Sample records for metabolic scaling theory
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Scaling of Metabolic Scaling within Physical Limits
Directory of Open Access Journals (Sweden)
Douglas S. Glazier
2014-10-01
Full Text Available Both the slope and elevation of scaling relationships between log metabolic rate and log body size vary taxonomically and in relation to physiological or developmental state, ecological lifestyle and environmental conditions. Here I discuss how the recently proposed metabolic-level boundaries hypothesis (MLBH provides a useful conceptual framework for explaining and predicting much, but not all of this variation. This hypothesis is based on three major assumptions: (1 various processes related to body volume and surface area exert state-dependent effects on the scaling slope for metabolic rate in relation to body mass; (2 the elevation and slope of metabolic scaling relationships are linked; and (3 both intrinsic (anatomical, biochemical and physiological and extrinsic (ecological factors can affect metabolic scaling. According to the MLBH, the diversity of metabolic scaling relationships occurs within physical boundary limits related to body volume and surface area. Within these limits, specific metabolic scaling slopes can be predicted from the metabolic level (or scaling elevation of a species or group of species. In essence, metabolic scaling itself scales with metabolic level, which is in turn contingent on various intrinsic and extrinsic conditions operating in physiological or evolutionary time. The MLBH represents a “meta-mechanism” or collection of multiple, specific mechanisms that have contingent, state-dependent effects. As such, the MLBH is Darwinian in approach (the theory of natural selection is also meta-mechanistic, in contrast to currently influential metabolic scaling theory that is Newtonian in approach (i.e., based on unitary deterministic laws. Furthermore, the MLBH can be viewed as part of a more general theory that includes other mechanisms that may also affect metabolic scaling.
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DEFF Research Database (Denmark)
Hirst, Andrew G.; Glazier, Douglas S.; Atkinson, David
2014-01-01
Metabolism fuels all of life’s activities, from biochemical reactions to ecological interactions. According to two intensely debated theories, body size affects metabolism via geometrical influences on the transport of resources and wastes. However, these theories differ crucially in whether...... the size dependence of metabolism is derived from material transport across external surfaces, or through internal resource-transport networks. We show that when body shape changes during growth, these models make opposing predictions. These models are tested using pelagic invertebrates, because...... these animals exhibit highly variable intraspecific scaling relationships for metabolic rate and body shape. Metabolic scaling slopes of diverse integument-breathing species were significantly positively correlated with degree of body flattening or elongation during ontogeny, as expected from surface area...
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Plant interactions alter the predictions of metabolic scaling theory
DEFF Research Database (Denmark)
Lin, Yue; Berger, Uta; Grimm, Volker
2013-01-01
Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of 24/3 between mean individual biomass and density during densitydependent mortality (self-thinning). Empirical tests have...... processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive....... of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories...
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Plant interactions alter the predictions of metabolic scaling theory.
Directory of Open Access Journals (Sweden)
Yue Lin
Full Text Available Metabolic scaling theory (MST is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of -4/3 between mean individual biomass and density during density-dependent mortality (self-thinning. Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms' internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric, and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than -4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive.
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Shape shifting predicts ontogenetic changes in metabolic scaling in diverse aquatic invertebrates.
Glazier, Douglas S; Hirst, Andrew G; Atkinson, David
2015-03-07
Metabolism fuels all biological activities, and thus understanding its variation is fundamentally important. Much of this variation is related to body size, which is commonly believed to follow a 3/4-power scaling law. However, during ontogeny, many kinds of animals and plants show marked shifts in metabolic scaling that deviate from 3/4-power scaling predicted by general models. Here, we show that in diverse aquatic invertebrates, ontogenetic shifts in the scaling of routine metabolic rate from near isometry (bR = scaling exponent approx. 1) to negative allometry (bR < 1), or the reverse, are associated with significant changes in body shape (indexed by bL = the scaling exponent of the relationship between body mass and body length). The observed inverse correlations between bR and bL are predicted by metabolic scaling theory that emphasizes resource/waste fluxes across external body surfaces, but contradict theory that emphasizes resource transport through internal networks. Geometric estimates of the scaling of surface area (SA) with body mass (bA) further show that ontogenetic shifts in bR and bA are positively correlated. These results support new metabolic scaling theory based on SA influences that may be applied to ontogenetic shifts in bR shown by many kinds of animals and plants. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
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Size structure, not metabolic scaling rules, determines fisheries reference points
DEFF Research Database (Denmark)
Andersen, Ken Haste; Beyer, Jan
2015-01-01
Impact assessments of fishing on a stock require parameterization of vital rates: growth, mortality and recruitment. For 'data-poor' stocks, vital rates may be estimated from empirical size-based relationships or from life-history invariants. However, a theoretical framework to synthesize...... these empirical relations is lacking. Here, we combine life-history invariants, metabolic scaling and size-spectrum theory to develop a general size- and trait-based theory for demography and recruitment of exploited fish stocks. Important concepts are physiological or metabolic scaled mortalities and flux...... is that larger species have a higher egg production per recruit than small species. This means that density dependence is stronger for large than for small species and has the consequence that fisheries reference points that incorporate recruitment do not obey metabolic scaling rules. This result implies...
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The scaling of maximum and basal metabolic rates of mammals and birds
Barbosa, Lauro A.; Garcia, Guilherme J. M.; da Silva, Jafferson K. L.
2006-01-01
Allometric scaling is one of the most pervasive laws in biology. Its origin, however, is still a matter of dispute. Recent studies have established that maximum metabolic rate scales with an exponent larger than that found for basal metabolism. This unpredicted result sets a challenge that can decide which of the concurrent hypotheses is the correct theory. Here, we show that both scaling laws can be deduced from a single network model. Besides the 3/4-law for basal metabolism, the model predicts that maximum metabolic rate scales as M, maximum heart rate as M, and muscular capillary density as M, in agreement with data.
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Unified theory of interspecific allometric scaling
International Nuclear Information System (INIS)
Silva, Jafferson K L da; Barbosa, Lauro A; Silva, Paulo Roberto
2007-01-01
A general simple theory for the interspecific allometric scaling is developed in the d + 1-dimensional space (d biological lengths and a physiological time) of metabolic states of organisms. It is assumed that natural selection shaped the metabolic states in such a way that the mass and energy d + 1-densities are size-invariant quantities (independent of body mass). The different metabolic states (basal and maximum) are described by considering that the biological lengths and the physiological time are related by different transport processes of energy and mass. In the basal metabolism, transportation occurs by ballistic and diffusion processes. In d = 3, the 3/4 law occurs if the ballistic movement is the dominant process, while the 2/3 law appears when both transport processes are equivalent. Accelerated movement during the biological time is related to the maximum aerobic sustained metabolism, which is characterized by the scaling exponent 2d/(2d + 1) (6/7 in d = 3). The results are in good agreement with empirical data and a verifiable empirical prediction about the aorta blood velocity in maximum metabolic rate conditions is made. (fast track communication)
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Effects of Contingency versus Constraints on the Body-Mass Scaling of Metabolic Rate
Directory of Open Access Journals (Sweden)
Douglas S. Glazier
2018-01-01
Full Text Available I illustrate the effects of both contingency and constraints on the body-mass scaling of metabolic rate by analyzing the significantly different influences of ambient temperature (Ta on metabolic scaling in ectothermic versus endothermic animals. Interspecific comparisons show that increasing Ta results in decreasing metabolic scaling slopes in ectotherms, but increasing slopes in endotherms, a pattern uniquely predicted by the metabolic-level boundaries hypothesis, as amended to include effects of the scaling of thermal conductance in endotherms outside their thermoneutral zone. No other published theoretical model explicitly predicts this striking variation in metabolic scaling, which I explain in terms of contingent effects of Ta and thermoregulatory strategy in the context of physical and geometric constraints related to the scaling of surface area, volume, and heat flow across surfaces. My analysis shows that theoretical models focused on an ideal 3/4-power law, as explained by a single universally applicable mechanism, are clearly inadequate for explaining the diversity and environmental sensitivity of metabolic scaling. An important challenge is to develop a theory of metabolic scaling that recognizes the contingent effects of multiple mechanisms that are modulated by several extrinsic and intrinsic factors within specified constraints.
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A quantitative theory of solid tumor growth, metabolic rate and vascularization.
Directory of Open Access Journals (Sweden)
Alexander B Herman
Full Text Available The relationships between cellular, structural and dynamical properties of tumors have traditionally been studied separately. Here, we construct a quantitative, predictive theory of solid tumor growth, metabolic rate, vascularization and necrosis that integrates the relationships between these properties. To accomplish this, we develop a comprehensive theory that describes the interface and integration of the tumor vascular network and resource supply with the cardiovascular system of the host. Our theory enables a quantitative understanding of how cells, tissues, and vascular networks act together across multiple scales by building on recent theoretical advances in modeling both healthy vasculature and the detailed processes of angiogenesis and tumor growth. The theory explicitly relates tumor vascularization and growth to metabolic rate, and yields extensive predictions for tumor properties, including growth rates, metabolic rates, degree of necrosis, blood flow rates and vessel sizes. Besides these quantitative predictions, we explain how growth rates depend on capillary density and metabolic rate, and why similar tumors grow slower and occur less frequently in larger animals, shedding light on Peto's paradox. Various implications for potential therapeutic strategies and further research are discussed.
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Critical PO2 is size-independent in insects: implications for the metabolic theory of ecology.
Harrison, Jon F; Klok, C J; Waters, James S
2014-10-01
Insects, and all animals, exhibit hypometric scaling of metabolic rate, with larger species having lower mass-specific metabolic rates. The metabolic theory of ecology (MTE) is based on models ascribing hypometric scaling of metabolic rate to constrained O 2 supply systems in larger animals. We compiled critical PO 2 of metabolic and growth rates for more than 40 insect species with a size range spanning four orders of magnitude. Critical PO 2 values vary from far below 21kPa for resting animals to near 21kPa for growing or flying animals and are size-independent, demonstrating that supply capacity matches oxygen demand. These data suggest that hypometric scaling of resting metabolic rate in insects is not driven by constraints on oxygen availability. Copyright © 2014 Elsevier Inc. All rights reserved.
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Bridging food webs, ecosystem metabolism, and biogeochemistry using ecological stoichiometry theory
DEFF Research Database (Denmark)
Welti, Nina; Striebel, Maren; Ulseth, Amber J.
2017-01-01
process rates). ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency......, we propose that using ES to link nutrient cycling, trophic dynamics, and ecosystem metabolism would allow for a more holistic understanding of ecosystem functions in a changing environment....
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Directory of Open Access Journals (Sweden)
Tyson L Swetnam
Full Text Available A significant concern about Metabolic Scaling Theory (MST in real forests relates to consistent differences between the values of power law scaling exponents of tree primary size measures used to estimate mass and those predicted by MST. Here we consider why observed scaling exponents for diameter and height relationships deviate from MST predictions across three semi-arid conifer forests in relation to: (1 tree condition and physical form, (2 the level of inter-tree competition (e.g. open vs closed stand structure, (3 increasing tree age, and (4 differences in site productivity. Scaling exponent values derived from non-linear least-squares regression for trees in excellent condition (n = 381 were above the MST prediction at the 95% confidence level, while the exponent for trees in good condition were no different than MST (n = 926. Trees that were in fair or poor condition, characterized as diseased, leaning, or sparsely crowned had exponent values below MST predictions (n = 2,058, as did recently dead standing trees (n = 375. Exponent value of the mean-tree model that disregarded tree condition (n = 3,740 was consistent with other studies that reject MST scaling. Ostensibly, as stand density and competition increase trees exhibited greater morphological plasticity whereby the majority had characteristically fair or poor growth forms. Fitting by least-squares regression biases the mean-tree model scaling exponent toward values that are below MST idealized predictions. For 368 trees from Arizona with known establishment dates, increasing age had no significant impact on expected scaling. We further suggest height to diameter ratios below MST relate to vertical truncation caused by limitation in plant water availability. Even with environmentally imposed height limitation, proportionality between height and diameter scaling exponents were consistent with the predictions of MST.
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Swetnam, Tyson L; O'Connor, Christopher D; Lynch, Ann M
2016-01-01
A significant concern about Metabolic Scaling Theory (MST) in real forests relates to consistent differences between the values of power law scaling exponents of tree primary size measures used to estimate mass and those predicted by MST. Here we consider why observed scaling exponents for diameter and height relationships deviate from MST predictions across three semi-arid conifer forests in relation to: (1) tree condition and physical form, (2) the level of inter-tree competition (e.g. open vs closed stand structure), (3) increasing tree age, and (4) differences in site productivity. Scaling exponent values derived from non-linear least-squares regression for trees in excellent condition (n = 381) were above the MST prediction at the 95% confidence level, while the exponent for trees in good condition were no different than MST (n = 926). Trees that were in fair or poor condition, characterized as diseased, leaning, or sparsely crowned had exponent values below MST predictions (n = 2,058), as did recently dead standing trees (n = 375). Exponent value of the mean-tree model that disregarded tree condition (n = 3,740) was consistent with other studies that reject MST scaling. Ostensibly, as stand density and competition increase trees exhibited greater morphological plasticity whereby the majority had characteristically fair or poor growth forms. Fitting by least-squares regression biases the mean-tree model scaling exponent toward values that are below MST idealized predictions. For 368 trees from Arizona with known establishment dates, increasing age had no significant impact on expected scaling. We further suggest height to diameter ratios below MST relate to vertical truncation caused by limitation in plant water availability. Even with environmentally imposed height limitation, proportionality between height and diameter scaling exponents were consistent with the predictions of MST.
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Genome scale metabolic modeling of cancer
DEFF Research Database (Denmark)
Nilsson, Avlant; Nielsen, Jens
2017-01-01
of metabolism which allows simulation and hypotheses testing of metabolic strategies. It has successfully been applied to many microorganisms and is now used to study cancer metabolism. Generic models of human metabolism have been reconstructed based on the existence of metabolic genes in the human genome......Cancer cells reprogram metabolism to support rapid proliferation and survival. Energy metabolism is particularly important for growth and genes encoding enzymes involved in energy metabolism are frequently altered in cancer cells. A genome scale metabolic model (GEM) is a mathematical formalization...
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Why allometric variation in mammalian metabolism is curvilinear on the logarithmic scale.
Packard, Gary C
2017-11-01
Studies performed over the last 20 years have repeatedly documented a slight convex curvature (relative to the x-axis) in double-logarithmic plots of basal metabolic rate (BMR) versus body mass in mammals. This curvilinear pattern has usually been interpreted in the context of a simple, two-parameter power function on the arithmetic scale, y = a × x b , with the exponent in the equation supposedly increasing systematically with body size. An equation of this form has caused concern among ecologists because a variable exponent is inconsistent with an assumption underlying the metabolic theory of ecology (MTE). However, the appearance of an exponent that varies with body size is an artifact resulting from the widespread use of logarithmic transformations in allometric analyses. Curvature in the distribution on the logarithmic scale actually is caused by a requirement for an explicit, non-zero intercept-and not a variable exponent-in the model describing the distribution on the arithmetic scale. Thus, the MTE need not be revised to accommodate an exponent that varies with body size in the scaling of mammalian BMR, but the theory may need to be tweaked to accommodate an intercept in the allometric equation. In general, any bivariate dataset that is well described by a three-parameter power equation on the arithmetic scale will follow a curvilinear path when displayed on the logarithmic scale. Consequently, reports of curvilinearity in log domain (i.e., "complex allometry") need to be revisited because conclusions from those investigations are likely to be flawed. © 2018 Wiley Periodicals, Inc.
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Genome scale engineering techniques for metabolic engineering.
Liu, Rongming; Bassalo, Marcelo C; Zeitoun, Ramsey I; Gill, Ryan T
2015-11-01
Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.
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Exercise-induced maximum metabolic rate scaled to body mass by ...
African Journals Online (AJOL)
Exercise-induced maximum metabolic rate scaled to body mass by the fractal ... rate scaling is that exercise-induced maximum aerobic metabolic rate (MMR) is ... muscle stress limitation, and maximized oxygen delivery and metabolic rates.
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Directory of Open Access Journals (Sweden)
Painter Page R
2005-08-01
Full Text Available Abstract Background A prominent theoretical explanation for 3/4-power allometric scaling of metabolism proposes that the nutrient exchange surface of capillaries has properties of a space-filling fractal. The theory assumes that nutrient exchange surface area has a fractal dimension equal to or greater than 2 and less than or equal to 3 and that the volume filled by the exchange surface area has a fractal dimension equal to or greater than 3 and less than or equal to 4. Results It is shown that contradicting predictions can be derived from the assumptions of the model. When errors in the model are corrected, it is shown to predict that metabolic rate is proportional to body mass (proportional scaling. Conclusion The presence of space-filling fractal nutrient exchange surfaces does not provide a satisfactory explanation for 3/4-power metabolic rate scaling.
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Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering.
Ando, David; Garcia Martin, Hector
2018-01-01
Accelerating the Design-Build-Test-Learn (DBTL) cycle in synthetic biology is critical to achieving rapid and facile bioengineering of organisms for the production of, e.g., biofuels and other chemicals. The Learn phase involves using data obtained from the Test phase to inform the next Design phase. As part of the Learn phase, mathematical models of metabolic fluxes give a mechanistic level of comprehension to cellular metabolism, isolating the principle drivers of metabolic behavior from the peripheral ones, and directing future experimental designs and engineering methodologies. Furthermore, the measurement of intracellular metabolic fluxes is specifically noteworthy as providing a rapid and easy-to-understand picture of how carbon and energy flow throughout the cell. Here, we present a detailed guide to performing metabolic flux analysis in the Learn phase of the DBTL cycle, where we show how one can take the isotope labeling data from a 13 C labeling experiment and immediately turn it into a determination of cellular fluxes that points in the direction of genetic engineering strategies that will advance the metabolic engineering process.For our modeling purposes we use the Joint BioEnergy Institute (JBEI) Quantitative Metabolic Modeling (jQMM) library, which provides an open-source, python-based framework for modeling internal metabolic fluxes and making actionable predictions on how to modify cellular metabolism for specific bioengineering goals. It presents a complete toolbox for performing different types of flux analysis such as Flux Balance Analysis, 13 C Metabolic Flux Analysis, and it introduces the capability to use 13 C labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale 13 C Metabolic Flux Analysis (2S- 13 C MFA) [1]. In addition to several other capabilities, the jQMM is also able to predict the effects of knockouts using the MoMA and ROOM methodologies. The use of the jQMM library is
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Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model
DEFF Research Database (Denmark)
Olivares Hernandez, Roberto
Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been construc......Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been...
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Little string theory from double-scaling limits of field theories
International Nuclear Information System (INIS)
Ling, Henry; Shieh, H.-H.; Anders, Greg van
2007-01-01
We show that little string theory on S 5 can be obtained as double-scaling limits of the maximally supersymmetric Yang-Mills theories on R x S 2 and R x S 3 /Z k . By matching the gauge theory parameters with those in the dual supergravity solutions found by Lin and Maldacena, we determine the limits in the gauge theories that correspond to decoupling of NS5-brane degrees of freedom. We find that for the theory on R x S 2 , the 't Hooft coupling must be scaled like ln 3 N, and on R x S 3 /Z k , like ln 2 N. Accordingly, taking these limits in these field theories gives Lagrangian definitions of little string theory on S 5
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Metabolic engineering of strains: from industrial-scale to lab-scale chemical production.
Sun, Jie; Alper, Hal S
2015-03-01
A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5-50 g/L), and lab-scale (0-5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.
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Riel, van N.A.W.; Giuseppin, M.L.F.; Verrips, C.T.
2000-01-01
The theory of dynamic optimal metabolic control (DOMC), as developed by Giuseppin and Van Riel (Metab. Eng., 2000), is applied to model the central nitrogen metabolism (CNM) in Saccharomyces cerevisiae. The CNM represents a typical system encountered in advanced metabolic engineering. The CNM is the
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Zomorrodi, Ali R; Segrè, Daniel
2017-11-16
Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.
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Mokken scale analysis : Between the Guttman scale and parametric item response theory
van Schuur, Wijbrandt H.
2003-01-01
This article introduces a model of ordinal unidimensional measurement known as Mokken scale analysis. Mokken scaling is based on principles of Item Response Theory (IRT) that originated in the Guttman scale. I compare the Mokken model with both Classical Test Theory (reliability or factor analysis)
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Non-Abelian gauge field theory in scale relativity
International Nuclear Information System (INIS)
Nottale, Laurent; Celerier, Marie-Noeelle; Lehner, Thierry
2006-01-01
Gauge field theory is developed in the framework of scale relativity. In this theory, space-time is described as a nondifferentiable continuum, which implies it is fractal, i.e., explicitly dependent on internal scale variables. Owing to the principle of relativity that has been extended to scales, these scale variables can themselves become functions of the space-time coordinates. Therefore, a coupling is expected between displacements in the fractal space-time and the transformations of these scale variables. In previous works, an Abelian gauge theory (electromagnetism) has been derived as a consequence of this coupling for global dilations and/or contractions. We consider here more general transformations of the scale variables by taking into account separate dilations for each of them, which yield non-Abelian gauge theories. We identify these transformations with the usual gauge transformations. The gauge fields naturally appear as a new geometric contribution to the total variation of the action involving these scale variables, while the gauge charges emerge as the generators of the scale transformation group. A generalized action is identified with the scale-relativistic invariant. The gauge charges are the conservative quantities, conjugates of the scale variables through the action, which find their origin in the symmetries of the ''scale-space.'' We thus found in a geometric way and recover the expression for the covariant derivative of gauge theory. Adding the requirement that under the scale transformations the fermion multiplets and the boson fields transform such that the derived Lagrangian remains invariant, we obtain gauge theories as a consequence of scale symmetries issued from a geometric space-time description
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Shape shifting predicts ontogenetic changes in metabolic scaling in diverse aquatic invertebrates
DEFF Research Database (Denmark)
Glazier, Douglas S.; Hirst, Andrew G.; Atkinson, D.
2016-01-01
in metabolic scaling that deviate from 3/4-power scaling predicted by general models. Here, we show that in diverse aquatic invertebrates, ontogenetic shifts in the scaling of routine metabolic rate from near isometry (bR = scaling exponent approx. 1) to negative allometry (bR
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Bridging Food Webs, Ecosystem Metabolism, and Biogeochemistry Using Ecological Stoichiometry Theory
Directory of Open Access Journals (Sweden)
Nina Welti
2017-07-01
Full Text Available Although aquatic ecologists and biogeochemists are well aware of the crucial importance of ecosystem functions, i.e., how biota drive biogeochemical processes and vice-versa, linking these fields in conceptual models is still uncommon. Attempts to explain the variability in elemental cycling consequently miss an important biological component and thereby impede a comprehensive understanding of the underlying processes governing energy and matter flow and transformation. The fate of multiple chemical elements in ecosystems is strongly linked by biotic demand and uptake; thus, considering elemental stoichiometry is important for both biogeochemical and ecological research. Nonetheless, assessments of ecological stoichiometry (ES often focus on the elemental content of biota rather than taking a more holistic view by examining both elemental pools and fluxes (e.g., organismal stoichiometry and ecosystem process rates. ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency to connect food webs, ecosystem metabolism, and biogeochemistry, as they are inherently concatenated by the transfer of carbon, nitrogen, and phosphorous through biotic and abiotic nutrient transformation and fluxes. Several new studies exist that demonstrate the connections between food web ecology, biogeochemistry, and ecosystem metabolism. In addition to a general introduction into the topic, this paper presents examples of how these fields can be combined with a focus on ES. In this review, a series of concepts have guided the discussion: (1 changing biogeochemistry affects trophic interactions and ecosystem processes by altering the elemental ratios of key species and assemblages; (2 changing trophic dynamics influences the transformation and
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Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network
Mart?n-Jim?nez, Cynthia A.; Salazar-Barreto, Diego; Barreto, George E.; Gonz?lez, Janneth
2017-01-01
Astrocytes are the most abundant cells of the central nervous system; they have a predominant role in maintaining brain metabolism. In this sense, abnormal metabolic states have been found in different neuropathological diseases. Determination of metabolic states of astrocytes is difficult to model using current experimental approaches given the high number of reactions and metabolites present. Thus, genome-scale metabolic networks derived from transcriptomic data can be used as a framework t...
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Babin, Anatoli
2016-01-01
In this monograph, the authors present their recently developed theory of electromagnetic interactions. This neoclassical approach extends the classical electromagnetic theory down to atomic scales and allows the explanation of various non-classical phenomena in the same framework. While the classical Maxwell–Lorentz electromagnetism theory succeeds in describing the physical reality at macroscopic scales, it struggles at atomic scales. Here, quantum mechanics traditionally takes over to describe non-classical phenomena such as the hydrogen spectrum and de Broglie waves. By means of modifying the classical theory, the approach presented here is able to consistently explain quantum-mechanical effects, and while similar to quantum mechanics in some respects, this neoclassical theory also differs markedly from it. In particular, the newly developed framework omits probabilistic interpretations of the wave function and features a new fundamental spatial scale which, at the size of the free electron, is much lar...
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Next-generation genome-scale models for metabolic engineering
DEFF Research Database (Denmark)
King, Zachary A.; Lloyd, Colton J.; Feist, Adam M.
2015-01-01
Constraint-based reconstruction and analysis (COBRA) methods have become widely used tools for metabolic engineering in both academic and industrial laboratories. By employing a genome-scale in silico representation of the metabolic network of a host organism, COBRA methods can be used to predict...... examples of applying COBRA methods to strain optimization are presented and discussed. Then, an outlook is provided on the next generation of COBRA models and the new types of predictions they will enable for systems metabolic engineering....
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Use of genome-scale microbial models for metabolic engineering
DEFF Research Database (Denmark)
Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens
2004-01-01
Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metaboli...... network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction....
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Identifying all moiety conservation laws in genome-scale metabolic networks.
De Martino, Andrea; De Martino, Daniele; Mulet, Roberto; Pagnani, Andrea
2014-01-01
The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.
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Identifying all moiety conservation laws in genome-scale metabolic networks.
Directory of Open Access Journals (Sweden)
Andrea De Martino
Full Text Available The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.
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McAnulty, Michael J; Yen, Jiun Y; Freedman, Benjamin G; Senger, Ryan S
2012-05-14
Genome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential metabolic engineering strategies in silico. A new method called "flux balance analysis with flux ratios (FBrAtio)" was developed in this research and applied to a new genome-scale model of Clostridium acetobutylicum ATCC 824 (iCAC490) that contains 707 metabolites and 794 reactions. FBrAtio was used to model wild-type metabolism and metabolically engineered strains of C. acetobutylicum where only flux ratio constraints and thermodynamic reversibility of reactions were required. The FBrAtio approach allowed solutions to be found through standard linear programming. Five flux ratio constraints were required to achieve a qualitative picture of wild-type metabolism for C. acetobutylicum for the production of: (i) acetate, (ii) lactate, (iii) butyrate, (iv) acetone, (v) butanol, (vi) ethanol, (vii) CO2 and (viii) H2. Results of this simulation study coincide with published experimental results and show the knockdown of the acetoacetyl-CoA transferase increases butanol to acetone selectivity, while the simultaneous over-expression of the aldehyde/alcohol dehydrogenase greatly increases ethanol production. FBrAtio is a promising new method for constraining genome-scale models using internal flux ratios. The method was effective for modeling wild-type and engineered strains of C. acetobutylicum.
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Wang, Zhiqiang; Ji, Mingfei; Deng, Jianming; Milne, Richard I; Ran, Jinzhi; Zhang, Qiang; Fan, Zhexuan; Zhang, Xiaowei; Li, Jiangtao; Huang, Heng; Cheng, Dongliang; Niklas, Karl J
2015-06-01
Simultaneous and accurate measurements of whole-plant instantaneous carbon-use efficiency (ICUE) and annual total carbon-use efficiency (TCUE) are difficult to make, especially for trees. One usually estimates ICUE based on the net photosynthetic rate or the assumed proportional relationship between growth efficiency and ICUE. However, thus far, protocols for easily estimating annual TCUE remain problematic. Here, we present a theoretical framework (based on the metabolic scaling theory) to predict whole-plant annual TCUE by directly measuring instantaneous net photosynthetic and respiratory rates. This framework makes four predictions, which were evaluated empirically using seedlings of nine Picea taxa: (i) the flux rates of CO(2) and energy will scale isometrically as a function of plant size, (ii) whole-plant net and gross photosynthetic rates and the net primary productivity will scale isometrically with respect to total leaf mass, (iii) these scaling relationships will be independent of ambient temperature and humidity fluctuations (as measured within an experimental chamber) regardless of the instantaneous net photosynthetic rate or dark respiratory rate, or overall growth rate and (iv) TCUE will scale isometrically with respect to instantaneous efficiency of carbon use (i.e., the latter can be used to predict the former) across diverse species. These predictions were experimentally verified. We also found that the ranking of the nine taxa based on net photosynthetic rates differed from ranking based on either ICUE or TCUE. In addition, the absolute values of ICUE and TCUE significantly differed among the nine taxa, with both ICUE and temperature-corrected ICUE being highest for Picea abies and lowest for Picea schrenkiana. Nevertheless, the data are consistent with the predictions of our general theoretical framework, which can be used to access annual carbon-use efficiency of different species at the level of an individual plant based on simple, direct
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Gaussian-3 theory using scaled energies
International Nuclear Information System (INIS)
Curtiss, Larry A.; Raghavachari, Krishnan; Redfern, Paul C.; Pople, John A.
2000-01-01
A modification of Guassian-3 (G3) theory using multiplicative scale factors, instead of the additive higher level correction, is presented. In this method, referred to as G3S, the correlation energy is scaled by five parameters and the Hartree-Fock energy by one parameter. The six parameters are fitted to the G2/97 test set of 299 energies and the resulting mean absolute deviation from experiment is 0.99 kcal/mol compared to 1.01 kcal/mol for G3 theory. The G3S method has the advantage compared to G3 theory in that it can be used for studying potential energy surfaces where the products and reactants have a different number of paired electrons. In addition, versions of the computationally less intensive G3(MP3) and G3(MP2) methods that use scaled energies are also presented. These methods, referred to as G3S(MP3) and G3S(MP2), have mean absolute deviations of 1.16 and 1.35 kcal/mol, respectively. (c) 2000 American Institute of Physics
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Scaling of Theory-of-Mind Tasks
Wellman, Henry M.; Liu, David
2004-01-01
Two studies address the sequence of understandings evident in preschoolers' developing theory of mind. The first, preliminary study provides a meta-analysis of research comparing different types of mental state understandings (e.g., desires vs. beliefs, ignorance vs. false belief). The second, primary study tests a theory-of-mind scale for…
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Bays, Harold
2005-05-01
Excessive fat (adiposity) and dysfunctional fat (adiposopathy) constitute the most common worldwide epidemics of our time -- and perhaps of all time. Ongoing efforts to explain how the micro (adipocyte) and macro (body organ) biologic systems interact through function and dysfunction in promoting Type 2 diabetes mellitus, hypertension and dyslipidemia are not unlike the mechanistic and philosophical thinking processes involved in reconciling the micro (quantum physics) and macro (general relativity) theories in physics. Currently, the term metabolic syndrome refers to a constellation of consequences often associated with excess body fat and is an attempt to unify the associations known to exist between the four fundamental metabolic diseases of obesity, hyperglycemia (including Type 2 diabetes mellitus), hypertension and dyslipidemia. However, the association of adiposity with these metabolic disorders is not absolute and the metabolic syndrome does not describe underlying causality, nor does the metabolic syndrome necessarily reflect any reasonably related pathophysiologic process. Just as with quantum physics, general relativity and the four fundamental forces of the universe, the lack of an adequate unifying theory of micro causality and macro consequence is unsatisfying, and in medicine, impairs the development of agents that may globally improve both obesity and obesity-related metabolic disease. Emerging scientific and clinical evidence strongly supports the novel concept that it is not adiposity alone, but rather it is adiposopathy that is the underlying cause of most cases of Type 2 diabetes mellitus, hypertension and dyslipidemia. Adiposopathy is a plausible Theory of Everything for mankind's greatest metabolic epidemics.
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Astrophysical tests of scale-covariant gravity theories
International Nuclear Information System (INIS)
Mansfield, V.N.; Malin, S.
1980-01-01
Starting from the most general form of the conservation laws in scale-covariant gravitation theory, a conservation of energy equation appropriate for stars is derived. Applications to white dwarfs and neutron stars reveal serious difficulties for some choices of gauge that have been frequently employed in the literature on scale-covariant gravity. We also show how to restrict some of the possible gauges that result from theories which are independent of the Large Numbers Hypothesis
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Directory of Open Access Journals (Sweden)
Jensen Paul A
2011-09-01
Full Text Available Abstract Background Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model. Results We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae. Conclusion The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.
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Directory of Open Access Journals (Sweden)
Katsunori Yoshikawa
Full Text Available Arthrospira (Spirulina platensis is a promising feedstock and host strain for bioproduction because of its high accumulation of glycogen and superior characteristics for industrial production. Metabolic simulation using a genome-scale metabolic model and flux balance analysis is a powerful method that can be used to design metabolic engineering strategies for the improvement of target molecule production. In this study, we constructed a genome-scale metabolic model of A. platensis NIES-39 including 746 metabolic reactions and 673 metabolites, and developed novel strategies to improve the production of valuable metabolites, such as glycogen and ethanol. The simulation results obtained using the metabolic model showed high consistency with experimental results for growth rates under several trophic conditions and growth capabilities on various organic substrates. The metabolic model was further applied to design a metabolic network to improve the autotrophic production of glycogen and ethanol. Decreased flux of reactions related to the TCA cycle and phosphoenolpyruvate reaction were found to improve glycogen production. Furthermore, in silico knockout simulation indicated that deletion of genes related to the respiratory chain, such as NAD(PH dehydrogenase and cytochrome-c oxidase, could enhance ethanol production by using ammonium as a nitrogen source.
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Analysis of Aspergillus nidulans metabolism at the genome-scale
DEFF Research Database (Denmark)
David, Helga; Ozcelik, İlknur Ş; Hofmann, Gerald
2008-01-01
of relevant secondary metabolites, was reconstructed based on detailed metabolic reconstructions available for A. niger and Saccharomyces cerevisiae, and information on the genetics, biochemistry and physiology of A. nidulans. Thereby, it was possible to identify metabolic functions without a gene associated...... a function. Results: In this work, we have manually assigned functions to 472 orphan genes in the metabolism of A. nidulans, by using a pathway-driven approach and by employing comparative genomics tools based on sequence similarity. The central metabolism of A. nidulans, as well as biosynthetic pathways......, in an objective and systematic manner. The functional assignments served as a basis to develop a mathematical model, linking 666 genes (both previously and newly annotated) to metabolic roles. The model was used to simulate metabolic behavior and additionally to integrate, analyze and interpret large-scale gene...
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Reconstruction of genome-scale human metabolic models using omics data
DEFF Research Database (Denmark)
Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup
2015-01-01
used to describe metabolic phenotypes of healthy and diseased human tissues and cells, and to predict therapeutic targets. Here we review recent trends in genome-scale human metabolic modeling, including various generic and tissue/cell type-specific human metabolic models developed to date, and methods......, databases and platforms used to construct them. For generic human metabolic models, we pay attention to Recon 2 and HMR 2.0 with emphasis on data sources used to construct them. Draft and high-quality tissue/cell type-specific human metabolic models have been generated using these generic human metabolic...... refined through gap filling, reaction directionality assignment and the subcellular localization of metabolic reactions. We review relevant tools for this model refinement procedure as well. Finally, we suggest the direction of further studies on reconstructing an improved human metabolic model....
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Do Performance-Safety Tradeoffs Cause Hypometric Metabolic Scaling in Animals?
Harrison, Jon F
2017-09-01
Hypometric scaling of aerobic metabolism in animals has been widely attributed to constraints on oxygen (O 2 ) supply in larger animals, but recent findings demonstrate that O 2 supply balances with need regardless of size. Larger animals also do not exhibit evidence of compensation for O 2 supply limitation. Because declining metabolic rates (MRs) are tightly linked to fitness, this provides significant evidence against the hypothesis that constraints on supply drive hypometric scaling. As an alternative, ATP demand might decline in larger animals because of performance-safety tradeoffs. Larger animals, which typically reproduce later, exhibit risk-reducing strategies that lower MR. Conversely, smaller animals are more strongly selected for growth and costly neurolocomotory performance, elevating metabolism. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Maldonado, Elaina M; Leoncikas, Vytautas; Fisher, Ciarán P; Moore, J Bernadette; Plant, Nick J; Kierzek, Andrzej M
2017-11-01
The scope of physiologically based pharmacokinetic (PBPK) modeling can be expanded by assimilation of the mechanistic models of intracellular processes from systems biology field. The genome scale metabolic networks (GSMNs) represent a whole set of metabolic enzymes expressed in human tissues. Dynamic models of the gene regulation of key drug metabolism enzymes are available. Here, we introduce GSMNs and review ongoing work on integration of PBPK, GSMNs, and metabolic gene regulation. We demonstrate example models. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.
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Integration of expression data in genome-scale metabolic network reconstructions
Directory of Open Access Journals (Sweden)
Anna S. Blazier
2012-08-01
Full Text Available With the advent of high-throughput technologies, the field of systems biology has amassed an abundance of omics data, quantifying thousands of cellular components across a variety of scales, ranging from mRNA transcript levels to metabolite quantities. Methods are needed to not only integrate this omics data but to also use this data to heighten the predictive capabilities of computational models. Several recent studies have successfully demonstrated how flux balance analysis (FBA, a constraint-based modeling approach, can be used to integrate transcriptomic data into genome-scale metabolic network reconstructions to generate predictive computational models. In this review, we summarize such FBA-based methods for integrating expression data into genome-scale metabolic network reconstructions, highlighting their advantages as well as their limitations.
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Exercise-induced maximum metabolic rate scaled to body mass by ...
African Journals Online (AJOL)
user
2016-10-27
Oct 27, 2016 ... maximum aerobic metabolic rate (MMR) is proportional to the fractal extent ... metabolic rate with body mass can be obtained by taking body .... blood takes place. ..... MMR and BMR is that MMR is owing mainly to respiration in skeletal .... the spectra of surface area scaling strategies of cells and organisms:.
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Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis
Directory of Open Access Journals (Sweden)
Balagurunathan Balaji
2012-02-01
Full Text Available Abstract Background Fermentation of xylose, the major component in hemicellulose, is essential for economic conversion of lignocellulosic biomass to fuels and chemicals. The yeast Scheffersomyces stipitis (formerly known as Pichia stipitis has the highest known native capacity for xylose fermentation and possesses several genes for lignocellulose bioconversion in its genome. Understanding the metabolism of this yeast at a global scale, by reconstructing the genome scale metabolic model, is essential for manipulating its metabolic capabilities and for successful transfer of its capabilities to other industrial microbes. Results We present a genome-scale metabolic model for Scheffersomyces stipitis, a native xylose utilizing yeast. The model was reconstructed based on genome sequence annotation, detailed experimental investigation and known yeast physiology. Macromolecular composition of Scheffersomyces stipitis biomass was estimated experimentally and its ability to grow on different carbon, nitrogen, sulphur and phosphorus sources was determined by phenotype microarrays. The compartmentalized model, developed based on an iterative procedure, accounted for 814 genes, 1371 reactions, and 971 metabolites. In silico computed growth rates were compared with high-throughput phenotyping data and the model could predict the qualitative outcomes in 74% of substrates investigated. Model simulations were used to identify the biosynthetic requirements for anaerobic growth of Scheffersomyces stipitis on glucose and the results were validated with published literature. The bottlenecks in Scheffersomyces stipitis metabolic network for xylose uptake and nucleotide cofactor recycling were identified by in silico flux variability analysis. The scope of the model in enhancing the mechanistic understanding of microbial metabolism is demonstrated by identifying a mechanism for mitochondrial respiration and oxidative phosphorylation. Conclusion The genome-scale
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A general model for metabolic scaling in self-similar asymmetric networks.
Directory of Open Access Journals (Sweden)
Alexander Byers Brummer
2017-03-01
Full Text Available How a particular attribute of an organism changes or scales with its body size is known as an allometry. Biological allometries, such as metabolic scaling, have been hypothesized to result from selection to maximize how vascular networks fill space yet minimize internal transport distances and resistances. The West, Brown, Enquist (WBE model argues that these two principles (space-filling and energy minimization are (i general principles underlying the evolution of the diversity of biological networks across plants and animals and (ii can be used to predict how the resulting geometry of biological networks then governs their allometric scaling. Perhaps the most central biological allometry is how metabolic rate scales with body size. A core assumption of the WBE model is that networks are symmetric with respect to their geometric properties. That is, any two given branches within the same generation in the network are assumed to have identical lengths and radii. However, biological networks are rarely if ever symmetric. An open question is: Does incorporating asymmetric branching change or influence the predictions of the WBE model? We derive a general network model that relaxes the symmetric assumption and define two classes of asymmetrically bifurcating networks. We show that asymmetric branching can be incorporated into the WBE model. This asymmetric version of the WBE model results in several theoretical predictions for the structure, physiology, and metabolism of organisms, specifically in the case for the cardiovascular system. We show how network asymmetry can now be incorporated in the many allometric scaling relationships via total network volume. Most importantly, we show that the 3/4 metabolic scaling exponent from Kleiber's Law can still be attained within many asymmetric networks.
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A scale distortion theory of anchoring.
Frederick, Shane W; Mochon, Daniel
2012-02-01
We propose that anchoring is often best interpreted as a scaling effect--that the anchor changes how the response scale is used, not how the focal stimulus is perceived. Of importance, we maintain that this holds true even for so-called objective scales (e.g., pounds, calories, meters, etc.). In support of this theory of scale distortion, we show that prior exposure to a numeric standard changes respondents' use of that specific response scale but does not generalize to conceptually affiliated judgments rendered on similar scales. Our findings highlight the necessity of distinguishing response language effects from representational effects in places where the need for that distinction has often been assumed away.
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Directory of Open Access Journals (Sweden)
Zixiang Xu
Full Text Available Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective.
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On the character of scale symmetry breaking in gauge theories
International Nuclear Information System (INIS)
Gusijnin, V.P.; Kushnir, V.A.; Miransky, V.A.
1988-01-01
The problem of scale symmetry breaking in gauge theories is discussed. It is shown that the phenomenon of spontaneous breaking of scale symmetry in gauge theories is incompatible with the PCAAC dynamics. 12 refs
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Metingear: a development environment for annotating genome-scale metabolic models.
May, John W; James, A Gordon; Steinbeck, Christoph
2013-09-01
Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format. Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.
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A protocol for generating a high-quality genome-scale metabolic reconstruction.
Thiele, Ines; Palsson, Bernhard Ø
2010-01-01
Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.
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The evolving Planck mass in classically scale-invariant theories
Energy Technology Data Exchange (ETDEWEB)
Kannike, K.; Raidal, M.; Spethmann, C.; Veermäe, H. [National Institute of Chemical Physics and Biophysics,Rävala 10, 10143 Tallinn (Estonia)
2017-04-05
We consider classically scale-invariant theories with non-minimally coupled scalar fields, where the Planck mass and the hierarchy of physical scales are dynamically generated. The classical theories possess a fixed point, where scale invariance is spontaneously broken. In these theories, however, the Planck mass becomes unstable in the presence of explicit sources of scale invariance breaking, such as non-relativistic matter and cosmological constant terms. We quantify the constraints on such classical models from Big Bang Nucleosynthesis that lead to an upper bound on the non-minimal coupling and require trans-Planckian field values. We show that quantum corrections to the scalar potential can stabilise the fixed point close to the minimum of the Coleman-Weinberg potential. The time-averaged motion of the evolving fixed point is strongly suppressed, thus the limits on the evolving gravitational constant from Big Bang Nucleosynthesis and other measurements do not presently constrain this class of theories. Field oscillations around the fixed point, if not damped, contribute to the dark matter density of the Universe.
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The evolving Planck mass in classically scale-invariant theories
Kannike, K.; Raidal, M.; Spethmann, C.; Veermäe, H.
2017-04-01
We consider classically scale-invariant theories with non-minimally coupled scalar fields, where the Planck mass and the hierarchy of physical scales are dynamically generated. The classical theories possess a fixed point, where scale invariance is spontaneously broken. In these theories, however, the Planck mass becomes unstable in the presence of explicit sources of scale invariance breaking, such as non-relativistic matter and cosmological constant terms. We quantify the constraints on such classical models from Big Bang Nucleosynthesis that lead to an upper bound on the non-minimal coupling and require trans-Planckian field values. We show that quantum corrections to the scalar potential can stabilise the fixed point close to the minimum of the Coleman-Weinberg potential. The time-averaged motion of the evolving fixed point is strongly suppressed, thus the limits on the evolving gravitational constant from Big Bang Nucleosynthesis and other measurements do not presently constrain this class of theories. Field oscillations around the fixed point, if not damped, contribute to the dark matter density of the Universe.
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Genome-scale metabolic models as platforms for strain design and biological discovery.
Mienda, Bashir Sajo
2017-07-01
Genome-scale metabolic models (GEMs) have been developed and used in guiding systems' metabolic engineering strategies for strain design and development. This strategy has been used in fermentative production of bio-based industrial chemicals and fuels from alternative carbon sources. However, computer-aided hypotheses building using established algorithms and software platforms for biological discovery can be integrated into the pipeline for strain design strategy to create superior strains of microorganisms for targeted biosynthetic goals. Here, I described an integrated workflow strategy using GEMs for strain design and biological discovery. Specific case studies of strain design and biological discovery using Escherichia coli genome-scale model are presented and discussed. The integrated workflow presented herein, when applied carefully would help guide future design strategies for high-performance microbial strains that have existing and forthcoming genome-scale metabolic models.
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Determining the Control Circuitry of Redox Metabolism at the Genome-Scale
DEFF Research Database (Denmark)
Federowicz, Stephen; Kim, Donghyuk; Ebrahim, Ali
2014-01-01
-scale metabolic model to show that ArcA and Fnr regulate >80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Based on the data, we propose a feedforward with feedback trim regulatory scheme, given the extensive repression of catabolic genes...
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Graph-based linear scaling electronic structure theory
Energy Technology Data Exchange (ETDEWEB)
Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.; Swart, Pieter J.; Germann, Timothy C.; Bock, Nicolas [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Mniszewski, Susan M.; Mohd-Yusof, Jamal; Wall, Michael E.; Djidjev, Hristo [Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Rubensson, Emanuel H. [Division of Scientific Computing, Department of Information Technology, Uppsala University, Box 337, SE-751 05 Uppsala (Sweden)
2016-06-21
We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.
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Experimental signature of scaling violation implied by field theories
International Nuclear Information System (INIS)
Tung, W.
1975-01-01
Renormalizable field theories are found to predict a surprisingly specific pattern of scaling violation in deep inelastic scattering. Comparison with experiments is discussed. The feasibility of distinguishing asymptotically free field theories from conventional field theories is evaluated
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DEFF Research Database (Denmark)
Backman, Tyler W.H.; Ando, David; Singh, Jahnavi
2018-01-01
for a minimum of fluxes into core metabolism to satisfy these experimental constraints. Together, these methods accelerate and automate the identification of a biologically reasonable set of core reactions for use with 13C MFA or 2S- 13C MFA, as well as provide for a substantially lower set of flux bounds......Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13C Metabolic Flux Analysis (13C MFA) and Two-Scale 13C Metabolic Flux Analysis (2S-13C MFA) are two techniques used...
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Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism
Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D.
2011-01-01
The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species. PMID:21755001
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Scaling algebras and renormalization group in algebraic quantum field theory
International Nuclear Information System (INIS)
Buchholz, D.; Verch, R.
1995-01-01
For any given algebra of local observables in Minkowski space an associated scaling algebra is constructed on which renormalization group (scaling) transformations act in a canonical manner. The method can be carried over to arbitrary spacetime manifolds and provides a framework for the systematic analysis of the short distance properties of local quantum field theories. It is shown that every theory has a (possibly non-unique) scaling limit which can be classified according to its classical or quantum nature. Dilation invariant theories are stable under the action of the renormalization group. Within this framework the problem of wedge (Bisognano-Wichmann) duality in the scaling limit is discussed and some of its physical implications are outlined. (orig.)
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A model for allometric scaling of mammalian metabolism with ambient heat loss
Kwak, Ho Sang
2016-02-02
Background Allometric scaling, which represents the dependence of biological trait or process relates on body size, is a long-standing subject in biological science. However, there has been no study to consider heat loss to the ambient and an insulation layer representing mammalian skin and fur for the derivation of the scaling law of metabolism. Methods A simple heat transfer model is proposed to analyze the allometry of mammalian metabolism. The present model extends existing studies by incorporating various external heat transfer parameters and additional insulation layers. The model equations were solved numerically and by an analytic heat balance approach. Results A general observation is that the present heat transfer model predicted the 2/3 surface scaling law, which is primarily attributed to the dependence of the surface area on the body mass. External heat transfer effects introduced deviations in the scaling law, mainly due to natural convection heat transfer which becomes more prominent at smaller mass. These deviations resulted in a slight modification of the scaling exponent to a value smaller than 2/3. Conclusion The finding that additional radiative heat loss and the consideration of an outer insulation fur layer attenuate these deviation effects and render the scaling law closer to 2/3 provides in silico evidence for a functional impact of heat transfer mode on the allometric scaling law in mammalian metabolism.
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Metabolic activation and carcinogenicity of polycyclic hydrocarbons: A new quantum mechanical theory
International Nuclear Information System (INIS)
Mohammad, S.N.
1986-01-01
This investigation aims to describe a quantum mechanical theory of cancer, which, on the basis of certain electronic indices calculated for the parent compound, would give prediction of its P-450 mediated metabolic activation and would provide better representation of its relative carcinogenic potency when activated to its PUM. The author's theory is based on the assumption that electronic charge distribution of activated species resembles at least qualitatively the charge distribution of the parent compound, and a careful analysis of electronic characteristics of the parent compound would suffice to give reasonable estimation of the carcinogenic activities of the metabolic products. The details of the theoretical method is given and the results for some alternant and non-alternant PAHs are presented
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Directory of Open Access Journals (Sweden)
Sriram Chandrasekaran
2017-12-01
Full Text Available Summary: Metabolism is an emerging stem cell hallmark tied to cell fate, pluripotency, and self-renewal, yet systems-level understanding of stem cell metabolism has been limited by the lack of genome-scale network models. Here, we develop a systems approach to integrate time-course metabolomics data with a computational model of metabolism to analyze the metabolic state of naive and primed murine pluripotent stem cells. Using this approach, we find that one-carbon metabolism involving phosphoglycerate dehydrogenase, folate synthesis, and nucleotide synthesis is a key pathway that differs between the two states, resulting in differential sensitivity to anti-folates. The model also predicts that the pluripotency factor Lin28 regulates this one-carbon metabolic pathway, which we validate using metabolomics data from Lin28-deficient cells. Moreover, we identify and validate metabolic reactions related to S-adenosyl-methionine production that can differentially impact histone methylation in naive and primed cells. Our network-based approach provides a framework for characterizing metabolic changes influencing pluripotency and cell fate. : Chandrasekaran et al. use computational modeling, metabolomics, and metabolic inhibitors to discover metabolic differences between various pluripotent stem cell states and infer their impact on stem cell fate decisions. Keywords: systems biology, stem cell biology, metabolism, genome-scale modeling, pluripotency, histone methylation, naive (ground state, primed state, cell fate, metabolic network
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Directory of Open Access Journals (Sweden)
Tyler W. H. Backman
2018-01-01
Full Text Available Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13 C Metabolic Flux Analysis ( 13 C MFA and Two-Scale 13 C Metabolic Flux Analysis (2S- 13 C MFA are two techniques used to determine such fluxes. Both operate on the simplifying approximation that metabolic flux from peripheral metabolism into central “core” carbon metabolism is minimal, and can be omitted when modeling isotopic labeling in core metabolism. The validity of this “two-scale” or “bow tie” approximation is supported both by the ability to accurately model experimental isotopic labeling data, and by experimentally verified metabolic engineering predictions using these methods. However, the boundaries of core metabolism that satisfy this approximation can vary across species, and across cell culture conditions. Here, we present a set of algorithms that (1 systematically calculate flux bounds for any specified “core” of a genome-scale model so as to satisfy the bow tie approximation and (2 automatically identify an updated set of core reactions that can satisfy this approximation more efficiently. First, we leverage linear programming to simultaneously identify the lowest fluxes from peripheral metabolism into core metabolism compatible with the observed growth rate and extracellular metabolite exchange fluxes. Second, we use Simulated Annealing to identify an updated set of core reactions that allow for a minimum of fluxes into core metabolism to satisfy these experimental constraints. Together, these methods accelerate and automate the identification of a biologically reasonable set of core reactions for use with 13 C MFA or 2S- 13 C MFA, as well as provide for a substantially lower set of flux bounds for fluxes into the core as compared with previous methods. We provide an open source Python implementation of these algorithms at https://github.com/JBEI/limitfluxtocore.
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Metabolite coupling in genome-scale metabolic networks
Directory of Open Access Journals (Sweden)
Palsson Bernhard Ø
2006-03-01
Full Text Available Abstract Background Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and proteomic data. These networks have been manually curated based on legacy data and elementally and charge balanced. Comparative analysis of these well curated networks is now possible. Pairs of metabolites often appear together in several network reactions, linking them topologically. This co-occurrence of pairs of metabolites in metabolic reactions is termed herein "metabolite coupling." These metabolite pairs can be directly computed from the stoichiometric matrix, S. Metabolite coupling is derived from the matrix ŜŜT, whose off-diagonal elements indicate the number of reactions in which any two metabolites participate together, where Ŝ is the binary form of S. Results Metabolite coupling in the studied networks was found to be dominated by a relatively small group of highly interacting pairs of metabolites. As would be expected, metabolites with high individual metabolite connectivity also tended to be those with the highest metabolite coupling, as the most connected metabolites couple more often. For metabolite pairs that are not highly coupled, we show that the number of reactions a pair of metabolites shares across a metabolic network closely approximates a line on a log-log scale. We also show that the preferential coupling of two metabolites with each other is spread across the spectrum of metabolites and is not unique to the most connected metabolites. We provide a measure for determining which metabolite pairs couple more often than would be expected based on their individual connectivity in the network and show that these metabolites often derive their principal biological functions from existing in pairs. Thus, analysis of metabolite coupling provides information beyond that which is found from studying the individual connectivity of individual
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Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization.
Nair, Govind; Jungreuthmayer, Christian; Zanghellini, Jürgen
2017-02-01
Knockout strategies, particularly the concept of constrained minimal cut sets (cMCSs), are an important part of the arsenal of tools used in manipulating metabolic networks. Given a specific design, cMCSs can be calculated even in genome-scale networks. We would however like to find not only the optimal intervention strategy for a given design but the best possible design too. Our solution (PSOMCS) is to use particle swarm optimization (PSO) along with the direct calculation of cMCSs from the stoichiometric matrix to obtain optimal designs satisfying multiple objectives. To illustrate the working of PSOMCS, we apply it to a toy network. Next we show its superiority by comparing its performance against other comparable methods on a medium sized E. coli core metabolic network. PSOMCS not only finds solutions comparable to previously published results but also it is orders of magnitude faster. Finally, we use PSOMCS to predict knockouts satisfying multiple objectives in a genome-scale metabolic model of E. coli and compare it with OptKnock and RobustKnock. PSOMCS finds competitive knockout strategies and designs compared to other current methods and is in some cases significantly faster. It can be used in identifying knockouts which will force optimal desired behaviors in large and genome scale metabolic networks. It will be even more useful as larger metabolic models of industrially relevant organisms become available.
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The necessity of a theory of biology for tissue engineering: metabolism-repair systems.
Ganguli, Suman; Hunt, C Anthony
2004-01-01
Since there is no widely accepted global theory of biology, tissue engineering and bioengineering lack a theoretical understanding of the systems being engineered. By default, tissue engineering operates with a "reductionist" theoretical approach, inherited from traditional engineering of non-living materials. Long term, that approach is inadequate, since it ignores essential aspects of biology. Metabolism-repair systems are a theoretical framework which explicitly represents two "functional" aspects of living organisms: self-repair and self-replication. Since repair and replication are central to tissue engineering, we advance metabolism-repair systems as a potential theoretical framework for tissue engineering. We present an overview of the framework, and indicate directions to pursue for extending it to the context of tissue engineering. We focus on biological networks, both metabolic and cellular, as one such direction. The construction of these networks, in turn, depends on biological protocols. Together these concepts may help point the way to a global theory of biology appropriate for tissue engineering.
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A global evaluation of metabolic theory as an explanation for terrestrial species richness gradients
DEFF Research Database (Denmark)
Hawkins, Bradford A.; Albuquerque, Fabio S.; Araújo, Miguel B.
2007-01-01
We compiled 46 broadscale data sets of species richness for a wide range of terrestrial plant, invertebrate, and ectothermic vertebrate groups in all parts of the world to test the ability of metabolic theory to account for observed diversity gradients. The theory makes two related predictions: (...
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On the scaling limits in the Euclidean (quantum) field theory
International Nuclear Information System (INIS)
Gielerak, R.
1983-01-01
The author studies the concept of scaling limits in the context of the constructive field theory. He finds that the domain of attraction of a free massless Euclidean scalar field in the two-dimensional space time contains almost all Euclidean self-interacting models of quantum fields so far constructed. The renormalized scaling limit of the Wick polynomials of several self-interacting Euclidean field theory models are shown to be the same as in the free field theory. (Auth.)
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Renormalization Group Theory of Bolgiano Scaling in Boussinesq Turbulence
Rubinstein, Robert
1994-01-01
Bolgiano scaling in Boussinesq turbulence is analyzed using the Yakhot-Orszag renormalization group. For this purpose, an isotropic model is introduced. Scaling exponents are calculated by forcing the temperature equation so that the temperature variance flux is constant in the inertial range. Universal amplitudes associated with the scaling laws are computed by expanding about a logarithmic theory. Connections between this formalism and the direct interaction approximation are discussed. It is suggested that the Yakhot-Orszag theory yields a lowest order approximate solution of a regularized direct interaction approximation which can be corrected by a simple iterative procedure.
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Predicting growth of the healthy infant using a genome scale metabolic model.
Nilsson, Avlant; Mardinoglu, Adil; Nielsen, Jens
2017-01-01
An estimated 165 million children globally have stunted growth, and extensive growth data are available. Genome scale metabolic models allow the simulation of molecular flux over each metabolic enzyme, and are well adapted to analyze biological systems. We used a human genome scale metabolic model to simulate the mechanisms of growth and integrate data about breast-milk intake and composition with the infant's biomass and energy expenditure of major organs. The model predicted daily metabolic fluxes from birth to age 6 months, and accurately reproduced standard growth curves and changes in body composition. The model corroborates the finding that essential amino and fatty acids do not limit growth, but that energy is the main growth limiting factor. Disruptions to the supply and demand of energy markedly affected the predicted growth, indicating that elevated energy expenditure may be detrimental. The model was used to simulate the metabolic effect of mineral deficiencies, and showed the greatest growth reduction for deficiencies in copper, iron, and magnesium ions which affect energy production through oxidative phosphorylation. The model and simulation method were integrated to a platform and shared with the research community. The growth model constitutes another step towards the complete representation of human metabolism, and may further help improve the understanding of the mechanisms underlying stunting.
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Nonperturbative scale anomaly and composite operators in gauge field theories
International Nuclear Information System (INIS)
Gusynin, V.P.; Miranskij, V.A.
1987-01-01
In non-asymptotically free gauge theories with a non-trivial ultraviolet fixed point scale symmetry breaking (the scale anomaly) caused by the nonperturbative PCAC dynamics is studied. In the two-loop approximation the analytical expression for the gluon condensate is obtained. It is shown that the form of the anomaly depends on the type of the phase of a theory to which it relates. The hypothesis about the soft behaviour at small distances of composite operators in such theories is confirmed. 14 refs.; 1 fig
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In Silico Genome-Scale Reconstruction and Validation of the Staphylococcus aureus Metabolic Network
Heinemann, Matthias; Kümmel, Anne; Ruinatscha, Reto; Panke, Sven
2005-01-01
A genome-scale metabolic model of the Gram-positive, facultative anaerobic opportunistic pathogen Staphylococcus aureus N315 was constructed based on current genomic data, literature, and physiological information. The model comprises 774 metabolic processes representing approximately 23% of all
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Scaling theory and the classification of phase transitions
International Nuclear Information System (INIS)
Hilfer, R.
1992-01-01
In this paper, the recent classification theory for phase transitions and its relation with the foundations of statistical physics is reviewed. First it is outlined how Ehrenfests classification scheme can be generalized into a general thermodynamic classification theory for phase transitions. The classification theory implies scaling and multiscaling thereby eliminating the need to postulate the scaling hypothesis as a fourth law of thermodynamics. The new classification has also led to the discovery and distinction of nonequilibrium transitions within equilibrium statistical physics. Nonequilibrium phase transitions are distinguished from equilibrium transitions by orders less than unity and by the fact the equilibrium thermodynamics and statistical mechanics become inapplicable at the critical point. The latter fact requires a change in the Gibbs assumption underlying the canonical and grandcanonical ensembles in order to recover the thermodynamic description in the critical limit
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Toward the automated generation of genome-scale metabolic networks in the SEED.
DeJongh, Matthew; Formsma, Kevin; Boillot, Paul; Gould, John; Rycenga, Matthew; Best, Aaron
2007-04-26
Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis). We have implemented our tools and database within the SEED, an open-source software environment for comparative genome annotation and analysis. Our method sets the
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Toward the automated generation of genome-scale metabolic networks in the SEED
Directory of Open Access Journals (Sweden)
Gould John
2007-04-01
Full Text Available Abstract Background Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. Results We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis. We have implemented our tools and database within the SEED, an open-source software environment for comparative
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The physics of musical scales: Theory and experiment
Durfee, Dallin S.; Colton, John S.
2015-10-01
The theory of musical scales involves mathematical ratios, harmonic resonators, beats, and human perception and provides an interesting application of the physics of waves and sound. We first review the history and physics of musical scales, with an emphasis on four historically important scales: twelve-tone equal temperament, Pythagorean, quarter-comma meantone, and Ptolemaic just intonation. We then present an easy way for students and teachers to directly experience the qualities of different scales using MIDI synthesis.
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Another scheme for quantization of scale invariant gauge theories
International Nuclear Information System (INIS)
Hortacsu, M.
1987-10-01
A new scheme is proposed for the quantization of scale invariant gauge theories for all even dimensions when they are minimally coupled to a spinor field. A cut-off procedure suggests an algorithm which may regularize the theory. (author). 10 refs
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Allometric scaling and cell ratios in multi-organ in vitro models of human metabolism
Directory of Open Access Journals (Sweden)
Nadia eUcciferri
2014-12-01
Full Text Available Intelligent in vitro models able to recapitulate the physiological interactions between tissues in the body have enormous potential as they enable detailed studies on specific two-way or higher order tissue communication. These models are the first step towards building an integrated picture of systemic metabolism and signalling in physiological or pathological conditions. However the rational design of in vitro models of cell-cell or cell-tissue interaction is difficult as quite often cell culture experiments are driven by the device used, rather than by design considerations. Indeed very little research has been carried out on in vitro models of metabolism connecting different cell or tissue types in a physiologically and metabolically relevant manner. Here we analyse the physiologic relationship between cells, cell metabolism and exchange in the human body using allometric rules, downscaling them to an organ-on-a plate device. In particular, in order to establish appropriate cell ratios in the system in a rational manner, two different allometric scaling models (Cell Number Scaling Model, CNSM, and Metabolic and Surface Scaling model, MSSM are proposed and applied to a two compartment model of hepatic-vascular metabolic cross-talk. The theoretical scaling studies illustrate that the design and hence relevance of multi-organ models is principally determined by experimental constraints. Two experimentally feasible model configurations are then implemented in a multi-compartment organ-on-a plate device. An analysis of the metabolic response of the two configurations demonstrates that their glucose and lipid balance is quite different, with only one of the two models recapitulating physiological-like homeostasis. In conclusion, not only do cross-talk and physical stimuli play an important role in in vitro models, but the numeric relationship between cells is also crucial to recreate in vitro interactions which can be extrapolated to the in vivo
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Allometric Scaling and Cell Ratios in Multi-Organ in vitro Models of Human Metabolism
International Nuclear Information System (INIS)
Ucciferri, Nadia; Sbrana, Tommaso; Ahluwalia, Arti
2014-01-01
Intelligent in vitro models able to recapitulate the physiological interactions between tissues in the body have enormous potential as they enable detailed studies on specific two-way or higher order tissue communication. These models are the first step toward building an integrated picture of systemic metabolism and signaling in physiological or pathological conditions. However, the rational design of in vitro models of cell–cell or cell–tissue interaction is difficult as quite often cell culture experiments are driven by the device used, rather than by design considerations. Indeed, very little research has been carried out on in vitro models of metabolism connecting different cell or tissue types in a physiologically and metabolically relevant manner. Here, we analyze the physiological relationship between cells, cell metabolism, and exchange in the human body using allometric rules, downscaling them to an organ-on-a-plate device. In particular, in order to establish appropriate cell ratios in the system in a rational manner, two different allometric scaling models (cell number scaling model and metabolic and surface scaling model) are proposed and applied to a two compartment model of hepatic-vascular metabolic cross-talk. The theoretical scaling studies illustrate that the design and hence relevance of multi-organ models is principally determined by experimental constraints. Two experimentally feasible model configurations are then implemented in a multi-compartment organ-on-a-plate device. An analysis of the metabolic response of the two configurations demonstrates that their glucose and lipid balance is quite different, with only one of the two models recapitulating physiological-like homeostasis. In conclusion, not only do cross-talk and physical stimuli play an important role in in vitro models, but the numeric relationship between cells is also crucial to recreate in vitro interactions, which can be extrapolated to the in vivo reality.
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Allometric Scaling and Cell Ratios in Multi-Organ in vitro Models of Human Metabolism
Energy Technology Data Exchange (ETDEWEB)
Ucciferri, Nadia [CNR Institute of Clinical Physiology, Pisa (Italy); Interdepartmental Research Center “E. Piaggio”, University of Pisa, Pisa (Italy); Sbrana, Tommaso [Interdepartmental Research Center “E. Piaggio”, University of Pisa, Pisa (Italy); Ahluwalia, Arti, E-mail: arti.ahluwalia@unipi.it [CNR Institute of Clinical Physiology, Pisa (Italy); Interdepartmental Research Center “E. Piaggio”, University of Pisa, Pisa (Italy)
2014-12-17
Intelligent in vitro models able to recapitulate the physiological interactions between tissues in the body have enormous potential as they enable detailed studies on specific two-way or higher order tissue communication. These models are the first step toward building an integrated picture of systemic metabolism and signaling in physiological or pathological conditions. However, the rational design of in vitro models of cell–cell or cell–tissue interaction is difficult as quite often cell culture experiments are driven by the device used, rather than by design considerations. Indeed, very little research has been carried out on in vitro models of metabolism connecting different cell or tissue types in a physiologically and metabolically relevant manner. Here, we analyze the physiological relationship between cells, cell metabolism, and exchange in the human body using allometric rules, downscaling them to an organ-on-a-plate device. In particular, in order to establish appropriate cell ratios in the system in a rational manner, two different allometric scaling models (cell number scaling model and metabolic and surface scaling model) are proposed and applied to a two compartment model of hepatic-vascular metabolic cross-talk. The theoretical scaling studies illustrate that the design and hence relevance of multi-organ models is principally determined by experimental constraints. Two experimentally feasible model configurations are then implemented in a multi-compartment organ-on-a-plate device. An analysis of the metabolic response of the two configurations demonstrates that their glucose and lipid balance is quite different, with only one of the two models recapitulating physiological-like homeostasis. In conclusion, not only do cross-talk and physical stimuli play an important role in in vitro models, but the numeric relationship between cells is also crucial to recreate in vitro interactions, which can be extrapolated to the in vivo reality.
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Allometric Scaling and Cell Ratios in Multi-Organ in vitro Models of Human Metabolism.
Ucciferri, Nadia; Sbrana, Tommaso; Ahluwalia, Arti
2014-01-01
Intelligent in vitro models able to recapitulate the physiological interactions between tissues in the body have enormous potential as they enable detailed studies on specific two-way or higher order tissue communication. These models are the first step toward building an integrated picture of systemic metabolism and signaling in physiological or pathological conditions. However, the rational design of in vitro models of cell-cell or cell-tissue interaction is difficult as quite often cell culture experiments are driven by the device used, rather than by design considerations. Indeed, very little research has been carried out on in vitro models of metabolism connecting different cell or tissue types in a physiologically and metabolically relevant manner. Here, we analyze the physiological relationship between cells, cell metabolism, and exchange in the human body using allometric rules, downscaling them to an organ-on-a-plate device. In particular, in order to establish appropriate cell ratios in the system in a rational manner, two different allometric scaling models (cell number scaling model and metabolic and surface scaling model) are proposed and applied to a two compartment model of hepatic-vascular metabolic cross-talk. The theoretical scaling studies illustrate that the design and hence relevance of multi-organ models is principally determined by experimental constraints. Two experimentally feasible model configurations are then implemented in a multi-compartment organ-on-a-plate device. An analysis of the metabolic response of the two configurations demonstrates that their glucose and lipid balance is quite different, with only one of the two models recapitulating physiological-like homeostasis. In conclusion, not only do cross-talk and physical stimuli play an important role in in vitro models, but the numeric relationship between cells is also crucial to recreate in vitro interactions, which can be extrapolated to the in vivo reality.
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Testing the Grandchildren's Received Affection Scale using Affection Exchange Theory.
Mansson, Daniel H
2013-04-01
The purpose of this study was to test the Grandchildren's Received Affection Scale (GRAS) using Affection Exchange Theory (Floyd, 2006). In accordance with Affection Exchange Theory, it was hypothesized that grandchildren's scores on the Trait Affection Received Scale (i.e., the extent to which individuals by nature receive affection) would be related significantly and positively to their reports of received affection from their grandparents (i.e., their scores on the GRAS). Additionally, a research question was asked to explore if grandchildren's received affection from their grandparents is dependent on their grandparent's biological sex or lineage (i.e., maternal vs paternal). Thus, young adult grandchildren (N = 422) completed the GRAS and the Trait Affection Received Scale. The results of zero-order Pearson correlational analyses provided support for the hypothesis, whereas the results of MANOVAs tests only partially support extant grandparent-grandchild theory and research. These findings broaden the scope of Affection Exchange Theory and also bolster the GRAS's utility in future grandparent-grandchild affectionate communication research.
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A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.
Directory of Open Access Journals (Sweden)
Hojung Nam
2014-09-01
Full Text Available Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH, succinate dehydrogenase (SDH, and fumarate hydratase (FH that produce oncometabolites that competitively inhibit epigenetic regulation. In this study, we demonstrate in silico predictions of oncometabolites that have the potential to dysregulate epigenetic controls in nine types of cancer by incorporating massive scale genetic mutation information (collected from more than 1,700 cancer genomes, expression profiling data, and deploying Recon 2 to reconstruct context-specific genome-scale metabolic models. Our analysis predicted 15 compounds and 24 substructures of potential oncometabolites that could result from the loss-of-function and gain-of-function mutations of metabolic enzymes, respectively. These results suggest a substantial potential for discovering unidentified oncometabolites in various forms of cancers.
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Advanced computational workflow for the multi-scale modeling of the bone metabolic processes.
Dao, Tien Tuan
2017-06-01
Multi-scale modeling of the musculoskeletal system plays an essential role in the deep understanding of complex mechanisms underlying the biological phenomena and processes such as bone metabolic processes. Current multi-scale models suffer from the isolation of sub-models at each anatomical scale. The objective of this present work was to develop a new fully integrated computational workflow for simulating bone metabolic processes at multi-scale levels. Organ-level model employs multi-body dynamics to estimate body boundary and loading conditions from body kinematics. Tissue-level model uses finite element method to estimate the tissue deformation and mechanical loading under body loading conditions. Finally, cell-level model includes bone remodeling mechanism through an agent-based simulation under tissue loading. A case study on the bone remodeling process located on the human jaw was performed and presented. The developed multi-scale model of the human jaw was validated using the literature-based data at each anatomical level. Simulation outcomes fall within the literature-based ranges of values for estimated muscle force, tissue loading and cell dynamics during bone remodeling process. This study opens perspectives for accurately simulating bone metabolic processes using a fully integrated computational workflow leading to a better understanding of the musculoskeletal system function from multiple length scales as well as to provide new informative data for clinical decision support and industrial applications.
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Broddrick, Jared T.; Rubin, Benjamin E.; Welkie, David G.; Du, Niu; Mih, Nathan; Diamond, Spencer; Lee, Jenny J.; Golden, Susan S.; Palsson, Bernhard O.
2016-01-01
The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism. The model explicitly describes photon absorption and accounts for shading, resulting in the characteristic linear growth curve of photoautotrophs. GEM predictions of gene essentiality were compared with data obtained from recent dense-transposon mutagenesis experiments. This dataset allowed major improvements to the accuracy of the model. Furthermore, discrepancies between GEM predictions and the in vivo dataset revealed biological characteristics, such as the importance of a truncated, linear TCA pathway, low flux toward amino acid synthesis from photorespiration, and knowledge gaps within nucleotide metabolism. Coupling of strong experimental support and photoautotrophic modeling methods thus resulted in a highly accurate model of S. elongatus metabolism that highlights previously unknown areas of S. elongatus biology. PMID:27911809
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Scaling in the sine-Gordon theory
International Nuclear Information System (INIS)
Ben-Abraham, S.I.
1976-01-01
It is shown that both the classical and the quantum sine-Gordon theory depend on a single scaling parameter and therefore the coupling constant cannot be freely chosen. To introduce a meaningful coupling constant it is proposed to include higher Fourier terms in the sine-Gordon potential. The two term case is exactly solvable. (Auth.)
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Genome-scale metabolic representation of Amycolatopsis balhimycina
DEFF Research Database (Denmark)
Vongsangnak, Wanwipa; Figueiredo, L. F.; Förster, Jochen
2012-01-01
Infection caused by methicillin‐resistant Staphylococcus aureus (MRSA) is an increasing societal problem. Typically, glycopeptide antibiotics are used in the treatment of these infections. The most comprehensively studied glycopeptide antibiotic biosynthetic pathway is that of balhimycin...... to reconstruct a genome‐scale metabolic model for the organism. Here we generated an almost complete A. balhimycina genome sequence comprising 10,562,587 base pairs assembled into 2,153 contigs. The high GC‐genome (∼69%) includes 8,585 open reading frames (ORFs). We used our integrative toolbox called SEQTOR...
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The relationship between body mass and field metabolic rate among individual birds and mammals.
Hudson, Lawrence N; Isaac, Nick J B; Reuman, Daniel C
2013-09-01
1. The power-law dependence of metabolic rate on body mass has major implications at every level of ecological organization. However, the overwhelming majority of studies examining this relationship have used basal or resting metabolic rates, and/or have used data consisting of species-averaged masses and metabolic rates. Field metabolic rates are more ecologically relevant and are probably more directly subject to natural selection than basal rates. Individual rates might be more important than species-average rates in determining the outcome of ecological interactions, and hence selection. 2. We here provide the first comprehensive database of published field metabolic rates and body masses of individual birds and mammals, containing measurements of 1498 animals of 133 species in 28 orders. We used linear mixed-effects models to answer questions about the body mass scaling of metabolic rate and its taxonomic universality/heterogeneity that have become classic areas of controversy. Our statistical approach allows mean scaling exponents and taxonomic heterogeneity in scaling to be analysed in a unified way while simultaneously accounting for nonindependence in the data due to shared evolutionary history of related species. 3. The mean power-law scaling exponents of metabolic rate vs. body mass relationships were 0.71 [95% confidence intervals (CI) 0.625-0.795] for birds and 0.64 (95% CI 0.564-0.716) for mammals. However, these central tendencies obscured meaningful taxonomic heterogeneity in scaling exponents. The primary taxonomic level at which heterogeneity occurred was the order level. Substantial heterogeneity also occurred at the species level, a fact that cannot be revealed by species-averaged data sets used in prior work. Variability in scaling exponents at both order and species levels was comparable to or exceeded the differences 3/4-2/3 = 1/12 and 0.71-0.64. 4. Results are interpreted in the light of a variety of existing theories. In particular, results
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Net Community Metabolism and Seawater Carbonate Chemistry Scale Non-intuitively with Coral Cover
Directory of Open Access Journals (Sweden)
Heather N. Page
2017-05-01
Full Text Available Coral cover and reef health have been declining globally as reefs face local and global stressors including higher temperature and ocean acidification (OA. Ocean warming and acidification will alter rates of benthic reef metabolism (i.e., primary production, respiration, calcification, and CaCO3 dissolution, but our understanding of community and ecosystem level responses is limited in terms of functional, spatial, and temporal scales. Furthermore, dramatic changes in coral cover and benthic metabolism could alter seawater carbonate chemistry on coral reefs, locally alleviating or exacerbating OA. This study examines how benthic metabolic rates scale with changing coral cover (0–100%, and the subsequent influence of these coral communities on seawater carbonate chemistry based on mesocosm experiments in Bermuda and Hawaii. In Bermuda, no significant differences in benthic metabolism or seawater carbonate chemistry were observed for low (40% and high (80% coral cover due to large variability within treatments. In contrast, significant differences were detected between treatments in Hawaii with benthic metabolic rates increasing with increasing coral cover. Observed increases in daily net community calcification and nighttime net respiration scaled proportionally with coral cover. This was not true for daytime net community organic carbon production rates, which increased the most between 0 and 20% coral cover and then less so between 20 and 100%. Consequently, diel variability in seawater carbonate chemistry increased with increasing coral cover, but absolute values of pH, Ωa, and pCO2 were not significantly different during daytime. To place the results of the mesocosm experiments into a broader context, in situ seawater carbon dioxide (CO2 at three reef sites in Bermuda and Hawaii were also evaluated; reefs with higher coral cover experienced a greater range of diel CO2 levels, complementing the mesocosm results. The results from this study
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Large-scale structure in the universe: Theory vs observations
International Nuclear Information System (INIS)
Kashlinsky, A.; Jones, B.J.T.
1990-01-01
A variety of observations constrain models of the origin of large scale cosmic structures. We review here the elements of current theories and comment in detail on which of the current observational data provide the principal constraints. We point out that enough observational data have accumulated to constrain (and perhaps determine) the power spectrum of primordial density fluctuations over a very large range of scales. We discuss the theories in the light of observational data and focus on the potential of future observations in providing even (and ever) tighter constraints. (orig.)
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The effective field theory of cosmological large scale structures
Energy Technology Data Exchange (ETDEWEB)
Carrasco, John Joseph M. [Stanford Univ., Stanford, CA (United States); Hertzberg, Mark P. [Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States); Senatore, Leonardo [Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)
2012-09-20
Large scale structure surveys will likely become the next leading cosmological probe. In our universe, matter perturbations are large on short distances and small at long scales, i.e. strongly coupled in the UV and weakly coupled in the IR. To make precise analytical predictions on large scales, we develop an effective field theory formulated in terms of an IR effective fluid characterized by several parameters, such as speed of sound and viscosity. These parameters, determined by the UV physics described by the Boltzmann equation, are measured from N-body simulations. We find that the speed of sound of the effective fluid is c2s ≈ 10–6c2 and that the viscosity contributions are of the same order. The fluid describes all the relevant physics at long scales k and permits a manifestly convergent perturbative expansion in the size of the matter perturbations δ(k) for all the observables. As an example, we calculate the correction to the power spectrum at order δ(k)4. As a result, the predictions of the effective field theory are found to be in much better agreement with observation than standard cosmological perturbation theory, already reaching percent precision at this order up to a relatively short scale k ≃ 0.24h Mpc–1.
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Electrodynamics in scale-covariant gravity theory
International Nuclear Information System (INIS)
Mansfield, V.N.; Malin, S.
1980-01-01
Utilizing the inherent scale-invariance of Maxwell's Equations, classical electrodynamics is incorporated into the theory of scale-invariant gravity. In this incorporation the gravitational constant G is shown to transform like β -2 (β is the gauge function), the generalized Lorentz Force Law is derived, the electric charge is shown to be invariant under gauge transformation, and matter creation is shown to be a necessity. In all nontrivial gauges a modified version of QED is obtained. The deviation from standard QED, however, is shown to be beyond the range of experimental detection when G α β -2 . (orig.)
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Divergence of perturbation theory in large scale structures
Pajer, Enrico; van der Woude, Drian
2018-05-01
We make progress towards an analytical understanding of the regime of validity of perturbation theory for large scale structures and the nature of some non-perturbative corrections. We restrict ourselves to 1D gravitational collapse, for which exact solutions before shell crossing are known. We review the convergence of perturbation theory for the power spectrum, recently proven by McQuinn and White [1], and extend it to non-Gaussian initial conditions and the bispectrum. In contrast, we prove that perturbation theory diverges for the real space two-point correlation function and for the probability density function (PDF) of the density averaged in cells and all the cumulants derived from it. We attribute these divergences to the statistical averaging intrinsic to cosmological observables, which, even on very large and "perturbative" scales, gives non-vanishing weight to all extreme fluctuations. Finally, we discuss some general properties of non-perturbative effects in real space and Fourier space.
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Environmental versatility promotes modularity in genome-scale metabolic networks.
Samal, Areejit; Wagner, Andreas; Martin, Olivier C
2011-08-24
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. For such networks, we define a network module as a maximal set of reactions that are fully coupled, i.e., whose fluxes can only vary in fixed proportions. This definition overcomes limitations of purely graph based analyses of metabolism by exploiting the functional links between reactions. We call a metabolic network viable in a given chemical environment if it can synthesize all of an organism's biomass compounds from nutrients in this environment. An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. Using recently developed techniques to randomly sample large numbers of viable metabolic networks from a vast space of metabolic networks, we use flux balance analysis to study in silico metabolic networks that differ in their versatility. We find that highly versatile networks are also highly modular. They contain more modules and more reactions that are organized into modules. Most or all reactions in a module are associated with the same biochemical pathways. Modules that arise in highly versatile networks generally involve reactions that process nutrients or closely related chemicals. We also observe that the metabolism of E. coli is significantly more modular than even our most versatile networks. Our work shows that modularity in metabolic networks can be a by-product of functional constraints, e.g., the need to sustain life in multiple
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Environmental versatility promotes modularity in genome-scale metabolic networks
Directory of Open Access Journals (Sweden)
Wagner Andreas
2011-08-01
Full Text Available Abstract Background The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. For such networks, we define a network module as a maximal set of reactions that are fully coupled, i.e., whose fluxes can only vary in fixed proportions. This definition overcomes limitations of purely graph based analyses of metabolism by exploiting the functional links between reactions. We call a metabolic network viable in a given chemical environment if it can synthesize all of an organism's biomass compounds from nutrients in this environment. An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. Results Using recently developed techniques to randomly sample large numbers of viable metabolic networks from a vast space of metabolic networks, we use flux balance analysis to study in silico metabolic networks that differ in their versatility. We find that highly versatile networks are also highly modular. They contain more modules and more reactions that are organized into modules. Most or all reactions in a module are associated with the same biochemical pathways. Modules that arise in highly versatile networks generally involve reactions that process nutrients or closely related chemicals. We also observe that the metabolism of E. coli is significantly more modular than even our most versatile networks. Conclusions Our work shows that modularity in metabolic networks can be a by-product of functional
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A model for allometric scaling of mammalian metabolism with ambient heat loss
Kwak, Ho Sang; Im, Hong G.; Shim, Eun Bo
2016-01-01
The finding that additional radiative heat loss and the consideration of an outer insulation fur layer attenuate these deviation effects and render the scaling law closer to 2/3 provides in silico evidence for a functional impact of heat transfer mode on the allometric scaling law in mammalian metabolism.
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Novel insights into obesity and diabetes through genome-scale metabolic modeling
Directory of Open Access Journals (Sweden)
Leif eVäremo
2013-04-01
Full Text Available The growing prevalence of metabolic diseases, such as obesity and diabetes, are putting a high strain on global healthcare systems as well as increasing the demand for efficient treatment strategies. More than 360 million people worldwide are suffering from type 2 diabetes and, with the current trends, the projection is that 10% of the global adult population will be affected by 2030. In light of the systemic properties of metabolic diseases as well as the interconnected nature of metabolism, it is necessary to begin taking a holistic approach to study these diseases. Human genome-scale metabolic models (GEMs are topological and mathematical representations of cell metabolism and have proven to be valuable tools in the area of systems biology. Successful applications of GEMs include the process of gaining further biological and mechanistic understanding of diseases, finding potential biomarkers and identifying new drug targets. This review will focus on the modeling of human metabolism in the field of obesity and diabetes, showing its vast range of applications of clinical importance as well as point out future challenges.
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On the Renormalization of the Effective Field Theory of Large Scale Structures
Pajer, Enrico; Zaldarriaga, Matias
2013-01-01
Standard perturbation theory (SPT) for large-scale matter inhomogeneities is unsatisfactory for at least three reasons: there is no clear expansion parameter since the density contrast is not small on all scales; it does not fully account for deviations at large scales from a perfect pressureless fluid induced by short-scale non-linearities; for generic initial conditions, loop corrections are UV-divergent, making predictions cutoff dependent and hence unphysical. The Effective Field Theory o...
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Finite size scaling and lattice gauge theory
International Nuclear Information System (INIS)
Berg, B.A.
1986-01-01
Finite size (Fisher) scaling is investigated for four dimensional SU(2) and SU(3) lattice gauge theories without quarks. It allows to disentangle violations of (asymptotic) scaling and finite volume corrections. Mass spectrum, string tension, deconfinement temperature and lattice β-function are considered. For appropriate volumes, Monte Carlo investigations seem to be able to control the finite volume continuum limit. Contact is made with Luescher's small volume expansion and possibly also with the asymptotic large volume behavior. 41 refs., 19 figs
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Genome scale metabolic network reconstruction of Spirochaeta cellobiosiphila
Directory of Open Access Journals (Sweden)
Bharat Manna
2017-10-01
Full Text Available Substantial rise in the global energy demand is one of the biggest challenges in this century. Environmental pollution due to rapid depletion of the fossil fuel resources and its alarming impact on the climate change and Global Warming have motivated researchers to look for non-petroleum-based sustainable, eco-friendly, renewable, low-cost energy alternatives, such as biofuel. Lignocellulosic biomass is one of the most promising bio-resources with huge potential to contribute to this worldwide energy demand. However, the complex organization of the Cellulose, Hemicellulose and Lignin in the Lignocellulosic biomass requires extensive pre-treatment and enzymatic hydrolysis followed by fermentation, raising overall production cost of biofuel. This encourages researchers to design cost-effective approaches for the production of second generation biofuels. The products from enzymatic hydrolysis of cellulose are mostly glucose monomer or cellobiose unit that are subjected to fermentation. Spirochaeta genus is a well-known group of obligate or facultative anaerobes, living primarily on carbohydrate metabolism. Spirochaeta cellobiosiphila sp. is a facultative anaerobe under this genus, which uses a variety of monosaccharides and disaccharides as energy sources. However, most rapid growth occurs on cellobiose and fermentation yields significant amount of ethanol, acetate, CO2, H2 and small amounts of formate. It is predicted to be promising microbial machinery for industrial fermentation processes for biofuel production. The metabolic pathways that govern cellobiose metabolism in Spirochaeta cellobiosiphila are yet to be explored. The function annotation of the genome sequence of Spirochaeta cellobiosiphila is in progress. In this work we aim to map all the metabolic activities for reconstruction of genome-scale metabolic model of Spirochaeta cellobiosiphila.
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Use of density functional theory in drug metabolism studies
DEFF Research Database (Denmark)
Rydberg, Patrik; Jørgensen, Flemming Steen; Olsen, Lars
2014-01-01
INTRODUCTION: The cytochrome P450 enzymes (CYPs) metabolize many drug compounds. They catalyze a wide variety of reactions, and potentially, a large number of different metabolites can be generated. Density functional theory (DFT) has, over the past decade, been shown to be a powerful tool...... isoforms. This is probably due to the fact that the binding of the substrates is not the major determinant. When binding of the substrate plays a significant role, the well-known issue of determining the free energy of binding is the challenge. How approaches taking the protein environment into account...
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Sequential Progressions in a Theory of Mind Scale: Longitudinal Perspectives
Wellman, Henry M.; Fuxi, Fang; Peterson, Candida C.
2011-01-01
Consecutive re-testings of 92 U.S. preschoolers (n = 30), Chinese preschoolers (n = 31), and deaf children (n = 31) examined whether the sequences of development apparent in cross-sectional results with a theory-of-mind scale also appeared in longitudinal assessment. Longitudinal data confirmed that theory-of-mind progressions apparent in cross-sectional scaling data also characterized longitudinal sequences of understanding for individual children. The match between cross-sectional and longitudinal sequences appeared for children who exhibit different progressions across cultures (U.S. vs. China) and for children with substantial delays (deaf children of hearing parents). Moreover, greater scale distances reflected larger longitudinal age differences. PMID:21428982
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Characterizing steady states of genome-scale metabolic networks in continuous cell cultures.
Directory of Open Access Journals (Sweden)
Jorge Fernandez-de-Cossio-Diaz
2017-11-01
Full Text Available In the continuous mode of cell culture, a constant flow carrying fresh media replaces culture fluid, cells, nutrients and secreted metabolites. Here we present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct accumulation. We provide a method to determine the steady states of this system that is tractable for metabolic networks of arbitrary complexity. We demonstrate our approach in a toy model first, and then in a genome-scale metabolic network of the Chinese hamster ovary cell line, obtaining results that are in qualitative agreement with experimental observations. We derive a number of consequences from the model that are independent of parameter values. The ratio between cell density and dilution rate is an ideal control parameter to fix a steady state with desired metabolic properties. This conclusion is robust even in the presence of multi-stability, which is explained in our model by a negative feedback loop due to toxic byproduct accumulation. A complex landscape of steady states emerges from our simulations, including multiple metabolic switches, which also explain why cell-line and media benchmarks carried out in batch culture cannot be extrapolated to perfusion. On the other hand, we predict invariance laws between continuous cell cultures with different parameters. A practical consequence is that the chemostat is an ideal experimental model for large-scale high-density perfusion cultures, where the complex landscape of metabolic transitions is faithfully reproduced.
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Energy Technology Data Exchange (ETDEWEB)
Kubo, R; Takahashi, Y; Yokoyama, K
1975-01-01
In a wide class of neutral vector field theories, in which massive and massless fields are described in a unified way and a unique massless limit exists to quantum electrodynamics in covariant gauges, the commutability of the scale transformation and the massless limit is examined. It is shown that there occurs no anomaly with respect to the assignment for scale dimensions of relevant fields. Connection of scale transformation and gauge transformation is also discussed.
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SCALE Sensitivity Calculations Using Contributon Theory
International Nuclear Information System (INIS)
Rearden, Bradley T.; Perfetti, Chris; Williams, Mark L.; Petrie, Lester M. Jr.
2010-01-01
The SCALE TSUNAMI-3D sensitivity and uncertainty analysis sequence computes the sensitivity of k-eff to each constituent multigroup cross section using adjoint techniques with the KENO Monte Carlo codes. A new technique to simultaneously obtain the product of the forward and adjoint angular flux moments within a single Monte Carlo calculation has been developed and implemented in the SCALE TSUNAMI-3D analysis sequence. A new concept in Monte Carlo theory has been developed for this work, an eigenvalue contributon estimator, which is an extension of previously developed fixed-source contributon estimators. A contributon is a particle for which the forward solution is accumulated, and its importance to the response, which is equivalent to the adjoint solution, is simultaneously accumulated. Thus, the contributon is a particle coupled with its contribution to the response, in this case k-eff. As implemented in SCALE, the contributon provides the importance of a particle exiting at any energy or direction for each location, energy and direction at which the forward flux solution is sampled. Although currently implemented for eigenvalue calculations in multigroup mode in KENO, this technique is directly applicable to continuous-energy calculations for many other responses such as fixed-source sensitivity analysis and quantification of reactor kinetics parameters. This paper provides the physical bases of eigenvalue contributon theory, provides details of implementation into TSUNAMI-3D, and provides results of sample calculations.
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Jiang, Zhenhong; He, Fei; Zhang, Ziding
2017-07-01
Through large-scale transcriptional data analyses, we highlighted the importance of plant metabolism in plant immunity and identified 26 metabolic pathways that were frequently influenced by the infection of 14 different pathogens. Reprogramming of plant metabolism is a common phenomenon in plant defense responses. Currently, a large number of transcriptional profiles of infected tissues in Arabidopsis (Arabidopsis thaliana) have been deposited in public databases, which provides a great opportunity to understand the expression patterns of metabolic pathways during plant defense responses at the systems level. Here, we performed a large-scale transcriptome analysis based on 135 previously published expression samples, including 14 different pathogens, to explore the expression pattern of Arabidopsis metabolic pathways. Overall, metabolic genes are significantly changed in expression during plant defense responses. Upregulated metabolic genes are enriched on defense responses, and downregulated genes are enriched on photosynthesis, fatty acid and lipid metabolic processes. Gene set enrichment analysis (GSEA) identifies 26 frequently differentially expressed metabolic pathways (FreDE_Paths) that are differentially expressed in more than 60% of infected samples. These pathways are involved in the generation of energy, fatty acid and lipid metabolism as well as secondary metabolite biosynthesis. Clustering analysis based on the expression levels of these 26 metabolic pathways clearly distinguishes infected and control samples, further suggesting the importance of these metabolic pathways in plant defense responses. By comparing with FreDE_Paths from abiotic stresses, we find that the expression patterns of 26 FreDE_Paths from biotic stresses are more consistent across different infected samples. By investigating the expression correlation between transcriptional factors (TFs) and FreDE_Paths, we identify several notable relationships. Collectively, the current study
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Scaling theory of quantum resistance distributions in disordered systems
International Nuclear Information System (INIS)
Jayannavar, A.M.
1991-01-01
The large scale distribution of quantum Ohmic resistance of a disorderd one-dimensional conductor is derived explicitly. It is shown that in the thermodynamic limit this distribution is characterized by two independent parameters for strong disorder, leading to a two-parameter scaling theory of localization. Only in the limit of weak disorder single parameter scaling consistent with existing theoretical treatments is recovered. (author). 33 refs., 4 figs
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Scaling theory of quantum resistance distributions in disordered systems
International Nuclear Information System (INIS)
Jayannavar, A.M.
1990-05-01
We have derived explicitly, the large scale distribution of quantum Ohmic resistance of a disordered one-dimensional conductor. We show that in the thermodynamic limit this distribution is characterized by two independent parameters for strong disorder, leading to a two-parameter scaling theory of localization. Only in the limit of weak disorder we recover single parameter scaling, consistent with existing theoretical treatments. (author). 32 refs, 4 figs
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Deconfinement phase transition and finite-size scaling in SU(2) lattice gauge theory
International Nuclear Information System (INIS)
Mogilevskij, O.A.
1988-01-01
Calculation technique for deconfinement phase transition parameters based on application of finite-size scaling theory is suggested. The essence of the technique lies in plotting of universal scaling function on the basis of numerical data obtained at different-size final lattices and discrimination of phase transition parameters for infinite lattice system. Finite-size scaling technique was developed as applied to spin system theory. β critical index for Polyakov loop and SU(2) deconfinement temperature of lattice gauge theory are calculated on the basis of finite-size scaling technique. The obtained value agrees with critical index of magnetization in Ising three-dimensional model
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Genome-scale metabolic models applied to human health and disease.
Cook, Daniel J; Nielsen, Jens
2017-11-01
Advances in genome sequencing, high throughput measurement of gene and protein expression levels, data accessibility, and computational power have allowed genome-scale metabolic models (GEMs) to become a useful tool for understanding metabolic alterations associated with many different diseases. Despite the proven utility of GEMs, researchers confront multiple challenges in the use of GEMs, their application to human health and disease, and their construction and simulation in an organ-specific and disease-specific manner. Several approaches that researchers are taking to address these challenges include using proteomic and transcriptomic-informed methods to build GEMs for individual organs, diseases, and patients and using constraints on model behavior during simulation to match observed metabolic fluxes. We review the challenges facing researchers in the use of GEMs, review the approaches used to address these challenges, and describe advances that are on the horizon and could lead to a better understanding of human metabolism. WIREs Syst Biol Med 2017, 9:e1393. doi: 10.1002/wsbm.1393 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.
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Quantum no-scale regimes in string theory
Coudarchet, Thibaut; Fleming, Claude; Partouche, Hervé
2018-05-01
We show that in generic no-scale models in string theory, the flat, expanding cosmological evolutions found at the quantum level can be attracted to a "quantum no-scale regime", where the no-scale structure is restored asymptotically. In this regime, the quantum effective potential is dominated by the classical kinetic energies of the no-scale modulus and dilaton. We find that this natural preservation of the classical no-scale structure at the quantum level occurs when the initial conditions of the evolutions sit in a subcritical region of their space. On the contrary, supercritical initial conditions yield solutions that have no analogue at the classical level. The associated intrinsically quantum universes are sentenced to collapse and their histories last finite cosmic times. Our analysis is done at 1-loop, in perturbative heterotic string compactified on tori, with spontaneous supersymmetry breaking implemented by a stringy version of the Scherk-Schwarz mechanism.
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Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm
Energy Technology Data Exchange (ETDEWEB)
Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane; Zarecki, Raphy; Ruppin, Eytan; Hanson, Andrew D.; Henry, Christopher S.
2015-03-10
There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.
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Enumeration of smallest intervention strategies in genome-scale metabolic networks.
Directory of Open Access Journals (Sweden)
Axel von Kamp
2014-01-01
Full Text Available One ultimate goal of metabolic network modeling is the rational redesign of biochemical networks to optimize the production of certain compounds by cellular systems. Although several constraint-based optimization techniques have been developed for this purpose, methods for systematic enumeration of intervention strategies in genome-scale metabolic networks are still lacking. In principle, Minimal Cut Sets (MCSs; inclusion-minimal combinations of reaction or gene deletions that lead to the fulfilment of a given intervention goal provide an exhaustive enumeration approach. However, their disadvantage is the combinatorial explosion in larger networks and the requirement to compute first the elementary modes (EMs which itself is impractical in genome-scale networks. We present MCSEnumerator, a new method for effective enumeration of the smallest MCSs (with fewest interventions in genome-scale metabolic network models. For this we combine two approaches, namely (i the mapping of MCSs to EMs in a dual network, and (ii a modified algorithm by which shortest EMs can be effectively determined in large networks. In this way, we can identify the smallest MCSs by calculating the shortest EMs in the dual network. Realistic application examples demonstrate that our algorithm is able to list thousands of the most efficient intervention strategies in genome-scale networks for various intervention problems. For instance, for the first time we could enumerate all synthetic lethals in E.coli with combinations of up to 5 reactions. We also applied the new algorithm exemplarily to compute strain designs for growth-coupled synthesis of different products (ethanol, fumarate, serine by E.coli. We found numerous new engineering strategies partially requiring less knockouts and guaranteeing higher product yields (even without the assumption of optimal growth than reported previously. The strength of the presented approach is that smallest intervention strategies can be
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Network Thermodynamic Curation of Human and Yeast Genome-Scale Metabolic Models
Martínez, Verónica S.; Quek, Lake-Ee; Nielsen, Lars K.
2014-01-01
Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. PMID:25028891
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DEFF Research Database (Denmark)
Geng, Jun; Nielsen, Jens
2017-01-01
The arising prevalence of metabolic diseases calls for a holistic approach for analysis of the underlying nature of abnormalities in cellular functions. Through mathematic representation and topological analysis of cellular metabolism, GEnome scale metabolic Models (GEMs) provide a promising fram...... that correctly describe interactions between cells or tissues, and we therefore discuss how GEMs can be integrated with blood circulation models. Finally, we end the review with proposing some possible future research directions....
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Perturbation theory instead of large scale shell model calculations
International Nuclear Information System (INIS)
Feldmeier, H.; Mankos, P.
1977-01-01
Results of large scale shell model calculations for (sd)-shell nuclei are compared with a perturbation theory provides an excellent approximation when the SU(3)-basis is used as a starting point. The results indicate that perturbation theory treatment in an SU(3)-basis including 2hω excitations should be preferable to a full diagonalization within the (sd)-shell. (orig.) [de
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Non-equilibrium mean-field theories on scale-free networks
International Nuclear Information System (INIS)
Caccioli, Fabio; Dall'Asta, Luca
2009-01-01
Many non-equilibrium processes on scale-free networks present anomalous critical behavior that is not explained by standard mean-field theories. We propose a systematic method to derive stochastic equations for mean-field order parameters that implicitly account for the degree heterogeneity. The method is used to correctly predict the dynamical critical behavior of some binary spin models and reaction–diffusion processes. The validity of our non-equilibrium theory is further supported by showing its relation with the generalized Landau theory of equilibrium critical phenomena on networks
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Vongsangnak, Wanwipa; Klanchui, Amornpan; Tawornsamretkit, Iyarest; Tatiyaborwornchai, Witthawin; Laoteng, Kobkul; Meechai, Asawin
2016-06-01
We present a novel genome-scale metabolic model iWV1213 of Mucor circinelloides, which is an oleaginous fungus for industrial applications. The model contains 1213 genes, 1413 metabolites and 1326 metabolic reactions across different compartments. We demonstrate that iWV1213 is able to accurately predict the growth rates of M. circinelloides on various nutrient sources and culture conditions using Flux Balance Analysis and Phenotypic Phase Plane analysis. Comparative analysis of three oleaginous genome-scale models, including M. circinelloides (iWV1213), Mortierella alpina (iCY1106) and Yarrowia lipolytica (iYL619_PCP) revealed that iWV1213 possesses a higher number of genes involved in carbohydrate, amino acid, and lipid metabolisms that might contribute to its versatility in nutrient utilization. Moreover, the identification of unique and common active reactions among the Zygomycetes oleaginous models using Flux Variability Analysis unveiled a set of gene/enzyme candidates as metabolic engineering targets for cellular improvement. Thus, iWV1213 offers a powerful metabolic engineering tool for multi-level omics analysis, enabling strain optimization as a cell factory platform of lipid-based production. Copyright © 2016 Elsevier B.V. All rights reserved.
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Scaling theory of depinning in the Sneppen model
International Nuclear Information System (INIS)
Maslov, S.; Paczuski, M.
1994-01-01
We develop a scaling theory for the critical depinning behavior of the Sneppen interface model [Phys. Rev. Lett. 69, 3539 (1992)]. This theory is based on a ''gap'' equation that describes the self-organization process to a critical state of the depinning transition. All of the critical exponents can be expressed in terms of two independent exponents, ν parallel (d) and ν perpendicular (d), characterizing the divergence of the parallel and perpendicular correlation lengths as the interface approaches its dynamical attractor
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Sadhukhan, Priyanka P; Raghunathan, Anu
2014-01-01
Genome Scale Metabolic Modeling methods represent one way to compute whole cell function starting from the genome sequence of an organism and contribute towards understanding and predicting the genotype-phenotype relationship. About 80 models spanning all the kingdoms of life from archaea to eukaryotes have been built till date and used to interrogate cell phenotype under varying conditions. These models have been used to not only understand the flux distribution in evolutionary conserved pathways like glycolysis and the Krebs cycle but also in applications ranging from value added product formation in Escherichia coli to predicting inborn errors of Homo sapiens metabolism. This chapter describes a protocol that delineates the process of genome scale metabolic modeling for analysing host-pathogen behavior and interaction using flux balance analysis (FBA). The steps discussed in the process include (1) reconstruction of a metabolic network from the genome sequence, (2) its representation in a precise mathematical framework, (3) its translation to a model, and (4) the analysis using linear algebra and optimization. The methods for biological interpretations of computed cell phenotypes in the context of individual host and pathogen models and their integration are also discussed.
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Cordes, Henrik; Thiel, Christoph; Baier, Vanessa; Blank, Lars M; Kuepfer, Lars
2018-01-01
Drug-induced perturbations of the endogenous metabolic network are a potential root cause of cellular toxicity. A mechanistic understanding of such unwanted side effects during drug therapy is therefore vital for patient safety. The comprehensive assessment of such drug-induced injuries requires the simultaneous consideration of both drug exposure at the whole-body and resulting biochemical responses at the cellular level. We here present a computational multi-scale workflow that combines whole-body physiologically based pharmacokinetic (PBPK) models and organ-specific genome-scale metabolic network (GSMN) models through shared reactions of the xenobiotic metabolism. The applicability of the proposed workflow is illustrated for isoniazid, a first-line antibacterial agent against Mycobacterium tuberculosis , which is known to cause idiosyncratic drug-induced liver injuries (DILI). We combined GSMN models of a human liver with N-acetyl transferase 2 (NAT2)-phenotype-specific PBPK models of isoniazid. The combined PBPK-GSMN models quantitatively describe isoniazid pharmacokinetics, as well as intracellular responses, and changes in the exometabolome in a human liver following isoniazid administration. Notably, intracellular and extracellular responses identified with the PBPK-GSMN models are in line with experimental and clinical findings. Moreover, the drug-induced metabolic perturbations are distributed and attenuated in the metabolic network in a phenotype-dependent manner. Our simulation results show that a simultaneous consideration of both drug pharmacokinetics at the whole-body and metabolism at the cellular level is mandatory to explain drug-induced injuries at the patient level. The proposed workflow extends our mechanistic understanding of the biochemistry underlying adverse events and may be used to prevent drug-induced injuries in the future.
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Network thermodynamic curation of human and yeast genome-scale metabolic models.
Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K
2014-07-15
Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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On the renormalization of the effective field theory of large scale structures
International Nuclear Information System (INIS)
Pajer, Enrico; Zaldarriaga, Matias
2013-01-01
Standard perturbation theory (SPT) for large-scale matter inhomogeneities is unsatisfactory for at least three reasons: there is no clear expansion parameter since the density contrast is not small on all scales; it does not fully account for deviations at large scales from a perfect pressureless fluid induced by short-scale non-linearities; for generic initial conditions, loop corrections are UV-divergent, making predictions cutoff dependent and hence unphysical. The Effective Field Theory of Large Scale Structures successfully addresses all three issues. Here we focus on the third one and show explicitly that the terms induced by integrating out short scales, neglected in SPT, have exactly the right scale dependence to cancel all UV-divergences at one loop, and this should hold at all loops. A particularly clear example is an Einstein deSitter universe with no-scale initial conditions P in ∼ k n . After renormalizing the theory, we use self-similarity to derive a very simple result for the final power spectrum for any n, excluding two-loop corrections and higher. We show how the relative importance of different corrections depends on n. For n ∼ −1.5, relevant for our universe, pressure and dissipative corrections are more important than the two-loop corrections
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On the renormalization of the effective field theory of large scale structures
Energy Technology Data Exchange (ETDEWEB)
Pajer, Enrico [Department of Physics, Princeton University, Princeton, NJ 08544 (United States); Zaldarriaga, Matias, E-mail: enrico.pajer@gmail.com, E-mail: matiasz@ias.edu [Institute for Advanced Study, Princeton, NJ 08544 (United States)
2013-08-01
Standard perturbation theory (SPT) for large-scale matter inhomogeneities is unsatisfactory for at least three reasons: there is no clear expansion parameter since the density contrast is not small on all scales; it does not fully account for deviations at large scales from a perfect pressureless fluid induced by short-scale non-linearities; for generic initial conditions, loop corrections are UV-divergent, making predictions cutoff dependent and hence unphysical. The Effective Field Theory of Large Scale Structures successfully addresses all three issues. Here we focus on the third one and show explicitly that the terms induced by integrating out short scales, neglected in SPT, have exactly the right scale dependence to cancel all UV-divergences at one loop, and this should hold at all loops. A particularly clear example is an Einstein deSitter universe with no-scale initial conditions P{sub in} ∼ k{sup n}. After renormalizing the theory, we use self-similarity to derive a very simple result for the final power spectrum for any n, excluding two-loop corrections and higher. We show how the relative importance of different corrections depends on n. For n ∼ −1.5, relevant for our universe, pressure and dissipative corrections are more important than the two-loop corrections.
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Renormalization and scaling behaviour of eikonal perturbation theories. [Eikonal approximation
Energy Technology Data Exchange (ETDEWEB)
Din, A M [Chalmers Tekniska Hoegskola, Goeteborg (Sweden). Institutionen foer Teoretisk Fysik; Nielsen, N K [Aarhus Univ. (Denmark)
1975-01-04
Some observations on the renormalization and scaling behaviour of the charged-particle propagator in scalar quantum electrodynamics, in the ordinary eikonal approximation as well as in the eikonal perturbation theory, are reported. The conclusions indicate that scaling behaviour is not realized in the simple sense.
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Genome-scale modeling for metabolic engineering.
Simeonidis, Evangelos; Price, Nathan D
2015-03-01
We focus on the application of constraint-based methodologies and, more specifically, flux balance analysis in the field of metabolic engineering, and enumerate recent developments and successes of the field. We also review computational frameworks that have been developed with the express purpose of automatically selecting optimal gene deletions for achieving improved production of a chemical of interest. The application of flux balance analysis methods in rational metabolic engineering requires a metabolic network reconstruction and a corresponding in silico metabolic model for the microorganism in question. For this reason, we additionally present a brief overview of automated reconstruction techniques. Finally, we emphasize the importance of integrating metabolic networks with regulatory information-an area which we expect will become increasingly important for metabolic engineering-and present recent developments in the field of metabolic and regulatory integration.
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Sequential Progressions in a Theory-of-Mind Scale: Longitudinal Perspectives
Wellman, Henry M.; Fang, Fuxi; Peterson, Candida C.
2011-01-01
Consecutive retestings of 92 U.S. preschoolers (n = 30), Chinese preschoolers (n = 31), and deaf children (n = 31) examined whether the sequences of development apparent in cross-sectional results with a theory-of-mind scale also appeared in longitudinal assessment. Longitudinal data confirmed that theory-of-mind progressions apparent in…
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Scaling of theory-of-mind understandings in Chinese children.
Wellman, Henry M; Fang, Fuxi; Liu, David; Zhu, Liqi; Liu, Guoxiong
2006-12-01
Prior research demonstrates that understanding of theory of mind develops at different paces in children raised in different cultures. Are these differences simply differences in timing, or do they represent different patterns of cultural learning? That is, to what extent are sequences of theory-of-mind understanding universal, and to what extent are they culture-specific? We addressed these questions by using a theory-of-mind scale to examine performance of 140 Chinese children living in Beijing and to compare their performance with that of 135 English-speaking children living in the United States and Australia. Results reveal a common sequence of understanding, as well as sociocultural differences in children's developing theories of mind.
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International Nuclear Information System (INIS)
Dash, Satyakam; Mueller, Thomas J.; Venkataramanan, Keerthi P.; Papoutsakis, Eleftherios T.; Maranas, Costas D.
2014-01-01
Clostridia are anaerobic Gram-positive Firmicutes containing broad and flexible systems for substrate utilization, which have been used successfully to produce a range of industrial compounds. Clostridium acetobutylicum has been used to produce butanol on an industrial scale through acetone-butanol-ethanol (ABE) fermentation. A genome-scale metabolic (GSM) model is a powerful tool for understanding the metabolic capacities of an organism and developing metabolic engineering strategies for strain development. The integration of stress related specific transcriptomics information with the GSM model provides opportunities for elucidating the focal points of regulation
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BPS ZN string tensions, sine law and Casimir scaling, and integrable field theories
International Nuclear Information System (INIS)
Kneipp, Marco A. C.
2007-01-01
We consider a Yang-Mills-Higgs theory with spontaneous symmetry breaking of the gauge group G→U(1) r →C G , with C G being the center of G. We study two vacua solutions of the theory which produce this symmetry breaking. We show that for one of these vacua, the theory in the Coulomb phase has the mass spectrum of particles and monopoles which is exactly the same as the mass spectrum of particles and solitons of two-dimensional affine Toda field theory, for suitable coupling constants. That result holds also for N=4 super Yang-Mills theories. On the other hand, in the Higgs phase, we show that for each of the two vacua the ratio of the tensions of the BPS Z N strings satisfy either the Casimir scaling or the sine law scaling for G=SU(N). These results are extended to other gauge groups: for the Casimir scaling, the ratios of the tensions are equal to the ratios of the quadratic Casimir constant of specific representations; for the sine law scaling, the tensions are proportional to the components of the left Perron-Frobenius eigenvector of Cartan matrix K ij and the ratios of tensions are equal to the ratios of the soliton masses of affine Toda field theories
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Levering, J.; Fiedler, T.; Sieg, A.; van Grinsven, K.W.A.; Hering, S.; Veith, N.; Olivier, B.G.; Klett, L.; Hugenholtz, J.; Teusink, B.; Kreikemeyer, B.; Kummer, U.
2016-01-01
Genome-scale metabolic models comprise stoichiometric relations between metabolites, as well as associations between genes and metabolic reactions and facilitate the analysis of metabolism. We computationally reconstructed the metabolic network of the lactic acid bacterium Streptococcus pyogenes
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Branco Dos Santos, Filipe; Olivier, Brett G; Boele, Joost; Smessaert, Vincent; De Rop, Philippe; Krumpochova, Petra; Klau, Gunnar W; Giera, Martin; Dehottay, Philippe; Teusink, Bas; Goffin, Philippe
2017-08-25
Whooping cough is a highly-contagious respiratory disease caused by Bordetella pertussi s. Despite vaccination, its incidence has been rising alarmingly, and yet, the physiology of B. pertussis remains poorly understood. We combined genome-scale metabolic reconstruction, a novel optimization algorithm and experimental data to probe the full metabolic potential of this pathogen, using strain Tohama I as a reference. Experimental validation showed that B. pertussis secretes a significant proportion of nitrogen as arginine and purine nucleosides, which may contribute to modulation of the host response. We also found that B. pertussis can be unexpectedly versatile, being able to metabolize many compounds while displaying minimal nutrient requirements. It can grow without cysteine - using inorganic sulfur sources such as thiosulfate - and it can grow on organic acids such as citrate or lactate as sole carbon sources, providing in vivo demonstration that its TCA cycle is functional. Although the metabolic reconstruction of eight additional strains indicates that the structural genes underlying this metabolic flexibility are widespread, experimental validation suggests a role of strain-specific regulatory mechanisms in shaping metabolic capabilities. Among five alternative strains tested, three were shown to grow on substrate combinations requiring a functional TCA cycle, but only one could use thiosulfate. Finally, the metabolic model was used to rationally design growth media with over two-fold improvements in pertussis toxin production. This study thus provides novel insights into B. pertussis physiology, and highlights the potential, but also limitations of models solely based on metabolic gene content. IMPORTANCE The metabolic capabilities of Bordetella pertussis - the causative agent of whooping cough - were investigated from a systems-level perspective. We constructed a comprehensive genome-scale metabolic model for B. pertussis , and challenged its predictions
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Theory of finite-entanglement scaling at one-dimensional quantum critical points.
Pollmann, Frank; Mukerjee, Subroto; Turner, Ari M; Moore, Joel E
2009-06-26
Studies of entanglement in many-particle systems suggest that most quantum critical ground states have infinitely more entanglement than noncritical states. Standard algorithms for one-dimensional systems construct model states with limited entanglement, which are a worse approximation to quantum critical states than to others. We give a quantitative theory of previously observed scaling behavior resulting from finite entanglement at quantum criticality. Finite-entanglement scaling in one-dimensional systems is governed not by the scaling dimension of an operator but by the "central charge" of the critical point. An important ingredient is the universal distribution of density-matrix eigenvalues at a critical point [P. Calabrese and A. Lefevre, Phys. Rev. A 78, 032329 (2008)10.1103/PhysRevA.78.032329]. The parameter-free theory is checked against numerical scaling at several quantum critical points.
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Scale-covariant theory of gravitation and astrophysical applications
International Nuclear Information System (INIS)
Canuto, V.; Adams, P.J.; Hsieh, S.; Tsiang, E.
1977-01-01
By associating the mathematical operation of scale transformation with the physics of using different dynamical systems to measure space-time distances, we formulate a scale-covariant theory of gravitation. Corresponding to each dynamical system of units is a gauge condition which determines the otherwise arbitrary gauge function. For gravitational units, the gauge condition is chosen so that the standard Einstein equations are recovered. Assuming the atomic units, derivable from atomic dynamics, to be distinct from the gravitational units, a different gauge condition must be imposed. It is suggested that Dirac's large-number hypothesis be used for the determination of this condition so that gravitational phenomena can be described in atomic units. The result allows a natural interpretation of the possible variation of the gravitational constant without compromising the validity of general relativity. A geometrical interpretation of the scale-covariant theory is possible if the covariant tensors in Riemannian space are replaced by cocovariant cotensors in an integrable Weyl space. A scale-invariant action principle is constructed from the metrical potentials of the integrable Weyl space. Application of the dynamical equations in atomic units to cosmology yields a family of homogeneous solutions characterized by R approx. t for large cosmological times. Equations of motion in atomic units are solved for spherically symmetric gravitational fields. Expressions for perihelion shift and light deflection are derived. They do not differ from the predictions of general relativity except for secular variations, having the age of the universe as a time scale. Similar variations of periods and radii for planetary orbits are also derived
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A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism
Hefzi, Hooman
2016-11-23
Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell-line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show that the metabolic resources in CHO are more than three times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.
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Quasi-potential and Two-Scale Large Deviation Theory for Gillespie Dynamics
Li, Tiejun; Li, Fangting; Li, Xianggang; Lu, Cheng
2016-01-01
theory for Gillespie-type jump dynamics. In the application to a typical genetic switching model, the two-scale large deviation theory is developed to take into account the fast switching of DNA states. The comparison with other proposals are also
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A quantization scheme for scale-invariant pure gauge theories
International Nuclear Information System (INIS)
Hortacsu, M.
1988-01-01
A scheme is suggested for the quantization of the recently proposed scale-invariant gauge theories in higher dimensions. The model is minimally coupled to a spinor field. Regularization algorithms are proposed. (orig.)
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Boomerang RG flows in M-theory with intermediate scaling
Donos, Aristomenis; Gauntlett, Jerome P.; Rosen, Christopher; Sosa-Rodriguez, Omar
2017-07-01
We construct novel RG flows of D=11 supergravity that asymptotically approach AdS 4 × S 7 in the UV with deformations that break spatial translations in the dual field theory. In the IR the solutions return to exactly the same AdS 4 × S 7 vacuum, with a renormalisation of relative length scales, and hence we refer to the flows as `boomerang RG flows'. For sufficiently large deformations, on the way to the IR the solutions also approach two distinct intermediate scaling regimes, each with hyperscaling violation. The first regime is Lorentz invariant with dynamical exponent z = 1 while the second has z = 5/2. Neither ofthe two intermediatescaling regimesare associatedwith exact hyperscaling violation solutions of D = 11 supergravity. The RG flow solutions are constructed using the four dimensional N = 2 STU gauged supergravity theory with vanishing gauge fields, but non-vanishing scalar and pseudoscalar fields. In the ABJM dual field theory the flows are driven by spatially modulated deformation parameters for scalar and fermion bilinear operators.
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Time-sliced perturbation theory for large scale structure I: general formalism
Energy Technology Data Exchange (ETDEWEB)
Blas, Diego; Garny, Mathias; Sibiryakov, Sergey [Theory Division, CERN, CH-1211 Genève 23 (Switzerland); Ivanov, Mikhail M., E-mail: diego.blas@cern.ch, E-mail: mathias.garny@cern.ch, E-mail: mikhail.ivanov@cern.ch, E-mail: sergey.sibiryakov@cern.ch [FSB/ITP/LPPC, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne (Switzerland)
2016-07-01
We present a new analytic approach to describe large scale structure formation in the mildly non-linear regime. The central object of the method is the time-dependent probability distribution function generating correlators of the cosmological observables at a given moment of time. Expanding the distribution function around the Gaussian weight we formulate a perturbative technique to calculate non-linear corrections to cosmological correlators, similar to the diagrammatic expansion in a three-dimensional Euclidean quantum field theory, with time playing the role of an external parameter. For the physically relevant case of cold dark matter in an Einstein-de Sitter universe, the time evolution of the distribution function can be found exactly and is encapsulated by a time-dependent coupling constant controlling the perturbative expansion. We show that all building blocks of the expansion are free from spurious infrared enhanced contributions that plague the standard cosmological perturbation theory. This paves the way towards the systematic resummation of infrared effects in large scale structure formation. We also argue that the approach proposed here provides a natural framework to account for the influence of short-scale dynamics on larger scales along the lines of effective field theory.
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Chemical theory and modelling through density across length scales
International Nuclear Information System (INIS)
Ghosh, Swapan K.
2016-01-01
One of the concepts that has played a major role in the conceptual as well as computational developments covering all the length scales of interest in a number of areas of chemistry, physics, chemical engineering and materials science is the concept of single-particle density. Density functional theory has been a versatile tool for the description of many-particle systems across length scales. Thus, in the microscopic length scale, an electron density based description has played a major role in providing a deeper understanding of chemical binding in atoms, molecules and solids. Density concept has been used in the form of single particle number density in the intermediate mesoscopic length scale to obtain an appropriate picture of the equilibrium and dynamical processes, dealing with a wide class of problems involving interfacial science and soft condensed matter. In the macroscopic length scale, however, matter is usually treated as a continuous medium and a description using local mass density, energy density and other related property density functions has been found to be quite appropriate. The basic ideas underlying the versatile uses of the concept of density in the theory and modelling of materials and phenomena, as visualized across length scales, along with selected illustrative applications to some recent areas of research on hydrogen energy, soft matter, nucleation phenomena, isotope separation, and separation of mixture in condensed phase, will form the subject matter of the talk. (author)
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The corrections to scaling within Mazenko's theory in the limit of low ...
Indian Academy of Sciences (India)
functions'. In fact both the scaling functions and scaling exponents describe only the leading behaviour in the theory of scaling phenomena. There may be, and usually are, subdominant corrections, known as corrections to scaling. These corrections cannot be neglected in practice if more accurate values for exponents and ...
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Environmental versatility promotes modularity in large scale metabolic networks
Samal A.; Wagner Andreas; Martin O.C.
2011-01-01
Abstract Background The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chem...
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Agren, Rasmus; Liu, Liming; Shoaie, Saeed; Vongsangnak, Wanwipa; Nookaew, Intawat; Nielsen, Jens
2013-01-01
We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium chrysogenum Wisconsin54-1255. The model was validated in a bibliomic study of in total 440 references, and it comprises 1471 unique biochemical reactions and 1006 ORFs. It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production. PMID:23555215
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Basal metabolic rate scaled to body mass within species by the ...
African Journals Online (AJOL)
Basal metabolic rate scaled to body mass within species by the fractal dimension of the vascular system and body composition. ... The postulate bd = c is shown to hold for both these species within the limits of experimental error, with the crucian carp evidence being especially convincing, since b, c and d are estimated from ...
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Basal metabolic rate scaled to body mass between species by the ...
African Journals Online (AJOL)
The principal reason that basal metabolic rate (BMR) and MMR scale with different power exponents to whole body mass is that MMR is due mainly to respiration in skeletal muscle during exercise and BMR to respiration in the viscera during rest. It follows, therefore, from the self-similarity of the vascular system that BMR is ...
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Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production
Directory of Open Access Journals (Sweden)
Brooks J Paul
2010-03-01
Full Text Available Abstract Background Microorganisms possess diverse metabolic capabilities that can potentially be leveraged for efficient production of biofuels. Clostridium thermocellum (ATCC 27405 is a thermophilic anaerobe that is both cellulolytic and ethanologenic, meaning that it can directly use the plant sugar, cellulose, and biochemically convert it to ethanol. A major challenge in using microorganisms for chemical production is the need to modify the organism to increase production efficiency. The process of properly engineering an organism is typically arduous. Results Here we present a genome-scale model of C. thermocellum metabolism, iSR432, for the purpose of establishing a computational tool to study the metabolic network of C. thermocellum and facilitate efforts to engineer C. thermocellum for biofuel production. The model consists of 577 reactions involving 525 intracellular metabolites, 432 genes, and a proteomic-based representation of a cellulosome. The process of constructing this metabolic model led to suggested annotation refinements for 27 genes and identification of areas of metabolism requiring further study. The accuracy of the iSR432 model was tested using experimental growth and by-product secretion data for growth on cellobiose and fructose. Analysis using this model captures the relationship between the reduction-oxidation state of the cell and ethanol secretion and allowed for prediction of gene deletions and environmental conditions that would increase ethanol production. Conclusions By incorporating genomic sequence data, network topology, and experimental measurements of enzyme activities and metabolite fluxes, we have generated a model that is reasonably accurate at predicting the cellular phenotype of C. thermocellum and establish a strong foundation for rational strain design. In addition, we are able to draw some important conclusions regarding the underlying metabolic mechanisms for observed behaviors of C. thermocellum
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Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics.
Nottale, Laurent; Auffray, Charles
2008-05-01
In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, which aims at describing the effects of a non-differentiable and fractal (i.e., explicitly scale dependent) geometry of space-time. The first paper of this series was devoted, in this new framework, to the construction from first principles of scale laws of increasing complexity, and to the discussion of some tentative applications of these laws to biological systems. In this second review and perspective paper, we describe the effects induced by the internal fractal structures of trajectories on motion in standard space. Their main consequence is the transformation of classical dynamics into a generalized, quantum-like self-organized dynamics. A Schrödinger-type equation is derived as an integral of the geodesic equation in a fractal space. We then indicate how gauge fields can be constructed from a geometric re-interpretation of gauge transformations as scale transformations in fractal space-time. Finally, we introduce a new tentative development of the theory, in which quantum laws would hold also in scale space, introducing complexergy as a measure of organizational complexity. Initial possible applications of this extended framework to the processes of morphogenesis and the emergence of prokaryotic and eukaryotic cellular structures are discussed. Having founded elements of the evolutionary, developmental, biochemical and cellular theories on the first principles of scale relativity theory, we introduce proposals for the construction of an integrative theory of life and for the design and implementation of novel macroscopic quantum-type experiments and devices, and discuss their potential
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The algebraic construction of the scale-invariant asymtotic theory
International Nuclear Information System (INIS)
Gatto, R.; Sartori, G.
1975-01-01
The procedure proposed in the preceding paper to construct the asymptotic scale-invariant theory is applied to massive free fields. The contracted fields (of the asymptotic theory) are calculated in terms of the original fields by two different procedures. The contracted charges are calculated and their general relation to the original charges is verified. The problem of defining a vacuum state for the contracted fields and charges is solved. The relation to the problem of non-equivalent representations of the commutator relations is pointed out
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Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.
Directory of Open Access Journals (Sweden)
Elena Vinay-Lara
Full Text Available Lactobacillus casei strains are widely used in industry and the utility of this organism in these industrial applications is strain dependent. Hence, tools capable of predicting strain specific phenotypes would have utility in the selection of strains for specific industrial processes. Genome-scale metabolic models can be utilized to better understand genotype-phenotype relationships and to compare different organisms. To assist in the selection and development of strains with enhanced industrial utility, genome-scale models for L. casei ATCC 334, a well characterized strain, and strain 12A, a corn silage isolate, were constructed. Draft models were generated from RAST genome annotations using the Model SEED database and refined by evaluating ATP generating cycles, mass-and-charge-balances of reactions, and growth phenotypes. After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors. We conclude that the metabolic capabilities of the two networks are highly similar. The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes. The developed L. casei ATCC 334 and 12A metabolic models will enable better understanding of the physiology of these organisms and be valuable tools in the development and selection of strains with enhanced utility in a variety of industrial applications.
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Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
DEFF Research Database (Denmark)
Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim
2008-01-01
Background: Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome sequence of A. oryzae with 12,074 annotated genes was released but the number...... to a genome scale metabolic model of A. oryzae. Results: Our assembled EST sequences we identified 1,046 newly predicted genes in the A. oryzae genome. Furthermore, it was possible to assign putative protein functions to 398 of the newly predicted genes. Noteworthy, our annotation strategy resulted...... model was validated and shown to correctly describe the phenotypic behavior of A. oryzae grown on different carbon sources. Conclusion: A much enhanced annotation of the A. oryzae genome was performed and a genomescale metabolic model of A. oryzae was reconstructed. The model accurately predicted...
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Directory of Open Access Journals (Sweden)
María P. Cortés
2017-12-01
Full Text Available Piscirickettsia salmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with highly adverse impact in the Chilean salmon farming industry. The development of effective treatment and control methods for piscireckttsiosis is still a challenge. To meet it the number of studies on P. salmonis has grown in the last couple of years but many aspects of the pathogen’s biology are still poorly understood. Studies on its metabolism are scarce and only recently a metabolic model for reference strain LF-89 was developed. We present a new genome-scale model for P. salmonis LF-89 with more than twice as many genes as in the previous model and incorporating specific elements of the fish pathogen metabolism. Comparative analysis with models of different bacterial pathogens revealed a lower flexibility in P. salmonis metabolic network. Through constraint-based analysis, we determined essential metabolites required for its growth and showed that it can benefit from different carbon sources tested experimentally in new defined media. We also built an additional model for strain A1-15972, and together with an analysis of P. salmonis pangenome, we identified metabolic features that differentiate two main species clades. Both models constitute a knowledge-base for P. salmonis metabolism and can be used to guide the efficient culture of the pathogen and the identification of specific drug targets.
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Deriving metabolic engineering strategies from genome-scale modeling with flux ratio constraints.
Yen, Jiun Y; Nazem-Bokaee, Hadi; Freedman, Benjamin G; Athamneh, Ahmad I M; Senger, Ryan S
2013-05-01
Optimized production of bio-based fuels and chemicals from microbial cell factories is a central goal of systems metabolic engineering. To achieve this goal, a new computational method of using flux balance analysis with flux ratios (FBrAtio) was further developed in this research and applied to five case studies to evaluate and design metabolic engineering strategies. The approach was implemented using publicly available genome-scale metabolic flux models. Synthetic pathways were added to these models along with flux ratio constraints by FBrAtio to achieve increased (i) cellulose production from Arabidopsis thaliana; (ii) isobutanol production from Saccharomyces cerevisiae; (iii) acetone production from Synechocystis sp. PCC6803; (iv) H2 production from Escherichia coli MG1655; and (v) isopropanol, butanol, and ethanol (IBE) production from engineered Clostridium acetobutylicum. The FBrAtio approach was applied to each case to simulate a metabolic engineering strategy already implemented experimentally, and flux ratios were continually adjusted to find (i) the end-limit of increased production using the existing strategy, (ii) new potential strategies to increase production, and (iii) the impact of these metabolic engineering strategies on product yield and culture growth. The FBrAtio approach has the potential to design "fine-tuned" metabolic engineering strategies in silico that can be implemented directly with available genomic tools. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Marchetti, Luca; Manca, Vincenzo
2015-04-15
MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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ONETEP: linear-scaling density-functional theory with plane-waves
International Nuclear Information System (INIS)
Haynes, P D; Mostof, A A; Skylaris, C-K; Payne, M C
2006-01-01
This paper provides a general overview of the methodology implemented in onetep (Order-N Electronic Total Energy Package), a parallel density-functional theory code for largescale first-principles quantum-mechanical calculations. The distinctive features of onetep are linear-scaling in both computational effort and resources, obtained by making well-controlled approximations which enable simulations to be performed with plane-wave accuracy. Titanium dioxide clusters of increasing size designed to mimic surfaces are studied to demonstrate the accuracy and scaling of onetep
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Scaling Theory of Polyelectrolyte Nanogels
International Nuclear Information System (INIS)
Qu Li-Jian
2017-01-01
The present paper develops the scaling theory of polyelectrolyte nanogels in dilute and semidilute solutions. The dependencies of the nanogel dimension on branching topology, charge fraction, subchain length, segment number, solution concentration are obtained. For a single polyelectrolyte nanogel in salt free solution, the nanogel may be swelled by the Coulombic repulsion (the so-called polyelectrolyte regime) or the osmotic counterion pressure (the so-called osmotic regime). Characteristics and boundaries between different regimes of a single polyelectrolyte nanogel are summarized. In dilute solution, the nanogels in polyelectrolyte regime will distribute orderly with the increase of concentration. While the nanogels in osmotic regime will always distribute randomly. Different concentration dependencies of the size of a nanogel in polyelectrolyte regime and in osmotic regime are also explored. (paper)
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Directory of Open Access Journals (Sweden)
Mark Graham Poolman
2014-11-01
Full Text Available Previously we have used a genome scale model of rice metabolism to describe how metabolism reconfigures at different light intensities in an expanding leaf of rice. Although this established that the metabolism of the leaf was adequatelyrepresented, in the model, the scenario was not that of the typical function of the leaf --- to provide material for the rest of the plant. Here we extend our analysis to explore the transition to a source leaf as export of photosynthate increases at the expense of making leaf biomass precursors, again as a function of light intensity. In particular we investigate whether, when the leaf is making a smaller range of compounds for export to the phloem, the same changes occur in the interactions between mitochondrial and chloroplast metabolism as seen in biomass synthesis for growth when light intensity increases. Our results show that the same changes occur qualitatively, though there are slight quantitative differences reflecting differences in the energy and redox requirements for the different metabolic outputs.
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Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
DEFF Research Database (Denmark)
Ghaffari, Pouyan; Mardinoglu, Adil; Asplund, Anna
2015-01-01
Human cancer cell lines are used as important model systems to study molecular mechanisms associated with tumor growth, hereunder how genomic and biological heterogeneity found in primary tumors affect cellular phenotypes. We reconstructed Genome scale metabolic models (GEMs) for eleven cell lines...... based on RNA-Seq data and validated the functionality of these models with data from metabolite profiling. We used cell line-specific GEMs to analyze the differences in the metabolism of cancer cell lines, and to explore the heterogeneous expression of the metabolic subsystems. Furthermore, we predicted...... for inhibition of cell growth may provide leads for the development of efficient cancer treatment strategies....
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Development and psychometric validation of social cognitive theory scales in an oral health context.
Jones, Kelly; Parker, Eleanor J; Steffens, Margaret A; Logan, Richard M; Brennan, David; Jamieson, Lisa M
2016-04-01
This study aimed to develop and evaluate scales reflecting potentially modifiable social cognitive theory-based risk indicators associated with homeless populations' oral health. The scales are referred to as the social cognitive theory risk scales in an oral health context (SCTOH) and are referred to as SCTOH(SE), SCTOH(K) and SCTOH(F), respectively. The three SCTOH scales assess the key constructs of social cognitive theory: self-efficacy, knowledge and fatalism. The reliability and validity of the three scales were evaluated in a convenience sample of 248 homeless participants (age range 17-78 years, 79% male) located in a metropolitan setting in Australia. The scales were supported by exploratory factor analysis and established three distinct and internally consistent domains of social cognition: oral health-related self-efficacy, oral health-related knowledge and oral health-related fatalism, with Cronbach's alphas of 0.95, 0.85 and Spearman's-Brown ρ of 0.69. Concurrent ability was confirmed by each SCTOH scale's association with oral health status in the expected directions. The three SCTOH scales appear to be internally valid and reliable. If confirmed by further research, these scales could potentially be used for tailored educational and cognitive-behavioural interventions to reduce oral health inequalities among homeless and other vulnerable populations. © 2015 Public Health Association of Australia.
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Chiral symmetry breaking and nonperturbative scale anomaly in gauge field theories
International Nuclear Information System (INIS)
Miranskij, V.A.; Gusynin, V.P.
1987-01-01
The nonperturbative dynamics of chiral and scale symmetry breaking in asymtotically free and non-asymptotically free (with an ultraviolet stable fixed point) vector-like gauge theories is investigated. In the two-loop approximation analytical expressions for the chiral and gluon condensates are obtained. The hypothesis about a soft behaviour at small distances of composite operators in non-asymptotically free gauge theories with a fixed point is put forward and substantiated. It is shown that in these theories the form of the scale anomaly depends on the type of the phase in coupling constant to which it relates. A new dilaton effective lagrangian for glueball and chiral fields is suggested. The mass relation for the single scalar fermion-antifermion bound state is obtained. The important ingredient of this approach is a large (d≅ 2) dynamical dimension of composite chiral fields. The application of this approach to QCD and technicolour models is discussed
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Directory of Open Access Journals (Sweden)
Fenja Klevenhusen
2015-10-01
Full Text Available Left displaced abomasum (LDA is a severe metabolic disease of cattle with a strong negative impact on production efficiency of dairy farms. Metabolic and inflammatory alterations associated with this disease have been reported in earlier studies, conducted mostly in large dairy farms. This research aimed to: (1 evaluate metabolic and inflammatory responses in dairy cows affected by LDA in small-scaled dairy farms; and (2 establish an Animals 2015, 5 1022 association between lactation number and milk production with the outcome of metabolic variables. The cows with LDA had lower serum calcium (Ca, but greater concentrations of non-esterified fatty acids (NEFA and beta-hydroxy-butyrate (BHBA, in particular when lactation number was >2. Cows with LDA showed elevated levels of aspartate aminotransferase, glutamate dehydrogenase, and serum amyloid A (SAA, regardless of lactation number. In addition, this study revealed strong associations between milk yield and the alteration of metabolic profile but not with inflammation in the sick cows. Results indicate metabolic alterations, liver damage, and inflammation in LDA cows kept under small-scale farm conditions. Furthermore, the data suggest exacerbation of metabolic profile and Ca metabolism but not of inflammation and liver health with increasing lactation number and milk yield in cows affected by LDA.
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Klevenhusen, Fenja; Humer, Elke; Metzler-Zebeli, Barbara; Podstatzky-Lichtenstein, Leopold; Wittek, Thomas; Zebeli, Qendrim
2015-10-13
Left displaced abomasum (LDA) is a severe metabolic disease of cattle with a strong negative impact on production efficiency of dairy farms. Metabolic and inflammatory alterations associated with this disease have been reported in earlier studies, conducted mostly in large dairy farms. This research aimed to: (1) evaluate metabolic and inflammatory responses in dairy cows affected by LDA in small-scaled dairy farms; and (2) establish an Animals 2015, 5 1022 association between lactation number and milk production with the outcome of metabolic variables. The cows with LDA had lower serum calcium (Ca), but greater concentrations of non-esterified fatty acids (NEFA) and beta-hydroxy-butyrate (BHBA), in particular when lactation number was >2. Cows with LDA showed elevated levels of aspartate aminotransferase, glutamate dehydrogenase, and serum amyloid A (SAA), regardless of lactation number. In addition, this study revealed strong associations between milk yield and the alteration of metabolic profile but not with inflammation in the sick cows. Results indicate metabolic alterations, liver damage, and inflammation in LDA cows kept under small-scale farm conditions. Furthermore, the data suggest exacerbation of metabolic profile and Ca metabolism but not of inflammation and liver health with increasing lactation number and milk yield in cows affected by LDA.
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Departures from scaling in SU(2) lattice gauge theory
International Nuclear Information System (INIS)
Gutbrod, F.
1987-01-01
High statistics Monte Carlo Data in SU(2) lattice gauge theory are presented. At β = 2.6 and β = 2.7 large deviations form scaling are observed for Creutz ratios, when 12 4 and 24 4 lattice data are compared. There is a trend towards a restauration of asymptotic scaling with increasing β, which vanishes if at the higher value of β larger loops are considered than at lower β. The static qanti q-potential and an upper limit for the string tension are given. (orig.)
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Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02.
Guo, Jing; Zhang, Hong; Wang, Cheng; Chang, Ji-Wei; Chen, Ling-Ling
2016-05-01
We constructed the genome-scale metabolic network of Bacillus licheniformis (B. licheniformis) WX-02 by combining genomic annotation, high-throughput phenotype microarray (PM) experiments and literature-based metabolic information. The accuracy of the metabolic network was assessed by an OmniLog PM experiment. The final metabolic model iWX1009 contains 1009 genes, 1141 metabolites and 1762 reactions, and the predicted metabolic phenotypes showed an agreement rate of 76.8% with experimental PM data. In addition, key metabolic features such as growth yield, utilization of different substrates and essential genes were identified by flux balance analysis. A total of 195 essential genes were predicted from LB medium, among which 149 were verified with the experimental essential gene set of B. subtilis 168. With the removal of 5 reactions from the network, pathways for poly-γ-glutamic acid (γ-PGA) synthesis were optimized and the γ-PGA yield reached 83.8 mmol/h. Furthermore, the important metabolites and pathways related to γ-PGA synthesis and bacterium growth were comprehensively analyzed. The present study provides valuable clues for exploring the metabolisms and metabolic regulation of γ-PGA synthesis in B. licheniformis WX-02. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
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Genome-scale modelling of microbial metabolism with temporal and spatial resolution.
Henson, Michael A
2015-12-01
Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.
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Systematic construction of kinetic models from genome-scale metabolic networks.
Directory of Open Access Journals (Sweden)
Natalie J Stanford
Full Text Available The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments.
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Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks
Smallbone, Kieran; Klipp, Edda; Mendes, Pedro; Liebermeister, Wolfram
2013-01-01
The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments. PMID:24324546
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Romeny, Bart M Haar
2008-01-01
Front-End Vision and Multi-Scale Image Analysis is a tutorial in multi-scale methods for computer vision and image processing. It builds on the cross fertilization between human visual perception and multi-scale computer vision (`scale-space') theory and applications. The multi-scale strategies recognized in the first stages of the human visual system are carefully examined, and taken as inspiration for the many geometric methods discussed. All chapters are written in Mathematica, a spectacular high-level language for symbolic and numerical manipulations. The book presents a new and effective
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Thermodynamic scaling of dynamics in polymer melts: predictions from the generalized entropy theory.
Xu, Wen-Sheng; Freed, Karl F
2013-06-21
Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of a unique scaling function of the ratio ρ(γ)∕T, where ρ is the density, T is the temperature, and γ is a material dependent constant. Interest in the scaling is also heightened because the exponent γ enters prominently into considerations of the relative contributions to the dynamics from pressure effects (e.g., activation barriers) vs. volume effects (e.g., free volume). Although this scaling is clearly of great practical use, a molecular understanding of the scaling remains elusive. Providing this molecular understanding would greatly enhance the utility of the empirically observed scaling in assisting the rational design of materials by describing how controllable molecular factors, such as monomer structures, interactions, flexibility, etc., influence the scaling exponent γ and, hence, the dynamics. Given the successes of the generalized entropy theory in elucidating the influence of molecular details on the universal properties of glass-forming polymers, this theory is extended here to investigate the thermodynamic scaling in polymer melts. The predictions of theory are in accord with the appearance of thermodynamic scaling for pressures not in excess of ~50 MPa. (The failure at higher pressures arises due to inherent limitations of a lattice model.) In line with arguments relating the magnitude of γ to the steepness of the repulsive part of the intermolecular potential, the abrupt, square-well nature of the lattice model interactions lead, as expected, to much larger values of the scaling exponent. Nevertheless, the theory is employed to study how individual molecular parameters affect the scaling exponent in order to extract a molecular understanding of the information content contained in the exponent. The chain
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Item Response Theory Models for Wording Effects in Mixed-Format Scales
Wang, Wen-Chung; Chen, Hui-Fang; Jin, Kuan-Yu
2015-01-01
Many scales contain both positively and negatively worded items. Reverse recoding of negatively worded items might not be enough for them to function as positively worded items do. In this study, we commented on the drawbacks of existing approaches to wording effect in mixed-format scales and used bi-factor item response theory (IRT) models to…
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An Item Response Theory Analysis of the Community of Inquiry Scale
Horzum, Mehmet Baris; Uyanik, Gülden Kaya
2015-01-01
The aim of this study is to examine validity and reliability of Community of Inquiry Scale commonly used in online learning by the means of Item Response Theory. For this purpose, Community of Inquiry Scale version 14 is applied on 1,499 students of a distance education center's online learning programs at a Turkish state university via internet.…
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Renormalization group scale-setting from the action—a road to modified gravity theories
International Nuclear Information System (INIS)
Domazet, Silvije; Štefančić, Hrvoje
2012-01-01
The renormalization group (RG) corrected gravitational action in Einstein–Hilbert and other truncations is considered. The running scale of the RG is treated as a scalar field at the level of the action and determined in a scale-setting procedure recently introduced by Koch and Ramirez for the Einstein–Hilbert truncation. The scale-setting procedure is elaborated for other truncations of the gravitational action and applied to several phenomenologically interesting cases. It is shown how the logarithmic dependence of the Newton's coupling on the RG scale leads to exponentially suppressed effective cosmological constant and how the scale-setting in particular RG-corrected gravitational theories yields the effective f(R) modified gravity theories with negative powers of the Ricci scalar R. The scale-setting at the level of the action at the non-Gaussian fixed point in Einstein–Hilbert and more general truncations is shown to lead to universal effective action quadratic in the Ricci tensor. (paper)
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Renormalization group scale-setting from the action—a road to modified gravity theories
Domazet, Silvije; Štefančić, Hrvoje
2012-12-01
The renormalization group (RG) corrected gravitational action in Einstein-Hilbert and other truncations is considered. The running scale of the RG is treated as a scalar field at the level of the action and determined in a scale-setting procedure recently introduced by Koch and Ramirez for the Einstein-Hilbert truncation. The scale-setting procedure is elaborated for other truncations of the gravitational action and applied to several phenomenologically interesting cases. It is shown how the logarithmic dependence of the Newton's coupling on the RG scale leads to exponentially suppressed effective cosmological constant and how the scale-setting in particular RG-corrected gravitational theories yields the effective f(R) modified gravity theories with negative powers of the Ricci scalar R. The scale-setting at the level of the action at the non-Gaussian fixed point in Einstein-Hilbert and more general truncations is shown to lead to universal effective action quadratic in the Ricci tensor.
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Association of metabolic syndrome and change in Unified Parkinson's Disease Rating Scale scores.
Leehey, Maureen; Luo, Sheng; Sharma, Saloni; Wills, Anne-Marie A; Bainbridge, Jacquelyn L; Wong, Pei Shieen; Simon, David K; Schneider, Jay; Zhang, Yunxi; Pérez, Adriana; Dhall, Rohit; Christine, Chadwick W; Singer, Carlos; Cambi, Franca; Boyd, James T
2017-10-24
To explore the association between metabolic syndrome and the Unified Parkinson's Disease Rating Scale (UPDRS) scores and, secondarily, the Symbol Digit Modalities Test (SDMT). This is a secondary analysis of data from 1,022 of 1,741 participants of the National Institute of Neurological Disorders and Stroke Exploratory Clinical Trials in Parkinson Disease Long-Term Study 1, a randomized, placebo-controlled trial of creatine. Participants were categorized as having or not having metabolic syndrome on the basis of modified criteria from the National Cholesterol Education Program Adult Treatment Panel III. Those who had the same metabolic syndrome status at consecutive annual visits were included. The change in UPDRS and SDMT scores from randomization to 3 years was compared in participants with and without metabolic syndrome. Participants with metabolic syndrome (n = 396) compared to those without (n = 626) were older (mean [SD] 63.9 [8.1] vs 59.9 [9.4] years; p metabolic syndrome experienced an additional 0.6- (0.2) unit annual increase in total UPDRS ( p = 0.02) and 0.5- (0.2) unit increase in motor UPDRS ( p = 0.01) scores compared with participants without metabolic syndrome. There was no difference in the change in SDMT scores. Persons with Parkinson disease meeting modified criteria for metabolic syndrome experienced a greater increase in total UPDRS scores over time, mainly as a result of increases in motor scores, compared to those who did not. Further studies are needed to confirm this finding. NCT00449865. © 2017 American Academy of Neurology.
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Theory-based scaling of the SOL width in circular limited tokamak plasmas
International Nuclear Information System (INIS)
Halpern, F.D.; Ricci, P.; Labit, B.; Furno, I.; Jolliet, S.; Loizu, J.; Mosetto, A.; Arnoux, G.; Silva, C.; Gunn, J.P.; Horacek, J.; Kočan, M.; LaBombard, B.
2013-01-01
A theory-based scaling for the characteristic length of a circular, limited tokamak scrape-off layer (SOL) is obtained by considering the balance between parallel losses and non-linearly saturated resistive ballooning mode turbulence driving anomalous perpendicular transport. The SOL size increases with plasma size, resistivity, and safety factor q. The scaling is verified against flux-driven non-linear turbulence simulations, which reveal good agreement within a wide range of dimensionless parameters, including parameters closely matching the TCV tokamak. An initial comparison of the theory against experimental data from several tokamaks also yields good agreement. (letter)
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Eliminating infinities in the λφ4 theory by simple scaling
International Nuclear Information System (INIS)
Aragao, Cristiane M.L. de; Carneiro, C.E.I.
2006-01-01
We present an alternative method to remove infinities in the perturbative φ 4 theory. In our method, the renormalization is performed in two stages. Firstly, the infinities are eliminated by rescaling the Lagrangian. The Green functions obtained from this rescaled Lagrangian are finite to all orders in perturbation. Secondly, we fix the values of parameters of the resulting finite theory at a certain mass scale by using the standard renormalization conditions. This second stage allows us to derive renormalization equations which yields the critical behavior of the theory. We show that our method does not change the critical behavior of the λφ 4 theory in 4-ε dimensions. In particular, we recover the usual critical exponents
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2012-01-01
Background Over the last decade, the genome-scale metabolic models have been playing increasingly important roles in elucidating metabolic characteristics of biological systems for a wide range of applications including, but not limited to, system-wide identification of drug targets and production of high value biochemical compounds. However, these genome-scale metabolic models must be able to first predict known in vivo phenotypes before it is applied towards these applications with high confidence. One benchmark for measuring the in silico capability in predicting in vivo phenotypes is the use of single-gene mutant libraries to measure the accuracy of knockout simulations in predicting mutant growth phenotypes. Results Here we employed a systematic and iterative process, designated as Reconciling In silico/in vivo mutaNt Growth (RING), to settle discrepancies between in silico prediction and in vivo observations to a newly reconstructed genome-scale metabolic model of the fission yeast, Schizosaccharomyces pombe, SpoMBEL1693. The predictive capabilities of the genome-scale metabolic model in predicting single-gene mutant growth phenotypes were measured against the single-gene mutant library of S. pombe. The use of RING resulted in improving the overall predictive capability of SpoMBEL1693 by 21.5%, from 61.2% to 82.7% (92.5% of the negative predictions matched the observed growth phenotype and 79.7% the positive predictions matched the observed growth phenotype). Conclusion This study presents validation and refinement of a newly reconstructed metabolic model of the yeast S. pombe, through improving the metabolic model’s predictive capabilities by reconciling the in silico predicted growth phenotypes of single-gene knockout mutants, with experimental in vivo growth data. PMID:22631437
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Finite-size scaling theory and quantum hamiltonian Field theory: the transverse Ising model
International Nuclear Information System (INIS)
Hamer, C.J.; Barber, M.N.
1979-01-01
Exact results for the mass gap, specific heat and susceptibility of the one-dimensional transverse Ising model on a finite lattice are generated by constructing a finite matrix representation of the Hamiltonian using strong-coupling eigenstates. The critical behaviour of the limiting infinite chain is analysed using finite-size scaling theory. In this way, excellent estimates (to within 1/2% accuracy) are found for the critical coupling and the exponents α, ν and γ
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Validation of Theory of Consumption Values Scales for Deal Sites
DEFF Research Database (Denmark)
Sudzina, Frantisek
2016-01-01
Deal sites became a widely used artefact. But there is still only a limited number of papers investigating their adoption and use. Most of the research published on the topic is qualitative. It is typical for an early stage of investigation of any new artefact. The Theory of Consumption Values ex...... explains purchase behavior. The aim of this paper is to validate scales for the Theory of Consumption Values for deal sites. This should pave a way for quantitative investigation of motives for purchasing using deal sites....
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Bontempo, Robert
1993-01-01
Describes a method for assessing the quality of translations based on item response theory (IRT). Results from the IRT technique with French and Chinese versions of a scale measuring individualism-collectivism for samples of 250 U.S., 357 French, and 290 Chinese undergraduates show how several biased items are detected. (SLD)
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[Scale Relativity Theory in living beings morphogenesis: fratal, determinism and chance].
Chaline, J
2012-10-01
The Scale Relativity Theory has many biological applications from linear to non-linear and, from classical mechanics to quantum mechanics. Self-similar laws have been used as model for the description of a huge number of biological systems. Theses laws may explain the origin of basal life structures. Log-periodic behaviors of acceleration or deceleration can be applied to branching macroevolution, to the time sequences of major evolutionary leaps. The existence of such a law does not mean that the role of chance in evolution is reduced, but instead that randomness and contingency may occur within a framework which may itself be structured in a partly statistical way. The scale relativity theory can open new perspectives in evolution. Copyright © 2012 Elsevier Masson SAS. All rights reserved.
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A flux-scaling scenario for high-scale moduli stabilization in string theory
Directory of Open Access Journals (Sweden)
Ralph Blumenhagen
2015-08-01
Full Text Available Tree-level moduli stabilization via geometric and non-geometric fluxes in type IIB orientifolds on Calabi–Yau manifolds is investigated. The focus is on stable non-supersymmetric minima, where all moduli are fixed except for some massless axions. The scenario includes the purely axionic orientifold-odd moduli. A set of vacua allowing for parametric control over the moduli vacuum expectation values and their masses is presented, featuring a specific scaling with the fluxes. Uplift mechanisms and supersymmetry breaking soft masses on MSSM-like D7-branes are discussed as well. This scenario provides a complete effective framework for realizing the idea of F-term axion monodromy inflation in string theory. It is argued that, with all masses close to the Planck and GUT scales, one is confronted with working at the threshold of controlling all mass hierarchies.
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A flux-scaling scenario for high-scale moduli stabilization in string theory
Energy Technology Data Exchange (ETDEWEB)
Blumenhagen, Ralph [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Font, Anamaría [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Arnold Sommerfeld Center for Theoretical Physics, LMU, Theresienstr. 37, 80333 München (Germany); Fuchs, Michael [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Herschmann, Daniela, E-mail: herschma@mpp.mpg.de [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Plauschinn, Erik [Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova (Italy); Sekiguchi, Yuta; Wolf, Florian [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Arnold Sommerfeld Center for Theoretical Physics, LMU, Theresienstr. 37, 80333 München (Germany)
2015-08-15
Tree-level moduli stabilization via geometric and non-geometric fluxes in type IIB orientifolds on Calabi–Yau manifolds is investigated. The focus is on stable non-supersymmetric minima, where all moduli are fixed except for some massless axions. The scenario includes the purely axionic orientifold-odd moduli. A set of vacua allowing for parametric control over the moduli vacuum expectation values and their masses is presented, featuring a specific scaling with the fluxes. Uplift mechanisms and supersymmetry breaking soft masses on MSSM-like D7-branes are discussed as well. This scenario provides a complete effective framework for realizing the idea of F-term axion monodromy inflation in string theory. It is argued that, with all masses close to the Planck and GUT scales, one is confronted with working at the threshold of controlling all mass hierarchies.
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F-theory, GUTs, and the weak scale
International Nuclear Information System (INIS)
Heckman, Jonathan J.; Vafa, Cumrun
2009-01-01
In this paper we study a deformation of gauge mediated supersymmetry breaking in a class of local F-theory GUT models where the scale of supersymmetry breaking determines the value of the μ term. Geometrically correlating these two scales constrains the soft SUSY breaking parameters of the MSSM. In this scenario, the hidden SUSY breaking sector involves an anomalous U(1) Peccei-Quinn symmetry which forbids bare μ and Bμ terms. This sector typically breaks supersymmetry at the desired range of energy scales through a simple stringy hybrid of a Fayet and Polonyi model. A variant of the Giudice-Masiero mechanism generates the value μ ∼ 10 2 -10 3 GeV when the hidden sector scale of supersymmetry breaking is F 1/2 ∼ 10 8.5 GeV. Further, the Bμ problem is solved due to the mild hierarchy between the GUT scale and Planck scale. These models relate SUSY breaking with the QCD axion, and solve the strong CP problem through an axion with decay constant f a ∼ M GUT cμ/Λ, where Λ ∼ 10 5 GeV is the characteristic scale of gaugino mass unification in gauge mediated models, and the ratio μ/Λ ∼ M GUT /M pl ∼ 10 -3 . We find f a ∼ 10 12 GeV, which is near the high end of the phenomenologically viable window. Here, the axino is the goldstino mode which is eaten by the gravitino. The gravitino is the LSP with a mass of about 10 1 -10 2 MeV, and a bino-like neutralino is (typically) the NLSP with mass of about 10 2 -10 3 GeV. Compatibility with electroweak symmetry breaking also determines the value of tanβ ∼ 30±7.
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Xu, Zixiang; Sun, Jibin; Wu, Qiaqing; Zhu, Dunming
2017-12-11
Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry. In addition, the shortest pathways may not be the pathways with high yield. At the same time, a pathway, which exists in stoichiometry, may not be feasible in thermodynamics. By using mixed integer programming strategy, we put forward an algorithm to identify all the smallest balanced pathways which convert the source compound to the target compound in large-scale metabolic networks. The resulting pathways by our method can finely satisfy the stoichiometric constraints and non-decomposability condition. Especially, the functions of high yield and thermodynamics feasibility have been considered in our approach. This tool is tailored to direct the metabolic engineering practice to enlarge the metabolic potentials of industrial strains by integrating the extensive metabolic network information built from systems biology dataset.
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Scaling Theory of Polyelectrolyte Nanogels
Qu, Li-Jian
2017-08-01
The present paper develops the scaling theory of polyelectrolyte nanogels in dilute and semidilute solutions. The dependencies of the nanogel dimension on branching topology, charge fraction, subchain length, segment number, solution concentration are obtained. For a single polyelectrolyte nanogel in salt free solution, the nanogel may be swelled by the Coulombic repulsion (the so-called polyelectrolyte regime) or the osmotic counterion pressure (the so-called osmotic regime). Characteristics and boundaries between different regimes of a single polyelectrolyte nanogel are summarized. In dilute solution, the nanogels in polyelectrolyte regime will distribute orderly with the increase of concentration. While the nanogels in osmotic regime will always distribute randomly. Different concentration dependencies of the size of a nanogel in polyelectrolyte regime and in osmotic regime are also explored. Supported by China Earthquake Administration under Grant No. 20150112 and National Natural Science Foundation of China under Grant No. 21504014
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Ontogenetic scaling of fish metabolism in the mouse-to-elephant mass magnitude range
DEFF Research Database (Denmark)
Moran, Damian; Wells, R.M.G.
2007-01-01
, and are therefore not statistically comparable. In this study the metabolic rate of yellowtail kingfish was measured from 0.6 mg-2.2 kg, a mass range comparable to that between a mouse and an elephant. Linear regression of the log transformed data resulted in a scaling exponent of 0.90 and high correlation...
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Detailed treatment of scaling violations in asymptotically free gauge theories
International Nuclear Information System (INIS)
Hinchliffe, I.; Llewellyn Smith, C.H.
1977-01-01
Scaling violations in lepto-production are discussed on the basis of asymptotically free gauge theories. Detailed attention is given to the problems of operator mixing and data parametrisation. All the electro-/muo-production data for F 2 can be accommodated. The calculated values for Fsub(L) are also compatible with the data in the region where the theory may be trusted. It is shown that the FNAL data for sigmasup(anti γ)/sigmasup(γ) and sup(anti γ) can be explained if the freedom to input rather large amounts of antiquarks is exploited. It is therefore premature to conclude that new flavours are required. Predictions are given for very high energies which are relevant for possible new experimental facilities. The consequences of a conjecture about the possible pattern of scaling violations in the production of W's, Z's and μ-pairs are explored. Some theoretical problems and uncertainties in testing asymptotic freedom are discussed. (Auth.)
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Systematic renormalization of the effective theory of Large Scale Structure
International Nuclear Information System (INIS)
Abolhasani, Ali Akbar; Mirbabayi, Mehrdad; Pajer, Enrico
2016-01-01
A perturbative description of Large Scale Structure is a cornerstone of our understanding of the observed distribution of matter in the universe. Renormalization is an essential and defining step to make this description physical and predictive. Here we introduce a systematic renormalization procedure, which neatly associates counterterms to the UV-sensitive diagrams order by order, as it is commonly done in quantum field theory. As a concrete example, we renormalize the one-loop power spectrum and bispectrum of both density and velocity. In addition, we present a series of results that are valid to all orders in perturbation theory. First, we show that while systematic renormalization requires temporally non-local counterterms, in practice one can use an equivalent basis made of local operators. We give an explicit prescription to generate all counterterms allowed by the symmetries. Second, we present a formal proof of the well-known general argument that the contribution of short distance perturbations to large scale density contrast δ and momentum density π(k) scale as k 2 and k, respectively. Third, we demonstrate that the common practice of introducing counterterms only in the Euler equation when one is interested in correlators of δ is indeed valid to all orders.
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Theory of critical phenomena in finite-size systems scaling and quantum effects
Brankov, Jordan G; Tonchev, Nicholai S
2000-01-01
The aim of this book is to familiarise the reader with the rich collection of ideas, methods and results available in the theory of critical phenomena in systems with confined geometry. The existence of universal features of the finite-size effects arising due to highly correlated classical or quantum fluctuations is explained by the finite-size scaling theory. This theory (1) offers an interpretation of experimental results on finite-size effects in real systems; (2) gives the most reliable tool for extrapolation to the thermodynamic limit of data obtained by computer simulations; (3) reveals
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Conservation laws and radiation in the scale covariant theory of gravitation
International Nuclear Information System (INIS)
Beesham, A.
1988-01-01
The conservation laws for mass, energy, and momentum are derived in the scale covariant theory of gravitation. The entropy problem which exists in the standard Friedmann-Lemaitre-Robertson-Walker models can be solved in the present context. Since the weak and strong energy conditions may be violated, a big bang singularity may be avoided, in contrast to general relativity. Since beta is shown to be constant during the radiation-dominated era, the difficulties in the theory associated with nucleosynthesis are avoided. 10 references
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Scaling theory put into practice: First-principles modeling of transport in doped silicon nanowires
DEFF Research Database (Denmark)
Markussen, Troels; Rurali, R.; Jauho, Antti-Pekka
2007-01-01
We combine the ideas of scaling theory and universal conductance fluctuations with density-functional theory to analyze the conductance properties of doped silicon nanowires. Specifically, we study the crossover from ballistic to diffusive transport in boron or phosphorus doped Si nanowires...
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Titov, V N
2013-01-01
Virchow's cellular pathology indirectly points at structural units between cells and organs in vivo and at universal mechanisms underlying the condition of health or disease. In order to substantiate similarity of pathogeneses of atherosclerosis, diabetes mellitus, metabolic syndrome and obesity we suggest a phylogenetic theory which includes: 1) consideration of physiological and pathological processes in vivo from the viewpoint of biological functions and biological reactions. 2) Phylogenesis of metabolic regulation at the levels of: a) cells (autocrine), b) paracrine cell communities, i.e., structural and functional units of each organ (paracrine), and c) the entire organism. Biological functions are: trophology, homeostasis, endoecology ( of the intercellular medium), adaptation, locomotion, reproduction, and cognition. 3) A three-step successive phylogenesis of biological functions and pathological responses. Methodological approaches in phylogenesis are: a) succession of biological functions and reactions and b) biological subordination where phylogenetically late humoral mediators cannot abolish the effects of phylogenetically early mediators. Incompliance of humoral regulation at different steps of phylogenesis, autocrine, paracrine and the organism levels is the basis for similarity between pathogeneses of all metabolic pandemias, including essential hypertension and insulin resistance syndrome.
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Determining the control circuitry of redox metabolism at the genome-scale.
Directory of Open Access Journals (Sweden)
Stephen Federowicz
2014-04-01
Full Text Available Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regulated during electron acceptor shifts. Here we propose a qualitative model that accounts for the full breadth of regulated genes by detailing how two global transcription factors (TFs, ArcA and Fnr of E. coli, sense key metabolic redox ratios and act on a genome-wide basis to regulate anabolic, catabolic, and energy generation pathways. We first fill gaps in our knowledge of this transcriptional regulatory network by carrying out ChIP-chip and gene expression experiments to identify 463 regulatory events. We then interfaced this reconstructed regulatory network with a highly curated genome-scale metabolic model to show that ArcA and Fnr regulate >80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Based on the data, we propose a feedforward with feedback trim regulatory scheme, given the extensive repression of catabolic genes by ArcA and extensive activation of chemiosmotic genes by Fnr. We further corroborated this regulatory scheme by showing a 0.71 r(2 (p<1e-6 correlation between changes in metabolic flux and changes in regulatory activity across fermentative and nitrate respiratory conditions. Finally, we are able to relate the proposed model to a wealth of previously generated data by contextualizing the existing transcriptional regulatory network.
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Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S
2017-08-15
Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
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Revisiting a model of ontogenetic growth: estimating model parameters from theory and data.
Moses, Melanie E; Hou, Chen; Woodruff, William H; West, Geoffrey B; Nekola, Jeffery C; Zuo, Wenyun; Brown, James H
2008-05-01
The ontogenetic growth model (OGM) of West et al. provides a general description of how metabolic energy is allocated between production of new biomass and maintenance of existing biomass during ontogeny. Here, we reexamine the OGM, make some minor modifications and corrections, and further evaluate its ability to account for empirical variation on rates of metabolism and biomass in vertebrates both during ontogeny and across species of varying adult body size. We show that the updated version of the model is internally consistent and is consistent with other predictions of metabolic scaling theory and empirical data. The OGM predicts not only the near universal sigmoidal form of growth curves but also the M(1/4) scaling of the characteristic times of ontogenetic stages in addition to the curvilinear decline in growth efficiency described by Brody. Additionally, the OGM relates the M(3/4) scaling across adults of different species to the scaling of metabolic rate across ontogeny within species. In providing a simple, quantitative description of how energy is allocated to growth, the OGM calls attention to unexplained variation, unanswered questions, and opportunities for future research.
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On the GUT scale of F-theory SU(5)
International Nuclear Information System (INIS)
Leontaris, G.K.; Vlachos, N.D.
2011-01-01
In F-theory GUTs, threshold corrections from Kaluza-Klein (KK) massive modes arising from gauge and matter multiplets play an important role in the determination of the weak mixing angle and the strong gauge coupling of the effective low energy model. In this Letter we further explore the induced modifications on the gauge couplings running and the GUT scale. In particular, we focus on the KK-contributions from matter curves and analyze the conditions on the chiral and Higgs matter spectrum which imply a GUT scale consistent with the minimal unification scenario. As an application, we present an explicit computation of these thresholds for matter fields residing on specific non-trivial Riemann surfaces.
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Kong, Hyung-Sik; Lee, Kang-Sook; Yim, Eun-Shil; Lee, Seon-Young; Cho, Hyun-Young; Lee, Bin Na; Park, Jee Young
2013-10-21
The purpose of this study was to identify the risk factors of metabolic syndrome (MS) and to analyze the relationship between the risk factors of MS and medical cost of major diseases related to MS in Korean workers, according to the scale of the enterprise. Data was obtained from annual physical examinations, health insurance qualification and premiums, and health insurance benefits of 4,094,217 male and female workers who underwent medical examinations provided by the National Health Insurance Corporation in 2009. Logistic regression analyses were used to the identify risk factors of MS and multiple regression was used to find factors associated with medical expenditures due to major diseases related to MS. The study found that low-income workers were more likely to work in small-scale enterprises. The prevalence rate of MS in males and females, respectively, was 17.2% and 9.4% in small-scale enterprises, 15.9% and 8.9% in medium-scale enterprises, and 15.9% and 5.5% in large-scale enterprises. The risks of MS increased with age, lower income status, and smoking in small-scale enterprise workers. The medical costs increased in workers with old age and past smoking history. There was also a gender difference in the pattern of medical expenditures related to MS. Health promotion programs to manage metabolic syndrome should be developed to focus on workers who smoke, drink, and do little exercise in small scale enterprises.
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Characterizing Sources of Uncertainty in Item Response Theory Scale Scores
Yang, Ji Seung; Hansen, Mark; Cai, Li
2012-01-01
Traditional estimators of item response theory scale scores ignore uncertainty carried over from the item calibration process, which can lead to incorrect estimates of the standard errors of measurement (SEMs). Here, the authors review a variety of approaches that have been applied to this problem and compare them on the basis of their statistical…
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International Nuclear Information System (INIS)
Edelen, D.G.B.
1986-01-01
Homogeneous scaling of the group space of the Poincare group, P 10 , is shown to induce scalings of all geometric quantities associated with the local action of P 10 . The field equations for both the translation and the Lorentz rotation compensating fields reduce to O(1) equations if the scaling parameter is set equal to the general relativistic gravitational coupling constant 8πGc -4 . Standard expansions of all field variables in power series in the scaling parameter give the following results. The zeroth-order field equations are exactly the classical field equations for matter fields on Minkowski space subject to local action of an internal symmetry group (classical gauge theory). The expansion process is shown to break P 10 -gauge covariance of the theory, and hence solving the zeroth-order field equations imposes an implicit system of P 10 -gauge conditions. Explicit systems of field equations are obtained for the first- and higher-order approximations. The first-order translation field equations are driven by the momentum-energy tensor of the matter and internal compensating fields in the zeroth order (classical gauge theory), while the first-order Lorentz rotation field equations are driven by the spin currents of the same classical gauge theory. Field equations for the first-order gravitational corrections to the matter fields and the gauge fields for the internal symmetry group are obtained. Direct Poincare gauge theory is thus shown to satisfy the first two of the three-part acid test of any unified field theory. Satisfaction of the third part of the test, at least for finite neighborhoods, seems probable
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Mih, Nathan; Brunk, Elizabeth; Bordbar, Aarash; Palsson, Bernhard O
2016-07-01
Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies. Recently, genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include the three-dimensional structure of proteins. The integration of these molecular-level details, such as the physical, structural, and dynamical properties of proteins, notably expands the computational description of biochemical network-level properties and the possibility of understanding and predicting whole cell phenotypes. In this study, we present a multi-scale modeling framework that describes biological processes which range in scale from atomistic details to an entire metabolic network. Using this approach, we can understand how genetic variation, which impacts the structure and reactivity of a protein, influences both native and drug-induced metabolic states. As a proof-of-concept, we study three enzymes (catechol-O-methyltransferase, glucose-6-phosphate dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase) and their respective genetic variants which have clinically relevant associations. Using all-atom molecular dynamic simulations enables the sampling of long timescale conformational dynamics of the proteins (and their mutant variants) in complex with their respective native metabolites or drug molecules. We find that changes in a protein's structure due to a mutation influences protein binding affinity to metabolites and/or drug molecules, and inflicts large-scale changes in metabolism.
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Features and New Physical Scales in Primordial Observables: Theory and Observation
Chluba, Jens; Patil, Subodh P.
2015-01-01
All cosmological observations to date are consistent with adiabatic, Gaussian and nearly scale invariant initial conditions. These findings provide strong evidence for a particular symmetry breaking pattern in the very early universe (with a close to vanishing order parameter, $\\epsilon$), widely accepted as conforming to the predictions of the simplest realizations of the inflationary paradigm. However, given that our observations are only privy to perturbations, in inferring something about the background that gave rise to them, it should be clear that many different underlying constructions project onto the same set of cosmological observables. Features in the primordial correlation functions, if present, would offer a unique and discriminating window onto the parent theory in which the mechanism that generated the initial conditions is embedded. In certain contexts, simple linear response theory allows us to infer new characteristic scales from the presence of features that can break the aforementioned de...
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Dilts, Thomas E.; Weisberg, Peter J.; Leitner, Phillip; Matocq, Marjorie D.; Inman, Richard D.; Nussear, Ken E.; Esque, Todd C.
2016-01-01
Conservation planning and biodiversity management require information on landscape connectivity across a range of spatial scales from individual home ranges to large regions. Reduction in landscape connectivity due changes in land-use or development is expected to act synergistically with alterations to habitat mosaic configuration arising from climate change. We illustrate a multi-scale connectivity framework to aid habitat conservation prioritization in the context of changing land use and climate. Our approach, which builds upon the strengths of multiple landscape connectivity methods including graph theory, circuit theory and least-cost path analysis, is here applied to the conservation planning requirements of the Mohave ground squirrel. The distribution of this California threatened species, as for numerous other desert species, overlaps with the proposed placement of several utility-scale renewable energy developments in the American Southwest. Our approach uses information derived at three spatial scales to forecast potential changes in habitat connectivity under various scenarios of energy development and climate change. By disentangling the potential effects of habitat loss and fragmentation across multiple scales, we identify priority conservation areas for both core habitat and critical corridor or stepping stone habitats. This approach is a first step toward applying graph theory to analyze habitat connectivity for species with continuously-distributed habitat, and should be applicable across a broad range of taxa.
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Interdisciplinary Pathways for Urban Metabolism Research
Newell, J. P.
2011-12-01
With its rapid rise as a metaphor to express coupled natural-human systems in cities, the concept of urban metabolism is evolving into a series of relatively distinct research frameworks amongst various disciplines, with varying definitions, theories, models, and emphases. In industrial ecology, housed primarily within the disciplinary domain of engineering, urban metabolism research has focused on quantifying material and energy flows into, within, and out of cities, using methodologies such as material flow analysis and life cycle assessment. In the field of urban ecology, which is strongly influenced by ecology and urban planning, research focus has been placed on understanding and modeling the complex patterns and processes of human-ecological systems within urban areas. Finally, in political ecology, closely aligned with human geography and anthropology, scholars theorize about the interwoven knots of social and natural processes, material flows, and spatial structures that form the urban metabolism. This paper offers three potential interdisciplinary urban metabolism research tracks that might integrate elements of these three "ecologies," thereby bridging engineering and the social and physical sciences. First, it presents the idea of infrastructure ecology, which explores the complex, emergent interdependencies between gray (water and wastewater, transportation, etc) and green (e.g. parks, greenways) infrastructure systems, as nested within a broader socio-economic context. For cities to be sustainable and resilient over time-space, the theory follows, these is a need to understand and redesign these infrastructure linkages. Second, there is the concept of an urban-scale carbon metabolism model which integrates consumption-based material flow analysis (including goods, water, and materials), with the carbon sink and source dynamics of the built environment (e.g. buildings, etc) and urban ecosystems. Finally, there is the political ecology of the material
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Iyigun, Emine; Tastan, Sevinc; Ayhan, Hatice; Kose, Gulsah; Acikel, Cengizhan
2016-06-01
This study aimed to determine the validity and reliability levels of the Planned Behavior Theory Scale as related to a testicular self-examination. The study was carried out in a health-profession higher-education school in Ankara, Turkey, from April to June 2012. The study participants comprised 215 male students. Study data were collected by using a questionnaire, a planned behavior theory scale related to testicular self-examination, and Champion's Health Belief Model Scale (CHBMS). The sub-dimensions of the planned behavior theory scale, namely those of intention, attitude, subjective norms and self-efficacy, were found to have Cronbach's alpha values of between 0.81 and 0.89. Exploratory factor analysis showed that items of the scale had five factors that accounted for 75% of the variance. Of these, the sub-dimension of intention was found to have the highest level of contribution. A significant correlation was found between the sub-dimensions of the testicular self-examination planned behavior theory scale and those of CHBMS (p Planned Behavior Theory Scale is a valid and reliable measurement for Turkish society.
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Irani, Zahra Azimzadeh; Kerkhoven, Eduard J; Shojaosadati, Seyed Abbas; Nielsen, Jens
2016-05-01
Pichia pastoris is used for commercial production of human therapeutic proteins, and genome-scale models of P. pastoris metabolism have been generated in the past to study the metabolism and associated protein production by this yeast. A major challenge with clinical usage of recombinant proteins produced by P. pastoris is the difference in N-glycosylation of proteins produced by humans and this yeast. However, through metabolic engineering, a P. pastoris strain capable of producing humanized N-glycosylated proteins was constructed. The current genome-scale models of P. pastoris do not address native nor humanized N-glycosylation, and we therefore developed ihGlycopastoris, an extension to the iLC915 model with both native and humanized N-glycosylation for recombinant protein production, but also an estimation of N-glycosylation of P. pastoris native proteins. This new model gives a better prediction of protein yield, demonstrates the effect of the different types of N-glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required for using these models to understand and optimize protein production processes. © 2015 Wiley Periodicals, Inc.
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Scaling theory for the quasideterministic limit of continuous bifurcations.
Kessler, David A; Shnerb, Nadav M
2012-05-01
Deterministic rate equations are widely used in the study of stochastic, interacting particles systems. This approach assumes that the inherent noise, associated with the discreteness of the elementary constituents, may be neglected when the number of particles N is large. Accordingly, it fails close to the extinction transition, when the amplitude of stochastic fluctuations is comparable with the size of the population. Here we present a general scaling theory of the transition regime for spatially extended systems. We demonstrate this through a detailed study of two fundamental models for out-of-equilibrium phase transitions: the Susceptible-Infected-Susceptible (SIS) that belongs to the directed percolation equivalence class and the Susceptible-Infected-Recovered (SIR) model belonging to the dynamic percolation class. Implementing the Ginzburg criteria we show that the width of the fluctuation-dominated region scales like N^{-κ}, where N is the number of individuals per site and κ=2/(d_{u}-d), d_{u} is the upper critical dimension. Other exponents that control the approach to the deterministic limit are shown to be calculable once κ is known. The theory is extended to include the corrections to the front velocity above the transition. It is supported by the results of extensive numerical simulations for systems of various dimensionalities.
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Higgs mass scales and matter-antimatter oscillations in grand unified theories
International Nuclear Information System (INIS)
Senjanovic, G.
1982-01-01
A general discussion of mass scales in grand unified theories is presented, with special emphasis on Higgs scalars which mediate neutron-antineutron (n-anti n) and hydrogen-antihydrogen (H-anti H) oscillations. It is shown that the analogue of survival hypothesis for fermions naturally makes such particles superheavy, thus leading to unobservable lifetimes. If this hypothesis is relaxed, an interesting possibility of potentially observable n-anti n and H-anti H transitions, mutually related arises in the context of SU(5) theory with spontaneously broken B-L symmetry
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Neutral Theory and Scale-Free Neural Dynamics
Martinello, Matteo; Hidalgo, Jorge; Maritan, Amos; di Santo, Serena; Plenz, Dietmar; Muñoz, Miguel A.
2017-10-01
Neural tissues have been consistently observed to be spontaneously active and to generate highly variable (scale-free distributed) outbursts of activity in vivo and in vitro. Understanding whether these heterogeneous patterns of activity stem from the underlying neural dynamics operating at the edge of a phase transition is a fascinating possibility, as criticality has been argued to entail many possible important functional advantages in biological computing systems. Here, we employ a well-accepted model for neural dynamics to elucidate an alternative scenario in which diverse neuronal avalanches, obeying scaling, can coexist simultaneously, even if the network operates in a regime far from the edge of any phase transition. We show that perturbations to the system state unfold dynamically according to a "neutral drift" (i.e., guided only by stochasticity) with respect to the background of endogenous spontaneous activity, and that such a neutral dynamics—akin to neutral theories of population genetics and of biogeography—implies marginal propagation of perturbations and scale-free distributed causal avalanches. We argue that causal information, not easily accessible to experiments, is essential to elucidate the nature and statistics of neural avalanches, and that neutral dynamics is likely to play an important role in the cortex functioning. We discuss the implications of these findings to design new empirical approaches to shed further light on how the brain processes and stores information.
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Watching More Closely: Shot Scale Affects Film Viewers’ Theory of Mind Tendency But Not Ability
Rooney, Brendan; Bálint, Katalin E.
2018-01-01
Recent research debates the effects of exposure to narrative fiction on recognition of mental states in others and self, referred to as Theory of Mind. The current study explores the mechanisms by which such effects could occur in fictional film. Using manipulated film scenes, we conducted a between subject experiment (N = 136) exploring how film shot-scale affects viewers’ Theory of Mind. Specifically, in our methods we distinguish between the trait Theory of Mind abilities (ToM ability), and the state-like tendency to recognize mental states in others and self (ToM tendency). Results showed that close-up shots (compared to long shots) of a character was associated with higher levels of Theory of Mind tendency, when the facial expression was sad but not when it was neutral. And this effect did not transfer to other characters in the film. There was also no observable effect of character depiction on viewers’ general Theory of Mind ability. Together the findings suggest that formal and content features of shot scale can elicit Theory of Mind responses by directing attention toward character mental states rather than improving viewers’ general Theory of Mind ability. PMID:29387032
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Watching More Closely: Shot Scale Affects Film Viewers’ Theory of Mind Tendency But Not Ability
Directory of Open Access Journals (Sweden)
Brendan Rooney
2018-01-01
Full Text Available Recent research debates the effects of exposure to narrative fiction on recognition of mental states in others and self, referred to as Theory of Mind. The current study explores the mechanisms by which such effects could occur in fictional film. Using manipulated film scenes, we conducted a between subject experiment (N = 136 exploring how film shot-scale affects viewers’ Theory of Mind. Specifically, in our methods we distinguish between the trait Theory of Mind abilities (ToM ability, and the state-like tendency to recognize mental states in others and self (ToM tendency. Results showed that close-up shots (compared to long shots of a character was associated with higher levels of Theory of Mind tendency, when the facial expression was sad but not when it was neutral. And this effect did not transfer to other characters in the film. There was also no observable effect of character depiction on viewers’ general Theory of Mind ability. Together the findings suggest that formal and content features of shot scale can elicit Theory of Mind responses by directing attention toward character mental states rather than improving viewers’ general Theory of Mind ability.
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Dark energy and modified gravity in the Effective Field Theory of Large-Scale Structure
Cusin, Giulia; Lewandowski, Matthew; Vernizzi, Filippo
2018-04-01
We develop an approach to compute observables beyond the linear regime of dark matter perturbations for general dark energy and modified gravity models. We do so by combining the Effective Field Theory of Dark Energy and Effective Field Theory of Large-Scale Structure approaches. In particular, we parametrize the linear and nonlinear effects of dark energy on dark matter clustering in terms of the Lagrangian terms introduced in a companion paper [1], focusing on Horndeski theories and assuming the quasi-static approximation. The Euler equation for dark matter is sourced, via the Newtonian potential, by new nonlinear vertices due to modified gravity and, as in the pure dark matter case, by the effects of short-scale physics in the form of the divergence of an effective stress tensor. The effective fluid introduces a counterterm in the solution to the matter continuity and Euler equations, which allows a controlled expansion of clustering statistics on mildly nonlinear scales. We use this setup to compute the one-loop dark-matter power spectrum.
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Friedmann cosmology with a cosmological 'constant' in the scale covariant theory
International Nuclear Information System (INIS)
Beesham, A.
1986-01-01
Homogeneous isotropic cosmologies in the presence of a cosmological 'constant' are studied in the scale covariant theory. A class of solutions is obtained for kappa = 0 for models filled with dust, radiation or stiff matter. For kappa not= 0, solutions are presented for the radiation models. (author)
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International Nuclear Information System (INIS)
Svistun, R.P.; Babej, Yu.I.; Tkachenko, N.N.
1976-01-01
Statistical theories of the scale effect in the fatigue failure of 40KH18N9T, 10 and 20 steels have been verified. The theories are shown to be not invariably suitable for a satisfactory exlanation of the fatigue strength of the samples with respect to their dimensions. One of the main reasons for displaying the scale effect in the process of steel fatigue is the sample self-heating, i.e. a temperature factor which in many cases overlaps a statistical one
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Energy Technology Data Exchange (ETDEWEB)
Svistun, R P; Babei, Yu I; Tkachenko, N N [AN Ukrainskoj SSR, Lvov. Fiziko-Mekhanicheskij Inst.; L' vovskij Lesotekhnicheskij Inst. (Ukrainian SSR))
1976-01-01
Statistical theories of the scale effect in the fatigue failure of 40KH18N9T, 10 and 20 steels have been verified. The theories are shown to be not invariably suitable for a satisfactory exlanation of the fatigue strength of the samples with respect to their dimensions. One of the main reasons for displaying the scale effect in the process of steel fatigue is the sample self-heating, i.e. a temperature factor which in many cases overlaps a statistical one.
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A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks.
Röhl, Annika; Bockmayr, Alexander
2017-01-03
Constraint-based analysis has become a widely used method to study metabolic networks. While some of the associated algorithms can be applied to genome-scale network reconstructions with several thousands of reactions, others are limited to small or medium-sized models. In 2015, Erdrich et al. introduced a method called NetworkReducer, which reduces large metabolic networks to smaller subnetworks, while preserving a set of biological requirements that can be specified by the user. Already in 2001, Burgard et al. developed a mixed-integer linear programming (MILP) approach for computing minimal reaction sets under a given growth requirement. Here we present an MILP approach for computing minimum subnetworks with the given properties. The minimality (with respect to the number of active reactions) is not guaranteed by NetworkReducer, while the method by Burgard et al. does not allow specifying the different biological requirements. Our procedure is about 5-10 times faster than NetworkReducer and can enumerate all minimum subnetworks in case there exist several ones. This allows identifying common reactions that are present in all subnetworks, and reactions appearing in alternative pathways. Applying complex analysis methods to genome-scale metabolic networks is often not possible in practice. Thus it may become necessary to reduce the size of the network while keeping important functionalities. We propose a MILP solution to this problem. Compared to previous work, our approach is more efficient and allows computing not only one, but even all minimum subnetworks satisfying the required properties.
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Directory of Open Access Journals (Sweden)
Nathan Mih
2016-07-01
Full Text Available Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies. Recently, genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include the three-dimensional structure of proteins. The integration of these molecular-level details, such as the physical, structural, and dynamical properties of proteins, notably expands the computational description of biochemical network-level properties and the possibility of understanding and predicting whole cell phenotypes. In this study, we present a multi-scale modeling framework that describes biological processes which range in scale from atomistic details to an entire metabolic network. Using this approach, we can understand how genetic variation, which impacts the structure and reactivity of a protein, influences both native and drug-induced metabolic states. As a proof-of-concept, we study three enzymes (catechol-O-methyltransferase, glucose-6-phosphate dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase and their respective genetic variants which have clinically relevant associations. Using all-atom molecular dynamic simulations enables the sampling of long timescale conformational dynamics of the proteins (and their mutant variants in complex with their respective native metabolites or drug molecules. We find that changes in a protein's structure due to a mutation influences protein binding affinity to metabolites and/or drug molecules, and inflicts large-scale changes in metabolism.
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Inflationary perturbations in no-scale theories
Energy Technology Data Exchange (ETDEWEB)
Salvio, Alberto [CERN, Theoretical Physics Department, Geneva (Switzerland)
2017-04-15
We study the inflationary perturbations in general (classically) scale-invariant theories. Such scenario is motivated by the hierarchy problem and provides natural inflationary potentials and dark matter candidates. We analyse in detail all sectors (the scalar, vector and tensor perturbations) giving general formulae for the potentially observable power spectra, as well as for the curvature spectral index n{sub s} and the tensor-to-scalar ratio r. We show that the conserved Hamiltonian for all perturbations does not feature negative energies even in the presence of the Weyl-squared term if the appropriate quantisation is performed and argue that this term does not lead to phenomenological problems at least in some relevant setups. The general formulae are then applied to a concrete no-scale model, which includes the Higgs and a scalar, ''the planckion'', whose vacuum expectation value generates the Planck mass. Inflation can be triggered by a combination of the planckion and the Starobinsky scalar and we show that no tension with observations is present even in the case of pure planckion inflation, if the coefficient of the Weyl-squared term is large enough. In general, even quadratic inflation is allowed in this case. Moreover, the Weyl-squared term leads to an isocurvature mode, which currently satisfies the observational bounds, but it may be detectable with future experiments. (orig.)
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Directory of Open Access Journals (Sweden)
Benjamin eMerlet
2016-02-01
Full Text Available This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc and flat file formats (SBML and Matlab files. We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics and Glasgow Polyomics on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks.In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks.In order to achieve this goal we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.
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Levering, Jennifer; Fiedler, Tomas; Sieg, Antje; van Grinsven, Koen W A; Hering, Silvio; Veith, Nadine; Olivier, Brett G; Klett, Lara; Hugenholtz, Jeroen; Teusink, Bas; Kreikemeyer, Bernd; Kummer, Ursula
2016-08-20
Genome-scale metabolic models comprise stoichiometric relations between metabolites, as well as associations between genes and metabolic reactions and facilitate the analysis of metabolism. We computationally reconstructed the metabolic network of the lactic acid bacterium Streptococcus pyogenes M49. Initially, we based the reconstruction on genome annotations and already existing and curated metabolic networks of Bacillus subtilis, Escherichia coli, Lactobacillus plantarum and Lactococcus lactis. This initial draft was manually curated with the final reconstruction accounting for 480 genes associated with 576 reactions and 558 metabolites. In order to constrain the model further, we performed growth experiments of wild type and arcA deletion strains of S. pyogenes M49 in a chemically defined medium and calculated nutrient uptake and production fluxes. We additionally performed amino acid auxotrophy experiments to test the consistency of the model. The established genome-scale model can be used to understand the growth requirements of the human pathogen S. pyogenes and define optimal and suboptimal conditions, but also to describe differences and similarities between S. pyogenes and related lactic acid bacteria such as L. lactis in order to find strategies to reduce the growth of the pathogen and propose drug targets. Copyright © 2016 Elsevier B.V. All rights reserved.
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Quasi-potential and Two-Scale Large Deviation Theory for Gillespie Dynamics
Li, Tiejun
2016-01-07
The construction of energy landscape for bio-dynamics is attracting more and more attention recent years. In this talk, I will introduce the strategy to construct the landscape from the connection to rare events, which relies on the large deviation theory for Gillespie-type jump dynamics. In the application to a typical genetic switching model, the two-scale large deviation theory is developed to take into account the fast switching of DNA states. The comparison with other proposals are also discussed. We demonstrate different diffusive limits arise when considering different regimes for genetic translation and switching processes.
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Conductance of finite systems and scaling in localization theory
Suslov, I. M.
2012-11-01
The conductance of finite systems plays a central role in the scaling theory of localization (Abrahams et al., Phys. Rev. Lett. 42, 673 (1979)). Usually it is defined by the Landauer-type formulas, which remain open the following questions: (a) exclusion of the contact resistance in the many-channel case; (b) correspondence of the Landauer conductance with internal properties of the system; (c) relation with the diffusion coefficient D(ω, q) of an infinite system. The answers to these questions are obtained below in the framework of two approaches: (1) self-consistent theory of localization by Vollhardt and Wölfle, and (2) quantum mechanical analysis based on the shell model. Both approaches lead to the same definition for the conductance of a finite system, closely related to the Thouless definition. In the framework of the self-consistent theory, the relations of finite-size scaling are derived and the Gell-Mann-Low functions β( g) for space dimensions d = 1, 2, 3 are calculated. In contrast to the previous attempt by Vollhardt and Wölfle (1982), the metallic and localized phase are considered from the same standpoint, and the conductance of a finite system has no singularity at the critical point. In the 2D case, the expansion of β( g) in 1/ g coincides with results of the σ-model approach on the two-loop level and depends on the renormalization scheme in higher loops; the use of dimensional regularization for transition to dimension d = 2 + ɛ looks incompatible with the physical essence of the problem. The results are compared with numerical and physical experiments. A situation in higher dimensions and the conditions for observation of the localization law σ(ω) ∝ - iω for conductivity are discussed.
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Conductance of finite systems and scaling in localization theory
International Nuclear Information System (INIS)
Suslov, I. M.
2012-01-01
The conductance of finite systems plays a central role in the scaling theory of localization (Abrahams et al., Phys. Rev. Lett. 42, 673 (1979)). Usually it is defined by the Landauer-type formulas, which remain open the following questions: (a) exclusion of the contact resistance in the many-channel case; (b) correspondence of the Landauer conductance with internal properties of the system; (c) relation with the diffusion coefficient D(ω, q) of an infinite system. The answers to these questions are obtained below in the framework of two approaches: (1) self-consistent theory of localization by Vollhardt and Wölfle, and (2) quantum mechanical analysis based on the shell model. Both approaches lead to the same definition for the conductance of a finite system, closely related to the Thouless definition. In the framework of the self-consistent theory, the relations of finite-size scaling are derived and the Gell-Mann-Low functions β(g) for space dimensions d = 1, 2, 3 are calculated. In contrast to the previous attempt by Vollhardt and Wölfle (1982), the metallic and localized phase are considered from the same standpoint, and the conductance of a finite system has no singularity at the critical point. In the 2D case, the expansion of β(g) in 1/g coincides with results of the σ-model approach on the two-loop level and depends on the renormalization scheme in higher loops; the use of dimensional regularization for transition to dimension d = 2 + ε looks incompatible with the physical essence of the problem. The results are compared with numerical and physical experiments. A situation in higher dimensions and the conditions for observation of the localization law σ(ω) ∝ −iω for conductivity are discussed.
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Cosmological tests of a scale covariant theory of gravitation
International Nuclear Information System (INIS)
Owen, J.R.
1979-01-01
The Friedmann models with #betta# = 0 are subjected to several optical and radio tests within the standard and scale covariant theories of gravitation. Within standard cosmology, both interferometric and scintillation data are interpreted in terms of selection effects and evolution. Within the context of scale covariant cosmology are derived: (1) the full solution to Einstein's gravitational equations in atomic units for a matter dominated universe, (2) the study of the magnitude vs. redshift relation for elliptical galaxies, (3) the derivation of the evolutionary parameter used in (2), (4) the isophotal angular diameter vs. redshift relation, (5) the metric angular diameter vs. redshift relation, (6) the N(m) vs. magnitude relation for QSO's and their m vs z relation, and finally (7) the integrated and differential expressions for the number count vs. radio flux test. The results, both in graphical and tabular form, are presented for four gauges (i.e. parametrized relations between atomic and gravitational units). No contradiction between the new theory and the data is found with any of the tests studied. For some gauges, which are suggested by a recent analysis of the time variation of the Moon's period which is discussed in the text in terms of the new theory, the effect of the deceleration parameter on cosmological predictions is enhanced over standard cosmology and it is possible to say that the data are more easily reconciled with an open universe. Within the same gauge, the main features of both the N(m) vs. m and m-z test are accounted for by the same simple evolutionary parametrization whereas different evolutionary rates were indicated by interpretation within standard cosmology. The same consistency, lacking in standard cosmology on this level of analysis, is achieved for the integrated and differential number count - radio flux tests within the same gauge
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A simplified density matrix minimization for linear scaling self-consistent field theory
International Nuclear Information System (INIS)
Challacombe, M.
1999-01-01
A simplified version of the Li, Nunes and Vanderbilt [Phys. Rev. B 47, 10891 (1993)] and Daw [Phys. Rev. B 47, 10895 (1993)] density matrix minimization is introduced that requires four fewer matrix multiplies per minimization step relative to previous formulations. The simplified method also exhibits superior convergence properties, such that the bulk of the work may be shifted to the quadratically convergent McWeeny purification, which brings the density matrix to idempotency. Both orthogonal and nonorthogonal versions are derived. The AINV algorithm of Benzi, Meyer, and Tuma [SIAM J. Sci. Comp. 17, 1135 (1996)] is introduced to linear scaling electronic structure theory, and found to be essential in transformations between orthogonal and nonorthogonal representations. These methods have been developed with an atom-blocked sparse matrix algebra that achieves sustained megafloating point operations per second rates as high as 50% of theoretical, and implemented in the MondoSCF suite of linear scaling SCF programs. For the first time, linear scaling Hartree - Fock theory is demonstrated with three-dimensional systems, including water clusters and estane polymers. The nonorthogonal minimization is shown to be uncompetitive with minimization in an orthonormal representation. An early onset of linear scaling is found for both minimal and double zeta basis sets, and crossovers with a highly optimized eigensolver are achieved. Calculations with up to 6000 basis functions are reported. The scaling of errors with system size is investigated for various levels of approximation. copyright 1999 American Institute of Physics
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The maximum sizes of large scale structures in alternative theories of gravity
Energy Technology Data Exchange (ETDEWEB)
Bhattacharya, Sourav [IUCAA, Pune University Campus, Post Bag 4, Ganeshkhind, Pune, 411 007 India (India); Dialektopoulos, Konstantinos F. [Dipartimento di Fisica, Università di Napoli ' Federico II' , Complesso Universitario di Monte S. Angelo, Edificio G, Via Cinthia, Napoli, I-80126 Italy (Italy); Romano, Antonio Enea [Instituto de Física, Universidad de Antioquia, Calle 70 No. 52–21, Medellín (Colombia); Skordis, Constantinos [Department of Physics, University of Cyprus, 1 Panepistimiou Street, Nicosia, 2109 Cyprus (Cyprus); Tomaras, Theodore N., E-mail: sbhatta@iitrpr.ac.in, E-mail: kdialekt@gmail.com, E-mail: aer@phys.ntu.edu.tw, E-mail: skordis@ucy.ac.cy, E-mail: tomaras@physics.uoc.gr [Institute of Theoretical and Computational Physics and Department of Physics, University of Crete, 70013 Heraklion (Greece)
2017-07-01
The maximum size of a cosmic structure is given by the maximum turnaround radius—the scale where the attraction due to its mass is balanced by the repulsion due to dark energy. We derive generic formulae for the estimation of the maximum turnaround radius in any theory of gravity obeying the Einstein equivalence principle, in two situations: on a spherically symmetric spacetime and on a perturbed Friedman-Robertson-Walker spacetime. We show that the two formulae agree. As an application of our formula, we calculate the maximum turnaround radius in the case of the Brans-Dicke theory of gravity. We find that for this theory, such maximum sizes always lie above the ΛCDM value, by a factor 1 + 1/3ω, where ω>> 1 is the Brans-Dicke parameter, implying consistency of the theory with current data.
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International Nuclear Information System (INIS)
Senjanovic, G.
1982-07-01
It is demonstrated that the spontaneous breakdown of CP invariance in grand unified theories requires the presence of intermediate mass scales. The simplest realization is provided by weakly broken left-right symmetry in the context of SU(2)sub(L) x SU(2)sub(R) x U(1)sub(B-L) model embedded in grand unified theories. (author)
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Scaling Law for Photon Transmission through Optically Turbid Slabs Based on Random Walk Theory
Directory of Open Access Journals (Sweden)
Xuesong Li
2012-03-01
Full Text Available Past work has demonstrated the value of a random walk theory (RWT to solve multiple-scattering problems arising in numerous contexts. This paper’s goal is to investigate the application range of the RWT using Monte Carlo simulations and extending it to anisotropic media using scaling laws. Meanwhile, this paper also reiterates rules for converting RWT formulas to real physical dimensions, and corrects some errors which appear in an earlier publication. The RWT theory, validated by the Monte Carlo simulations and combined with the scaling law, is expected to be useful to study multiple scattering and to greatly reduce the computation cost.
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2014-01-01
Background Abnormal states in human liver metabolism are major causes of human liver diseases ranging from hepatitis to hepatic tumor. The accumulation in relevant data makes it feasible to derive a large-scale human liver metabolic network (HLMN) and to discover important biological principles or drug-targets based on network analysis. Some studies have shown that interesting biological phenomenon and drug-targets could be discovered by applying structural controllability analysis (which is a newly prevailed concept in networks) to biological networks. The exploration on the connections between structural controllability theory and the HLMN could be used to uncover valuable information on the human liver metabolism from a fresh perspective. Results We applied structural controllability analysis to the HLMN and detected driver metabolites. The driver metabolites tend to have strong ability to influence the states of other metabolites and weak susceptibility to be influenced by the states of others. In addition, the metabolites were classified into three classes: critical, high-frequency and low-frequency driver metabolites. Among the identified 36 critical driver metabolites, 27 metabolites were found to be essential; the high-frequency driver metabolites tend to participate in different metabolic pathways, which are important in regulating the whole metabolic systems. Moreover, we explored some other possible connections between the structural controllability theory and the HLMN, and find that transport reactions and the environment play important roles in the human liver metabolism. Conclusion There are interesting connections between the structural controllability theory and the human liver metabolism: driver metabolites have essential biological functions; the crucial role of extracellular metabolites and transport reactions in controlling the HLMN highlights the importance of the environment in the health of human liver metabolism. PMID:24885538
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Directory of Open Access Journals (Sweden)
Bushell Michael E
2011-05-01
Full Text Available Abstract Background Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment. Results Here, we present Acorn, an open source (GNU GPL grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a
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A Polytomous Item Response Theory Analysis of Social Physique Anxiety Scale
Fletcher, Richard B.; Crocker, Peter
2014-01-01
The present study investigated the social physique anxiety scale's factor structure and item properties using confirmatory factor analysis and item response theory. An additional aim was to identify differences in response patterns between groups (gender). A large sample of high school students aged 11-15 years (N = 1,529) consisting of n =…
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Maino, James L.; Kearney, Michael R.
2017-03-01
A key strength of the DEB approach, in contrast to other metabolic theories, is that its foundational principles are general to all of life. Other theories have attempted to explain patterns in metabolism in terms of taxon-specific processes, such as the geometry of vascular network supply constraints [1,2], or heat dissipation requirements of endotherms [3], but DEB theory presents constraints on metabolic processes that apply to a wide range of taxa, including bacteria, invertebrates, birds, or mammals [4]. The price of this generalisability is abstraction, but there is much to gain from a general and unifying metabolic theory. Abstracting individuals into simple energy processors would seem to overlook many other important aspects of their biology, such as their unique phylogeny, physiology, or ethology, but this strategy has facilitated great advances in one of the grand challenges in biology: making sense of interacting phenomena occurring across wide scales in space, time, and organisational complexity. The study of cells, individuals, communities and ecosystems have benefited from such a regime [5,6]. Similarly, the simple abstraction of partitioning individual organisms into compartments of reserve biomass and structural biomass allows one to account for an astounding variety of energetic transformations that occur between species and as an organism develops.
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Taousser, Fatima; Defoort, Michael; Djemai, Mohamed
2016-01-01
This paper investigates the consensus problem for linear multi-agent system with fixed communication topology in the presence of intermittent communication using the time-scale theory. Since each agent can only obtain relative local information intermittently, the proposed consensus algorithm is based on a discontinuous local interaction rule. The interaction among agents happens at a disjoint set of continuous-time intervals. The closed-loop multi-agent system can be represented using mixed linear continuous-time and linear discrete-time models due to intermittent information transmissions. The time-scale theory provides a powerful tool to combine continuous-time and discrete-time cases and study the consensus protocol under a unified framework. Using this theory, some conditions are derived to achieve exponential consensus under intermittent information transmissions. Simulations are performed to validate the theoretical results.
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Geček, Sunčana
2017-03-01
Jusup and colleagues in the recent review on physics of metabolic organization [1] discuss in detail motivational considerations and common assumptions of Dynamic Energy Budget (DEB) theory, supply readers with a practical guide to DEB-based modeling, demonstrate the construction and dynamics of the standard DEB model, and illustrate several applications. The authors make a step forward from the existing literature by seamlessly bridging over the dichotomy between (i) thermodynamic foundations of the theory (which are often more accessible and understandable to physicists and mathematicians), and (ii) the resulting bioenergetic models (mostly used by biologists in real-world applications).
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Energy Technology Data Exchange (ETDEWEB)
Mehralian, Fahimeh [Mechanical Engineering Department, Shahrekord University, Shahrekord (Iran, Islamic Republic of); Tadi Beni, Yaghoub, E-mail: tadi@eng.sku.ac.ir [Faculty of Engineering, Shahrekord University, Shahrekord (Iran, Islamic Republic of); Karimi Zeverdejani, Mehran [Mechanical Engineering Department, Shahrekord University, Shahrekord (Iran, Islamic Republic of)
2017-06-01
Featured by two small length scale parameters, nonlocal strain gradient theory is utilized to investigate the free vibration of nanotubes. A new size-dependent shell model formulation is developed by using the first order shear deformation theory. The governing equations and boundary conditions are obtained using Hamilton's principle and solved for simply supported boundary condition. As main purpose of this study, since the values of two small length scale parameters are still unknown, they are calibrated by the means of molecular dynamics simulations (MDs). Then, the influences of different parameters such as nonlocal parameter, scale factor, length and thickness on vibration characteristics of nanotubes are studied. It is also shown that increase in thickness and decrease in length parameters intensify the effect of nonlocal parameter and scale factor.
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Planar plane-wave matrix theory at the four loop order: integrability without BMN scaling
International Nuclear Information System (INIS)
Fischbacher, Thomas; Klose, Thomas; Plefka, Jan
2005-01-01
We study SU(N) plane-wave matrix theory up to fourth perturbative order in its large N planar limit. The effective hamiltonian in the closed su(2) subsector of the model is explicitly computed through a specially tailored computer program to perform large scale distributed symbolic algebra and generation of planar graphs. The number of graphs here was in the deep billions. The outcome of our computation establishes the four-loop integrability of the planar plane-wave matrix model. To elucidate the integrable structure we apply the recent technology of the perturbative asymptotic Bethe ansatz to our model. The resulting S-matrix turns out to be structurally similar but nevertheless distinct to the so far considered long-range spin-chain S-matrices of Inozemtsev, Beisert-Dippel-Staudacher and Arutyunov-Frolov-Staudacher in the AdS/CFT context. In particular our result displays a breakdown of BMN scaling at the four-loop order. That is, while there exists an appropriate identification of the matrix theory mass parameter with the coupling constant of the N=4 superconformal Yang-Mills theory which yields an eighth order lattice derivative for well separated impurities (naively implying BMN scaling) the detailed impurity contact interactions ruin this scaling property at the four-loop order. Moreover we study the issue of 'wrapping' interactions, which show up for the first time at this loop-order through a Konishi descendant length four operator. (author)
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Agren, Rasmus; Otero, José Manuel; Nielsen, Jens
2013-07-01
In this work, we describe the application of a genome-scale metabolic model and flux balance analysis for the prediction of succinic acid overproduction strategies in Saccharomyces cerevisiae. The top three single gene deletion strategies, Δmdh1, Δoac1, and Δdic1, were tested using knock-out strains cultivated anaerobically on glucose, coupled with physiological and DNA microarray characterization. While Δmdh1 and Δoac1 strains failed to produce succinate, Δdic1 produced 0.02 C-mol/C-mol glucose, in close agreement with model predictions (0.03 C-mol/C-mol glucose). Transcriptional profiling suggests that succinate formation is coupled to mitochondrial redox balancing, and more specifically, reductive TCA cycle activity. While far from industrial titers, this proof-of-concept suggests that in silico predictions coupled with experimental validation can be used to identify novel and non-intuitive metabolic engineering strategies.
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Merlet, Benjamin; Paulhe, Nils; Vinson, Florence; Frainay, Clément; Chazalviel, Maxime; Poupin, Nathalie; Gloaguen, Yoann; Giacomoni, Franck; Jourdan, Fabien
2016-01-01
This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.
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Nisbet, Roger M.
2017-03-01
Jusup et al. [1] provide a comprehensive review of Dynamic Energy Budget (DEB) theory - a theory of metabolic organization that has its roots in a model by S.A.L.M Kooijman [2] and has evolved over three decades into a remarkable general theory whose use appears to be growing exponentially. The definitive text on DEB theory [3] is a challenging (though exceptionally rewarding) read, and previous reviews (e.g. [4,5]) have provided focused summaries of some of its main themes, targeted at specific groups of readers. The strong case for a further review is well captured in the abstract: ;Hitherto, the foundations were more accessible to physicists or mathematicians, and the applications to biologists, causing a dichotomy in what always should have been a single body of work.; In response to this need, Jusup et al. provide a review that combines a lucid, rigorous exposition of the core components of DEB theory with a diverse collection of DEB applications. They also highlight some recent advances, notably the rapidly growing on-line database of DEB model parameters (451 species on 15 August 2016 according to [1], now, just a few months later, over 500 species).
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Fang, Yilin; Yabusaki, Steven B.; Lipton, Mary S.; Long, Philip E.
2012-01-01
Accurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within an in silico model using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model of Geobacter metallireducens—specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment. PMID:23042184
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Rolland, Jonathan; Loiseau, Oriane; Romiguier, Jonathan; Salamin, Nicolas
2016-05-20
The metabolic theory of ecology stipulates that molecular evolutionary rates should correlate with temperature and latitude in ectothermic organisms. Previous studies have shown that most groups of vertebrates, such as amphibians, turtles and even endothermic mammals, have higher molecular evolutionary rates in regions where temperature is high. However, the association between molecular evolutionary rates and temperature or latitude has never been tested in Squamata. We used a large dataset including the spatial distributions and environmental variables for 1,651 species of Squamata and compared the contrast of the rates of molecular evolution with the contrast of temperature and latitude between sister species. Using major axis regressions and a new algorithm to choose independent sister species pairs, we found that temperature and absolute latitude were not associated with molecular evolutionary rates. This absence of association in such a diverse ectothermic group questions the mechanisms explaining current pattern of species diversity in Squamata and challenges the presupposed universality of the metabolic theory of ecology.
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2016-03-15
RESEARCH ARTICLE Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism Francisco G...jaques.reifman.civ@mail.mil Abstract A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm -based infections that are difficult to...eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic
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National Research Council Canada - National Science Library
Grodzicker, Terri; Stewart, David J; Stillman, Bruce
2011-01-01
...), cellular, organ system (cardiovascular, bone), and organismal (timing and life span) scales. Diseases impacted by metabolic imbalance or dysregulation that were covered in detail included diabetes, obesity, metabolic syndrome, and cancer...
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McGill, Anne-Thea
2014-01-01
Metabolic syndrome (MetS) predicts type II diabetes mellitus (TIIDM), cardiovascular disease (CVD) and cancer, and their rates have escalated over the last few decades. Obesity related co-morbidities also overlap the concept of the metabolic syndrome (MetS). However, understanding of the syndrome's underlying causes may have been misapprehended. The current paper follows on from a theory review by McGill, A-T in Archives of Public Health, 72: 30. This accompanying paper utilises research on human evolution and new biochemistry to theorise on why MetS and obesity arise and how they affect the population. The basis of this composite unifying theory is that the proportionately large, energy-demanding human brain may have driven co-adaptive mechanisms to provide, or conserve, energy for the brain. A 'dual system' is proposed. 1) The enlarged, complex cortico-limbic-striatal system increases dietary energy by developing strong neural self-reward/motivation pathways for the acquisition of energy dense food, and (2) the nuclear factor-erythroid 2-related factor 2 (NRF2) cellular protection system amplifies antioxidant, antitoxicant and repair activity by employing plant chemicals. In humans who consume a nutritious diet, the NRF2 system has become highly energy efficient. Other relevant human-specific co-adaptations are explored. In order to 'test' this composite unifying theory it is important to show that the hypothesis and sub-theories pertain throughout the whole of human evolution and history up till the current era. Corollaries of the composite unifying theory of MetS are examined with respect to past under-nutrition and malnutrition since agriculture began 10,000 years ago. The effects of man-made pollutants on degenerative change are examined. Projections are then made from current to future patterns on the state of 'insufficient micronutrient and/or unbalanced high energy malnutrition with central obesity and metabolic dysregulation' or 'malnubesity'. Forecasts
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Arandia-Gorostidi, Nestor; Huete-Stauffer, Tamara Megan; Alonso-Sá ez, Laura; Moran, Xose Anxelu G.
2017-01-01
in general lower than 0.65 eV, the value predicted by the Metabolic Theory of Ecology (MTE). Contrary to MTE predictions, carrying capacity tended to increase with warming for all bacterial groups. Our analysis confirms that resource availability is key when
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Constraints on Interacting Scalars in 2T Field Theory and No Scale Models in 1T Field Theory
Bars, Itzhak
2010-01-01
In this paper I determine the general form of the physical and mathematical restrictions that arise on the interactions of gravity and scalar fields in the 2T field theory setting, in d+2 dimensions, as well as in the emerging shadows in d dimensions. These constraints on scalar fields follow from an underlying Sp(2,R) gauge symmetry in phase space. Determining these general constraints provides a basis for the construction of 2T supergravity, as well as physical applications in 1T-field theory, that are discussed briefly here, and more detail elsewhere. In particular, no scale models that lead to a vanishing cosmological constant at the classical level emerge naturally in this setting.
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International Nuclear Information System (INIS)
Vardoulakis, I.; Kourkoulis, S.K.; Exadaktylos, G.
1998-01-01
A gradient bending theory is developed based on a strain energy function that includes the classical Bernoulli-Euler term, the shape correction term (microstructural length scale) introduced by Timoshenko, and a term associated with surface energy (micromaterial length scale) accounting for the bending moment gradient effect. It is shown that the last term is capable to interpret the size effect in three-point bending (3PB), namely the decrease of the failure load with decreasing beam length for the same aspect ratio. This theory is used to describe the mechanical behaviour of Dionysos-Pentelikon marble in 3PB. Series of tests with prismatic marble beams of the same aperture but with different lengths were conducted and it was concluded that the present theory predicts well the size effect. (orig.)
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The role of instantons in scale-invariant gauge theories
International Nuclear Information System (INIS)
Affleck, I.
1980-01-01
Instanton calculations in scale-invariant gauge theories, such as QCD, have long been plagued by divergences at large distances where strong coupling effects are important. Furthermore, Witten has argued that quantum effects may cause the instanton gas to disappear and has displayed this phenomenon in the CPsup(N-1) model at large N. It is argued here that instantons can play a role in calculations involving an inherent infrared cut-off, and this is demonstrated in the CPsup(N-1) model for large N at a finite temperature. Some results on finite-temperature QED are also obtained in passing. (orig.)
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Catalonia's energy metabolism: Using the MuSIASEM approach at different scales
International Nuclear Information System (INIS)
Ramos-Martin, Jesus; Canellas-Bolta, Silvia; Giampietro, Mario; Gamboa, Gonzalo
2009-01-01
This paper applies the so-called Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM), based on Georgescu-Roegen's fund-flow model, to the Spanish region of Catalonia. It arrives to the conclusion that within the context of the end of cheap oil, the current development model of the Catalan economy, based on the growth of low-productivity sectors such as services and construction, must be changed. The change is needed not only because of the increasing scarcity of affordable energy and the increasing environmental impact of present development, but also because of the aging population. Moreover, the situation experienced by Catalonia is similar to that of other European countries and many other developed countries. This implies that we can expect a wave of major structural changes in the economy of developed countries worldwide. To make things more challenging, according to current trends, the energy intensity and exosomatic energy metabolism of Catalonia will keep increasing in the near future. To avoid a reduction in the standard of living of Catalans due to a reduction in the available energy it is important that the Government of Catalonia implement major adjustments and conservation efforts in both the household and paid-work sectors.
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diCenzo, George C; Finan, Turlough M
2018-01-01
The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration. Subsequent expression of the site-specific recombinase mediates recombination between the two target sequences, resulting in the excision of the intervening region and its loss from the genome. We further illustrate how this deletion system can be readily adapted to function as a large-scale in vivo cloning procedure, in which the region excised from the genome is captured as a replicative plasmid. We next provide a procedure for the metabolic analysis of bacterial large-scale genome deletion mutants using the Biolog Phenotype MicroArray™ system. Finally, a pipeline is described, and a sample Matlab script is provided, for the integration of the obtained data with a draft metabolic reconstruction for the refinement of the reactions and gene-protein-reaction relationships in a metabolic reconstruction.
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Vispoel, Walter P; Morris, Carrie A; Kilinc, Murat
2018-01-01
We applied a new approach to Generalizability theory (G-theory) involving parallel splits and repeated measures to evaluate common uses of the Paulhus Deception Scales based on polytomous and four types of dichotomous scoring. G-theory indices of reliability and validity accounting for specific-factor, transient, and random-response measurement error supported use of polytomous over dichotomous scores as contamination checks; as control, explanatory, and outcome variables; as aspects of construct validation; and as indexes of environmental effects on socially desirable responding. Polytomous scoring also provided results for flagging faking as dependable as those when using dichotomous scoring methods. These findings argue strongly against the nearly exclusive use of dichotomous scoring for the Paulhus Deception Scales in practice and underscore the value of G-theory in demonstrating this. We provide guidelines for applying our G-theory techniques to other objectively scored clinical assessments, for using G-theory to estimate how changes to a measure might improve reliability, and for obtaining software to conduct G-theory analyses free of charge.
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Teusink, B.; Wiersma, A.; Molenaar, D.; Francke, C.; Vos, de W.M.; Siezen, R.J.; Smid, E.J.
2006-01-01
A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete model includes 721 genes, 643 reactions, and 531 metabolites. Different stoichiometric modeling techniques were used for
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The string tension and the scaling behavior of SU(2) gauge theory on a random lattice
International Nuclear Information System (INIS)
Qui Zhaoming; Ren Haichang; Academia Sinica, Beijing; Wang Xiaoqun; Yang Zhixing; Zhao Enping
1987-01-01
The SU(2) gauge theory on an 8 4 random lattice has been studied by the Monte Carlo method. The string tensions have been evaluated. They display the expected scaling behavior for β = 1.2-1.3. The scale parameter Λ RAN has been determined approximately. (orig.)
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Banavar, Jayanth
2009-03-01
The unity of life is expressed not only in the universal basis of inheritance and energetics at the molecular level, but also in the pervasive scaling of traits with body size at the whole-organism level. More than 75 years ago, Kleiber and Brody and Proctor independently showed that the metabolic rates, B, of mammals and birds scale as the three-quarter power of their mass, M. Subsequent studies showed that most biological rates and times scale as M-1/4 and M^1/4 respectively, and that these so called quarter-power scaling relations hold for a variety of organisms, from unicellular prokaryotes and eukaryotes to trees and mammals. The wide applicability of Kleiber's law, across the 22 orders of magnitude of body mass from minute bacteria to giant whales and sequoias, raises the hope that there is some simple general explanation that underlies the incredible diversity of form and function. We will present a general theoretical framework for understanding the relationship between metabolic rate, B, and body mass, M. We show how the pervasive quarter-power biological scaling relations arise naturally from optimal directed resource supply systems. This framework robustly predicts that: 1) whole organism power and resource supply rate, B, scale as M^3/4; 2) most other rates, such as heart rate and maximal population growth rate scale as M-1/4; 3) most biological times, such as blood circulation time and lifespan, scale as M^1/4; and 4) the average velocity of flow through the network, v, such as the speed of blood and oxygen delivery, scales as M^1/12. Our framework is valid even when there is no underlying network. Our theory is applicable to unicellular organisms as well as to large animals and plants. This work was carried out in collaboration with Amos Maritan along with Jim Brown, John Damuth, Melanie Moses, Andrea Rinaldo, and Geoff West.
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A critical review on the scaling theory of dispersion
Zech, Alraune; Mai, Juliane; Attinger, Sabine; Dietrich, Peter; Teutsch, Georg; Fiori, Aldo; Rubin, Yoram
2014-05-01
The phenomenon of dispersive mixing of solutes in aquifers is subject of research since decades. The characterization of dispersivity at a particular field site is a prerequisite to predict the movement and spreading of a contaminant plume. Experimental investigations have shown, that field-scale dispersivities vary over orders of magnitude, which apparently depends on the scale of measurement. Gelhar et al. [1992] and Schulze-Makuch [2005] have reviewed a large number of transport experiments reported in the literature. Based on that data Schulze-Makuch [2005] performed a trend analysis of longitudinal dispersivity, fostering the empirical relationship of a power law between dispersivities and the scale of measurement without an upper bound. The goal of our study is to critically revisit not only the data used for the trend analysis but the power-law scale dependence of longitudinal dispersivity (e.g. Neuman [1990], Xu and Eckstein [1995]). Our particular focus is on the reported dispersivities of large amount (larger than 100m) and large measurement scales (in the order of kilometers). We aim to evaluate current theories of transport against a critical "mass" of field experiments and to bracket the conditions of their applicability. We further aim to evaluate the adequacy of the field sampling techniques that were employed from the perspective of more than 30 years development in modeling and field characterization. Given the tremendous progress in field data acquisition techniques and new insights gained, it is reasonable to expect that interpretations of past experiments may be flawed due to the limitations or inadequacy of field sampling techniques. Gelhar, L.W., C. Welty, and K.R. Rehfeldt, 1992, A critical review of data on field-scale dispersion in aquifers, Water Resources Research 28, No. 7: 1955-1974. Schulze-Makuch, D., 2005, Longitudinal dispersivity data and implications for scaling behavior, Ground Water, Vol. 43, No. 3, 443-456. Neuman, S.P., 1990
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Zuñiga, Cristal; Li, Chien-Ting; Huelsman, Tyler; Levering, Jennifer; Zielinski, Daniel C; McConnell, Brian O; Long, Christopher P; Knoshaug, Eric P; Guarnieri, Michael T; Antoniewicz, Maciek R; Betenbaugh, Michael J; Zengler, Karsten
2016-09-01
The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine. © 2016 American Society of Plant Biologists. All rights reserved.
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Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001
Energy Technology Data Exchange (ETDEWEB)
Navid, A; Almaas, E
2009-01-13
The gram-negative bacterium Yersinia pestis, the aetiological agent of bubonic plague, is one the deadliest pathogens known to man. Despite its historical reputation, plague is a modern disease which annually afflicts thousands of people. Public safety considerations greatly limit clinical experimentation on this organism and thus development of theoretical tools to analyze the capabilities of this pathogen is of utmost importance. Here, we report the first genome-scale metabolic model of Yersinia pestis biovar Mediaevalis based both on its recently annotated genome, and physiological and biochemical data from literature. Our model demonstrates excellent agreement with Y. pestis known metabolic needs and capabilities. Since Y. pestis is a meiotrophic organism, we have developed CryptFind, a systematic approach to identify all candidate cryptic genes responsible for known and theoretical meiotrophic phenomena. In addition to uncovering every known cryptic gene for Y. pestis, our analysis of the rhamnose fermentation pathway suggests that betB is the responsible cryptic gene. Despite all of our medical advances, we still do not have a vaccine for bubonic plague. Recent discoveries of antibiotic resistant strains of Yersinia pestis coupled with the threat of plague being used as a bioterrorism weapon compel us to develop new tools for studying the physiology of this deadly pathogen. Using our theoretical model, we can study the cell's phenotypic behavior under different circumstances and identify metabolic weaknesses which may be harnessed for the development of therapeutics. Additionally, the automatic identification of cryptic genes expands the usage of genomic data for pharmaceutical purposes.
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Zuñiga, Cristal; Li, Chien-Ting; Zielinski, Daniel C.; Guarnieri, Michael T.; Antoniewicz, Maciek R.; Zengler, Karsten
2016-01-01
The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine. PMID:27372244
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International Nuclear Information System (INIS)
Foot, Robert; Kobakhidze, Archil; Volkas, Raymond R.; McDonald, Kristian L.
2008-01-01
If scale invariance is a classical symmetry then both the Planck scale and the weak scale should emerge as quantum effects. We show that this can be realized in simple scale invariant theories with a hidden sector. The weak/Planck scale hierarchy emerges in the (technically natural) limit in which the hidden sector decouples from the ordinary sector. In this limit, finite corrections to the weak scale are consequently small, while quadratic divergences are absent by virtue of classical scale invariance, so there is no hierarchy problem
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Directory of Open Access Journals (Sweden)
Yuanzhi Shao
Full Text Available On the basis of two universal power-law scaling laws, i.e. the scaling dynamic hysteresis in physics and the allometric scaling metabolism in biosystem, we studied the dynamic response and the evolution of an immunosurveillant anti-tumor system subjected to a periodic external intervention, which is equivalent to the scheme of a radiotherapy or chemotherapy, within the framework of the growth dynamics of tumor. Under the modulation of either an abrupt or a gradual change external intervention, the population density of tumors exhibits a dynamic hysteresis to the intervention. The area of dynamic hysteresis loop characterizes a sort of dissipative-therapeutic relationship of the dynamic responding of treated tumors with the dose consumption of accumulated external intervention per cycle of therapy. Scaling the area of dynamic hysteresis loops against the intensity of an external intervention, we deduced a characteristic quantity which was defined as the theoretical therapeutic effectiveness of treated tumor and related with the destructive metabolism of tumor under treatment. The calculated dose-effectiveness profiles, namely the dose cumulant per cycle of intervention versus the therapeutic effectiveness, could be well scaled into a universal quadratic formula regardless of either an abrupt or a gradual change intervention involved. We present a new concept, i.e., the therapy-effect matrix and the dose cumulant matrix, to expound the new finding observed in the growth and regression dynamics of a modulated anti-tumor system.
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A computational comparison of theory and practice of scale intonation in Byzantine chant
DEFF Research Database (Denmark)
Panteli, Maria; Purwins, Hendrik
2013-01-01
Byzantine Chant performance practice is quantitatively compared to the Chrysanthine theory. The intonation of scale degrees is quantified, based on pitch class profiles. An analysis procedure is introduced that consists of the following steps: 1) Pitch class histograms are calculated via non-parametric...... kernel smoothing. 2) Histogram peaks are detected. 3) Phrase ending analysis aids the finding of the tonic to align histogram peaks. 4) The theoretical scale degrees are mapped to the practical ones. 5) A schema of statistical tests detects significant deviations of theoretical scale tuning from...... the estimated ones in performance practice. The analysis of 94 echoi shows a tendency of the singer to level theoretic particularities of the echos that stand out of the general norm in the octoechos: theoretically extremely large scale steps are diminished in performance....
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Engineering Cellular Metabolism
DEFF Research Database (Denmark)
Nielsen, Jens; Keasling, Jay
2016-01-01
Metabolic engineering is the science of rewiring the metabolism of cells to enhance production of native metabolites or to endow cells with the ability to produce new products. The potential applications of such efforts are wide ranging, including the generation of fuels, chemicals, foods, feeds...... of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation....
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Klamt, Steffen; Müller, Stefan; Regensburger, Georg; Zanghellini, Jürgen
2018-02-07
The optimization of metabolic rates (as linear objective functions) represents the methodical core of flux-balance analysis techniques which have become a standard tool for the study of genome-scale metabolic models. Besides (growth and synthesis) rates, metabolic yields are key parameters for the characterization of biochemical transformation processes, especially in the context of biotechnological applications. However, yields are ratios of rates, and hence the optimization of yields (as nonlinear objective functions) under arbitrary linear constraints is not possible with current flux-balance analysis techniques. Despite the fundamental importance of yields in constraint-based modeling, a comprehensive mathematical framework for yield optimization is still missing. We present a mathematical theory that allows one to systematically compute and analyze yield-optimal solutions of metabolic models under arbitrary linear constraints. In particular, we formulate yield optimization as a linear-fractional program. For practical computations, we transform the linear-fractional yield optimization problem to a (higher-dimensional) linear problem. Its solutions determine the solutions of the original problem and can be used to predict yield-optimal flux distributions in genome-scale metabolic models. For the theoretical analysis, we consider the linear-fractional problem directly. Most importantly, we show that the yield-optimal solution set (like the rate-optimal solution set) is determined by (yield-optimal) elementary flux vectors of the underlying metabolic model. However, yield- and rate-optimal solutions may differ from each other, and hence optimal (biomass or product) yields are not necessarily obtained at solutions with optimal (growth or synthesis) rates. Moreover, we discuss phase planes/production envelopes and yield spaces, in particular, we prove that yield spaces are convex and provide algorithms for their computation. We illustrate our findings by a small
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Gu, Deqing; Jian, Xingxing; Zhang, Cheng; Hua, Qiang
2017-01-01
Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named logical transformation of model (LTM) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.
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Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
DEFF Research Database (Denmark)
Förster, Jochen; Famili, I.; Fu, P.
2003-01-01
The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments...
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Comparison of relativity theories with observer-independent scales of both velocity and length/mass
International Nuclear Information System (INIS)
Amelino-Camelia, Giovanni; Benedetti, Dario; D'Andrea, Francesco; Procaccini, Andrea
2003-01-01
We consider the two most studied proposals of relativity theories with observer-independent scales of both velocity and length/mass: the one discussed by Amelino-Camelia as an illustrative example for the original proposal (Preprint gr-qc/0012051) of theories with two relativistic invariants, and an alternative more recently proposed by Magueijo and Smolin (Preprint hep-th/0112090). We show that these two relativistic theories are much more closely connected than it would appear on the basis of a naive analysis of their original formulations. In particular, in spite of adopting a rather different formal description of the deformed boost generators, they end up assigning the same dependence of momentum on rapidity, which can be described as the core feature of these relativistic theories. We show that this observation can be used to clarify the concepts of particle mass, particle velocity and energy-momentum conservation rules in these theories with two relativistic invariants
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Cosmological large-scale structures beyond linear theory in modified gravity
Energy Technology Data Exchange (ETDEWEB)
Bernardeau, Francis; Brax, Philippe, E-mail: francis.bernardeau@cea.fr, E-mail: philippe.brax@cea.fr [CEA, Institut de Physique Théorique, 91191 Gif-sur-Yvette Cédex (France)
2011-06-01
We consider the effect of modified gravity on the growth of large-scale structures at second order in perturbation theory. We show that modified gravity models changing the linear growth rate of fluctuations are also bound to change, although mildly, the mode coupling amplitude in the density and reduced velocity fields. We present explicit formulae which describe this effect. We then focus on models of modified gravity involving a scalar field coupled to matter, in particular chameleons and dilatons, where it is shown that there exists a transition scale around which the existence of an extra scalar degree of freedom induces significant changes in the coupling properties of the cosmic fields. We obtain the amplitude of this effect for realistic dilaton models at the tree-order level for the bispectrum, finding them to be comparable in amplitude to those obtained in the DGP and f(R) models.
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Warming increases the top-down effects and metabolism of a subtidal herbivore
Directory of Open Access Journals (Sweden)
Lindsey A. Carr
2013-07-01
Full Text Available Ecological theory and experiments indicate that warming can increase the relative strength of top-down effects via alterations to metabolic rates in several different systems, thereby resulting in decreased plant biomass at higher temperatures. However, the general influence of increased environmental temperature on top-down effects is not well understood in systems where organisms experience relatively large variation in temperature. Rapid ocean temperature changes are pervasive throughout the Galápagos Islands due to upwelling and downwelling of internal waves, ENSO events and seasonality. We measured the effect of large, but not uncommon, water temperature variation on the metabolism and grazing rate of a common subtidal herbivore and on photosynthesis of their algal prey in the Galápagos Islands in July 2012. We found that green urchin consumption and metabolism were greater at the higher temperature treatment (28°C, resulting in significantly less algal biomass. Our result that warming increased green urchin metabolic rates, even in a highly dynamic system, provides further support for a mechanistic link between environmental temperature and feeding rates. And further, our findings suggest individual response to temperature results in changes in top-down effects. And if this response is maintained over longer-time scales of days to weeks, this could translate to alterations of larger-scale ecological patterns, such as primary producer community composition and structure.
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Kleeorin, N.
2018-06-01
We discuss a mean-field theory of the generation of large-scale vorticity in a rotating density stratified developed turbulence with inhomogeneous kinetic helicity. We show that the large-scale non-uniform flow is produced due to either a combined action of a density stratified rotating turbulence and uniform kinetic helicity or a combined effect of a rotating incompressible turbulence and inhomogeneous kinetic helicity. These effects result in the formation of a large-scale shear, and in turn its interaction with the small-scale turbulence causes an excitation of the large-scale instability (known as a vorticity dynamo) due to a combined effect of the large-scale shear and Reynolds stress-induced generation of the mean vorticity. The latter is due to the effect of large-scale shear on the Reynolds stress. A fast rotation suppresses this large-scale instability.
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Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome
Kim, Woonsu; Park, Hyesun; Seo, Seongwon
2016-01-01
The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle. PMID
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West, Geoffrey
2013-04-01
Many of the most challenging, exciting and profound questions facing science and society, from the origins of life to global sustainability, fall under the banner of ``complex adaptive systems.'' This talk explores how scaling can be used to begin to develop physics-inspired quantitative, predictive, coarse-grained theories for understanding their structure, dynamics and organization based on underlying mathematisable principles. Remarkably, most physiological, organisational and life history phenomena in biology and socio-economic systems scale in a simple and ``universal'' fashion: metabolic rate scales approximately as the 3/4-power of mass over 27 orders of magnitude from complex molecules to the largest organisms. Time-scales (such as lifespans and growth-rates) and sizes (such as genome lengths and RNA densities) scale with exponents which are typically simple multiples of 1/4, suggesting that fundamental constraints underlie much of the generic structure and dynamics of living systems. These scaling laws follow from dynamical and geometrical properties of space-filling, fractal-like, hierarchical branching networks, presumed optimised by natural selection. This leads to a general framework that potentially captures essential features of diverse systems including vasculature, ontogenetic growth, cancer, aging and mortality, sleep, cell size, and DNA nucleotide substitution rates. Cities and companies also scale: wages, profits, patents, crime, disease, pollution, road lengths scale similarly across the globe, reflecting underlying universal social network dynamics which point to general principles of organization transcending their individuality. These have dramatic implications for global sustainability: innovation and wealth creation that fuel social systems, left unchecked, potentially sow the seeds for their inevitable collapse.
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Large-scale transportation network congestion evolution prediction using deep learning theory.
Ma, Xiaolei; Yu, Haiyang; Wang, Yunpeng; Wang, Yinhai
2015-01-01
Understanding how congestion at one location can cause ripples throughout large-scale transportation network is vital for transportation researchers and practitioners to pinpoint traffic bottlenecks for congestion mitigation. Traditional studies rely on either mathematical equations or simulation techniques to model traffic congestion dynamics. However, most of the approaches have limitations, largely due to unrealistic assumptions and cumbersome parameter calibration process. With the development of Intelligent Transportation Systems (ITS) and Internet of Things (IoT), transportation data become more and more ubiquitous. This triggers a series of data-driven research to investigate transportation phenomena. Among them, deep learning theory is considered one of the most promising techniques to tackle tremendous high-dimensional data. This study attempts to extend deep learning theory into large-scale transportation network analysis. A deep Restricted Boltzmann Machine and Recurrent Neural Network architecture is utilized to model and predict traffic congestion evolution based on Global Positioning System (GPS) data from taxi. A numerical study in Ningbo, China is conducted to validate the effectiveness and efficiency of the proposed method. Results show that the prediction accuracy can achieve as high as 88% within less than 6 minutes when the model is implemented in a Graphic Processing Unit (GPU)-based parallel computing environment. The predicted congestion evolution patterns can be visualized temporally and spatially through a map-based platform to identify the vulnerable links for proactive congestion mitigation.
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Recent development of linear scaling quantum theories in GAMESS
Energy Technology Data Exchange (ETDEWEB)
Choi, Cheol Ho [Kyungpook National Univ., Daegu (Korea, Republic of)
2003-06-01
Linear scaling quantum theories are reviewed especially focusing on the method adopted in GAMESS. The three key translation equations of the fast multipole method (FMM) are deduced from the general polypolar expansions given earlier by Steinborn and Rudenberg. Simplifications are introduced for the rotation-based FMM that lead to a very compact FMM formalism. The OPS (optimum parameter searching) procedure, a stable and efficient way of obtaining the optimum set of FMM parameters, is established with complete control over the tolerable error {epsilon}. In addition, a new parallel FMM algorithm requiring virtually no inter-node communication, is suggested which is suitable for the parallel construction of Fock matrices in electronic structure calculations.
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De Sitter and scaling solutions in a higher-order modified teleparallel theory
Energy Technology Data Exchange (ETDEWEB)
Paliathanasis, Andronikos, E-mail: anpaliat@phys.uoa.gr [Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia (Chile)
2017-08-01
The existence and the stability conditions for some exact relativistic solutions of special interest are studied in a higher-order modified teleparallel gravitational theory. The theory with the use of a Lagrange multiplier is equivalent with that of General Relativity with a minimally coupled noncanonical field. The conditions for the existence of de Sitter solutions and ideal gas solutions in the case of vacuum are studied as also the stability criteria. Furthermore, in the presence of matter the behaviour of scaling solutions is given. Finally, we discuss the degrees of freedom of the field equations and we reduce the field equations in an algebraic equation, where in order to demonstrate our result we show how this noncanonical scalar field can reproduce the Hubble function of Λ-cosmology.
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Uncovering transcriptional regulation of metabolism by using metabolic network topology
DEFF Research Database (Denmark)
Patil, Kiran Raosaheb; Nielsen, Jens
2005-01-01
in the metabolic network that follow a common transcriptional response. Thus, the algorithm enables identification of so-called reporter metabolites (metabolites around which the most significant transcriptional changes occur) and a set of connected genes with significant and coordinated response to genetic......Cellular response to genetic and environmental perturbations is often reflected and/or mediated through changes in the metabolism, because the latter plays a key role in providing Gibbs free energy and precursors for biosynthesis. Such metabolic changes are often exerted through transcriptional...... therefore developed an algorithm that is based on hypothesis-driven data analysis to uncover the transcriptional regulatory architecture of metabolic networks. By using information on the metabolic network topology from genome-scale metabolic reconstruction, we show that it is possible to reveal patterns...
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Fast flux module detection using matroid theory.
Reimers, Arne C; Bruggeman, Frank J; Olivier, Brett G; Stougie, Leen
2015-05-01
Flux balance analysis (FBA) is one of the most often applied methods on genome-scale metabolic networks. Although FBA uniquely determines the optimal yield, the pathway that achieves this is usually not unique. The analysis of the optimal-yield flux space has been an open challenge. Flux variability analysis is only capturing some properties of the flux space, while elementary mode analysis is intractable due to the enormous number of elementary modes. However, it has been found by Kelk et al. (2012) that the space of optimal-yield fluxes decomposes into flux modules. These decompositions allow a much easier but still comprehensive analysis of the optimal-yield flux space. Using the mathematical definition of module introduced by Müller and Bockmayr (2013b), we discovered useful connections to matroid theory, through which efficient algorithms enable us to compute the decomposition into modules in a few seconds for genome-scale networks. Using that every module can be represented by one reaction that represents its function, in this article, we also present a method that uses this decomposition to visualize the interplay of modules. We expect the new method to replace flux variability analysis in the pipelines for metabolic networks.
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Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming
2017-04-07
Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.
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Time-Sliced Perturbation Theory for Large Scale Structure I: General Formalism
Blas, Diego; Ivanov, Mikhail M.; Sibiryakov, Sergey
2016-01-01
We present a new analytic approach to describe large scale structure formation in the mildly non-linear regime. The central object of the method is the time-dependent probability distribution function generating correlators of the cosmological observables at a given moment of time. Expanding the distribution function around the Gaussian weight we formulate a perturbative technique to calculate non-linear corrections to cosmological correlators, similar to the diagrammatic expansion in a three-dimensional Euclidean quantum field theory, with time playing the role of an external parameter. For the physically relevant case of cold dark matter in an Einstein--de Sitter universe, the time evolution of the distribution function can be found exactly and is encapsulated by a time-dependent coupling constant controlling the perturbative expansion. We show that all building blocks of the expansion are free from spurious infrared enhanced contributions that plague the standard cosmological perturbation theory. This pave...
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International Nuclear Information System (INIS)
Rittenberg, V.
1983-01-01
Fischer's finite-size scaling describes the cross over from the singular behaviour of thermodynamic quantities at the critical point to the analytic behaviour of the finite system. Recent extensions of the method--transfer matrix technique, and the Hamiltonian formalism--are discussed in this paper. The method is presented, with equations deriving scaling function, critical temperature, and exponent v. As an application of the method, a 3-states Hamiltonian with Z 3 global symmetry is studied. Diagonalization of the Hamiltonian for finite chains allows one to estimate the critical exponents, and also to discover new phase transitions at lower temperatures. The critical points lambda, and indices v estimated for finite-scaling are given
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Energy Technology Data Exchange (ETDEWEB)
Kleinsmith, P E [Carnegie-Mellon Univ., Pittsburgh, Pa. (USA)
1976-04-01
Multiple spatial scaling is incorporated in a modified form of the Bogoliubov plasma cluster expansion; then this proposed reformulation of the plasma weak-coupling approximation is used to derive, from the BBGKY Hierarchy, a decoupled set of equations for the one-and two-particle distribution functions in the limit as the plasma parameter goes to zero. Because the reformulated cluster expansion permits retention of essential two-particle collisional information in the limiting equations, while simultaneously retaining the well-established Debye-scale relative ordering of the correlation functions, decoupling of the Hierarchy is accomplished without introduction of the divergence problems encountered in the Bogoliubov theory, as is indicated by an exact solution of the limiting equations for the equilibrium case. To establish additional links with existing plasma equilibrium theories, the two-particle equilibrium correlation function is used to calculate the interaction energy and the equation of state. The limiting equation for the equilibrium three-particle correlation function is then developed, and a formal solution is obtained.
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Kunicki, Zachary J; Schick, Melissa R; Spillane, Nichea S; Harlow, Lisa L
2018-06-01
Those who binge drink are at increased risk for alcohol-related consequences when compared to non-binge drinkers. Research shows individuals may face barriers to reducing their drinking behavior, but few measures exist to assess these barriers. This study created and validated the Barriers to Alcohol Reduction (BAR) scale. Participants were college students ( n = 230) who endorsed at least one instance of past-month binge drinking (4+ drinks for women or 5+ drinks for men). Using classical test theory, exploratory structural equation modeling found a two-factor structure of personal/psychosocial barriers and perceived program barriers. The sub-factors, and full scale had reasonable internal consistency (i.e., coefficient omega = 0.78 (personal/psychosocial), 0.82 (program barriers), and 0.83 (full measure)). The BAR also showed evidence for convergent validity with the Brief Young Adult Alcohol Consequences Questionnaire ( r = 0.39, p Theory (IRT) analysis showed the two factors separately met the unidimensionality assumption, and provided further evidence for severity of the items on the two factors. Results suggest that the BAR measure appears reliable and valid for use in an undergraduate student population of binge drinkers. Future studies may want to re-examine this measure in a more diverse sample.
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Quadery, Abrar H.; Doan, Baochi D.; Tucker, William C.; Dove, Adrienne R.; Schelling, Patrick K.
2017-10-01
The early stages of planet formation involve steps where submicron-sized dust particles collide to form aggregates. However, the mechanism through which millimeter-sized particles aggregate to kilometer-sized planetesimals is still not understood. Dust grain collision experiments carried out in the environment of the Earth lead to the prediction of a 'bouncing barrier' at millimeter-sizes. Theoretical models, e.g., Johnson-Kendall-Roberts and Derjaguin-Muller-Toporov theories, lack two key features, namely the chemistry of dust grain surfaces, and a mechanism for atomic-scale dissipation of energy. Moreover, interaction strengths in these models are parameterized based on experiments done in the Earth's environment. To address these issues, we performed atomic-scale simulations of collisions between nonhydroxylated and hydroxylated amorphous silica nanoparticles. We used the ReaxFF approach which enables modeling chemical reactions using an empirical potential. We found that nonhydroxylated nanograins tend to adhere with much higher probability than suggested by existing theories. By contrast, hydroxylated nanograins exhibit a strong tendency to bounce. Also, the interaction between dust grains has the characteristics of a strong chemical force instead of weak van der Waals forces. This suggests that the formation of strong chemical bonds and dissipation via internal atomic vibration may result in aggregation beyond what is expected based on our current understanding. Our results also indicate that experiments should more carefully consider surface conditions to mimic the space environment. We also report results of simulations with molten silica nanoparticles. It is found that molten particles are more likely to adhere due to viscous dissipation, which supports theories that suggest aggregation to kilometer scales might require grains to be in a molten state.
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Directory of Open Access Journals (Sweden)
Daugherty Sean
2009-09-01
Full Text Available Abstract Background Rhodoferax ferrireducens is a metabolically versatile, Fe(III-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about R. ferrireducens, the complete genome sequence of this organism was further annotated and then the physiology of R. ferrireducens was investigated with a constraint-based, genome-scale in silico metabolic model and laboratory studies. Results The iterative modeling and experimental approach unveiled exciting, previously unknown physiological features, including an expanded range of substrates that support growth, such as cellobiose and citrate, and provided additional insights into important features such as the stoichiometry of the electron transport chain and the ability to grow via fumarate dismutation. Further analysis explained why R. ferrireducens is unable to grow via photosynthesis or fermentation of sugars like other members of this genus and uncovered novel genes for benzoate metabolism. The genome also revealed that R. ferrireducens is well-adapted for growth in the subsurface because it appears to be capable of dealing with a number of environmental insults, including heavy metals, aromatic compounds, nutrient limitation and oxidative stress. Conclusion This study demonstrates that combining genome-scale modeling with the annotation of a new genome sequence can guide experimental studies and accelerate the understanding of the physiology of under-studied yet environmentally relevant microorganisms.
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Large-scale transportation network congestion evolution prediction using deep learning theory.
Directory of Open Access Journals (Sweden)
Xiaolei Ma
Full Text Available Understanding how congestion at one location can cause ripples throughout large-scale transportation network is vital for transportation researchers and practitioners to pinpoint traffic bottlenecks for congestion mitigation. Traditional studies rely on either mathematical equations or simulation techniques to model traffic congestion dynamics. However, most of the approaches have limitations, largely due to unrealistic assumptions and cumbersome parameter calibration process. With the development of Intelligent Transportation Systems (ITS and Internet of Things (IoT, transportation data become more and more ubiquitous. This triggers a series of data-driven research to investigate transportation phenomena. Among them, deep learning theory is considered one of the most promising techniques to tackle tremendous high-dimensional data. This study attempts to extend deep learning theory into large-scale transportation network analysis. A deep Restricted Boltzmann Machine and Recurrent Neural Network architecture is utilized to model and predict traffic congestion evolution based on Global Positioning System (GPS data from taxi. A numerical study in Ningbo, China is conducted to validate the effectiveness and efficiency of the proposed method. Results show that the prediction accuracy can achieve as high as 88% within less than 6 minutes when the model is implemented in a Graphic Processing Unit (GPU-based parallel computing environment. The predicted congestion evolution patterns can be visualized temporally and spatially through a map-based platform to identify the vulnerable links for proactive congestion mitigation.
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Wave-particle duality through an extended model of the scale relativity theory
International Nuclear Information System (INIS)
Ioannou, P D; Nica, P; Agop, M; Paun, V; Vizureanu, P
2008-01-01
Considering that the chaotic effect of associated wave packet on the particle itself results in movements on the fractal (continuous and non-differentiable) curves of fractal dimension D F , wave-particle duality through an extension of the scale relativity theory is given. It results through an equation of motion for the complex speed field, that in a fractal fluid, the convection, dissipation and dispersion are reciprocally compensating at any scale (differentiable or non-differentiable). From here, for an irrotational movement, a generalized Schroedinger equation is obtained. The absence of dispersion implies a generalized Navier-Stokes type equation, whereas, for the irrotational movement and the fractal dimension, D F = 2, the usual Schroedinger equation results. The absence of dissipation implies a generalized Korteweg-de Vries type equation. In such conjecture, at the differentiable scale, the duality is achieved through the flowing regimes of the fractal fluid, i.e. the wave character by means of the non-quasi-autonomous flowing regime and the particle character by means of the quasi-autonomous flowing regime. These flowing regimes are separated by '0.7 structure'. At the non-differentiable scale, a fractal potential acts as an energy accumulator and controls through the coherence the duality. The correspondence between the differentiable and non-differentiable scales implies a Cantor space-time. Moreover, the wave-particle duality implies at any scale a fractal.
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Item Response Theory Analyses of the Parent and Teacher Ratings of the DSM-IV ADHD Rating Scale
Gomez, Rapson
2008-01-01
The graded response model (GRM), which is based on item response theory (IRT), was used to evaluate the psychometric properties of the inattention and hyperactivity/impulsivity symptoms in an ADHD rating scale. To accomplish this, parents and teachers completed the DSM-IV ADHD Rating Scale (DARS; Gomez et al., "Journal of Child Psychology and…
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On Δβ and the search for asymptotic scaling in lattice gauge theory
International Nuclear Information System (INIS)
Petcher, D.
1986-01-01
An ansatz for the β-function of SU(3) lattice gauge theory in four dimensions whose parameters are determined by Monte Carlo data is used both to compare different sets of data for Δβ and to study systematic errors. The data for Δβ obtained from different values of the block spin renormalization group scaling factor are shown to be compatible within statistical errors. However the data is easily consistent with sizeable deviations (ca. 30% or more) from the two loop approximation to the renormalization group scaling formula for physical quantities in the region of coupling for which Δβ essentially takes on its asymptotic value. (orig.)
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On Δβ and the search for asymptotic scaling in lattice gauge theory
International Nuclear Information System (INIS)
Petcher, D.
1986-01-01
An ansatz for the β-function of SU(3) lattice gauge theory in four dimensions whose parameters are determined by Monte Carlo data is used both to compare different sets of data for Δβ and to study systematic errors. The data for Δβ obtained from different values of the block-spin renormalization group scaling factor are shown to be compatible within statistical errors. However the data is easily consistent with sizeable deviations (ca. 30% or more) from the two-loop approximation to the renormalization group scaling formula for physical quantities in the region of coupling for which Δβ essentially takes on its asymptotic value. (orig.)
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Scale dependence of the average potential around the maximum in Φ4 theories
International Nuclear Information System (INIS)
Tetradis, N.; Wetterich, C.
1992-04-01
The average potential describes the physics at a length scale k - 1 by averaging out the degrees of freedom with characteristic moments larger than k. The dependence on k can be described by differential evolution equations. We solve these equations for the nonconvex part of the potential around the origin in φ 4 theories, in the phase with spontaneous symmetry breaking. The average potential is real and approaches the convex effective potential in the limit k → 0. Our calculation is relevant for processes for which the shape of the potential at a given scale is important, such as tunneling phenomena or inflation. (orig.)
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van den Putte, B.; Saris, W.E.; Hoogstraten, J.
1995-01-01
Two experiments were carried out to test the theory of reasoned action of Fishbein and Ajzen. The measurements were done using two category scales and two psychophysical scales. No consistent difference in results was found between the four modalities. However, if the latter were used as multiple
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Norsigian, Charles J; Kavvas, Erol; Seif, Yara; Palsson, Bernhard O; Monk, Jonathan M
2018-01-01
Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of A. baumannii would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of A. baumannii AYE, named iCN718, that improves and standardizes previous A. baumannii AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an A. baumannii reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other A. baumannii strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen.
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Wu, Jiayuan; Hu, Liren; Zhang, Gaohua; Liang, Qilian; Meng, Qiong; Wan, Chonghua
2016-08-01
This research was designed to develop a nasopharyngeal cancer (NPC) scale based on quality of life (QOL) instruments for cancer patients (QLICP-NA). This scale was developed by using a modular approach and was evaluated by classical test and generalizability theories. Programmed decision procedures and theories on instrument development were applied to create QLICP-NA V2.0. A total of 121 NPC inpatients were assessed using QLICP-NA V2.0 to measure their QOL data from hospital admission until discharge. Scale validity, reliability, and responsiveness were evaluated by correlation, factor, parallel, multi-trait scaling, and t test analyses, as well as by generalizability (G) and decision (D) studies of the generalizability theory. Results of multi-trait scaling, correlation, factor, and parallel analyses indicated that QLICP-NA V2.0 exhibited good construct validity. The significant difference of QOL between the treated and untreated NPC patients indicated a good clinical validity of the questionnaire. The internal consistency (α) and test-retest reliability coefficients (intra-class correlations) of each domain, as well as the overall scale, were all >0.70. Ceiling effects were not found in all domains and most facets, except for common side effects (24.8 %) in the domain of common symptoms and side effects, tumor early symptoms (27.3 %) and therapeutic side effects (23.2 %) in specific domain, whereas floor effects did not exist in each domain/facet. The overall changes in the physical and social domains were significantly different between pre- and post-treatments with a moderate effective size (standard response mean) ranging from 0.21 to 0.27 (p theory. QLICP-NA V2.0 exhibited reasonable degrees of validity, reliability, and responsiveness. However, this scale must be further improved before it can be used as a practical instrument to evaluate the QOL of NPC patients in China.
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The natural selection of metabolism explains curvature in allometric scaling
Witting, Lars
2016-01-01
I simulate the evolution of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. I assume that the release of inter-specific competition by the extinction of dinosaurs 65 million years ago made it possible for each clade to diversity into a multitude of species across a wide range of niches. The natural selection of metabolism and mass was then fitted to explain the maximum observed body masses over time, as well as the current inter-spe...
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de la Torre, Andrea; Metivier, Aisha; Chu, Frances; Laurens, Lieve M L; Beck, David A C; Pienkos, Philip T; Lidstrom, Mary E; Kalyuzhnaya, Marina G
2015-11-25
Methane-utilizing bacteria (methanotrophs) are capable of growth on methane and are attractive systems for bio-catalysis. However, the application of natural methanotrophic strains to large-scale production of value-added chemicals/biofuels requires a number of physiological and genetic alterations. An accurate metabolic model coupled with flux balance analysis can provide a solid interpretative framework for experimental data analyses and integration. A stoichiometric flux balance model of Methylomicrobium buryatense strain 5G(B1) was constructed and used for evaluating metabolic engineering strategies for biofuels and chemical production with a methanotrophic bacterium as the catalytic platform. The initial metabolic reconstruction was based on whole-genome predictions. Each metabolic step was manually verified, gapfilled, and modified in accordance with genome-wide expression data. The final model incorporates a total of 841 reactions (in 167 metabolic pathways). Of these, up to 400 reactions were recruited to produce 118 intracellular metabolites. The flux balance simulations suggest that only the transfer of electrons from methanol oxidation to methane oxidation steps can support measured growth and methane/oxygen consumption parameters, while the scenario employing NADH as a possible source of electrons for particulate methane monooxygenase cannot. Direct coupling between methane oxidation and methanol oxidation accounts for most of the membrane-associated methane monooxygenase activity. However the best fit to experimental results is achieved only after assuming that the efficiency of direct coupling depends on growth conditions and additional NADH input (about 0.1-0.2 mol of incremental NADH per one mol of methane oxidized). The additional input is proposed to cover loss of electrons through inefficiency and to sustain methane oxidation at perturbations or support uphill electron transfer. Finally, the model was used for testing the carbon conversion
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Stability theory for dynamic equations on time scales
Martynyuk, Anatoly A
2016-01-01
This monograph is a first in the world to present three approaches for stability analysis of solutions of dynamic equations. The first approach is based on the application of dynamic integral inequalities and the fundamental matrix of solutions of linear approximation of dynamic equations. The second is based on the generalization of the direct Lyapunovs method for equations on time scales, using scalar, vector and matrix-valued auxiliary functions. The third approach is the application of auxiliary functions (scalar, vector, or matrix-valued ones) in combination with differential dynamic inequalities. This is an alternative comparison method, developed for time continuous and time discrete systems. In recent decades, automatic control theory in the study of air- and spacecraft dynamics and in other areas of modern applied mathematics has encountered problems in the analysis of the behavior of solutions of time continuous-discrete linear and/or nonlinear equations of perturbed motion. In the book “Men of Ma...
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International Nuclear Information System (INIS)
Tait, E W; Payne, M C; Ratcliff, L E; Haynes, P D; Hine, N D M
2016-01-01
Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree with those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. Finally, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable. (paper)
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International Nuclear Information System (INIS)
Cai Yifu; Qiu Taotao; Brandenberger, Robert; Zhang Xinmin
2009-01-01
We study the cosmology of a Lee-Wick type scalar field theory. First, we consider homogeneous and isotropic background solutions and find that they are nonsingular, leading to cosmological bounces. Next, we analyze the spectrum of cosmological perturbations which result from this model. Unless either the potential of the Lee-Wick theory or the initial conditions are finely tuned, it is impossible to obtain background solutions which have a sufficiently long period of inflation after the bounce. More interestingly, however, we find that in the generic noninflationary bouncing cosmology, perturbations created from quantum vacuum fluctuations in the contracting phase have the correct form to lead to a scale-invariant spectrum of metric inhomogeneities in the expanding phase. Since the background is nonsingular, the evolution of the fluctuations is defined unambiguously through the bounce. We also analyze the evolution of fluctuations which emerge from thermal initial conditions in the contracting phase. The spectrum of gravitational waves stemming from quantum vacuum fluctuations in the contracting phase is also scale-invariant, and the tensor to scalar ratio is not suppressed.
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Planck-scale induced left–right gauge theory at LHC and experimental tests
Directory of Open Access Journals (Sweden)
M.K. Parida
2016-05-01
Full Text Available Recent measurements at LHC have inspired searches for TeV scale left–right gauge theory originating from grand unified theories. We show that inclusion of Planck-scale induced effects due to dim.5 operator not only does away with all the additional intermediate symmetries, but also it predicts the minimal set of light Higgs scalars tailored after neutrino masses and dilepton, or trilepton signals. The heavy-light neutrino mixings are predicted from charged fermion mass fits in SO(10 and LFV constraints which lead to new predictions for dilepton or trilepton production signals. Including fine-structure constant matching and two-loop, and threshold effects predict MWR=g2R104.3±1.5±0.2 GeV and proton lifetime τp=1036.15±5.8±0.2 yrs with WR gauge boson coupling g2R=0.56–0.57. Predictions on lepton flavour and lepton number violations are accessible to ongoing experiments. Current CMS data on di-electron excess at s=8 TeV are found to be consistent with WR gauge boson mass MWR≥1.9–2.2 TeV which also agrees with the values obtained from dijet resonance production data. We also discuss plausible explanations for diboson production excesses observed at LHC and make predictions expected at s=14 TeV.
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Universality and scaling in SU(2) lattice gauge theory
International Nuclear Information System (INIS)
Michael, C.; Teper, M.; Oxford Univ.
1988-01-01
We calculate the lowest glueball masses and the string tension for both Manton's action and for Symanzik's tree-level improved action. We do so on large lattices and for small lattice spacings using techniques recently employed in an extensive investigation of the Wilson plaquette action. Comparing all these results we find that the ratios of the lightest masses are universal to a high degree of accuracy. In particular, we confirm that on large volumes the tensor glueball is heavier than the scalar glueball: m[2 + ] ≅ 1.5 m[0 + ]. We repeat these calculations for larger lattice spacings and find that the string tension follows 2-loop perturbation theory more closely in the case of these alternative actions than in the case of the standard plaquette action. Our attempt to repeat the analysis with Wilson's block-spin improved action foundered on the strong breakdown of positivity apparent in the calculated correlation functions. In all the cases which we were able to study the observed violations of scaling are in the same direction. This suggests that the causes of the scaling violations observed with Wilson's plaquette action are 'semi-universal'. It also weakens the implication of the observed universality for the question of how close we are to the continuum limit. (orig.)
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Directory of Open Access Journals (Sweden)
Shivendra G. Tewari
2017-08-01
Full Text Available Chloroquine, long the default first-line treatment against malaria, is now abandoned in large parts of the world because of widespread drug-resistance in Plasmodium falciparum. In spite of its importance as a cost-effective and efficient drug, a coherent understanding of the cellular mechanisms affected by chloroquine and how they influence the fitness and survival of the parasite remains elusive. Here, we used a systems biology approach to integrate genome-scale transcriptomics to map out the effects of chloroquine, identify targeted metabolic pathways, and translate these findings into mechanistic insights. Specifically, we first developed a method that integrates transcriptomic and metabolomic data, which we independently validated against a recently published set of such data for Krebs-cycle mutants of P. falciparum. We then used the method to calculate the effect of chloroquine treatment on the metabolic flux profiles of P. falciparum during the intraerythrocytic developmental cycle. The model predicted dose-dependent inhibition of DNA replication, in agreement with earlier experimental results for both drug-sensitive and drug-resistant P. falciparum strains. Our simulations also corroborated experimental findings that suggest differences in chloroquine sensitivity between ring- and schizont-stage P. falciparum. Our analysis also suggests that metabolic fluxes that govern reduced thioredoxin and phosphoenolpyruvate synthesis are significantly decreased and are pivotal to chloroquine-based inhibition of P. falciparum DNA replication. The consequences of impaired phosphoenolpyruvate synthesis and redox metabolism are reduced carbon fixation and increased oxidative stress, respectively, both of which eventually facilitate killing of the parasite. Our analysis suggests that a combination of chloroquine (or an analogue and another drug, which inhibits carbon fixation and/or increases oxidative stress, should increase the clearance of P
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Analysis of critical neutron- scattering data from iron and dynamical scaling theory
DEFF Research Database (Denmark)
Als-Nielsen, Jens Aage
1970-01-01
Experimental three- axis spectrometer data of critical neutron- scattering data from Fe are reanalyzed and compared with the recent theoretical prediction by P. Resibois and C. Piette. The reason why the spin- diffusion parameter did not obey the prediction of dynamical scaling theory is indicated....... Double- axis spectrometer data have previously been interpreted in terms of a non- Lorentzian susceptibility. It is shown that with proper corrections for the inelasticity of the scattering the data are consistent with a Lorentzian form of susceptibility....
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Bosco, Francesca M; Gabbatore, Ilaria; Tirassa, Maurizio; Testa, Silvia
2016-01-01
This research aimed at the evaluation of the psychometric properties of the Theory of Mind Assessment Scale (Th.o.m.a.s.). Th.o.m.a.s. is a semi-structured interview meant to evaluate a person's Theory of Mind (ToM). It is composed of several questions organized in four scales, each focusing on one of the areas of knowledge in which such faculty may manifest itself: Scale A (I-Me) investigates first-order first-person ToM; Scale B (Other-Self) investigates third-person ToM from an allocentric perspective; Scale C (I-Other) again investigates third-person ToM, but from an egocentric perspective; and Scale D (Other-Me) investigates second-order ToM. The psychometric proprieties of Th.o.m.a.s. were evaluated in a sample of 156 healthy persons: 80 preadolescent and adolescent (aged 11-17 years, 42 females) and 76 adults (aged from 20 to 67 years, 35 females). Th.o.m.a.s. scores show good inter-rater agreement and internal consistency; the scores increase with age. Evidence of criterion validity was found as Scale B scores were correlated with those of an independent instrument for the evaluation of ToM, the Strange Stories task. Confirmatory factor analysis (CFA) showed good fit of the four-factors theoretical model to the data, although the four factors were highly correlated. For each of the four scales, Rasch analyses showed that, with few exceptions, items fitted the Partial credit model and their functioning was invariant for gender and age. The results of this study, along with those of previous researches with clinical samples, show that Th.o.m.a.s. is a promising instrument to assess ToM in different populations.
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Item response theory analysis of the Lichtenberg Financial Decision Screening Scale.
Teresi, Jeanne A; Ocepek-Welikson, Katja; Lichtenberg, Peter A
2017-01-01
The focus of these analyses was to examine the psychometric properties of the Lichtenberg Financial Decision Screening Scale (LFDSS). The purpose of the screen was to evaluate the decisional abilities and vulnerability to exploitation of older adults. Adults aged 60 and over were interviewed by social, legal, financial, or health services professionals who underwent in-person training on the administration and scoring of the scale. Professionals provided a rating of the decision-making abilities of the older adult. The analytic sample included 213 individuals with an average age of 76.9 (SD = 10.1). The majority (57%) were female. Data were analyzed using item response theory (IRT) methodology. The results supported the unidimensionality of the item set. Several IRT models were tested. Ten ordinal and binary items evidenced a slightly higher reliability estimate (0.85) than other versions and better coverage in terms of the range of reliable measurement across the continuum of financial incapacity.
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Developing Scale for Assimilate the Integration between Learning Theories and E-learning.
Directory of Open Access Journals (Sweden)
George Maher Iskander
2014-03-01
Full Text Available As e-learning tend to get more and more significant for all kind of universities, researchers and consultants are becoming aware of the fact that a high technology approach and Blackboard do not guarantee successful teaching and learning. Thus, a move to pedagogy-based theories can be observed within the field of e-learning. This study describes the procedure of the development of an empirically-based psychometrically-sound instrument to measure instructional model for e-learning system at Middle East universities. In order to accelerate the acceptance of e-learning and implementation of institution-wide adoption of e-learning, it is important to understand students' perceptions with instructional model for e- learning. The 19-item scale developed shows a high probability of differentiating between positive and negative perceptions and the methods which can be used for embedding the traditional learning theories into e-learning.
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From genomes to in silico cells via metabolic networks
DEFF Research Database (Denmark)
Borodina, Irina; Nielsen, Jens
2005-01-01
Genome-scale metabolic models are the focal point of systems biology as they allow the collection of various data types in a form suitable for mathematical analysis. High-quality metabolic networks and metabolic networks with incorporated regulation have been successfully used for the analysis...... of phenotypes from phenotypic arrays and in gene-deletion studies. They have also been used for gene expression analysis guided by metabolic network structure, leading to the identification of commonly regulated genes. Thus, genome-scale metabolic modeling currently stands out as one of the most promising...
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Scaling of the quark-antiquark potential and improved actions in SU(2) lattice gauge theory
International Nuclear Information System (INIS)
Montvay, I.; Gutbrod, F.
1983-11-01
The scaling behaviour of the quark-antiquark potential is investigated by a high statistics Monte Carlo calculation in SU(2) lattice gauge theory. Besides the standard one-plaquette action we also use Symanzik's tree-level improved action and Wilson's block-spin improved action. No significant differences between Symanzik's action and the standard action have been observed. For small β Wilson's action scales differently. The string tension value chi extracted from the data corresponds to Λsub(latt) = (0.018 +- 0.001) √chi for the one-plaquette action. (orig.)
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International Nuclear Information System (INIS)
Frohlich, J.
1983-01-01
The author describes some recent techniques for constructing the continuum (= scaling) limit of lattice field theories, including the one- and two- component lambda/less than or equal to→/phi// 4 theories and the Ising and rotator models in a space (- imaginary time) of dimension d >greater than or equal to 4. These techniques should have applications to other related models, like the selfavoiding random walk in five or more dimensions and bond percolation in seven or more dimensions. Some plausible conjectures concerning the Gaussian nature of the scaling limit of the d greater than or equal to 2 dimensional rotator model and the d greater than or equal to 4 dimensional U(1) lattice gauge theory in the low temperature (weak coupling) phase are described
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Forests as Patrimonies? From Theory to Tangible Processes at Various Scales
Directory of Open Access Journals (Sweden)
Genevieve Michon
2012-09-01
Full Text Available Among theoretical fields addressing the conceptualization of interrelationships between nature and society, patrimonial approaches remain relatively unexplored. Stressing the multiplication of local dynamics where elements of nature are redefined as "patrimonies" (ranging from local patrimonies to world heritage by various social groups, this conceptual field tries to qualify these dynamics and their determiners to understand how they allow us to better address contemporary environmental challenges. Through a multidisciplinary approach in social sciences, centered on rural forests, we analyze the multiplication of patrimonial processes in forest development at various scales. First, we elaborate on the concept of patrimony and on patrimonial processes and present the current construction and dynamics of forest patrimonies. A crucial question concerns the links that form between the many spatial-temporal levels where these processes develop. Moreover, these patrimonial processes can be quite divergent, not only across scales from local to global, but also between "endogenous" (or bottom-up and "exogenous" (or top-down processes. We present two detailed examples in Morocco and Sumatra, where patrimonial constructions are developing simultaneously at various scales and through various actors who treat the forest in very different ways. Drawing from these examples, we discuss how and why the simultaneous development of different, often overlapping, patrimonial constructions along these scales allows collaboration or, conversely, can lead their holders into conflict. Lastly, we discuss the contribution of patrimonial concepts to resilience thinking and social-ecological systems theory.
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Directory of Open Access Journals (Sweden)
N. A. Brunsell
2011-08-01
Full Text Available A more thorough understanding of the multi-scale spatial structure of land surface heterogeneity will enhance understanding of the relationships and feedbacks between land surface conditions, mass and energy exchanges between the surface and the atmosphere, and regional meteorological and climatological conditions. The objectives of this study were to (1 quantify which spatial scales are dominant in determining the evapotranspiration flux between the surface and the atmosphere and (2 to quantify how different spatial scales of atmospheric and surface processes interact for different stages of the phenological cycle. We used the ALEXI/DisALEXI model for three days (DOY 181, 229 and 245 in 2002 over the Ft. Peck Ameriflux site to estimate the latent heat flux from Landsat, MODIS and GOES satellites. We then applied a multiresolution information theory methodology to quantify these interactions across different spatial scales and compared the dynamics across the different sensors and different periods. We note several important results: (1 spatial scaling characteristics vary with day, but are usually consistent for a given sensor, but (2 different sensors give different scalings, and (3 the different sensors exhibit different scaling relationships with driving variables such as fractional vegetation and near surface soil moisture. In addition, we note that while the dominant length scale of the vegetation index remains relatively constant across the dates, the contribution of the vegetation index to the derived latent heat flux varies with time. We also note that length scales determined from MODIS are consistently larger than those determined from Landsat, even at scales that should be detectable by MODIS. This may imply an inability of the MODIS sensor to accurately determine the fine scale spatial structure of the land surface. These results aid in identifying the dominant cross-scale nature of local to regional biosphere
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An Analysis of the Connectedness to Nature Scale Based on Item Response Theory.
Pasca, Laura; Aragonés, Juan I; Coello, María T
2017-01-01
The Connectedness to Nature Scale (CNS) is used as a measure of the subjective cognitive connection between individuals and nature. However, to date, it has not been analyzed at the item level to confirm its quality. In the present study, we conduct such an analysis based on Item Response Theory. We employed data from previous studies using the Spanish-language version of the CNS, analyzing a sample of 1008 participants. The results show that seven items presented appropriate indices of discrimination and difficulty, in addition to a good fit. The remaining six have inadequate discrimination indices and do not present a good fit. A second study with 321 participants shows that the seven-item scale has adequate levels of reliability and validity. Therefore, it would be appropriate to use a reduced version of the scale after eliminating the items that display inappropriate behavior, since they may interfere with research results on connectedness to nature.
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Razdan, Neil K; Koshy, David M; Prausnitz, John M
2017-11-07
A group-contribution method based on scaled-particle theory was developed to predict Henry's constants for six families of persistent organic pollutants: polychlorinated benzenes, polychlorinated biphenyls, polychlorinated dibenzodioxins, polychlorinated dibenzofurans, polychlorinated naphthalenes, and polybrominated diphenyl ethers. The group-contribution model uses limited experimental data to obtain group-interaction parameters for an easy-to-use method to predict Henry's constants for systems where reliable experimental data are scarce. By using group-interaction parameters obtained from data reduction, scaled-particle theory gives the partial molar Gibbs energy of dissolution, Δg̅ 2 , allowing calculation of Henry's constant, H 2 , for more than 700 organic pollutants. The average deviation between predicted values of log H 2 and experiment is 4%. Application of an approximate van't Hoff equation gives the temperature dependence of Henry's constants for polychlorinated biphenyls, polychlorinated naphthalenes, and polybrominated diphenyl ethers in the environmentally relevant range 0-40 °C.
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Directory of Open Access Journals (Sweden)
2007-01-01
Full Text Available Hysteresis is a rate-independent non-linearity that is expressed through thresholds, switches, and branches. Exceedance of a threshold, or the occurrence of a turning point in the input, switches the output onto a particular output branch. Rate-independent branching on a very large set of switches with non-local memory is the central concept in the new definition of hysteresis. Hysteretic loops are a special case. A self-consistent mathematical description of hydrological systems with hysteresis demands a new non-linear systems theory of adequate generality. The goal of this paper is to establish this and to show how this may be done. Two results are presented: a conceptual model for the hysteretic soil-moisture characteristic at the pedon scale and a hysteretic linear reservoir at the catchment scale. Both are based on the Preisach model. A result of particular significance is the demonstration that the independent domain model of the soil moisture characteristic due to Childs, Poulavassilis, Mualem and others, is equivalent to the Preisach hysteresis model of non-linear systems theory, a result reminiscent of the reduction of the theory of the unit hydrograph to linear systems theory in the 1950s. A significant reduction in the number of model parameters is also achieved. The new theory implies a change in modelling paradigm.
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Cosmological models with a hybrid scale factor in an extended gravity theory
Mishra, B.; Tripathy, S. K.; Tarai, Sankarsan
2018-03-01
A general formalism to investigate Bianchi type V Ih universes is developed in an extended theory of gravity. A minimally coupled geometry and matter field is considered with a rescaled function of f(R,T) substituted in place of the Ricci scalar R in the geometrical action. Dynamical aspects of the models are discussed by using a hybrid scale factor (HSF) that behaves as power law in an initial epoch and as an exponential form at late epoch. The power law behavior and the exponential behavior appear as two extreme cases of the present model.
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Ion, Bogdan; Kazim, Erum; Gauld, James
2014-01-01
Nicotinamidase (Nic) is a key zinc-dependent enzyme in NAD metabolism that catalyzes the hydrolysis of nicotinamide to give nicotinic acid. A multi-scale computational approach has been used to investigate the catalytic mechanism, substrate binding and roles of active site residues of Nic from Streptococcus pneumoniae (SpNic). In particular, density functional theory (DFT), molecular dynamics (MD) and ONIOM quantum mechanics/molecular mechanics (QM/MM) methods have been employed. The o...
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Huang, Yueng-Hsiang; Lee, Jin; Chen, Zhuo; Perry, MacKenna; Cheung, Janelle H; Wang, Mo
2017-06-01
Zohar and Luria's (2005) safety climate (SC) scale, measuring organization- and group- level SC each with 16 items, is widely used in research and practice. To improve the utility of the SC scale, we shortened the original full-length SC scales. Item response theory (IRT) analysis was conducted using a sample of 29,179 frontline workers from various industries. Based on graded response models, we shortened the original scales in two ways: (1) selecting items with above-average discriminating ability (i.e. offering more than 6.25% of the original total scale information), resulting in 8-item organization-level and 11-item group-level SC scales; and (2) selecting the most informative items that together retain at least 30% of original scale information, resulting in 4-item organization-level and 4-item group-level SC scales. All four shortened scales had acceptable reliability (≥0.89) and high correlations (≥0.95) with the original scale scores. The shortened scales will be valuable for academic research and practical survey implementation in improving occupational safety. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.
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Scale and scaling in agronomy and environmental sciences
Scale is of paramount importance in environmental studies, engineering, and design. The unique course covers the following topics: scale and scaling, methods and theories, scaling in soils and other porous media, scaling in plants and crops; scaling in landscapes and watersheds, and scaling in agro...
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Application of random matrix theory to biological networks
Energy Technology Data Exchange (ETDEWEB)
Luo Feng [Department of Computer Science, Clemson University, 100 McAdams Hall, Clemson, SC 29634 (United States); Department of Pathology, U.T. Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390-9072 (United States); Zhong Jianxin [Department of Physics, Xiangtan University, Hunan 411105 (China) and Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States)]. E-mail: zhongjn@ornl.gov; Yang Yunfeng [Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Scheuermann, Richard H. [Department of Pathology, U.T. Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390-9072 (United States); Zhou Jizhong [Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019 (United States) and Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States)]. E-mail: zhouj@ornl.gov
2006-09-25
We show that spectral fluctuation of interaction matrices of a yeast protein-protein interaction network and a yeast metabolic network follows the description of the Gaussian orthogonal ensemble (GOE) of random matrix theory (RMT). Furthermore, we demonstrate that while the global biological networks evaluated belong to GOE, removal of interactions between constituents transitions the networks to systems of isolated modules described by the Poisson distribution. Our results indicate that although biological networks are very different from other complex systems at the molecular level, they display the same statistical properties at network scale. The transition point provides a new objective approach for the identification of functional modules.
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Effective field theory analysis on μ problem in low-scale gauge mediation
International Nuclear Information System (INIS)
Zheng Sibo
2012-01-01
Supersymmetric models based on the scenario of gauge mediation often suffer from the well-known μ problem. In this paper, we reconsider this problem in low-scale gauge mediation in terms of effective field theory analysis. In this paradigm, all high energy input soft mass can be expressed via loop expansions. If the corrections coming from messenger thresholds are small, as we assume in this letter, then all RG evaluations can be taken as linearly approximation for low-scale supersymmetric breaking. Due to these observations, the parameter space can be systematically classified and studied after constraints coming from electro-weak symmetry breaking are imposed. We find that some old proposals in the literature are reproduced, and two new classes are uncovered. We refer to a microscopic model, where the specific relations among coefficients in one of the new classes are well motivated. Also, we discuss some primary phenomenologies.
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Metabolic engineering tools in model cyanobacteria.
Carroll, Austin L; Case, Anna E; Zhang, Angela; Atsumi, Shota
2018-03-26
Developing sustainable routes for producing chemicals and fuels is one of the most important challenges in metabolic engineering. Photoautotrophic hosts are particularly attractive because of their potential to utilize light as an energy source and CO 2 as a carbon substrate through photosynthesis. Cyanobacteria are unicellular organisms capable of photosynthesis and CO 2 fixation. While engineering in heterotrophs, such as Escherichia coli, has result in a plethora of tools for strain development and hosts capable of producing valuable chemicals efficiently, these techniques are not always directly transferable to cyanobacteria. However, recent efforts have led to an increase in the scope and scale of chemicals that cyanobacteria can produce. Adaptations of important metabolic engineering tools have also been optimized to function in photoautotrophic hosts, which include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9, 13 C Metabolic Flux Analysis (MFA), and Genome-Scale Modeling (GSM). This review explores innovations in cyanobacterial metabolic engineering, and highlights how photoautotrophic metabolism has shaped their development. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.
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Generalizability theory and item response theory
Glas, Cornelis A.W.; Eggen, T.J.H.M.; Veldkamp, B.P.
2012-01-01
Item response theory is usually applied to items with a selected-response format, such as multiple choice items, whereas generalizability theory is usually applied to constructed-response tasks assessed by raters. However, in many situations, raters may use rating scales consisting of items with a selected-response format. This chapter presents a short overview of how item response theory and generalizability theory were integrated to model such assessments. Further, the precision of the esti...
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El Naschie's ε (∞) space-time and scale relativity theory in the topological dimension D = 4
International Nuclear Information System (INIS)
Agop, M.; Murgulet, C.
2007-01-01
In the topological dimension D = 4 of the scale relativity theory, the self-structuring of a coherent quantum fluid implies the Golden mean renormalization group. Then, the transfinite set of El Naschie's ε (∞) space-time becomes the background of a new physics (the transfinite physics)
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Shiraishi, Junya; Miyato, Naoaki; Matsunaga, Go
2016-05-10
It is found that new channels of energy exchange between macro- and microscopic dynamics exist in plasmas. They are induced by macroscopic plasma flow. This finding is based on the kinetic-magnetohydrodynamic (MHD) theory, which analyses interaction between macroscopic (MHD-scale) motion and microscopic (particle-scale) dynamics. The kinetic-MHD theory is extended to include effects of macroscopic plasma flow self-consistently. The extension is realised by generalising an energy exchange term due to wave-particle resonance, denoted by δ WK. The first extension is generalisation of the particle's Lagrangian, and the second one stems from modification to the particle distribution function due to flow. These extensions lead to a generalised expression of δ WK, which affects the MHD stability of plasmas.
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Directory of Open Access Journals (Sweden)
Kim Pan-Jun
2011-08-01
Full Text Available Abstract Background Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis. Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications. Results We present the first genome-scale metabolic model (iCM925 for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test
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DEFF Research Database (Denmark)
Kjeldsen, Kjeld Raunkjær; Nielsen, J.
2009-01-01
A genome-scale metabolic model of the Gram-positive bacteria Corynebacterium glutamicum ATCC 13032 was constructed comprising 446 reactions and 411 metabolite, based on the annotated genome and available biochemical information. The network was analyzed using constraint based methods. The model...... was extensively validated against published flux data, and flux distribution values were found to correlate well between simulations and experiments. The split pathway of the lysine synthesis pathway of C. glutamicum was investigated, and it was found that the direct dehydrogenase variant gave a higher lysine...... yield than the alternative succinyl pathway at high lysine production rates. The NADPH demand of the network was not found to be critical for lysine production until lysine yields exceeded 55% (mmol lysine (mmol glucose)(-1)). The model was validated during growth on the organic acids acetate...
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Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
DEFF Research Database (Denmark)
Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.
2017-01-01
orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME......Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...... models have 70,000 constraints and variables and will grow larger). We have developed a quadrupleprecision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging...
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Chatterjee, Ankita; Kundu, Sudip
2015-01-01
Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air. PMID:26443104
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COULD SOCIOECONOMIC METABOLISM BE MOLDED BY TRANSACTION COSTS?
Directory of Open Access Journals (Sweden)
RALUCA I. IORGULESCU
2017-06-01
Full Text Available Two key issues that shape the economic development and growth of a country are the independence and effectiveness of the judicial system and the level of bureaucracy. The theory of transaction costs, developed, among others, by Douglass C. North, explores both. Increasing the independence and effectiveness of the judicial system reduces corruption and protects private property and economic freedom while reducing bureaucracy is absolutely necessary to increase a country's competitiveness by lowering the cost and increasing the speed of transactions. This paper introduces the transaction costs approach, the concept of ‘socioeconomic/societal metabolism’ and takes advantage of the Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM to examine how the ‘socioeconomic/societal metabolism’ could be impacted.
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A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism
DEFF Research Database (Denmark)
Hefzi, Hooman; Ang, Kok Siong; Hanscho, Michael
2016-01-01
Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways...
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Universality in quantum chaos and the one-parameter scaling theory.
García-García, Antonio M; Wang, Jiao
2008-02-22
The one-parameter scaling theory is adapted to the context of quantum chaos. We define a generalized dimensionless conductance, g, semiclassically and then study Anderson localization corrections by renormalization group techniques. This analysis permits a characterization of the universality classes associated to a metal (g-->infinity), an insulator (g-->0), and the metal-insulator transition (g-->g(c)) in quantum chaos provided that the classical phase space is not mixed. According to our results the universality class related to the metallic limit includes all the systems in which the Bohigas-Giannoni-Schmit conjecture holds but automatically excludes those in which dynamical localization effects are important. The universality class related to the metal-insulator transition is characterized by classical superdiffusion or a fractal spectrum in low dimensions (d < or = 2). Several examples are discussed in detail.
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Directory of Open Access Journals (Sweden)
Vashishta P.
2011-05-01
Full Text Available A linear-scaling algorithm based on a divide-and-conquer (DC scheme is designed to perform large-scale molecular-dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT. This scheme is applied to the thermite reaction at an Al/Fe2O3 interface. It is found that mass diffusion and reaction rate at the interface are enhanced by a concerted metal-oxygen flip mechanism. Preliminary simulations are carried out for an aluminum particle in water based on the conventional DFT, as a target system for large-scale DC-DFT simulations. A pair of Lewis acid and base sites on the aluminum surface preferentially catalyzes hydrogen production in a low activation-barrier mechanism found in the simulations
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Gravitational theory in atomic scale units in Dirac cosmology
International Nuclear Information System (INIS)
Davidson, W.
1984-01-01
The implication of Dirac's large numbers hypothesis (LNH) that there are two cosmological space-time metrics, gravitational (E) and atomic (A), is used to formulate the gravitational laws for a general mass system in atomic scale units within such a cosmology. The gravitational laws are illustrated in application to the case of a single spherical mass immersed in the smoothed out expanding universe. The condition is determined for such a metric to apply approximately just outside a typical member of a cosmic distribution of such masses. Conversely, the condition is given when the influence of the universe as a whole can be neglected outside such a mass. In the latter situation, which applies in particular to stars, a Schwarzschild-type metric is derived which incorporates variable G in accordance with the LNH. The dynamics of freely moving particles and photons in such a metric are examined according to the theory and observational tests are formulated. (author)
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Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test
DEFF Research Database (Denmark)
Pinu, Farhana R.; Granucci, Ninna; Daniell, James
2018-01-01
Introduction Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. Materials and Meth...
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Awang-Hashim, Rosna; Thaliah, Rajaletchumi; Kaur, Amrita
2017-01-01
Purpose: The cross-cultural significance of autonomy within self-determination theory is divisive on universal significance. This paper aims to report a sequential exploratory mixed methods study conducted to construct and validate a scale to investigate how, in Malaysian context, the construct of autonomy is conceptualized in comparison with the…
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Wu, Jianlan; Silbey, Robert J; Cao, Jianshu
2013-05-17
An asymptotic scaling theory is presented using the conceptual basis of trapping-free subspace (i.e., orthogonal subspace) to establish the generic mechanism of optimal efficiency of excitation energy transfer in light-harvesting systems. A quantum state orthogonal to the trap will exhibit noise-assisted transfer, clarifying the significance of initial preparation. For such an initial state, the efficiency is enhanced in the weak damping limit (⟨t⟩ ∼ 1/Γ), and suppressed in the strong damping limit (⟨t⟩ ∼ Γ), analogous to Kramers turnover in classical rate theory. An interpolating expression ⟨t⟩ = A/Γ + B + CΓ quantitatively describes the trapping time over the entire range of the dissipation strength, and predicts the optimal efficiency at Γ(opt) ∼ J for homogenous systems. In the presence of static disorder, the scaling law of transfer time with respect to dephasing rate changes from linear to square root, suggesting a weaker dependence on the environment. The prediction of the scaling theory is verified in a symmetric dendrimer system by numerically exact quantum calculations. Though formulated in the context of excitation energy transfer, the analysis and conclusions apply in general to open quantum processes, including electron transfer, fluorescence emission, and heat conduction.
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Generalizability theory and item response theory
Glas, Cornelis A.W.; Eggen, T.J.H.M.; Veldkamp, B.P.
2012-01-01
Item response theory is usually applied to items with a selected-response format, such as multiple choice items, whereas generalizability theory is usually applied to constructed-response tasks assessed by raters. However, in many situations, raters may use rating scales consisting of items with a
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Physics on all scales. Scalar-tensor theories of quantum gravity in particle physics and cosmology
Energy Technology Data Exchange (ETDEWEB)
Henz, Tobias
2016-05-10
In this thesis, we investigate dilaton quantum gravity using a functional renormalization group approach. We derive and discuss flow equations both in the background field approximation and using a vertex expansion as well as solve the fixed point equations globally to show how realistic gravity, connecting ultraviolet and infrared physics, can be realized on a pure fixed point trajectory by virtue of spontaneous breaking of scale invariance. The emerging physical system features a dynamically generated moving Planck scale resembling the Newton coupling as well as slow roll inflation with an exponentially decreasing effective cosmological constant that vanishes completely in the infrared. The moving Planck scale might make quantum gravity experimentally accessible at a different energy scale than previously believed. We therefore not only provide further evidence for the existence of a consistent quantum theory of gravity based on general relativity, but also offer potential solutions towards the hierarchy and cosmological constant problems, thereby opening up exciting opportunities for further research.
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Genome-scale reconstruction of the metabolic network in Yersinia pestis CO92
Navid, Ali; Almaas, Eivind
2007-03-01
The gram-negative bacterium Yersinia pestis is the causative agent of bubonic plague. Using publicly available genomic, biochemical and physiological data, we have developed a constraint-based flux balance model of metabolism in the CO92 strain (biovar Orientalis) of this organism. The metabolic reactions were appropriately compartmentalized, and the model accounts for the exchange of metabolites, as well as the import of nutrients and export of waste products. We have characterized the metabolic capabilities and phenotypes of this organism, after comparing the model predictions with available experimental observations to evaluate accuracy and completeness. We have also begun preliminary studies into how cellular metabolism affects virulence.
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Hirakawa, Teruo; Suzuki, Teppei; Bowler, David R; Miyazaki, Tsuyoshi
2017-10-11
We discuss the development and implementation of a constant temperature (NVT) molecular dynamics scheme that combines the Nosé-Hoover chain thermostat with the extended Lagrangian Born-Oppenheimer molecular dynamics (BOMD) scheme, using a linear scaling density functional theory (DFT) approach. An integration scheme for this canonical-ensemble extended Lagrangian BOMD is developed and discussed in the context of the Liouville operator formulation. Linear scaling DFT canonical-ensemble extended Lagrangian BOMD simulations are tested on bulk silicon and silicon carbide systems to evaluate our integration scheme. The results show that the conserved quantity remains stable with no systematic drift even in the presence of the thermostat.
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The validity and scalability of the Theory of Mind Scale with toddlers and preschoolers.
Hiller, Rachel M; Weber, Nathan; Young, Robyn L
2014-12-01
Despite the importance of theory of mind (ToM) for typical development, there remain 2 key issues affecting our ability to draw robust conclusions. One is the continued focus on false belief as the sole measure of ToM. The second is the lack of empirically validated measures of ToM as a broad construct. Our key aim was to examine the validity and reliability of the 5-item ToM scale (Peterson, Wellman, & Liu, 2005). In particular, we extended on previous research of this scale by assessing its scalability and validity for use with children from 2 years of age. Sixty-eight typically developing children (aged 24 to 61 months) were assessed on the scale's 5 tasks, along with a sixth Sally-Anne false-belief task. Our data replicated the scalability of the 5 tasks for a Rasch-but not Guttman-scale. Guttman analysis showed that a 4-item scale may be more suitable for this age range. Further, the tasks showed good internal consistency and validity for use with children as young as 2 years of age. Overall, the measure provides a valid and reliable tool for the assessment of ToM, and in particular, the longitudinal assessment of this ability as a construct. (c) 2014 APA, all rights reserved.
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Lei, Pingguang; Lei, Guanghe; Tian, Jianjun; Zhou, Zengfen; Zhao, Miao; Wan, Chonghua
2014-10-01
This paper is aimed to develop the irritable bowel syndrome (IBS) scale of the system of Quality of Life Instruments for Chronic Diseases (QLICD-IBS) by the modular approach and validate it by both classical test theory and generalizability theory. The QLICD-IBS was developed based on programmed decision procedures with multiple nominal and focus group discussions, in-depth interview, and quantitative statistical procedures. One hundred twelve inpatients with IBS were used to provide the data measuring QOL three times before and after treatments. The psychometric properties of the scale were evaluated with respect to validity, reliability, and responsiveness employing correlation analysis, factor analyses, multi-trait scaling analysis, t tests and also G studies and D studies of generalizability theory analysis. Multi-trait scaling analysis, correlation, and factor analyses confirmed good construct validity and criterion-related validity when using SF-36 as a criterion. Test-retest reliability coefficients (Pearson r and intra-class correlation (ICC)) for the overall score and all domains were higher than 0.80; the internal consistency α for all domains at two measurements were higher than 0.70 except for the social domain (0.55 and 0.67, respectively). The overall score and scores for all domains/facets had statistically significant changes after treatments with moderate or higher effect size standardized response mean (SRM) ranging from 0.72 to 1.02 at domain levels. G coefficients and index of dependability (Ф coefficients) confirmed the reliability of the scale further with more exact variance components. The QLICD-IBS has good validity, reliability, responsiveness, and some highlights and can be used as the quality of life instrument for patients with IBS.
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Nutrient Uptake and Metabolism Along a Large Scale Tropical Physical-Chemical Gradient
Tromboni, F.; Neres-Lima, V.; Saltarelli, W. A.; Miwa, A. C. P.; Cunha, D. G. F.
2016-12-01
Nutrient spiraling is a whole-system approach for estimating nutrient uptake that can be used to assess aquatic ecosystems' responses to environmental change and anthropogenic impacts. Historically research on nutrient dynamic uptake in streams has focused on single nutrient dynamics and only rarely the stoichiometric uptake has been considered and linked to carbon metabolism driven by autotrophic and heterotrophic production. We investigated the relationship between uptake of phosphate (PO43-), nitrate (NO3-) ammonium (NH4+) and total dissolve nitrogen (DIN)/ PO43-; and gross primary production (GPP), respiration (R), and net ecosystem productivity (NEP) in six relatively pristine streams with differences regarding canopy cover and physical characteristics, located in a large scale gradient from tropical Atlantic Forest to an Atlantic forest/Cerrado (Brazilian Savanna) transition. We carried out whole stream instantaneous additions of PO43-, NO3- and NH4+ added to each stream in combination, using the TASCC (Tracer Additions for Spiraling Curve Characterization) method. Metabolism measurements were performed in the same streams right after uptake was measured, using one-station open channel method and re-aeration estimations for those sites. We found different background concentrations in the streams located in the Atlantic forest compared with the transition area with Cerrado. In general PO43- and NO3- uptake increased with the decreasing of canopy cover, while a positive relation with background concentration better explained NH4+uptake. DIN/PO43- uptake increased with increasing R and NEP. Little work on functional characteristics of pristine streams has been conducted in this region and this work provides an initial characterization on nitrogen and phosphorus dynamics as well as their stoichiometric uptake in streams.
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Theory and evidence for using the economy-of-scale law in power plant economics
International Nuclear Information System (INIS)
Phung, D.L.
1987-05-01
This report compiles theory and evidence for the use of the economy-of-scale law in energy economics, particularly in the estimation of capital costs for coal-fired and nuclear power plants. The economy-of-scale law is widely used in its simplest form: cost is directly proportional to capacity raised to an exponent. An additive constant is an important component that is not generally taken into account. Also, the economy of scale is perforce valid only over a limited size range. The majority of engineering studies have estimated an economy of scale exponent of 0.7 to 0.9 for coal-fired plants and an exponent of 0.4 to 0.6 for nuclear plants in the capacity ranges of 400 to 1000 MWe. However, the majority of econometric analyses found little or no economy of scale for coal-fired plants and only a slight economy of scale for nuclear plants. This disparity is explained by the fact that economists have included regulatory and time-related costs in addition to the direct and indirect costs used by the engineers. Regulatory and time-related costs have become an increasingly larger portion of total costs during the last decade. In addition, these costs appeared to have either a very small economy of scale or to be increasing as the size of the power plant increased. We conclude that gains in economy of scale can only be made by reducing regulatory and time-related costs through design standardization and regulatory stability, in combination with more favorable economic conditions. 59 refs
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Context-specific metabolic networks are consistent with experiments.
Directory of Open Access Journals (Sweden)
Scott A Becker
2008-05-01
Full Text Available Reconstructions of cellular metabolism are publicly available for a variety of different microorganisms and some mammalian genomes. To date, these reconstructions are "genome-scale" and strive to include all reactions implied by the genome annotation, as well as those with direct experimental evidence. Clearly, many of the reactions in a genome-scale reconstruction will not be active under particular conditions or in a particular cell type. Methods to tailor these comprehensive genome-scale reconstructions into context-specific networks will aid predictive in silico modeling for a particular situation. We present a method called Gene Inactivity Moderated by Metabolism and Expression (GIMME to achieve this goal. The GIMME algorithm uses quantitative gene expression data and one or more presupposed metabolic objectives to produce the context-specific reconstruction that is most consistent with the available data. Furthermore, the algorithm provides a quantitative inconsistency score indicating how consistent a set of gene expression data is with a particular metabolic objective. We show that this algorithm produces results consistent with biological experiments and intuition for adaptive evolution of bacteria, rational design of metabolic engineering strains, and human skeletal muscle cells. This work represents progress towards producing constraint-based models of metabolism that are specific to the conditions where the expression profiling data is available.
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Directory of Open Access Journals (Sweden)
Dorines Rosario
2018-06-01
Full Text Available Dysbiosis in the gut microbiome composition may be promoted by therapeutic drugs such as metformin, the world’s most prescribed antidiabetic drug. Under metformin treatment, disturbances of the intestinal microbes lead to increased abundance of Escherichia spp., Akkermansia muciniphila, Subdoligranulum variabile and decreased abundance of Intestinibacter bartlettii. This alteration may potentially lead to adverse effects on the host metabolism, with the depletion of butyrate producer genus. However, an increased production of butyrate and propionate was verified in metformin-treated Type 2 diabetes (T2D patients. The mechanisms underlying these nutritional alterations and their relation with gut microbiota dysbiosis remain unclear. Here, we used Genome-scale Metabolic Models of the representative gut bacteria Escherichia spp., I. bartlettii, A. muciniphila, and S. variabile to elucidate their bacterial metabolism and its effect on intestinal nutrient pool, including macronutrients (e.g., amino acids and short chain fatty acids, minerals and chemical elements (e.g., iron and oxygen. We applied flux balance analysis (FBA coupled with synthetic lethality analysis interactions to identify combinations of reactions and extracellular nutrients whose absence prevents growth. Our analyses suggest that Escherichia sp. is the bacteria least vulnerable to nutrient availability. We have also examined bacterial contribution to extracellular nutrients including short chain fatty acids, amino acids, and gasses. For instance, Escherichia sp. and S. variabile may contribute to the production of important short chain fatty acids (e.g., acetate and butyrate, respectively involved in the host physiology under aerobic and anaerobic conditions. We have also identified pathway susceptibility to nutrient availability and reaction changes among the four bacteria using both FBA and flux variability analysis. For instance, lipopolysaccharide synthesis, nucleotide sugar
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On the consistency of scale among experiments, theory, and simulation
McClure, James E.; Dye, Amanda L.; Miller, Cass T.; Gray, William G.
2017-02-01
As a tool for addressing problems of scale, we consider an evolving approach known as the thermodynamically constrained averaging theory (TCAT), which has broad applicability to hydrology. We consider the case of modeling of two-fluid-phase flow in porous media, and we focus on issues of scale as they relate to various measures of pressure, capillary pressure, and state equations needed to produce solvable models. We apply TCAT to perform physics-based data assimilation to understand how the internal behavior influences the macroscale state of two-fluid porous medium systems. A microfluidic experimental method and a lattice Boltzmann simulation method are used to examine a key deficiency associated with standard approaches. In a hydrologic process such as evaporation, the water content will ultimately be reduced below the irreducible wetting-phase saturation determined from experiments. This is problematic since the derived closure relationships cannot predict the associated capillary pressures for these states. We demonstrate that the irreducible wetting-phase saturation is an artifact of the experimental design, caused by the fact that the boundary pressure difference does not approximate the true capillary pressure. Using averaging methods, we compute the true capillary pressure for fluid configurations at and below the irreducible wetting-phase saturation. Results of our analysis include a state function for the capillary pressure expressed as a function of fluid saturation and interfacial area.
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Tajparast, Mohammad; Frigon, Dominic
2013-01-01
Studying storage metabolism during feast-famine cycles of activated sludge treatment systems provides profound insight in terms of both operational issues (e.g., foaming and bulking) and process optimization for the production of value added by-products (e.g., bioplastics). We examined the storage metabolism (including poly-β-hydroxybutyrate [PHB], glycogen, and triacylglycerols [TAGs]) during feast-famine cycles using two genome-scale metabolic models: Rhodococcus jostii RHA1 (iMT1174) and Escherichia coli K-12 (iAF1260) for growth on glucose, acetate, and succinate. The goal was to develop the proper objective function (OF) for the prediction of the main storage compound produced in activated sludge for given feast-famine cycle conditions. For the flux balance analysis, combinations of three OFs were tested. For all of them, the main OF was to maximize growth rates. Two additional sub-OFs were used: (1) minimization of biochemical fluxes, and (2) minimization of metabolic adjustments (MoMA) between the feast and famine periods. All (sub-)OFs predicted identical substrate-storage associations for the feast-famine growth of the above-mentioned metabolic models on a given substrate when glucose and acetate were set as sole carbon sources (i.e., glucose-glycogen and acetate-PHB), in agreement with experimental observations. However, in the case of succinate as substrate, the predictions depended on the network structure of the metabolic models such that the E. coli model predicted glycogen accumulation and the R. jostii model predicted PHB accumulation. While the accumulation of both PHB and glycogen was observed experimentally, PHB showed higher dynamics during an activated sludge feast-famine growth cycle with succinate as substrate. These results suggest that new modeling insights between metabolic predictions and population ecology will be necessary to properly predict metabolisms likely to emerge within the niches of activated sludge communities. Nonetheless
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Control of fluxes in metabolic networks
Basler, Georg; Nikoloski, Zoran; Larhlimi, Abdelhalim; Barabási, Albert-László; Liu, Yang-Yu
2016-01-01
Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism. PMID:27197218
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Directory of Open Access Journals (Sweden)
Yali eWang
2015-06-01
Full Text Available Actinoplanes sp. SE50/110 produces the -glucosidase inhibitor acarbose, which is used to treat type 2 diabetes mellitus. To obtain a comprehensive understanding of its cellular metabolism, a genome-scale metabolic model of strain SE50/110, iYLW1028, was reconstructed on the bases of the genome annotation, biochemical databases, and extensive literature mining. Model iYLW1028 comprises 1028 genes, 1128 metabolites and 1219 reactions. 122 and 81 genes were essential for cell growth on acarbose synthesis and sucrose media, respectively, and the acarbose biosynthetic pathway in SE50/110 was expounded completely. Based on model predictions, the addition of arginine and histidine to the media increased acarbose production by 78% and 59%, respectively. Additionally, dissolved oxygen has a great effect on acarbose production based on model predictions. Furthermore, genes to be overexpressed for the overproduction of acarbose were identified, and the deletion of treY eliminated the formation of by-product component C. Model iYLW1028 is a useful platform for optimizing and systems metabolic engineering for acarbose production in Actinoplanes sp. SE50/110.
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International Nuclear Information System (INIS)
Kovacic, Zora; Giampietro, Mario
2017-01-01
As informal urban settlements grow in size and population across the developing world, the issue of how to design and implement effective policies to provide for the needs and the aspirations of dwellers becomes ever more pressing. This paper addresses the challenge of how to characterise in quantitative terms the complex and fast-changing phenomenon of informal urban settlements without falling into oversimplification and a narrow focus on the material deficits of informal settlements. Energy policies are taken as an example to illustrate the shortcomings of oversimplification in producing policy relevant information. We adopt a semantically open representation of informal settlements that can capture the diversity of adaptive strategies used by different settlement typologies, based on the societal metabolism approach. Results show that as settlements grow in size and complexity, they remain economically and politically marginalised and fail to integrate into the city. We argue that in the case of energy policy, the analysis must go beyond the definition of problems such as access to energy at the level of the individual, and focus on a multi-scale assessment including the household and community levels studying the capacity of the household to increase it energy throughput through exosomatic devices and infrastructure. - Highlights: • The policy challenges of fast changing informal urban settlements are assessed. • Metabolic patterns are used to assess and compare different typologies of slums. • Semantically open representations are used to capture the complexity of slums.
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Wan, Chonghua; Li, Hezhan; Fan, Xuejin; Yang, Ruixue; Pan, Jiahua; Chen, Wenru; Zhao, Rong
2014-06-04
Quality of life (QOL) for patients with coronary heart disease (CHD) is now concerned worldwide with the specific instruments being seldom and no one developed by the modular approach. This paper is aimed to develop the CHD scale of the system of Quality of Life Instruments for Chronic Diseases (QLICD-CHD) by the modular approach and validate it by both classical test theory and Generalizability Theory. The QLICD-CHD was developed based on programmed decision procedures with multiple nominal and focus group discussions, in-depth interview, pre-testing and quantitative statistical procedures. 146 inpatients with CHD were used to provide the data measuring QOL three times before and after treatments. The psychometric properties of the scale were evaluated with respect to validity, reliability and responsiveness employing correlation analysis, factor analyses, multi-trait scaling analysis, t-tests and also G studies and D studies of Genralizability Theory analysis. Multi-trait scaling analysis, correlation and factor analyses confirmed good construct validity and criterion-related validity when using SF-36 as a criterion. The internal consistency α and test-retest reliability coefficients (Pearson r and Intra-class correlations ICC) for the overall instrument and all domains were higher than 0.70 and 0.80 respectively; The overall and all domains except for social domain had statistically significant changes after treatments with moderate effect size SRM (standardized response mea) ranging from 0.32 to 0.67. G-coefficients and index of dependability (Ф coefficients) confirmed the reliability of the scale further with more exact variance components. The QLICD-CHD has good validity, reliability, and moderate responsiveness and some highlights, and can be used as the quality of life instrument for patients with CHD. However, in order to obtain better reliability, the numbers of items for social domain should be increased or the items' quality, not quantity, should be
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Density Functional Theory and Materials Modeling at Atomistic Length Scales
Directory of Open Access Journals (Sweden)
Swapan K. Ghosh
2002-04-01
Full Text Available Abstract: We discuss the basic concepts of density functional theory (DFT as applied to materials modeling in the microscopic, mesoscopic and macroscopic length scales. The picture that emerges is that of a single unified framework for the study of both quantum and classical systems. While for quantum DFT, the central equation is a one-particle Schrodinger-like Kohn-Sham equation, the classical DFT consists of Boltzmann type distributions, both corresponding to a system of noninteracting particles in the field of a density-dependent effective potential, the exact functional form of which is unknown. One therefore approximates the exchange-correlation potential for quantum systems and the excess free energy density functional or the direct correlation functions for classical systems. Illustrative applications of quantum DFT to microscopic modeling of molecular interaction and that of classical DFT to a mesoscopic modeling of soft condensed matter systems are highlighted.
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Clark, S. K.; Dodge, R. N.; Nybakken, G. H.
1972-01-01
The string theory was evaluated for predicting lateral tire dynamic properties as obtained from scaled model tests. The experimental data and string theory predictions are in generally good agreement using lateral stiffness and relaxation length values obtained from the static or slowly rolling tire. The results indicate that lateral forces and self-aligning torques are linearly proportional to tire lateral stiffness and to the amplitude of either steer or lateral displacement. In addition, the results show that the ratio of input excitation frequency to road speed is the proper independent variable by which frequency should be measured.
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Clinical update on metabolic syndrome
Directory of Open Access Journals (Sweden)
Juan Diego Hernández-Camacho
2017-12-01
Full Text Available Metabolic syndrome has been defined as a global issue since it affects a lot of people. Numerous factors are involved in metabolic syndrome development. It has been described that metabolic syndrome has negative consequences on health. Consequently, a lot of treatments have been proposed to palliate it such as drugs, surgery or life style changes where nutritional habits have shown to be an important point in its management. The current study reviews the literature existing about the actual epidemiology of metabolic syndrome, the components involucrate in its appearance and progression, the clinical consequences of metabolic syndrome and the nutritional strategies reported in its remission. A bibliographic search in PubMed and Medline was performed to identify eligible studies. Authors obtained that metabolic syndrome is present in population from developed and undeveloped areas in a huge scale. Environmental and genetic elements are involucrate in metabolic syndrome development. Metabolic syndrome exponentially increased risk of cardiovascular disease, some types of cancers, diabetes mellitus type 2, sleep disturbances, etc. Nutritional treatments play a crucial role in metabolic syndrome prevention, treatment and recovery.
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GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES
Directory of Open Access Journals (Sweden)
Radhakrishnan Mahadevan
2012-10-01
With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.
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International Nuclear Information System (INIS)
Edenstrasser, J.W.
1995-01-01
A multiple time-scale derivative expansion scheme is applied to the dimensionless Fokker--Planck equation and to Maxwell's equations, where the parameter range of a typical fusion plasma was assumed. Within kinetic theory, the four time scales considered are those of Larmor gyration, particle transit, collisions, and classical transport. The corresponding magnetohydrodynamic (MHD) time scales are those of ion Larmor gyration, Alfven, MHD collision, and resistive diffusion. The solution of the zeroth-order equations results in the force-free equilibria and ideal Ohm's law. The solution of the first-order equations leads under the assumption of a weak collisional plasma to the ideal MHD equations. On the MHD-collision time scale, not only the full set of the MHD transport equations is obtained, but also turbulent terms, where the related transport quantities are one order in the expansion parameter larger than those of classical transport. Finally, at the resistive diffusion time scale the known transport equations are arrived at including, however, also turbulent contributions. copyright 1995 American Institute of Physics
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Zadran, Sohila; Levine, Raphael D
2013-01-01
Metabolic engineering seeks to redirect metabolic pathways through the modification of specific biochemical reactions or the introduction of new ones with the use of recombinant technology. Many of the chemicals synthesized via introduction of product-specific enzymes or the reconstruction of entire metabolic pathways into engineered hosts that can sustain production and can synthesize high yields of the desired product as yields of natural product-derived compounds are frequently low, and chemical processes can be both energy and material expensive; current endeavors have focused on using biologically derived processes as alternatives to chemical synthesis. Such economically favorable manufacturing processes pursue goals related to sustainable development and "green chemistry". Metabolic engineering is a multidisciplinary approach, involving chemical engineering, molecular biology, biochemistry, and analytical chemistry. Recent advances in molecular biology, genome-scale models, theoretical understanding, and kinetic modeling has increased interest in using metabolic engineering to redirect metabolic fluxes for industrial and therapeutic purposes. The use of metabolic engineering has increased the productivity of industrially pertinent small molecules, alcohol-based biofuels, and biodiesel. Here, we highlight developments in the practical and theoretical strategies and technologies available for the metabolic engineering of simple systems and address current limitations.
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Lu, Hongzhong; Cao, Weiqiang; Ouyang, Liming; Xia, Jianye; Huang, Mingzhi; Chu, Ju; Zhuang, Yingping; Zhang, Siliang; Noorman, Henk
2017-03-01
Aspergillus niger is one of the most important cell factories for industrial enzymes and organic acids production. A comprehensive genome-scale metabolic network model (GSMM) with high quality is crucial for efficient strain improvement and process optimization. The lack of accurate reaction equations and gene-protein-reaction associations (GPRs) in the current best model of A. niger named GSMM iMA871, however, limits its application scope. To overcome these limitations, we updated the A. niger GSMM by combining the latest genome annotation and literature mining technology. Compared with iMA871, the number of reactions in iHL1210 was increased from 1,380 to 1,764, and the number of unique ORFs from 871 to 1,210. With the aid of our transcriptomics analysis, the existence of 63% ORFs and 68% reactions in iHL1210 can be verified when glucose was used as the only carbon source. Physiological data from chemostat cultivations, 13 C-labeled and molecular experiments from the published literature were further used to check the performance of iHL1210. The average correlation coefficients between the predicted fluxes and estimated fluxes from 13 C-labeling data were sufficiently high (above 0.89) and the prediction of cell growth on most of the reported carbon and nitrogen sources was consistent. Using the updated genome-scale model, we evaluated gene essentiality on synthetic and yeast extract medium, as well as the effects of NADPH supply on glucoamylase production in A. niger. In summary, the new A. niger GSMM iHL1210 contains significant improvements with respect to the metabolic coverage and prediction performance, which paves the way for systematic metabolic engineering of A. niger. Biotechnol. Bioeng. 2017;114: 685-695. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
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Theory and evidence of economies of scale in the development of waste management systems
International Nuclear Information System (INIS)
Chang, Shoou-Yuh; Rivera, A.L.
1989-01-01
Waste is a cost of doing business. This cost can be considered in terms of the potential adverse health and environmental impacts, or the waste management costs associated with avoiding, minimizing, and controlling those impacts. There is an anticipated increase in the cost of waste management as a result of the increasing requirements for regulatory compliance. To meet the total waste management capacity needs of the organization and the compliance requirements, low-level radioactive, hazardous, and mixed waste management will need demonstrated technologies strategically managed as a technology portfolio. The role of the decision maker is to select the optimum mix of technologies and facilities to provide the waste management capacity needed for the next twenty years. The waste management system resulting from this mix includes multiple small-scale fixed facilities, large-scale centralized facilities, and waste management subcontracts. This study was conducted to examine the theory and evidence of economies of scale in the development of waste management systems as as exploratory research on the economic considerations in the process of technology selection and implementation. 25 refs., 24 figs., 11 tabs
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Gas production in the Barnett Shale obeys a simple scaling theory.
Patzek, Tad W; Male, Frank; Marder, Michael
2013-12-03
Natural gas from tight shale formations will provide the United States with a major source of energy over the next several decades. Estimates of gas production from these formations have mainly relied on formulas designed for wells with a different geometry. We consider the simplest model of gas production consistent with the basic physics and geometry of the extraction process. In principle, solutions of the model depend upon many parameters, but in practice and within a given gas field, all but two can be fixed at typical values, leading to a nonlinear diffusion problem we solve exactly with a scaling curve. The scaling curve production rate declines as 1 over the square root of time early on, and it later declines exponentially. This simple model provides a surprisingly accurate description of gas extraction from 8,294 wells in the United States' oldest shale play, the Barnett Shale. There is good agreement with the scaling theory for 2,057 horizontal wells in which production started to decline exponentially in less than 10 y. The remaining 6,237 horizontal wells in our analysis are too young for us to predict when exponential decline will set in, but the model can nevertheless be used to establish lower and upper bounds on well lifetime. Finally, we obtain upper and lower bounds on the gas that will be produced by the wells in our sample, individually and in total. The estimated ultimate recovery from our sample of 8,294 wells is between 10 and 20 trillion standard cubic feet.
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Özenç, Emine Gül; Dogan, M. Cihangir
2014-01-01
This study aims to perform a validity-reliability test by developing the Functional Literacy Experience Scale based upon Ecological Theory (FLESBUET) for primary education students. The study group includes 209 fifth grade students at Sabri Taskin Primary School in the Kartal District of Istanbul, Turkey during the 2010-2011 academic year.…
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Suzuki, N.; Kitamura, K.; Nemoto, T.; Shimizu, N.; Wada, S.; Kondo, T.; Tabata, M. J.; Sodeyama, F.; Ijiri, K.; Hattori, A.
In osteoclastic activity during space flight as well as hind limb unloading by tail suspension, inconsistent results have been reported in an in vivo study. The bone matrix plays an important role in the response to physical stress. However, there is no suitable in vitro co-culture system of osteoblasts and osteoclasts including bone matrix. On the other hand, fish scale is a calcified tissue that contains osteoblasts, osteoclasts, and bone matrix, all of which are similar to those found in human bones. Recently, we developed a new in vitro model system using goldfish scale. This system can detect the activities of osteoclasts and osteoblasts with tartrate-resistant acid phosphatase and alkaline phosphatase as the respective markers and precisely analyze the co-relationship between osteoblasts and osteoclasts. Using this system, we analyzed the bone metabolism under various degrees of acceleration (0.5-, 1-, 2-, 4-, and 6-G) by vibration with a G-load apparatus. After loading for 5 and 10 min, the scales were incubated for 6 and 24 h. The osteoblastic and osteoclastic activities were then measured. The osteoblastic activities gradually increased corresponding to 1-G to 6-G acceleration. In addition, ER mRNA expression was the highest under 6-G acceleration. On the other hand, the osteoclastic activity decreased at 24 h of incubation under low acceleration (0.5- and 1-G). This change coincided with TRAP mRNA expression. Under 2-G acceleration, the strength of suppression in osteoclastic activity was the highest. The strength of the inhibitory action under 4- and 6-G acceleration was lower than that under 2-G acceleration. In our co-culture system, osteoblasts and osteoclasts in the scale sensitively responded to several degrees of acceleration. Therefore, we strongly believe that our in vitro co-culture system is useful for the analysis of bone metabolism under loading or unloading.
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Hamilton, Joshua J.; Dwivedi, Vivek; Reed, Jennifer L.
2013-01-01
Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. PMID:23870272
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A New Functional Health Literacy Scale for Japanese Young Adults Based on Item Response Theory.
Tsubakita, Takashi; Kawazoe, Nobuo; Kasano, Eri
2017-03-01
Health literacy predicts health outcomes. Despite concerns surrounding the health of Japanese young adults, to date there has been no objective assessment of health literacy in this population. This study aimed to develop a Functional Health Literacy Scale for Young Adults (funHLS-YA) based on item response theory. Each item in the scale requires participants to choose the most relevant term from 3 choices in relation to a target item, thus assessing objective rather than perceived health literacy. The 20-item scale was administered to 1816 university students and 1751 responded. Cronbach's α coefficient was .73. Difficulty and discrimination parameters of each item were estimated, resulting in the exclusion of 1 item. Some items showed different difficulty parameters for male and female participants, reflecting that some aspects of health literacy may differ by gender. The current 19-item version of funHLS-YA can reliably assess the objective health literacy of Japanese young adults.
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Wavelet-Based Quantum Field Theory
Directory of Open Access Journals (Sweden)
Mikhail V. Altaisky
2007-11-01
Full Text Available The Euclidean quantum field theory for the fields $phi_{Delta x}(x$, which depend on both the position $x$ and the resolution $Delta x$, constructed in SIGMA 2 (2006, 046, on the base of the continuous wavelet transform, is considered. The Feynman diagrams in such a theory become finite under the assumption there should be no scales in internal lines smaller than the minimal of scales of external lines. This regularisation agrees with the existing calculations of radiative corrections to the electron magnetic moment. The transition from the newly constructed theory to a standard Euclidean field theory is achieved by integration over the scale arguments.
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The O(epsilon2) scaling law for dsigma/dt in the Reggeon field theory
International Nuclear Information System (INIS)
Dash, J.W.; Grandou, Thierry.
1979-04-01
The two loop contributions were calculated within the epsilon-expansion to the Reggeon Field Theory scaling law for dsigma/dt, derived using the renormalization group and a general renormalization point for the Pomeron propagator. This generalizes the O(epsilon) work of Abarbanel, Bartels, Bronzan, and Sidhu. The invariance of the results under certain coupling constant rescalings is demonstrated. Some qualitative comments were made regarding phenomenological applications. Our amplitude in a certain limit approximates the form of the low energy diffractive amplitude advocated by Kane
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DEFF Research Database (Denmark)
Kim, Hyun Uk; Kim, Byoungjin; Seung, Do Young
2014-01-01
reactions are more frequently introduced into various microbial hosts. The genome-scale metabolic simulations of Escherichia coli strains engineered to produce 1,4-butanediol, 1,3-propanediol, and amorphadiene suggest that microbial metabolism shows much different responses to the introduced heterologous...... reactions in a strain-specific manner than typical gene knockouts in terms of the energetic status (e.g., ATP and biomass generation) and chemical production capacity. The 1,4-butanediol and 1,3-propanediol producers showed greater metabolic optimality than the wild-type strains and gene knockout mutants...... for the energetic status, while the amorphadiene producer was metabolically less optimal. For the optimal chemical production capacity, additional gene knockouts were most effective for the strain producing 1,3-propanediol, but not for the one producing 1,4-butanediol. These observations suggest that strains having...
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Inflation in a Scale Invariant Universe
Energy Technology Data Exchange (ETDEWEB)
Ferreira, Pedro G. [Oxford U.; Hill, Christopher T. [Fermilab; Noller, Johannes [Zurich U.; Ross, Graham G. [Oxford U., Theor. Phys.
2018-02-16
A scale-invariant universe can have a period of accelerated expansion at early times: inflation. We use a frame-invariant approach to calculate inflationary observables in a scale invariant theory of gravity involving two scalar fields - the spectral indices, the tensor to scalar ratio, the level of isocurvature modes and non-Gaussianity. We show that scale symmetry leads to an exact cancellation of isocurvature modes and that, in the scale-symmetry broken phase, this theory is well described by a single scalar field theory. We find the predictions of this theory strongly compatible with current observations.
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Sussman, Joshua; Beaujean, A. Alexander; Worrell, Frank C.; Watson, Stevie
2013-01-01
Item response models (IRMs) were used to analyze Cross Racial Identity Scale (CRIS) scores. Rasch analysis scores were compared with classical test theory (CTT) scores. The partial credit model demonstrated a high goodness of fit and correlations between Rasch and CTT scores ranged from 0.91 to 0.99. CRIS scores are supported by both methods.…
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Vaanholt, Lobke M.; Daan, Serge; Schubert, Kristin A.; Visser, G. Henk
2009-01-01
The proposition that increased energy expenditure shortens life has a long history. The rate-of-living theory ( Pearl 1928) states that life span and average mass-specific metabolic rate are inversely proportional. Originally based on interspecific allometric comparisons between species of mammals,
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Napolitano, Christopher M; Job, Veronika
2018-05-21
Why do some people struggle with self-control (colloquially called willpower) whereas others are able to sustain it during challenging circumstances? Recent research showed that a person's implicit theories of willpower-whether they think self-control capacity is a limited or nonlimited resource-predict sustained self-control on laboratory tasks and on goal-related outcomes in everyday life. The present research tests the Implicit Theory of Willpower for Strenuous Mental Activities Scale (or ITW-M) Scale for measurement invariance across samples and gender within each culture, and two cultural contexts (the U.S. and Switzerland/Germany). Across a series of multigroup confirmatory factor analyses, we found support for the measurement invariance of the ITW-M scale across samples within and across two cultures, as well as across men and women. Further, the analyses showed expected patterns of convergent (with life-satisfaction and trait-self-control) and discriminant validity (with implicit theory of intelligence). These results provide guidelines for future research and clinical practice using the ITW-M scale for the investigation of latent group differences, for example, between gender or cultures. (PsycINFO Database Record (c) 2018 APA, all rights reserved).
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Peterson, Candida C.; Wellman, Henry M.; Slaughter, Virginia
2013-01-01
Children aged 3 to 12 years (n=184) with typical development, deafness, autism or Asperger Syndrome took a series of theory-of-mind (ToM) tasks to confirm and extend previous developmental scaling evidence. A new sarcasm task, in the format of Wellman and Liu’s (2004) 5-step ToM scale, added a statistically reliable sixth step to the scale for all diagnostic groups. A key previous finding, divergence in task sequencing for children with autism, was confirmed. Comparisons among diagnostic groups, controlling age and language ability, showed that typical developers mastered the six ToM steps ahead of each of the three disabled groups, with implications for ToM theories. The final (sarcasm) task challenged even nondisabled 9-year-olds, demonstrating the new scale’s sensitivity to post-preschool ToM growth. PMID:22304467
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Topological analysis of metabolic control.
Sen, A K
1990-12-01
A topological approach is presented for the analysis of control and regulation in metabolic pathways. In this approach, the control structure of a metabolic pathway is represented by a weighted directed graph. From an inspection of the topology of the graph, the control coefficients of the enzymes are evaluated in a heuristic manner in terms of the enzyme elasticities. The major advantage of the topological approach is that it provides a visual framework for (1) calculating the control coefficients of the enzymes, (2) analyzing the cause-effect relationships of the individual enzymes, (3) assessing the relative importance of the enzymes in metabolic regulation, and (4) simplifying the structure of a given pathway, from a regulatory viewpoint. Results are obtained for (a) an unbranched pathway in the absence of feedback the feedforward regulation and (b) an unbranched pathway with feedback inhibition. Our formulation is based on the metabolic control theory of Kacser and Burns (1973) and Heinrich and Rapoport (1974).
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Random sampling of elementary flux modes in large-scale metabolic networks.
Machado, Daniel; Soons, Zita; Patil, Kiran Raosaheb; Ferreira, Eugénio C; Rocha, Isabel
2012-09-15
The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis. However, their application to large networks has been hampered by the combinatorial explosion in the number of modes. In this work, we develop a method for generating random samples of EMs without computing the whole set. Our algorithm is an adaptation of the canonical basis approach, where we add an additional filtering step which, at each iteration, selects a random subset of the new combinations of modes. In order to obtain an unbiased sample, all candidates are assigned the same probability of getting selected. This approach avoids the exponential growth of the number of modes during computation, thus generating a random sample of the complete set of EMs within reasonable time. We generated samples of different sizes for a metabolic network of Escherichia coli, and observed that they preserve several properties of the full EM set. It is also shown that EM sampling can be used for rational strain design. A well distributed sample, that is representative of the complete set of EMs, should be suitable to most EM-based methods for analysis and optimization of metabolic networks. Source code for a cross-platform implementation in Python is freely available at http://code.google.com/p/emsampler. dmachado@deb.uminho.pt Supplementary data are available at Bioinformatics online.
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Chaos, scaling and existence of a continuum limit in classical non-Abelian lattice gauge theory
International Nuclear Information System (INIS)
Nielsen, H.B.; Rugh, H.H.; Rugh, S.E.
1996-01-01
We discuss space-time chaos and scaling properties for classical non-Abelian gauge fields discretized on a spatial lattice. We emphasize that there is a open-quote no goclose quotes for simulating the original continuum classical gauge fields over a long time span since there is a never ending dynamical cascading towards the ultraviolet. We note that the temporal chaotic properties of the original continuum gauge fields and the lattice gauge system have entirely different scaling properties thereby emphasizing that they are entirely different dynamical systems which have only very little in common. Considered as a statistical system in its own right the lattice gauge system in a situation where it has reached equilibrium comes closest to what could be termed a open-quotes continuum limitclose quotes in the limit of very small energies (weak non-linearities). We discuss the lattice system both in the limit for small energies and in the limit of high energies where we show that there is a saturation of the temporal chaos as a pure lattice artifact. Our discussion focuses not only on the temporal correlations but to a large extent also on the spatial correlations in the lattice system. We argue that various conclusions of physics have been based on monitoring the non-Abelian lattice system in regimes where the fields are correlated over few lattice units only. This is further evidenced by comparison with results for Abelian lattice gauge theory. How the real time simulations of the classical lattice gauge theory may reach contact with the real time evolution of (semi-classical aspects of) the quantum gauge theory (e.g. Q.C.D.) is left an important question to be further examined
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Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling
International Nuclear Information System (INIS)
Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R.; Jijakli, Kenan; Salehi-Ashtiani, Kourosh
2014-01-01
Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.
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Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling
Energy Technology Data Exchange (ETDEWEB)
Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R. [Division of Science and Math, New York University Abu Dhabi, Abu Dhabi (United Arab Emirates); Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute, Abu Dhabi (United Arab Emirates); Jijakli, Kenan [Division of Science and Math, New York University Abu Dhabi, Abu Dhabi (United Arab Emirates); Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute, Abu Dhabi (United Arab Emirates); Engineering Division, Biofinery, Manhattan, KS (United States); Salehi-Ashtiani, Kourosh, E-mail: ksa3@nyu.edu [Division of Science and Math, New York University Abu Dhabi, Abu Dhabi (United Arab Emirates); Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute, Abu Dhabi (United Arab Emirates)
2014-12-10
Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.
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Prediction of lithium-ion battery capacity with metabolic grey model
International Nuclear Information System (INIS)
Chen, Lin; Lin, Weilong; Li, Junzi; Tian, Binbin; Pan, Haihong
2016-01-01
Given the popularity of Lithium-ion batteries in EVs (electric vehicles), predicting the capacity quickly and accurately throughout a battery's full life-time is still a challenging issue for ensuring the reliability of EVs. This paper proposes an approach in predicting the varied capacity with discharge cycles based on metabolic grey theory and consider issues from two perspectives: 1) three metabolic grey models will be presented, including MGM (metabolic grey model), MREGM (metabolic Residual-error grey model), and MMREGM (metabolic Markov-residual-error grey model); 2) the universality of these models will be explored under different conditions (such as various discharge rates and temperatures). Furthermore, the research findings in this paper demonstrate the excellent performance of the prediction depending on the three models; however, the precision of the MREGM model is inferior compared to the others. Therefore, we have obtained the conclusion in which the MGM model and the MMREGM model have excellent performances in predicting the capacity under a variety of load conditions, even using few data points for modeling. Also, the universality of the metabolic grey prediction theory is verified by predicting the capacity of batteries under different discharge rates and different temperatures. - Highlights: • The metabolic mechanism is introduced in a grey system for capacity prediction. • Three metabolic grey models are presented and studied. • The universality of these models under different conditions is assessed. • A few data points are required for predicting the capacity with these models.
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Effective quantum field theories
International Nuclear Information System (INIS)
Georgi, H.M.
1989-01-01
Certain dimensional parameters play a crucial role in the understanding of weak and strong interactions based on SU(2) x U(1) and SU(3) symmetry group theories and of grand unified theories (GUT's) based on SU(5). These parameters are the confinement scale of quantum chromodynamics and the breaking scales of SU(2) x U(1) and SU(5). The concepts of effective quantum field theories and renormalisability are discussed with reference to the economics and ethics of research. (U.K.)
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The terrestrial evolution of metabolism and life – by the numbers
O'Kelly Gregory C
2009-01-01
Abstract Background Allometric scaling relating body mass to metabolic rate by an exponent of the former (Kleiber's Law), commonly known as quarter-power scaling (QPS), is controversial for claims made on its behalf, especially that of its universality for all life. As originally formulated, Kleiber was based upon the study of heat; metabolic rate is quantified in watts (or calories per unit time). Techniques and technology for metabolic energy measurement have been refined but the math has n...
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Directory of Open Access Journals (Sweden)
Ankita Chatterjee
2017-11-01
Full Text Available To combat decrease in rice productivity under different stresses, an understanding of rice metabolism is needed. Though there are different genome scale metabolic models (GSMs of Oryza sativa japonica, no GSM with gene-protein-reaction association exist for Oryza sativa indica. Here, we report a GSM, OSI1136 of O.s. indica, which includes 3602 genes and 1136 metabolic reactions and transporters distributed across the cytosol, mitochondrion, peroxisome, and chloroplast compartments. Flux balance analysis of the model showed that for varying RuBisCO activity (Vc/Vo (i the activity of the chloroplastic malate valve increases to transport reducing equivalents out of the chloroplast under increased photorespiratory conditions and (ii glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase can act as source of cytosolic ATP under decreased photorespiration. Under increasing light conditions we observed metabolic flexibility, involving photorespiration, chloroplastic triose phosphate and the dicarboxylate transporters of the chloroplast and mitochondrion for redox and ATP exchanges across the intracellular compartments. Simulations under different enzymatic cost conditions revealed (i participation of peroxisomal glutathione-ascorbate cycle in photorespiratory H2O2 metabolism (ii different modes of the chloroplastic triose phosphate transporters and malate valve, and (iii two possible modes of chloroplastic Glu–Gln transporter which were related with the activity of chloroplastic and cytosolic isoforms of glutamine synthetase. Altogether, our results provide new insights into plant metabolism.
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Sunderland, Matthew; Batterham, Philip; Calear, Alison; Carragher, Natacha; Baillie, Andrew; Slade, Tim
2018-04-10
There is no standardized approach to the measurement of social anxiety. Researchers and clinicians are faced with numerous self-report scales with varying strengths, weaknesses, and psychometric properties. The lack of standardization makes it difficult to compare scores across populations that utilise different scales. Item response theory offers one solution to this problem via equating different scales using an anchor scale to set a standardized metric. This study is the first to equate several scales for social anxiety disorder. Data from two samples (n=3,175 and n=1,052), recruited from the Australian community using online advertisements, were utilised to equate a network of 11 self-report social anxiety scales via a fixed parameter item calibration method. Comparisons between actual and equated scores for most of the scales indicted a high level of agreement with mean differences <0.10 (equivalent to a mean difference of less than one point on the standardized metric). This study demonstrates that scores from multiple scales that measure social anxiety can be converted to a common scale. Re-scoring observed scores to a common scale provides opportunities to combine research from multiple studies and ultimately better assess social anxiety in treatment and research settings. Copyright © 2018. Published by Elsevier Inc.
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Evaporation of Liquid Droplet in Nano and Micro Scales from Statistical Rate Theory.
Duan, Fei; He, Bin; Wei, Tao
2015-04-01
The statistical rate theory (SRT) is applied to predict the average evaporation flux of liquid droplet after the approach is validated in the sessile droplet experiments of the water and heavy water. The steady-state experiments show a temperature discontinuity at the evaporating interface. The average evaporation flux is evaluated by individually changing the measurement at a liquid-vapor interface, including the interfacial liquid temperature, the interfacial vapor temperature, the vapor-phase pressure, and the droplet size. The parameter study shows that a higher temperature jump would reduce the average evaporation flux. The average evaporation flux can significantly be influenced by the interfacial liquid temperature and the vapor-phase pressure. The variation can switch the evaporation into condensation. The evaporation flux is found to remain relative constant if the droplet is larger than a micro scale, while the smaller diameters in nano scale can produce a much higher evaporation flux. In addition, a smaller diameter of droplets with the same liquid volume has a larger surface area. It is suggested that the evaporation rate increases dramatically as the droplet shrinks into nano size.
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Dash, Ranjan K; Li, Yanjun; Kim, Jaeyeon; Beard, Daniel A; Saidel, Gerald M; Cabrera, Marco E
2008-09-09
Control mechanisms of cellular metabolism and energetics in skeletal muscle that may become evident in response to physiological stresses such as reduction in blood flow and oxygen supply to mitochondria can be quantitatively understood using a multi-scale computational model. The analysis of dynamic responses from such a model can provide insights into mechanisms of metabolic regulation that may not be evident from experimental studies. For the purpose, a physiologically-based, multi-scale computational model of skeletal muscle cellular metabolism and energetics was developed to describe dynamic responses of key chemical species and reaction fluxes to muscle ischemia. The model, which incorporates key transport and metabolic processes and subcellular compartmentalization, is based on dynamic mass balances of 30 chemical species in both capillary blood and tissue cells (cytosol and mitochondria) domains. The reaction fluxes in cytosol and mitochondria are expressed in terms of a general phenomenological Michaelis-Menten equation involving the compartmentalized energy controller ratios ATP/ADP and NADH/NAD(+). The unknown transport and reaction parameters in the model are estimated simultaneously by minimizing the differences between available in vivo experimental data on muscle ischemia and corresponding model outputs in coupled with the resting linear flux balance constraints using a robust, nonlinear, constrained-based, reduced gradient optimization algorithm. With the optimal parameter values, the model is able to simulate dynamic responses to reduced blood flow and oxygen supply to mitochondria associated with muscle ischemia of several key metabolite concentrations and metabolic fluxes in the subcellular cytosolic and mitochondrial compartments, some that can be measured and others that can not be measured with the current experimental techniques. The model can be applied to test complex hypotheses involving dynamic regulation of cellular metabolism and
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Huhn, William Paul; Lange, Björn; Yu, Victor; Blum, Volker; Lee, Seyong; Yoon, Mina
Density-functional theory has been well established as the dominant quantum-mechanical computational method in the materials community. Large accurate simulations become very challenging on small to mid-scale computers and require high-performance compute platforms to succeed. GPU acceleration is one promising approach. In this talk, we present a first implementation of all-electron density-functional theory in the FHI-aims code for massively parallel GPU-based platforms. Special attention is paid to the update of the density and to the integration of the Hamiltonian and overlap matrices, realized in a domain decomposition scheme on non-uniform grids. The initial implementation scales well across nodes on ORNL's Titan Cray XK7 supercomputer (8 to 64 nodes, 16 MPI ranks/node) and shows an overall speed up in runtime due to utilization of the K20X Tesla GPUs on each Titan node of 1.4x, with the charge density update showing a speed up of 2x. Further acceleration opportunities will be discussed. Work supported by the LDRD Program of ORNL managed by UT-Battle, LLC, for the U.S. DOE and by the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725.
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Lawton IADL scale in dementia: can item response theory make it more informative?
McGrory, Sarah; Shenkin, Susan D; Austin, Elizabeth J; Starr, John M
2014-07-01
impairment of functional abilities represents a crucial component of dementia diagnosis. Current functional measures rely on the traditional aggregate method of summing raw scores. While this summary score provides a quick representation of a person's ability, it disregards useful information on the item level. to use item response theory (IRT) methods to increase the interpretive power of the Lawton Instrumental Activities of Daily Living (IADL) scale by establishing a hierarchy of item 'difficulty' and 'discrimination'. this cross-sectional study applied IRT methods to the analysis of IADL outcomes. Participants were 202 members of the Scottish Dementia Research Interest Register (mean age = 76.39, range = 56-93, SD = 7.89 years) with complete itemised data available. a Mokken scale with good reliability (Molenaar Sijtsama statistic 0.79) was obtained, satisfying the IRT assumption that the items comprise a single unidimensional scale. The eight items in the scale could be placed on a hierarchy of 'difficulty' (H coefficient = 0.55), with 'Shopping' being the most 'difficult' item and 'Telephone use' being the least 'difficult' item. 'Shopping' was the most discriminatory item differentiating well between patients of different levels of ability. IRT methods are capable of providing more information about functional impairment than a summed score. 'Shopping' and 'Telephone use' were identified as items that reveal key information about a patient's level of ability, and could be useful screening questions for clinicians. © The Author 2013. Published by Oxford University Press on behalf of the British Geriatrics Society. All rights reserved. For Permissions, please email: journals.permissions@ oup.com.
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Covariantized matrix theory for D-particles
Energy Technology Data Exchange (ETDEWEB)
Yoneya, Tamiaki [Institute of Physics, The University of Tokyo,3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); School of Graduate Studies, The Open University of Japan,2-11 Wakaba, Mihama-ku, Chiba 261-8586 (Japan)
2016-06-09
We reformulate the Matrix theory of D-particles in a manifestly Lorentz-covariant fashion in the sense of 11 dimesnional flat Minkowski space-time, from the viewpoint of the so-called DLCQ interpretation of the light-front Matrix theory. The theory is characterized by various symmetry properties including higher gauge symmetries, which contain the usual SU(N) symmetry as a special case and are extended from the structure naturally appearing in association with a discretized version of Nambu’s 3-bracket. The theory is scale invariant, and the emergence of the 11 dimensional gravitational length, or M-theory scale, is interpreted as a consequence of a breaking of the scaling symmetry through a super-selection rule. In the light-front gauge with the DLCQ compactification of 11 dimensions, the theory reduces to the usual light-front formulation. In the time-like gauge with the ordinary M-theory spatial compactification, it reduces to a non-Abelian Born-Infeld-like theory, which in the limit of large N becomes equivalent with the original BFSS theory.
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Hamilton, Joshua J; Dwivedi, Vivek; Reed, Jennifer L
2013-07-16
Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Is the rate of metabolic ageing and survival determined by Basal metabolic rate in the zebra finch?
Directory of Open Access Journals (Sweden)
Bernt Rønning
Full Text Available The relationship between energy metabolism and ageing is of great interest because aerobic metabolism is the primary source of reactive oxygen species which is believed to be of major importance in the ageing process. We conducted a longitudinal study on captive zebra finches where we tested the effect of age on basal metabolic rate (BMR, as well as the effect of BMR on the rate of metabolic ageing (decline in BMR with age and survival. Basal metabolic rate declined with age in both sexes after controlling for the effect of body mass, indicating a loss of functionality with age. This loss of functionality could be due to accumulated oxidative damage, believed to increase with increasing metabolic rate, c.f. the free radical theory of ageing. If so, we would expect the rate of metabolic ageing to increase and survival to decrease with increasing BMR. However, we found no effect of BMR on the rate of metabolic ageing. Furthermore, survival was not affected by BMR in the males. In female zebra finches there was a tendency for survival to decrease with increasing BMR, but the effect did not reach significance (P<0.1. Thus, the effect of BMR on the rate of functional deterioration with age, if any, was not strong enough to influence neither the rate of metabolic ageing nor survival in the zebra finches.
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Is the rate of metabolic ageing and survival determined by Basal metabolic rate in the zebra finch?
Rønning, Bernt; Moe, Børge; Berntsen, Henrik H; Noreen, Elin; Bech, Claus
2014-01-01
The relationship between energy metabolism and ageing is of great interest because aerobic metabolism is the primary source of reactive oxygen species which is believed to be of major importance in the ageing process. We conducted a longitudinal study on captive zebra finches where we tested the effect of age on basal metabolic rate (BMR), as well as the effect of BMR on the rate of metabolic ageing (decline in BMR with age) and survival. Basal metabolic rate declined with age in both sexes after controlling for the effect of body mass, indicating a loss of functionality with age. This loss of functionality could be due to accumulated oxidative damage, believed to increase with increasing metabolic rate, c.f. the free radical theory of ageing. If so, we would expect the rate of metabolic ageing to increase and survival to decrease with increasing BMR. However, we found no effect of BMR on the rate of metabolic ageing. Furthermore, survival was not affected by BMR in the males. In female zebra finches there was a tendency for survival to decrease with increasing BMR, but the effect did not reach significance (PBMR on the rate of functional deterioration with age, if any, was not strong enough to influence neither the rate of metabolic ageing nor survival in the zebra finches.
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Maltby, John; Day, Liz; Hall, Sophie S; Chivers, Sally
2017-10-01
Research suggests that trait resilience may be best understood within an ecological resilient systems theory, comprising engineering, ecological, and adaptive capacity resilience. However, there is no evidence as to how this theory translates to specific life domains. Data from two samples (the United States, n = 1,278; the United Kingdom, n = 211) facilitated five studies that introduce the Domain-Specific Resilient Systems Scales for assessing ecological resilient systems theory within work, health, marriage, friendships, and education. The Domain-Specific Resilient Systems Scales are found to predict unique variance in job satisfaction, lower job burnout, quality-of-life following illness, marriage commitment, and educational engagement, while controlling for factors including sex, age, personality, cognitive ability, and trait resilience. The findings also suggest a distinction between the three resilience dimensions in terms of the types of systems to which they contribute. Engineering resilience may contribute most to life domains where an established system needs to be maintained, for example, one's health. Ecological resilience may contribute most to life domains where the system needs sustainability in terms of present and future goal orientation, for example, one's work. Adaptive Capacity may contribute most to life domains where the system needs to be retained, preventing it from reaching a crisis state, for example, work burnout.
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Grigg, Kaine; Manderson, Lenore
2016-03-17
Racism and associated discrimination are pervasive and persistent challenges with multiple cumulative deleterious effects contributing to inequities in various health outcomes. Globally, research over the past decade has shown consistent associations between racism and negative health concerns. Such research confirms that race endures as one of the strongest predictors of poor health. Due to the lack of validated Australian measures of racist attitudes, RACES (Racism, Acceptance, and Cultural-Ethnocentrism Scale) was developed. Here, we examine RACES' psychometric properties, including the latent structure, utilising Item Response Theory (IRT). Unidimensional and Multidimensional Rating Scale Model (RSM) Rasch analyses were utilised with 296 Victorian primary school students and 182 adolescents and 220 adults from the Australian community. RACES was demonstrated to be a robust 24-item three-dimensional scale of Accepting Attitudes (12 items), Racist Attitudes (8 items), and Ethnocentric Attitudes (4 items). RSM Rasch analyses provide strong support for the instrument as a robust measure of racist attitudes in the Australian context, and for the overall factorial and construct validity of RACES across primary school children, adolescents, and adults. RACES provides a reliable and valid measure that can be utilised across the lifespan to evaluate attitudes towards all racial, ethnic, cultural, and religious groups. A core function of RACES is to assess the effectiveness of interventions to reduce community levels of racism and in turn inequities in health outcomes within Australia.
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Jacquet, Claire; Mouillot, David; Kulbicki, Michel; Gravel, Dominique
2017-02-01
The Theory of Island Biogeography (TIB) predicts how area and isolation influence species richness equilibrium on insular habitats. However, the TIB remains silent about functional trait composition and provides no information on the scaling of functional diversity with area, an observation that is now documented in many systems. To fill this gap, we develop a probabilistic approach to predict the distribution of a trait as a function of habitat area and isolation, extending the TIB beyond the traditional species-area relationship. We compare model predictions to the body-size distribution of piscivorous and herbivorous fishes found on tropical reefs worldwide. We find that small and isolated reefs have a higher proportion of large-sized species than large and connected reefs. We also find that knowledge of species body-size and trophic position improves the predictions of fish occupancy on tropical reefs, supporting both the allometric and trophic theory of island biogeography. The integration of functional ecology to island biogeography is broadly applicable to any functional traits and provides a general probabilistic approach to study the scaling of trait distribution with habitat area and isolation. © 2016 John Wiley & Sons Ltd/CNRS.
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Low-energy limit of two-scale field theories
International Nuclear Information System (INIS)
Leon, J.; Perez-Mercader, J.; Sanchez, M.F.
1991-01-01
We present a full and self-contained discussion of the decoupling theorem applied to several general models in four-dimensional field theory. We compute in each case the low-energy effective action and show the explicit one-loop expressions for each of the effective parameters. We find that for suitable conditions one can always build an effective low-energy theory where the conditions of the decoupling theorem are satisfied
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In silico method for modelling metabolism and gene product expression at genome scale
Energy Technology Data Exchange (ETDEWEB)
Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, Nathan E.; Orth, Jeffrey D.; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Zengler, Karsten; Palsson, Bernard O.
2012-07-03
Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.
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Single-polymer dynamics under constraints: scaling theory and computer experiment
International Nuclear Information System (INIS)
Milchev, Andrey
2011-01-01
The relaxation, diffusion and translocation dynamics of single linear polymer chains in confinement is briefly reviewed with emphasis on the comparison between theoretical scaling predictions and observations from experiment or, most frequently, from computer simulations. Besides cylindrical, spherical and slit-like constraints, related problems such as the chain dynamics in a random medium and the translocation dynamics through a nanopore are also considered. Another particular kind of confinement is imposed by polymer adsorption on attractive surfaces or selective interfaces-a short overview of single-chain dynamics is also contained in this survey. While both theory and numerical experiments consider predominantly coarse-grained models of self-avoiding linear chain molecules with typically Rouse dynamics, we also note some recent studies which examine the impact of hydrodynamic interactions on polymer dynamics in confinement. In all of the aforementioned cases we focus mainly on the consequences of imposed geometric restrictions on single-chain dynamics and try to check our degree of understanding by assessing the agreement between theoretical predictions and observations. (topical review)
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Cokley, K O
2000-04-01
This study examined the construct validity of the Academic Motivation Scale. Specifically, subscale correlations were examined to assess whether support for a continuum of self-determination would be provided. The three types of Intrinsic Motivation were significantly and positively correlated with each other .67, .62, and .58, while the three types of Extrinsic Motivation were significantly and positively intercorrelated .50, .49, and .45. The former subscales, however, correlated higher with Introjected Regulation than Identified Regulation, suggesting that Introjected Regulation may be indicative of more self-determined behavior than has previously been believed. Also, the Intrinsic Motivation To Accomplish subscale had a stronger relationship with two of the Extrinsic Motivation subscales, Identified Regulation and Introjected Regulation, than did the Extrinsic Motivation subscales with each other. This suggests that the differences between Extrinsic and Intrinsic Motivation are not as obvious as has been believed. Also, contrary to self-determination theory, Amotivation had a stronger negative correlation with Identified Regulation (r = -.31) than with any of the Intrinsic Motivation subscales (rs = -.27, -.19, and -.11).
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Improving Measurement Efficiency of the Inner EAR Scale with Item Response Theory.
Jessen, Annika; Ho, Andrew D; Corrales, C Eduardo; Yueh, Bevan; Shin, Jennifer J
2018-02-01
Objectives (1) To assess the 11-item Inner Effectiveness of Auditory Rehabilitation (Inner EAR) instrument with item response theory (IRT). (2) To determine whether the underlying latent ability could also be accurately represented by a subset of the items for use in high-volume clinical scenarios. (3) To determine whether the Inner EAR instrument correlates with pure tone thresholds and word recognition scores. Design IRT evaluation of prospective cohort data. Setting Tertiary care academic ambulatory otolaryngology clinic. Subjects and Methods Modern psychometric methods, including factor analysis and IRT, were used to assess unidimensionality and item properties. Regression methods were used to assess prediction of word recognition and pure tone audiometry scores. Results The Inner EAR scale is unidimensional, and items varied in their location and information. Information parameter estimates ranged from 1.63 to 4.52, with higher values indicating more useful items. The IRT model provided a basis for identifying 2 sets of items with relatively lower information parameters. Item information functions demonstrated which items added insubstantial value over and above other items and were removed in stages, creating a 8- and 3-item Inner EAR scale for more efficient assessment. The 8-item version accurately reflected the underlying construct. All versions correlated moderately with word recognition scores and pure tone averages. Conclusion The 11-, 8-, and 3-item versions of the Inner EAR scale have strong psychometric properties, and there is correlational validity evidence for the observed scores. Modern psychometric methods can help streamline care delivery by maximizing relevant information per item administered.
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Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine.
Aurich, Maike K; Thiele, Ines
2016-01-01
Modern high-throughput techniques offer immense opportunities to investigate whole-systems behavior, such as those underlying human diseases. However, the complexity of the data presents challenges in interpretation, and new avenues are needed to address the complexity of both diseases and data. Constraint-based modeling is one formalism applied in systems biology. It relies on a genome-scale reconstruction that captures extensive biochemical knowledge regarding an organism. The human genome-scale metabolic reconstruction is increasingly used to understand normal cellular and disease states because metabolism is an important factor in many human diseases. The application of human genome-scale reconstruction ranges from mere querying of the model as a knowledge base to studies that take advantage of the model's topology and, most notably, to functional predictions based on cell- and condition-specific metabolic models built based on omics data.An increasing number and diversity of biomedical questions are being addressed using constraint-based modeling and metabolic models. One of the most successful biomedical applications to date is cancer metabolism, but constraint-based modeling also holds great potential for inborn errors of metabolism or obesity. In addition, it offers great prospects for individualized approaches to diagnostics and the design of disease prevention and intervention strategies. Metabolic models support this endeavor by providing easy access to complex high-throughput datasets. Personalized metabolic models have been introduced. Finally, constraint-based modeling can be used to model whole-body metabolism, which will enable the elucidation of metabolic interactions between organs and disturbances of these interactions as either causes or consequence of metabolic diseases. This chapter introduces constraint-based modeling and describes some of its contributions to systems biomedicine.
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Data-driven integration of genome-scale regulatory and metabolic network models
Imam, Saheed; Schäuble, Sascha; Brooks, Aaron N.; Baliga, Nitin S.; Price, Nathan D.
2015-01-01
Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert—a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system. PMID:25999934
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Multi-scale modeling for sustainable chemical production
DEFF Research Database (Denmark)
Zhuang, Kai; Bakshi, Bhavik R.; Herrgard, Markus
2013-01-01
associated with the development and implementation of a su stainable biochemical industry. The temporal and spatial scales of modeling approaches for sustainable chemical production vary greatly, ranging from metabolic models that aid the design of fermentative microbial strains to material and monetary flow......With recent advances in metabolic engineering, it is now technically possible to produce a wide portfolio of existing petrochemical products from biomass feedstock. In recent years, a number of modeling approaches have been developed to support the engineering and decision-making processes...... models that explore the ecological impacts of all economic activities. Research efforts that attempt to connect the models at different scales have been limited. Here, we review a number of existing modeling approaches and their applications at the scales of metabolism, bioreactor, overall process...
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Masuda, Shumpei; Nakamura, Katsuhiro; Nakahara, Mikio
2018-02-01
We study phase imprinting on Bose-Einstein condensates (BECs) with the fast-forward scaling theory revealing a nontrivial scaling property in quantum dynamics. We introduce a wave packet with uniform momentum density (WPUM) which has peculiar properties but is short-lived. The fast-forward scaling theory is applied to derive the driving potential for creation of the WPUMs in a predetermined time. Fast manipulation is essential for the creation of WPUMs because of the instability of the state. We also study loading of a BEC into a predetermined Bloch state in the lowest band from the ground state of a periodic potential. Controlled linear potential is not sufficient for creation of the Bloch state with large wavenumber because the change in the amplitude of the order parameter is not negligible. We derive the exact driving potential for creation of predetermined Bloch states using the obtained theory.
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Renormalization group evolution of the universal theories EFT
International Nuclear Information System (INIS)
Wells, James D.; Zhang, Zhengkang
2016-01-01
The conventional oblique parameters analyses of precision electroweak data can be consistently cast in the modern framework of the Standard Model effective field theory (SMEFT) when restrictions are imposed on the SMEFT parameter space so that it describes universal theories. However, the usefulness of such analyses is challenged by the fact that universal theories at the scale of new physics, where they are matched onto the SMEFT, can flow to nonuniversal theories with renormalization group (RG) evolution down to the electroweak scale, where precision observables are measured. The departure from universal theories at the electroweak scale is not arbitrary, but dictated by the universal parameters at the matching scale. But to define oblique parameters, and more generally universal parameters at the electroweak scale that directly map onto observables, additional prescriptions are needed for the treatment of RG-induced nonuniversal effects. We perform a RG analysis of the SMEFT description of universal theories, and discuss the impact of RG on simplified, universal-theories-motivated approaches to fitting precision electroweak and Higgs data.
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International Nuclear Information System (INIS)
Aharony, Ofer; Komargodski, Zohar; Yankielowicz, Shimon
2016-01-01
We consider Euclidean Conformal Field Theories perturbed by quenched disorder, namely by random fluctuations in their couplings. Such theories are relevant for second-order phase transitions in the presence of impurities or other forms of disorder. Theories with quenched disorder often flow to new fixed points of the renormalization group. We begin with disorder in free field theories. Imry and Ma showed that disordered free fields can only exist for d>4. For d>4 we show that disorder leads to new fixed points which are not scale-invariant. We then move on to large-N theories (vector models or gauge theories in the ‘t Hooft limit). We compute exactly the beta function for the disorder, and the correlation functions of the disordered theory. We generalize the results of Imry and Ma by showing that such disordered theories exist only when disorder couples to operators of dimension Δ>d/4. Sometimes the disordered fixed points are not scale-invariant, and in other cases they have unconventional dependence on the disorder, including non-trivial effects due to irrelevant operators. Holography maps disorder in conformal theories to stochastic differential equations in a higher dimensional space. We use this dictionary to reproduce our field theory results. We also study the leading 1/N corrections, both by field theory methods and by holography. These corrections are particularly important when disorder scales with the number of degrees of freedom.
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Energy Technology Data Exchange (ETDEWEB)
Aharony, Ofer; Komargodski, Zohar [Department of Particle Physics and Astrophysics, Weizmann Institute of Science,Rehovot 7610001 (Israel); Yankielowicz, Shimon [School of Physics and Astronomy, Tel Aviv University,Ramat Aviv 69978 (Israel)
2016-04-04
We consider Euclidean Conformal Field Theories perturbed by quenched disorder, namely by random fluctuations in their couplings. Such theories are relevant for second-order phase transitions in the presence of impurities or other forms of disorder. Theories with quenched disorder often flow to new fixed points of the renormalization group. We begin with disorder in free field theories. Imry and Ma showed that disordered free fields can only exist for d>4. For d>4 we show that disorder leads to new fixed points which are not scale-invariant. We then move on to large-N theories (vector models or gauge theories in the ‘t Hooft limit). We compute exactly the beta function for the disorder, and the correlation functions of the disordered theory. We generalize the results of Imry and Ma by showing that such disordered theories exist only when disorder couples to operators of dimension Δ>d/4. Sometimes the disordered fixed points are not scale-invariant, and in other cases they have unconventional dependence on the disorder, including non-trivial effects due to irrelevant operators. Holography maps disorder in conformal theories to stochastic differential equations in a higher dimensional space. We use this dictionary to reproduce our field theory results. We also study the leading 1/N corrections, both by field theory methods and by holography. These corrections are particularly important when disorder scales with the number of degrees of freedom.
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Thermodynamics of the control of metabolism
Westerhoff, H. V.; Plomp, P. J.; Groen, A. K.; Wanders, R. J.
1987-01-01
A theory is presented, describing the control analysis of metabolic systems in terms of Gibbs free energies, extending earlier work of Kacser and Burns (25), and Heinrich and Rapoport (29). It is shown that relationships exist between flux control coefficients (the degree to which enzymes control
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Peterson, Candida C.; Wellman, Henry M.; Slaughter, Virginia
2012-01-01
Children aged 3-2 years (n = 184) with typical development, deafness, autism, or Asperger syndrome took a series of theory-of-mind (ToM) tasks to confirm and extend previous developmental scaling evidence. A new sarcasm task, in the format of H. M. Wellman and D. Liu's (2004) 5-step ToM Scale, added a statistically reliable 6th step to the scale…
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Peterson, Candida C.; Wellman, Henry M.; Slaughter, Virginia
2012-01-01
Children aged 3 to 12 years (n=184) with typical development, deafness, autism or Asperger Syndrome took a series of theory-of-mind (ToM) tasks to confirm and extend previous developmental scaling evidence. A new sarcasm task, in the format of Wellman and Liu’s (2004) 5-step ToM scale, added a statistically reliable sixth step to the scale for all diagnostic groups. A key previous finding, divergence in task sequencing for children with autism, was confirmed. Comparisons among diagnostic grou...
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Bordel, Sergio
2018-04-13
In order to choose optimal personalized anticancer treatments, transcriptomic data should be analyzed within the frame of biological networks. The best known human biological network (in terms of the interactions between its different components) is metabolism. Cancer cells have been known to have specific metabolic features for a long time and currently there is a growing interest in characterizing new cancer specific metabolic hallmarks. In this article it is presented a method to find personalized therapeutic windows using RNA-seq data and Genome Scale Metabolic Models. This method is implemented in the python library, pyTARG. Our predictions showed that the most anticancer selective (affecting 27 out of 34 considered cancer cell lines and only 1 out of 6 healthy mesenchymal stem cell lines) single metabolic reactions are those involved in cholesterol biosynthesis. Excluding cholesterol biosynthesis, all the considered cell lines can be selectively affected by targeting different combinations (from 1 to 5 reactions) of only 18 metabolic reactions, which suggests that a small subset of drugs or siRNAs combined in patient specific manners could be at the core of metabolism based personalized treatments.
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Directory of Open Access Journals (Sweden)
Eddy J Bautista
Full Text Available Primarily used for metabolic engineering and synthetic biology, genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism. Through a novel integration of flux balance analysis and genetic algorithms, a strategy to curate metabolic networks and facilitate identification of metabolic pathways that may not be directly inferable solely from genome annotation was developed. Specifically, metabolites involved in unknown reactions can be determined, and potentially erroneous pathways can be identified. The procedure developed allows for new fundamental insight into metabolism, as well as acting as a semi-automated curation methodology for genome-scale metabolic modeling. To validate the methodology, a genome-scale metabolic model for the bacterium Mycoplasma gallisepticum was created. Several reactions not predicted by the genome annotation were postulated and validated via the literature. The model predicted an average growth rate of 0.358±0.12[Formula: see text], closely matching the experimentally determined growth rate of M. gallisepticum of 0.244±0.03[Formula: see text]. This work presents a powerful algorithm for facilitating the identification and curation of previously known and new metabolic pathways, as well as presenting the first genome-scale reconstruction of M. gallisepticum.
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Data-driven integration of genome-scale regulatory and metabolic network models
Directory of Open Access Journals (Sweden)
Saheed eImam
2015-05-01
Full Text Available Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription and signaling have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert – a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.
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String theory as a Lilliputian world
International Nuclear Information System (INIS)
Ambjørn, J.; Makeenko, Y.
2016-01-01
Lattice regularizations of the bosonic string do not allow us to probe the tachyon. This has often been viewed as the reason why these theories have never managed to make any contact to standard continuum string theories when the dimension of spacetime is larger than two. We study the continuum string theory in large spacetime dimensions where simple mean field theory is reliable. By keeping carefully the cutoff we show that precisely the existence of a tachyon makes it possible to take a scaling limit which reproduces the lattice-string results. We compare this scaling limit with another scaling limit which reproduces standard continuum-string results. If the people working with lattice regularizations of string theories are akin to Gulliver they will view the standard string-world as a Lilliputian world no larger than a few lattice spacings.
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String theory as a Lilliputian world
Energy Technology Data Exchange (ETDEWEB)
Ambjørn, J., E-mail: ambjorn@nbi.dk [The Niels Bohr Institute, Copenhagen University, Blegdamsvej 17, DK-2100 Copenhagen (Denmark); IMAPP, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen (Netherlands); Makeenko, Y., E-mail: makeenko@nbi.dk [The Niels Bohr Institute, Copenhagen University, Blegdamsvej 17, DK-2100 Copenhagen (Denmark); Institute of Theoretical and Experimental Physics, B. Cheremushkinskaya 25, 117218 Moscow (Russian Federation)
2016-05-10
Lattice regularizations of the bosonic string do not allow us to probe the tachyon. This has often been viewed as the reason why these theories have never managed to make any contact to standard continuum string theories when the dimension of spacetime is larger than two. We study the continuum string theory in large spacetime dimensions where simple mean field theory is reliable. By keeping carefully the cutoff we show that precisely the existence of a tachyon makes it possible to take a scaling limit which reproduces the lattice-string results. We compare this scaling limit with another scaling limit which reproduces standard continuum-string results. If the people working with lattice regularizations of string theories are akin to Gulliver they will view the standard string-world as a Lilliputian world no larger than a few lattice spacings.
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Herrgård, Markus J.; Swainston, Neil; Dobson, Paul; Dunn, Warwick B.; Arga, K. Yalçin; Arvas, Mikko; Blüthgen, Nils; Borger, Simon; Costenoble, Roeland; Heinemann, Matthias; Hucka, Michael; Novère, Nicolas Le; Li, Peter; Liebermeister, Wolfram; Mo, Monica L.; Oliveira, Ana Paula; Petranovic, Dina; Pettifer, Stephen; Simeonidis, Evangelos; Smallbone, Kieran; Spasić, Irena; Weichart, Dieter; Brent, Roger; Broomhead, David S.; Westerhoff, Hans V.; Kırdar, Betül; Penttilä, Merja; Klipp, Edda; Palsson, Bernhard Ø.; Sauer, Uwe; Oliver, Stephen G.; Mendes, Pedro; Nielsen, Jens; Kell, Douglas B.
2008-01-01
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and
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A preliminary and qualitative study of resource ratio theory to nitrifying lab-scale bioreactors.
Bellucci, Micol; Ofiţeru, Irina D; Beneduce, Luciano; Graham, David W; Head, Ian M; Curtis, Thomas P
2015-05-01
The incorporation of microbial diversity in design would ideally require predictive theory that would relate operational parameters to the numbers and distribution of taxa. Resource ratio-theory (RRT) might be one such theory. Based on Monod kinetics, it explains diversity in function of resource-ratio and richness. However, to be usable in biological engineered system, the growth parameters of all the bacteria under consideration and the resource supply and diffusion parameters for all the relevant nutrients should be determined. This is challenging, but plausible, at least for low diversity groups with simple resource requirements like the ammonia oxidizing bacteria (AOB). One of the major successes of RRT was its ability to explain the 'paradox of enrichment' which states that diversity first increases and then decreases with resource richness. Here, we demonstrate that this pattern can be seen in lab-scale-activated sludge reactors and parallel simulations that incorporate the principles of RRT in a floc-based system. High and low ammonia and oxygen were supplied to continuous flow bioreactors with resource conditions correlating with the composition and diversity of resident AOB communities based on AOB 16S rDNA clone libraries. Neither the experimental work nor the simulations are definitive proof for the application of RRT in this context. However, it is sufficient evidence that such approach might work and justify a more rigorous investigation. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
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Metabolic engineering of biosynthetic pathway for production of renewable biofuels.
Singh, Vijai; Mani, Indra; Chaudhary, Dharmendra Kumar; Dhar, Pawan Kumar
2014-02-01
Metabolic engineering is an important area of research that involves editing genetic networks to overproduce a certain substance by the cells. Using a combination of genetic, metabolic, and modeling methods, useful substances have been synthesized in the past at industrial scale and in a cost-effective manner. Currently, metabolic engineering is being used to produce sufficient, economical, and eco-friendly biofuels. In the recent past, a number of efforts have been made towards engineering biosynthetic pathways for large scale and efficient production of biofuels from biomass. Given the adoption of metabolic engineering approaches by the biofuel industry, this paper reviews various approaches towards the production and enhancement of renewable biofuels such as ethanol, butanol, isopropanol, hydrogen, and biodiesel. We have also identified specific areas where more work needs to be done in the future.
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Absolute mass scale calibration in the inverse problem of the physical theory of fireballs.
Kalenichenko, V. V.
A method of the absolute mass scale calibration is suggested for solving the inverse problem of the physical theory of fireballs. The method is based on the data on the masses of the fallen meteorites whose fireballs have been photographed in their flight. The method may be applied to those fireballs whose bodies have not experienced considerable fragmentation during their destruction in the atmosphere and have kept their form well enough. Statistical analysis of the inverse problem solution for a sufficiently representative sample makes it possible to separate a subsample of such fireballs. The data on the Lost City and Innisfree meteorites are used to obtain calibration coefficients.
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Winslow, Luke; Zwart, Jacob A.; Batt, Ryan D.; Dugan, Hilary; Woolway, R. Iestyn; Corman, Jessica; Hanson, Paul C.; Read, Jordan S.
2016-01-01
Metabolism is a fundamental process in ecosystems that crosses multiple scales of organization from individual organisms to whole ecosystems. To improve sharing and reuse of published metabolism models, we developed LakeMetabolizer, an R package for estimating lake metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models). These tools have been organized into an R package that contains example data, example use-cases, and function documentation. The release package version is available on the Comprehensive R Archive Network (CRAN), and the full open-source GPL-licensed code is freely available for examination and extension online. With this unified, open-source, and freely available package, we hope to improve access and facilitate the application of metabolism in studies and management of lentic ecosystems.
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Directory of Open Access Journals (Sweden)
Slaviša M. Ilić
2011-10-01
Full Text Available This paper analyzes the effectiveness of possible models for queuing at gas stations, using a mathematical model of the large-scale queuing theory. Based on actual data collected and the statistical analysis of the expected intensity of vehicle arrivals and queuing at gas stations, the mathematical modeling of the real process of queuing was carried out and certain parameters quantified, in terms of perception of the weaknesses of the existing models and the possible benefits of an automated queuing model.
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Story of the string theory. From hadrons to Planck scale
International Nuclear Information System (INIS)
Petropoulos, P.M.
2010-01-01
Originally the string theory was devised to describe the scattering between hadron particles but was quickly put aside by the success of the quantum chromodynamics. Now string theory appears in the quantum gravity theory and has been involved in almost all attempts to define a physics beyond the standard model and to unify basic interactions. (A.C.)
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Energy Technology Data Exchange (ETDEWEB)
Friar, J.L.
1998-12-01
Nuclear scales are discussed from the nuclear physics viewpoint. The conventional nuclear potential is characterized as a black box that interpolates nucleon-nucleon (NN) data, while being constrained by the best possible theoretical input. The latter consists of the longer-range parts of the NN force (e.g., OPEP, TPEP, the {pi}-{gamma} force), which can be calculated using chiral perturbation theory and gauged using modern phase-shift analyses. The shorter-range parts of the force are effectively parameterized by moments of the interaction that are independent of the details of the force model, in analogy to chiral perturbation theory. Results of GFMC calculations in light nuclei are interpreted in terms of fundamental scales, which are in good agreement with expectations from chiral effective field theories. Problems with spin-orbit-type observables are noted.
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International Nuclear Information System (INIS)
Friar, J.L.
1998-01-01
Nuclear scales are discussed from the nuclear physics viewpoint. The conventional nuclear potential is characterized as a black box that interpolates nucleon-nucleon (NN) data, while being constrained by the best possible theoretical input. The latter consists of the longer-range parts of the NN force (e.g., OPEP, TPEP, the π-γ force), which can be calculated using chiral perturbation theory and gauged using modern phase-shift analyses. The shorter-range parts of the force are effectively parameterized by moments of the interaction that are independent of the details of the force model, in analogy to chiral perturbation theory. Results of GFMC calculations in light nuclei are interpreted in terms of fundamental scales, which are in good agreement with expectations from chiral effective field theories. Problems with spin-orbit-type observables are noted
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Scale invariant Volkov–Akulov supergravity
Energy Technology Data Exchange (ETDEWEB)
Ferrara, S., E-mail: sergio.ferrara@cern.ch [Th-Ph Department, CERN, CH-1211 Geneva 23 (Switzerland); INFN – Laboratori Nazionali di Frascati, Via Enrico Fermi 40, 00044 Frascati (Italy); Department of Physics and Astronomy, University of California, Los Angeles, CA 90095-1547 (United States); Porrati, M., E-mail: mp9@nyu.edu [Th-Ph Department, CERN, CH-1211 Geneva 23 (Switzerland); CCPP, Department of Physics, NYU, 4 Washington Pl., New York, NY 10003 (United States); Sagnotti, A., E-mail: sagnotti@sns.it [Th-Ph Department, CERN, CH-1211 Geneva 23 (Switzerland); Scuola Normale Superiore and INFN, Piazza dei Cavalieri 7, 56126 Pisa (Italy)
2015-10-07
A scale invariant goldstino theory coupled to supergravity is obtained as a standard supergravity dual of a rigidly scale-invariant higher-curvature supergravity with a nilpotent chiral scalar curvature. The bosonic part of this theory describes a massless scalaron and a massive axion in a de Sitter Universe.
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The energy metabolism of megacities
International Nuclear Information System (INIS)
Facchini, Angelo; Kennedy, Chris; Stewart, Iain; Mele, Renata
2017-01-01
Highlights: • Energy metabolism leads to a better management of energy use in megacities. • Insights on strategies to improve energy efficiency and reduce resource consumption. • We find a regionalization of energy flows and sectoral energy use. • Scaling law for energy Vs density suggests strategies for compact cities planning. • Supports development of models to reduce GHG emissions and increase resilience. - Abstract: Due to their sheer size and complexity, megacities are extreme examples in which both negative and positive aspects of urbanization co-exist and are amplified. Especially in emerging countries they are becoming the dominant paradigm of the future urbanization, representing a sustainability challenge both from the point of view of energy and resource consumption, and from the point of view of climate change adaptation and mitigation. In this paper we compare the energy metabolism in 27 of the world’s megacities including details of mobile and stationary energy consumption patterns, fuels used, as well as end-use patterns and electricity generation mix. Our results show that per capita total energy consumption scales with urban population density according to a power law characterized by the universal −3/4 scaling, pointing out that compact cities are more energy efficient with respect to dispersed cities. By comparing energy sources and sectoral end use, also focusing on electricity use and generation source, we found a significant regionalization of energy metabolism, and we discuss the implication for resilience, infrastructure planning, GHG emissions, and policies for infrastructure decarbonization. The comparison of the energy metabolism can lead to a more appropriate management of energy use patterns and electricity generation mix in megacities, giving insights on strategies to improve urban energy efficiency and reducing environmental pressure of megacities.
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Metabolic Control of Redox and Redox Control of Metabolism in Plants
Fernie, Alisdair R.
2014-01-01
Abstract Significance: Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression. Recent Advances: The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels. Critical Issues: It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels. Future Directions: Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and
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Guo, L; Han, S S; Liu, X; Cheng, Y; Xu, Z Z; Fan, J; Chen, J; Chen, S G; Becker, W; Blaga, C I; DiChiara, A D; Sistrunk, E; Agostini, P; DiMauro, L F
2013-01-04
A calculation of the second-order (rescattering) term in the S-matrix expansion of above-threshold ionization is presented for the case when the binding potential is the unscreened Coulomb potential. Technical problems related to the divergence of the Coulomb scattering amplitude are avoided in the theory by considering the depletion of the atomic ground state due to the applied laser field, which is well defined and does not require the introduction of a screening constant. We focus on the low-energy structure, which was observed in recent experiments with a midinfrared wavelength laser field. Both the spectra and, in particular, the observed scaling versus the Keldysh parameter and the ponderomotive energy are reproduced. The theory provides evidence that the origin of the structure lies in the long-range Coulomb interaction.
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Jordan, Pascal; Shedden-Mora, Meike C; Löwe, Bernd
2017-01-01
The Generalized Anxiety Disorder scale (GAD-7) is one of the most frequently used diagnostic self-report scales for screening, diagnosis and severity assessment of anxiety disorder. Its psychometric properties from the view of the Item Response Theory paradigm have rarely been investigated. We aimed to close this gap by analyzing the GAD-7 within a large sample of primary care patients with respect to its psychometric properties and its implications for scoring using Item Response Theory. Robust, nonparametric statistics were used to check unidimensionality of the GAD-7. A graded response model was fitted using a Bayesian approach. The model fit was evaluated using posterior predictive p-values, item information functions were derived and optimal predictions of anxiety were calculated. The sample included N = 3404 primary care patients (60% female; mean age, 52,2; standard deviation 19.2) The analysis indicated no deviations of the GAD-7 scale from unidimensionality and a decent fit of a graded response model. The commonly suggested ultra-brief measure consisting of the first two items, the GAD-2, was supported by item information analysis. The first four items discriminated better than the last three items with respect to latent anxiety. The information provided by the first four items should be weighted more heavily. Moreover, estimates corresponding to low to moderate levels of anxiety show greater variability. The psychometric validity of the GAD-2 was supported by our analysis.
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Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities.
Mahadevan, Radhakrishnan; Henson, Michael A
2012-01-01
Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.
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Deepening, and repairing, the metabolic rift.
Schneider, Mindi; McMichael, Philip
2010-01-01
This paper critically assesses the metabolic rift as a social, ecological, and historical concept describing the disruption of natural cycles and processes and ruptures in material human-nature relations under capitalism. As a social concept, the metabolic rift presumes that metabolism is understood in relation to the labour process. This conception, however, privileges the organisation of labour to the exclusion of the practice of labour, which we argue challenges its utility for analysing contemporary socio-environmental crises. As an ecological concept, the metabolic rift is based on outmoded understandings of (agro) ecosystems and inadequately describes relations and interactions between labour and ecological processes. Historically, the metabolic rift is integral to debates about the definitions and relations of capitalism, industrialism, and modernity as historical concepts. At the same time, it gives rise to an epistemic rift, insofar as the separation of the natural and social worlds comes to be expressed in social thought and critical theory, which have one-sidedly focused on the social. We argue that a reunification of the social and the ecological, in historical practice and in historical thought, is the key to repairing the metabolic rift, both conceptually and practically. The food sovereignty movement in this respect is exemplary.
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Multi-scale modeling for sustainable chemical production.
Zhuang, Kai; Bakshi, Bhavik R; Herrgård, Markus J
2013-09-01
With recent advances in metabolic engineering, it is now technically possible to produce a wide portfolio of existing petrochemical products from biomass feedstock. In recent years, a number of modeling approaches have been developed to support the engineering and decision-making processes associated with the development and implementation of a sustainable biochemical industry. The temporal and spatial scales of modeling approaches for sustainable chemical production vary greatly, ranging from metabolic models that aid the design of fermentative microbial strains to material and monetary flow models that explore the ecological impacts of all economic activities. Research efforts that attempt to connect the models at different scales have been limited. Here, we review a number of existing modeling approaches and their applications at the scales of metabolism, bioreactor, overall process, chemical industry, economy, and ecosystem. In addition, we propose a multi-scale approach for integrating the existing models into a cohesive framework. The major benefit of this proposed framework is that the design and decision-making at each scale can be informed, guided, and constrained by simulations and predictions at every other scale. In addition, the development of this multi-scale framework would promote cohesive collaborations across multiple traditionally disconnected modeling disciplines to achieve sustainable chemical production. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Dynamics of SU(N) supersymmetric gauge theory
Energy Technology Data Exchange (ETDEWEB)
Douglas, M R [Rutgers - the State Univ., Piscataway, NJ (United States). Dept. of Physics and Astronomy; Shenker, S H [Rutgers - the State Univ., Piscataway, NJ (United States). Dept. of Physics and Astronomy
1995-08-07
We study the physics of the Seiberg-Witten and Argyres-Faraggi-Klemm-Lerche-Theisen-Yankielowicz solutions of D=4, N=2 and N=1 SU(N) supersymmetric gauge theory. The N=1 theory is confining and its effective Lagrangian is a spontaneously broken U(1){sup N-1} abelian gauge theory. We identify some features of its physics which see this internal structure, including a spectrum of different string tensions. We discuss the limit N{yields}{infinity}, identify a scaling regime in which instanton and monopole effects survive, and give exact results for the crossover from weak to strong coupling along a scaling trajectory. We find a large hierarchy of mass scales in the scaling regime, including very light W bosons, and the absence of weak coupling. The light W`s leave a novel imprint on the effective dual magnetic theory. The effective Lagrangian appears to be inadequate to understand the conventional large N limit of the confining N=1 theory. (orig.).
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Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism
Zielinski, Daniel C.; Jamshidi, Neema; Corbett, Austin J.; Bordbar, Aarash; Thomas, Alex; Palsson, Bernhard O.
2017-01-01
Malignant transformation is often accompanied by significant metabolic changes. To identify drivers underlying these changes, we calculated metabolic flux states for the NCI60 cell line collection and correlated the variance between metabolic states of these lines with their other properties. The analysis revealed a remarkably consistent structure underlying high flux metabolism. The three primary uptake pathways, glucose, glutamine and serine, are each characterized by three features: (1) metabolite uptake sufficient for the stoichiometric requirement to sustain observed growth, (2) overflow metabolism, which scales with excess nutrient uptake over the basal growth requirement, and (3) redox production, which also scales with nutrient uptake but greatly exceeds the requirement for growth. We discovered that resistance to chemotherapeutic drugs in these lines broadly correlates with the amount of glucose uptake. These results support an interpretation of the Warburg effect and glutamine addiction as features of a growth state that provides resistance to metabolic stress through excess redox and energy production. Furthermore, overflow metabolism observed may indicate that mitochondrial catabolic capacity is a key constraint setting an upper limit on the rate of cofactor production possible. These results provide a greater context within which the metabolic alterations in cancer can be understood.
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Scale invariant Volkov–Akulov supergravity
Directory of Open Access Journals (Sweden)
S. Ferrara
2015-10-01
Full Text Available A scale invariant goldstino theory coupled to supergravity is obtained as a standard supergravity dual of a rigidly scale-invariant higher-curvature supergravity with a nilpotent chiral scalar curvature. The bosonic part of this theory describes a massless scalaron and a massive axion in a de Sitter Universe.
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Cognition and biology: perspectives from information theory.
Wallace, Rodrick
2014-02-01
The intimate relation between biology and cognition can be formally examined through statistical models constrained by the asymptotic limit theorems of communication theory, augmented by methods from statistical mechanics and nonequilibrium thermodynamics. Cognition, often involving submodules that act as information sources, is ubiquitous across the living state. Less metabolic free energy is consumed by permitting crosstalk between biological information sources than by isolating them, leading to evolutionary exaptations that assemble shifting, tunable cognitive arrays at multiple scales, and levels of organization to meet dynamic patterns of threat and opportunity. Cognition is thus necessary for life, but it is not sufficient: An organism represents a highly patterned outcome of path-dependent, blind, variation, selection, interaction, and chance extinction in the context of an adequate flow of free energy and an environment fit for development. Complex, interacting cognitive processes within an organism both record and instantiate those evolutionary and developmental trajectories.
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International Nuclear Information System (INIS)
Chris Quigg
2001-01-01
After a short essay on the current state of particle physics, the author reviews the antecedents of the modern picture of the weak and electromagnetic interactions and then undertakes a brief survey of the SU(2) L (circle-times) U(1) Y electroweak theory. The authors reviews the features of electroweak phenomenology at tree level and beyond, presents an introduction to the Higgs boson and the 1-TeV scale, and examines arguments for enlarging the electroweak theory. The author concludes with a brief look at low-scale gravity
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The riddle of sex: biological theories of sexual difference in the early twentieth-century.
Ha, Nathan Q
2011-01-01
At the turn of the twentieth century, biologists such as Oscar Riddle, Thomas Hunt Morgan, Frank Lillie, and Richard Goldschmidt all puzzled over the question of sexual difference, the distinction between male and female. They all offered competing explanations for the biological cause of this difference, and engaged in a fierce debate over the primacy of their respective theories. Riddle propounded a metabolic theory of sex dating from the late-nineteenth century suggesting that metabolism lay at the heart of sexual difference. Thomas Hunt Morgan insisted on the priority of chromosomes, Frank Lillie emphasized the importance of hormones, while Richard Goldschmidt supported a mixed model involving both chromosomes and hormones. In this paper, I will illustrate how the older metabolic theory of sex was displaced when those who argued for the relatively newer theories of chromosomes and hormones gradually formed an alliance that accommodated each other and excluded the metabolic theory of sex. By doing so, proponents of chromosomes and hormones established their authority over the question of sexual difference as they laid the foundations for the new disciplines of genetics and endocrinology. Their debate raised urgent questions about what constituted sexual difference, and how scientists envisioned the plasticity and controllability of this difference. These theories also had immediate political and cultural consequences at the turn of the twentieth century, especially for the eugenic and feminist movements, both of which were heavily invested in knowledge of sex and its determination, ascertainment, and command.
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Wilsonian effective action of superstring theory
Energy Technology Data Exchange (ETDEWEB)
Sen, Ashoke [Harish-Chandra Research Institute,Chhatnag Road, Jhusi, Allahabad 211019 (India); Homi Bhabha National Institute,Training School Complex, Anushakti Nagar, Mumbai 400085 (India)
2017-01-25
By integrating out the heavy fields in type II or heterotic string field theory one can construct the effective action for the light fields. This effective theory inherits all the algebraic structures of the parent theory and the effective action automatically satisfies the Batalin-Vilkovisky quantum master equation. This theory is manifestly ultraviolet finite, has only light fields as its explicit degrees of freedom, and the Feynman diagrams of this theory reproduce the exact scattering amplitudes of light states in string theory to any arbitrary order in perturbation theory. Furthermore in this theory the degrees of freedom of light fields above certain energy scale are also implicitly integrated out. This energy scale is determined by a particular parameter labelling a family of equivalent actions, and can be made arbitrarily low, leading to the interpretation of the effective action as the Wilsonian effective action.
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DGDFT: A massively parallel method for large scale density functional theory calculations.
Hu, Wei; Lin, Lin; Yang, Chao
2015-09-28
We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10(-4) Hartree/atom in terms of the error of energy and 6.2 × 10(-4) Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.
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DGDFT: A massively parallel method for large scale density functional theory calculations
International Nuclear Information System (INIS)
Hu, Wei; Yang, Chao; Lin, Lin
2015-01-01
We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10 −4 Hartree/atom in terms of the error of energy and 6.2 × 10 −4 Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail
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DGDFT: A massively parallel method for large scale density functional theory calculations
Energy Technology Data Exchange (ETDEWEB)
Hu, Wei, E-mail: whu@lbl.gov; Yang, Chao, E-mail: cyang@lbl.gov [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Lin, Lin, E-mail: linlin@math.berkeley.edu [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Department of Mathematics, University of California, Berkeley, California 94720 (United States)
2015-09-28
We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10{sup −4} Hartree/atom in terms of the error of energy and 6.2 × 10{sup −4} Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.
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J. de Haan (Hans)
2010-01-01
textabstractThis thesis is a treatise on a theory for societal transitions: pillar theory. Societal transitions are complex processes taking place in complex systems, large-scale, long-term processes in which societal systems radically change the way they are composed and function. Since we all are
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Absolute calibration of the mass scale in the inverse problem of the physical theory of fireballs
Kalenichenko, V. V.
1992-08-01
A method of the absolute calibration of the mass scale is proposed for solving the inverse problem of the physical theory of fireballs. The method is based on data on the masses of fallen meteorites whose fireballs have been photographed in flight. The method can be applied to fireballs whose bodies have not experienced significant fragmentation during their flight in the atmosphere and have kept their shape relatively well. Data on the Lost City and Innisfree meteorites are used to calculate the calibration coefficients.
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DEFF Research Database (Denmark)
Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S.
2017-01-01
analysis, new methods for the effective use of the ever more readily available and abundant -omics data (i.e. transcriptomics, proteomics and metabolomics) are urgently needed.Results: The jQMM library presented here provides an open-source, Python-based framework for modeling internal metabolic fluxes......, it introduces the capability to use C-13 labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale C-13 Metabolic Flux Analysis (2S-C-13 MFA). In addition, the library includes a demonstration of a method that uses proteomics data to produce actionable...... insights to increase biofuel production. Finally, the use of the jQMM library is illustrated through the addition of several Jupyter notebook demonstration files that enhance reproducibility and provide the capability to be adapted to the user's specific needs.Conclusions: jQMM will facilitate the design...
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Energy Technology Data Exchange (ETDEWEB)
Dai, J.C. [College of Mechanical and Electrical Engineering, Central South University, Changsha (China); School of Electromechanical Engineering, Hunan University of Science and Technology, Xiangtan (China); Hu, Y.P.; Liu, D.S. [School of Electromechanical Engineering, Hunan University of Science and Technology, Xiangtan (China); Long, X. [Hara XEMC Windpower Co., Ltd., Xiangtan (China)
2011-03-15
The aerodynamic loads for MW scale horizontal-axis wind turbines are calculated and analyzed in the established coordinate systems which are used to describe the wind turbine. In this paper, the blade element momentum (BEM) theory is employed and some corrections, such as Prandtl and Buhl models, are carried out. Based on the B-L semi-empirical dynamic stall (DS) model, a new modified DS model for NACA63-4xx airfoil is adopted. Then, by combing BEM modified theory with DS model, a set of calculation method of aerodynamic loads for large scale wind turbines is proposed, in which some influence factors such as wind shear, tower, tower and blade vibration are considered. The research results show that the presented dynamic stall model is good enough for engineering purpose; the aerodynamic loads are influenced by many factors such as tower shadow, wind shear, dynamic stall, tower and blade vibration, etc, with different degree; the single blade endures periodical changing loads but the variations of the rotor shaft power caused by the total aerodynamic torque in edgewise direction are very small. The presented study approach of aerodynamic loads calculation and analysis is of the university, and helpful for thorough research of loads reduction on large scale wind turbines. (author)
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Quantum field theory and statistical mechanics
International Nuclear Information System (INIS)
Jegerlehner, F.
1975-01-01
At first a heuristic understanding is given how the relation between quantum field theory and statistical mechanics near phase transitions comes about. A long range scale invariant theory is constructed, critical indices are calculated and the relations among them are proved, field theoretical Kadanoff-scale transformations are formulated and scaling corrections calculated. A precise meaning to many of Kadanoffs considerations and a model matching Wegners phenomenological scheme is given. It is shown, that soft parametrization is most transparent for the discussion of scaling behaviour. (BJ) [de
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Kinetic modeling of cell metabolism for microbial production.
Costa, Rafael S; Hartmann, Andras; Vinga, Susana
2016-02-10
Kinetic models of cellular metabolism are important tools for the rational design of metabolic engineering strategies and to explain properties of complex biological systems. The recent developments in high-throughput experimental data are leading to new computational approaches for building kinetic models of metabolism. Herein, we briefly survey the available databases, standards and software tools that can be applied for kinetic models of metabolism. In addition, we give an overview about recently developed ordinary differential equations (ODE)-based kinetic models of metabolism and some of the main applications of such models are illustrated in guiding metabolic engineering design. Finally, we review the kinetic modeling approaches of large-scale networks that are emerging, discussing their main advantages, challenges and limitations. Copyright © 2015 Elsevier B.V. All rights reserved.
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Flux balance analysis of genome-scale metabolic model of rice ...
Indian Academy of Sciences (India)
2015-09-28
Sep 28, 2015 ... biologists are also trying to understand the plant's systems level biochemistry ... metabolism to observe the effect of intracellular transporters' transport ..... [The information about this pathway and associated genes in .... 2013 A method for accounting for mainte- ... Biological control of rice diseases pp 1–11.
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Mean field theory of EM algorithm for Bayesian grey scale image restoration
International Nuclear Information System (INIS)
Inoue, Jun-ichi; Tanaka, Kazuyuki
2003-01-01
The EM algorithm for the Bayesian grey scale image restoration is investigated in the framework of the mean field theory. Our model system is identical to the infinite range random field Q-Ising model. The maximum marginal likelihood method is applied to the determination of hyper-parameters. We calculate both the data-averaged mean square error between the original image and its maximizer of posterior marginal estimate, and the data-averaged marginal likelihood function exactly. After evaluating the hyper-parameter dependence of the data-averaged marginal likelihood function, we derive the EM algorithm which updates the hyper-parameters to obtain the maximum likelihood estimate analytically. The time evolutions of the hyper-parameters and so-called Q function are obtained. The relation between the speed of convergence of the hyper-parameters and the shape of the Q function is explained from the viewpoint of dynamics
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Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini
2016-01-01
Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.
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Scaling of Advanced Theory-of-Mind Tasks
Osterhaus, Christopher; Koerber, Susanne; Sodian, Beate
2016-01-01
Advanced theory-of-mind (AToM) development was investigated in three separate studies involving 82, 466, and 402 elementary school children (8-, 9-, and 10-year-olds). Rasch and factor analyses assessed whether common conceptual development underlies higher-order false-belief understanding, social understanding, emotion recognition, and…
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Toward city-scale water quality control: building a theory for smart stormwater systems
Kerkez, B.; Mullapudi, A. M.; Wong, B. P.
2016-12-01
Urban stormwater systems are rarely designed as actual systems. Rather, it is often assumed that individual Best Management Practices (BMPs) will add up to achieve desired watershed outcomes. Given the rise of BMPs and green infrastructure, we ask: does doing "best" at the local scale guarantee the "best" at the global scale? Existing studies suggest that the system-level performance of distributed stormwater practices may actually adversely impact watersheds by increasing downstream erosion and reducing water quality. Optimizing spatial placement may not be sufficient, however, since precipitation variability and other sources of uncertainty can drive the overall system into undesirable states. To that end, it is also important to control the temporal behavior of the system, which can be achieved by equipping stormwater elements (ponds, wetlands, basins, bioswales, etc.) with "smart" sensors and valves. Rather than building new infrastructure, this permits for existing assets to be repurposed and controlled to adapt to individual storm events. While we have learned how to build and deploy the necessary sensing and control technologies, we do not have a framework or theory that combines our knowledge of hydrology, hydraulics, water quality and control. We discuss the development of such a framework and investigate how existing water domain knowledge can be transferred into a system-theoretic context to enable real-time, city-scale stormwater control. We apply this framework to water quality control in an urban watershed in southeast Michigan, which has been heavily instrumented and retrofitted for control over the past year.
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Giampietro, Mario; Sorman, Alevgül H
2013-01-01
The vast majority of the countries of the world are now facing an imminent energy crisis, particularly the USA, China, India, Japan and EU countries, but also developing countries having to boost their economic growth precisely when more powerful economies will prevent them from using the limited supply of fossil energy. Despite this crisis, current protocols of energy accounting have been developed for dealing with fossil energy exclusively and are therefore not useful for the analysis of alternative energy sources. The first part of the book illustrates the weakness of existing analyses of energy problems: the science of energy was born and developed neglecting the issue of scale. The authors argue that it is necessary to adopt more complex protocols of accounting and analysis in order to generate robust energy scenarios and effective assessments of the quality of alternative energy sources. The second part of the book introduces the concept of energetic metabolism of modern societies and uses empirical res...
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Generalized probabilistic scale space for image restoration.
Wong, Alexander; Mishra, Akshaya K
2010-10-01
A novel generalized sampling-based probabilistic scale space theory is proposed for image restoration. We explore extending the definition of scale space to better account for both noise and observation models, which is important for producing accurately restored images. A new class of scale-space realizations based on sampling and probability theory is introduced to realize this extended definition in the context of image restoration. Experimental results using 2-D images show that generalized sampling-based probabilistic scale-space theory can be used to produce more accurate restored images when compared with state-of-the-art scale-space formulations, particularly under situations characterized by low signal-to-noise ratios and image degradation.
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Effective quantum field theories
International Nuclear Information System (INIS)
Georgi, H.M.
1993-01-01
The most appropriate description of particle interactions in the language of quantum field theory depends on the energy at which the interactions are studied; the description is in terms of an ''effective field theory'' that contains explicit reference only to those particles that are actually important at the energy being studied. The various themes of the article are: local quantum field theory, quantum electrodynamics, new physics, dimensional parameters and renormalizability, socio-dynamics of particle theory, spontaneously broken gauge theories, scale dependence, grand unified and effective field theories. 2 figs
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Integration of Plant Metabolomics Data with Metabolic Networks: Progresses and Challenges.
Töpfer, Nadine; Seaver, Samuel M D; Aharoni, Asaph
2018-01-01
In the last decade, plant genome-scale modeling has developed rapidly and modeling efforts have advanced from representing metabolic behavior of plant heterotrophic cell suspensions to studying the complex interplay of cell types, tissues, and organs. A crucial driving force for such developments is the availability and integration of "omics" data (e.g., transcriptomics, proteomics, and metabolomics) which enable the reconstruction, extraction, and application of context-specific metabolic networks. In this chapter, we demonstrate a workflow to integrate gas chromatography coupled to mass spectrometry (GC-MS)-based metabolomics data of tomato fruit pericarp (flesh) tissue, at five developmental stages, with a genome-scale reconstruction of tomato metabolism. This method allows for the extraction of context-specific networks reflecting changing activities of metabolic pathways throughout fruit development and maturation.
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A note on finite-scale Navier–Stokes theory: The case of constant viscosity, strictly adiabatic flow
International Nuclear Information System (INIS)
Jordan, P.M.; Keiffer, R.S.
2015-01-01
We investigate the “piston problem” for the case of a viscous, but non-thermally conducting, gas with constant transport coefficients under the recently introduced generalization of the Navier–Stokes (NS) equations known as the finite-scale Navier–Stokes (FSNS) equations. Along with determining and analyzing the integral curves of the resulting kink-type traveling wave solutions (TWS)s, the present study also reveals the importance of the bulk viscosity vis-a-vis this special case of FSNS theory and highlights the impact that averaging has on the structure of the shock profile
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Egberink, Iris J L; Meijer, Rob R
2011-06-01
The authors investigated the psychometric properties of the subscales of the Self-Perception Profile for Children with item response theory (IRT) models using a sample of 611 children. Results from a nonparametric Mokken analysis and a parametric IRT approach for boys (n = 268) and girls (n = 343) were compared. The authors found that most scales formed weak scales and that measurement precision was relatively low and only present for latent trait values indicating low self-perception. The subscales Physical Appearance and Global Self-Worth formed one strong scale. Children seem to interpret Global Self-Worth items as if they measure Physical Appearance. Furthermore, the authors found that strong Mokken scales (such as Global Self-Worth) consisted mostly of items that repeat the same item content. They conclude that researchers should be very careful in interpreting the total scores on the different Self-Perception Profile for Children scales. Finally, implications for further research are discussed.
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Small numbers in supersymmetric theories of nature
International Nuclear Information System (INIS)
Graesser, Michael L.
1999-01-01
The Standard Model of particle interactions is a successful theory for describing the interactions of quarks, leptons and gauge bosons at microscopic distance scales. Despite these successes, the theory contains many unsatisfactory features. The origin of particle masses is a central mystery that has eluded experimental elucidation. In the Standard Model the known particles obtain their mass from the condensate of the so-called Higgs particle. Quantum corrections to the Higgs mass require an unnatural fine tuning in the Higgs mass of one part in 10 -32 to obtain the correct mass scale of electroweak physics. In addition, the origin of the vast hierarchy between the mass scales of the electroweak and quantum gravity physics is not explained in the current theory. Supersymmetric extensions to the Standard Model are not plagued by this fine tuning issue and may therefore be relevant in Nature. In the minimal supersymmetric Standard Model there is also a natural explanation for electroweak symmetry breaking. Supersymmetric Grand Unified Theories also correctly predict a parameter of the Standard Model. This provides non-trivial indirect evidence for these theories. The most general supersymmetric extension to the Standard Model however, is excluded by many physical processes, such as rare flavor changing processes, and the non-observation of the instability of the proton. These processes provide important information about the possible structure such a theory. In particular, certain parameters in this theory must be rather small. A physics explanation for why this is the case would be desirable. It is striking that the gauge couplings of the Standard Model unify if there is supersymmetry close to the weak scale. This suggests that at high energies Nature is described by a supersymmetric Grand Unified Theory. But the mass scale of unification must be introduced into the theory since it does not coincide with the probable mass scale of strong quantum gravity. The subject
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Yuan, H.; Cheung, C.Y. Maurice; Poolman, M.G.; Hilbers, P.A.J.; van Riel, N.A.W.
2016-01-01
Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the
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A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism
Hefzi, Hooman; Ang, Kok Siong; Hanscho, Michael; Bordbar, Aarash; Ruckerbauer, David; Lakshmanan, Meiyappan; Orellana, Camila A.; Baycin-Hizal, Deniz; Huang, Yingxiang; Ley, Daniel; Martinez, Veronica S.; Kyriakopoulos, Sarantos; Jimé nez, Natalia E.; Zielinski, Daniel C.; Quek, Lake-Ee; Wulff, Tune; Arnsdorf, Johnny; Li, Shangzhong; Lee, Jae Seong; Paglia, Giuseppe; Loira, Nicolas; Spahn, Philipp N.; Pedersen, Lasse E.; Gutierrez, Jahir M.; King, Zachary A.; Lund, Anne Mathilde; Nagarajan, Harish; Thomas, Alex; Abdel-Haleem, Alyaa M.; Zanghellini, Juergen; Kildegaard, Helene F.; Voldborg, Bjø rn G.; Gerdtzen, Ziomara P.; Betenbaugh, Michael J.; Palsson, Bernhard O.; Andersen, Mikael R.; Nielsen, Lars K.; Borth, Nicole; Lee, Dong-Yup; Lewis, Nathan E.
2016-01-01
Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess
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Mass corrections in string theory and lattice field theory
International Nuclear Information System (INIS)
Del Debbio, Luigi; Kerrane, Eoin; Russo, Rodolfo
2009-01-01
Kaluza-Klein (KK) compactifications of higher-dimensional Yang-Mills theories contain a number of 4-dimensional scalars corresponding to the internal components of the gauge field. While at tree level the scalar zero modes are massless, it is well known that quantum corrections make them massive. We compute these radiative corrections at 1 loop in an effective field theory framework, using the background field method and proper Schwinger-time regularization. In order to clarify the proper treatment of the sum over KK modes in the effective field theory approach, we consider the same problem in two different UV completions of Yang-Mills: string theory and lattice field theory. In both cases, when the compactification radius R is much bigger than the scale of the UV completion (R>>√(α ' ), a), we recover a mass renormalization that is independent of the UV scale and agrees with the one derived in the effective field theory approach. These results support the idea that the value of the mass corrections is, in this regime, universal for any UV completion that respects locality and gauge invariance. The string analysis suggests that this property holds also at higher loops. The lattice analysis suggests that the mass of the adjoint scalars appearing in N=2, 4 super Yang-Mills is highly suppressed, even if the lattice regularization breaks all supersymmetries explicitly. This is due to an interplay between the higher-dimensional gauge invariance and the degeneracy of bosonic and fermionic degrees of freedom.
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On classification of N=2 supersymmetric theories
International Nuclear Information System (INIS)
Cecotti, S.; Vafa, C.
1993-01-01
We find a relation between the spectrum of solitons of massive N=2 quantum field theories in d=2 and the scaling dimensions of chiral fields at the conformal point. The condition that the scaling dimensions be real imposes restrictions on the soliton numbers and leads to a classification program for symmetric N=2 conformal theories and their massive deformations in terms of a suitable generalization of Dynkin diagrams (which coincides with the A-D-E Dynkin diagrams for minimal models). The Landau-Ginzburg theories are a proper subset of this classification. In the particular case of LG theories we relate the soliton numbers with intersection of vanishing cycles of the corresponding singularity; the relation between soliton numbers and the scaling dimensions in this particular case is a well known application of Picard-Lefschetz theory. (orig.)
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International Nuclear Information System (INIS)
Krasnikov, N.V.
1987-01-01
Nonlocal gauge theories including gravity are considered. It is shown that the introduction of the additional nonlocal interaction makes γ 5 -anomalous theories meaningful. The introduction of such interaction leads to macrocausal unitary theory, which describes the interaction of massive vector fields with fermion fields. It is shown that nonlocal gauge theories with nonlocal scale Λ nl ≤(1-10) TeV can solve the gauge hierarchy problem. An example of nonlinear grand unified gauge model in which topologically nontrivial finite energy monopole solutions are absent is found
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[Modeling continuous scaling of NDVI based on fractal theory].
Luan, Hai-Jun; Tian, Qing-Jiu; Yu, Tao; Hu, Xin-Li; Huang, Yan; Du, Ling-Tong; Zhao, Li-Min; Wei, Xi; Han, Jie; Zhang, Zhou-Wei; Li, Shao-Peng
2013-07-01
Scale effect was one of the very important scientific problems of remote sensing. The scale effect of quantitative remote sensing can be used to study retrievals' relationship between different-resolution images, and its research became an effective way to confront the challenges, such as validation of quantitative remote sensing products et al. Traditional up-scaling methods cannot describe scale changing features of retrievals on entire series of scales; meanwhile, they are faced with serious parameters correction issues because of imaging parameters' variation of different sensors, such as geometrical correction, spectral correction, etc. Utilizing single sensor image, fractal methodology was utilized to solve these problems. Taking NDVI (computed by land surface radiance) as example and based on Enhanced Thematic Mapper Plus (ETM+) image, a scheme was proposed to model continuous scaling of retrievals. Then the experimental results indicated that: (a) For NDVI, scale effect existed, and it could be described by fractal model of continuous scaling; (2) The fractal method was suitable for validation of NDVI. All of these proved that fractal was an effective methodology of studying scaling of quantitative remote sensing.
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Evolution of metabolic network organization
Directory of Open Access Journals (Sweden)
Bonchev Danail
2010-05-01
Full Text Available Abstract Background Comparison of metabolic networks across species is a key to understanding how evolutionary pressures shape these networks. By selecting taxa representative of different lineages or lifestyles and using a comprehensive set of descriptors of the structure and complexity of their metabolic networks, one can highlight both qualitative and quantitative differences in the metabolic organization of species subject to distinct evolutionary paths or environmental constraints. Results We used a novel representation of metabolic networks, termed network of interacting pathways or NIP, to focus on the modular, high-level organization of the metabolic capabilities of the cell. Using machine learning techniques we identified the most relevant aspects of cellular organization that change under evolutionary pressures. We considered the transitions from prokarya to eukarya (with a focus on the transitions among the archaea, bacteria and eukarya, from unicellular to multicellular eukarya, from free living to host-associated bacteria, from anaerobic to aerobic, as well as the acquisition of cell motility or growth in an environment of various levels of salinity or temperature. Intuitively, we expect organisms with more complex lifestyles to have more complex and robust metabolic networks. Here we demonstrate for the first time that such organisms are not only characterized by larger, denser networks of metabolic pathways but also have more efficiently organized cross communications, as revealed by subtle changes in network topology. These changes are unevenly distributed among metabolic pathways, with specific categories of pathways being promoted to more central locations as an answer to environmental constraints. Conclusions Combining methods from graph theory and machine learning, we have shown here that evolutionary pressures not only affects gene and protein sequences, but also specific details of the complex wiring of functional modules
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An Asymptotic Derivation of Weakly Nonlinear Ray Theory
Indian Academy of Sciences (India)
The transport equation for the amplitude has been deduced with an error (2) where is the small parameter appearing in the high frequency approximation. On a length scale over which Choquet–Bruhat's theory is valid, this theory reduces to the former. The theory is valid on a much larger length scale and the leading ...
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Phase space properties of local observables and structure of scaling limits
International Nuclear Information System (INIS)
Buchholz, D.
1995-05-01
For any given algebra of local observables in relativistic quantum field theory there exists an associated scaling algebra which permits one to introduce renormalization group transformations and to construct the scaling (short distance) limit of the theory. On the basis of this result it is discussed how the phase space properties of a theory determine the structure of its scaling limit. Bounds on the number of local degrees of freedom appearing in the scaling limit are given which allow one to distinguish between theories with classical and quantum scaling limits. The results can also be used to establish physically significant algebraic properties of the scaling limit theories, such as the split property. (orig.)
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Roch, Loïc M; Baldridge, Kim K
2018-02-07
Correction for 'General optimization procedure towards the design of a new family of minimal parameter spin-component-scaled double-hybrid density functional theory' by Loïc M. Roch and Kim K. Baldridge, Phys. Chem. Chem. Phys., 2017, 19, 26191-26200.
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Peterson, Candida C.; Wellman, Henry M.
2009-01-01
We examined deaf and hearing children’s progression of steps in theory-of-mind (ToM) development including their understanding of social pretending. Ninety-three children (33 deaf; 60 hearing) aged 3 to 13 years were tested on a set of six closely-matched ToM tasks. Results showed that deaf children were delayed substantially behind hearing children in understanding pretending, false belief and other ToM concepts, in line with their delayed uptake of social pretend play. By using a scaling me...
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Tassé, Marc J.; Schalock, Robert L.; Thissen, David; Balboni, Giulia; Bersani, Henry, Jr.; Borthwick-Duffy, Sharon A.; Spreat, Scott; Widaman, Keith F.; Zhang, Dalun; Navas, Patricia
2016-01-01
The Diagnostic Adaptive Behavior Scale (DABS) was developed using item response theory (IRT) methods and was constructed to provide the most precise and valid adaptive behavior information at or near the cutoff point of making a decision regarding a diagnosis of intellectual disability. The DABS initial item pool consisted of 260 items. Using IRT…
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Deep inelastic scattering in an asymptotically free gauge theory
International Nuclear Information System (INIS)
Fujiwara, Tsutomu
1977-01-01
This paper reviews the success of the asymptotically free gauge theory which describes the deep inelastic lepton-hadron scattering. The asymptotically free gauge theory was discussed as well as the reason why the parton has the nature like free particles by the aid of the field theory. The asymptotically free gauge theory (AFGT) gives the prediction that the Bjorken scaling gives rise to logarithmic violation. The theory was applied to the exchange processes of single photon and two photons. First, this paper describes the approaches to the Bjorken scaling. The approaches are the discussion of the scaling law dependent on the model and the discussion of the scaling law independent of the model. The field theoretical treatment in described. This is called the method of the renormalization group introduced by Wilson. The asymptotically free gauge theory was formed on the basis of the Callan-Symanzik equation (CSE) and of the Weinberg's power counting theorem. The exact Bjorken scaling does not hold in the quantum field theory, at least there must be logarithmic violation. The pattern of the scaling violation cannot be clarified by the present data. Discussions concerning two gamma process are presented. The measurement of the photon-photon scattering process will give the judgement whether the prediction of the AFGT is correct or not. (Kato, T.)
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Asakura, Nobuhiko; Inui, Toshio
2016-01-01
Two apparently contrasting theories have been proposed to account for the development of children's theory of mind (ToM): theory-theory and simulation theory. We present a Bayesian framework that rationally integrates both theories for false belief reasoning. This framework exploits two internal models for predicting the belief states of others: one of self and one of others. These internal models are responsible for simulation-based and theory-based reasoning, respectively. The framework further takes into account empirical studies of a developmental ToM scale (e.g., Wellman and Liu, 2004): developmental progressions of various mental state understandings leading up to false belief understanding. By representing the internal models and their interactions as a causal Bayesian network, we formalize the model of children's false belief reasoning as probabilistic computations on the Bayesian network. This model probabilistically weighs and combines the two internal models and predicts children's false belief ability as a multiplicative effect of their early-developed abilities to understand the mental concepts of diverse beliefs and knowledge access. Specifically, the model predicts that children's proportion of correct responses on a false belief task can be closely approximated as the product of their proportions correct on the diverse belief and knowledge access tasks. To validate this prediction, we illustrate that our model provides good fits to a variety of ToM scale data for preschool children. We discuss the implications and extensions of our model for a deeper understanding of developmental progressions of children's ToM abilities.
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Directory of Open Access Journals (Sweden)
Andrew T Tredennick
Full Text Available Theoretical models of allometric scaling provide frameworks for understanding and predicting how and why the morphology and function of organisms vary with scale. It remains unclear, however, if the predictions of 'universal' scaling models for vascular plants hold across diverse species in variable environments. Phenomena such as competition and disturbance may drive allometric scaling relationships away from theoretical predictions based on an optimized tree. Here, we use a hierarchical Bayesian approach to calculate tree-specific, species-specific, and 'global' (i.e. interspecific scaling exponents for several allometric relationships using tree- and branch-level data harvested from three savanna sites across a rainfall gradient in Mali, West Africa. We use these exponents to provide a rigorous test of three plant scaling models (Metabolic Scaling Theory (MST, Geometric Similarity, and Stress Similarity in savanna systems. For the allometric relationships we evaluated (diameter vs. length, aboveground mass, stem mass, and leaf mass the empirically calculated exponents broadly overlapped among species from diverse environments, except for the scaling exponents for length, which increased with tree cover and density. When we compare empirical scaling exponents to the theoretical predictions from the three models we find MST predictions are most consistent with our observed allometries. In those situations where observations are inconsistent with MST we find that departure from theory corresponds with expected tradeoffs related to disturbance and competitive interactions. We hypothesize savanna trees have greater length-scaling exponents than predicted by MST due to an evolutionary tradeoff between fire escape and optimization of mechanical stability and internal resource transport. Future research on the drivers of systematic allometric variation could reconcile the differences between observed scaling relationships in variable ecosystems and
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Symmetry-guided large-scale shell-model theory
Czech Academy of Sciences Publication Activity Database
Launey, K. D.; Dytrych, Tomáš; Draayer, J. P.
2016-01-01
Roč. 89, JUL (2016), s. 101-136 ISSN 0146-6410 R&D Projects: GA ČR GA16-16772S Institutional support: RVO:61389005 Keywords : Ab intio shell -model theory * Symplectic symmetry * Collectivity * Clusters * Hoyle state * Orderly patterns in nuclei from first principles Subject RIV: BE - Theoretical Physics Impact factor: 11.229, year: 2016
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Ghanbarian, Behzad; Berg, Carl F.
2017-09-01
Accurate quantification of formation resistivity factor F (also called formation factor) provides useful insight into connectivity and pore space topology in fully saturated porous media. In particular the formation factor has been extensively used to estimate permeability in reservoir rocks. One of the widely applied models to estimate F is Archie's law (F = ϕ- m in which ϕ is total porosity and m is cementation exponent) that is known to be valid in rocks with negligible clay content, such as clean sandstones. In this study we compare formation factors determined by percolation and effective-medium theories as well as Archie's law with numerical simulations of electrical resistivity on digital rock models. These digital models represent Bentheimer and Fontainebleau sandstones and are derived either by reconstruction or directly from micro-tomographic images. Results show that the universal quadratic power law from percolation theory accurately estimates the calculated formation factor values in network models over the entire range of porosity. However, it crosses over to the linear scaling from the effective-medium approximation at the porosity of 0.75 in grid models. We also show that the effect of critical porosity, disregarded in Archie's law, is nontrivial, and the Archie model inaccurately estimates the formation factor in low-porosity homogeneous sandstones.
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Evolutionary programming as a platform for in silico metabolic engineering
Directory of Open Access Journals (Sweden)
Förster Jochen
2005-12-01
Full Text Available Abstract Background Through genetic engineering it is possible to introduce targeted genetic changes and hereby engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, owing to the complexity of metabolic networks, both in terms of structure and regulation, it is often difficult to predict the effects of genetic modifications on the resulting phenotype. Recently genome-scale metabolic models have been compiled for several different microorganisms where structural and stoichiometric complexity is inherently accounted for. New algorithms are being developed by using genome-scale metabolic models that enable identification of gene knockout strategies for obtaining improved phenotypes. However, the problem of finding optimal gene deletion strategy is combinatorial and consequently the computational time increases exponentially with the size of the problem, and it is therefore interesting to develop new faster algorithms. Results In this study we report an evolutionary programming based method to rapidly identify gene deletion strategies for optimization of a desired phenotypic objective function. We illustrate the proposed method for two important design parameters in industrial fermentations, one linear and other non-linear, by using a genome-scale model of the yeast Saccharomyces cerevisiae. Potential metabolic engineering targets for improved production of succinic acid, glycerol and vanillin are identified and underlying flux changes for the predicted mutants are discussed. Conclusion We show that evolutionary programming enables solving large gene knockout problems in relatively short computational time. The proposed algorithm also allows the optimization of non-linear objective functions or incorporation of non-linear constraints and additionally provides a family of close to optimal solutions. The identified metabolic engineering strategies suggest that non-intuitive genetic modifications span
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Generalized uncertainty principle as a consequence of the effective field theory
Energy Technology Data Exchange (ETDEWEB)
Faizal, Mir, E-mail: mirfaizalmir@gmail.com [Irving K. Barber School of Arts and Sciences, University of British Columbia – Okanagan, Kelowna, British Columbia V1V 1V7 (Canada); Department of Physics and Astronomy, University of Lethbridge, Lethbridge, Alberta T1K 3M4 (Canada); Ali, Ahmed Farag, E-mail: ahmed.ali@fsc.bu.edu.eg [Department of Physics, Faculty of Science, Benha University, Benha, 13518 (Egypt); Netherlands Institute for Advanced Study, Korte Spinhuissteeg 3, 1012 CG Amsterdam (Netherlands); Nassar, Ali, E-mail: anassar@zewailcity.edu.eg [Department of Physics, Zewail City of Science and Technology, 12588, Giza (Egypt)
2017-02-10
We will demonstrate that the generalized uncertainty principle exists because of the derivative expansion in the effective field theories. This is because in the framework of the effective field theories, the minimum measurable length scale has to be integrated away to obtain the low energy effective action. We will analyze the deformation of a massive free scalar field theory by the generalized uncertainty principle, and demonstrate that the minimum measurable length scale corresponds to a second more massive scale in the theory, which has been integrated away. We will also analyze CFT operators dual to this deformed scalar field theory, and observe that scaling of the new CFT operators indicates that they are dual to this more massive scale in the theory. We will use holographic renormalization to explicitly calculate the renormalized boundary action with counter terms for this scalar field theory deformed by generalized uncertainty principle, and show that the generalized uncertainty principle contributes to the matter conformal anomaly.
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Generalized uncertainty principle as a consequence of the effective field theory
Directory of Open Access Journals (Sweden)
Mir Faizal
2017-02-01
Full Text Available We will demonstrate that the generalized uncertainty principle exists because of the derivative expansion in the effective field theories. This is because in the framework of the effective field theories, the minimum measurable length scale has to be integrated away to obtain the low energy effective action. We will analyze the deformation of a massive free scalar field theory by the generalized uncertainty principle, and demonstrate that the minimum measurable length scale corresponds to a second more massive scale in the theory, which has been integrated away. We will also analyze CFT operators dual to this deformed scalar field theory, and observe that scaling of the new CFT operators indicates that they are dual to this more massive scale in the theory. We will use holographic renormalization to explicitly calculate the renormalized boundary action with counter terms for this scalar field theory deformed by generalized uncertainty principle, and show that the generalized uncertainty principle contributes to the matter conformal anomaly.
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Directory of Open Access Journals (Sweden)
Hong Yang
2014-09-01
Full Text Available Transposon mutagenesis, in combination with parallel sequencing, is becoming a powerful tool for en-masse mutant analysis. A probability generating function was used to explain observed miniHimar transposon insertion patterns, and gene essentiality calls were made by transposon insertion frequency analysis (TIFA. TIFA incorporated the observed genome and sequence motif bias of the miniHimar transposon. The gene essentiality calls were compared to: 1 previous genome-wide direct gene-essentiality assignments; and, 2 flux balance analysis (FBA predictions from an existing genome-scale metabolic model of Shewanella oneidensis MR-1. A three-way comparison between FBA, TIFA, and the direct essentiality calls was made to validate the TIFA approach. The refinement in the interpretation of observed transposon insertions demonstrated that genes without insertions are not necessarily essential, and that genes that contain insertions are not always nonessential. The TIFA calls were in reasonable agreement with direct essentiality calls for S. oneidensis, but agreed more closely with E. coli essentiality calls for orthologs. The TIFA gene essentiality calls were in good agreement with the MR-1 FBA essentiality predictions, and the agreement between TIFA and FBA predictions was substantially better than between the FBA and the direct gene essentiality predictions.
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Recent developments in the theory of critical phenomena
International Nuclear Information System (INIS)
Schroer, B.
1974-01-01
The work of Kadanoff, Wilson and Wegner, in the language of Euclidian field theory, is revised. In addition to Wilson's renormalization group method, which is based on the idea of eliminating short range fluctuations, the renormalization method of quantum field theory is discussed, which, in the present context, is called reparametrization (in order to avoid confusion). A reparametrization which is of particular interest in the theory of critical phenomena is the one which leads to scaling equations. New scaling equations which remain free of infrared divergences in two and three dimensions, are derived. The method allows a rather compact and unified discussion of Kadanoff's scaling laws and the related concept of global scaling fields, as well as the scale invariant correlation functions [pt
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Klok, C J; Chown, S L
2005-07-01
The influence of temperature on metabolic rate and characteristics of the gas exchange patterns of flightless, sub-Antarctic Ectemnorhinus-group species from Heard and Marion islands was investigated. All of the species showed cyclic gas exchange with no Flutter period, indicating that these species are not characterized by discontinuous gas exchange cycles. Metabolic rate estimates were substantially lower in this study than in a previous one of a subset of the species, demonstrating that open-system respirometry methods provide more representative estimates of standard metabolic rate than do many closed-system methods. We recommend that the latter, and especially constant-pressure methods, either be abandoned for estimates of standard metabolic rate in insects, or have their outputs subject to careful scrutiny, given the wide availability of the former. V(.)CO(2) increase with an increase in temperature (range: 0-15 degrees C) was modulated by an increase in cycle frequency, but typically not by an increase in burst volume. Previous investigations of temperature-related changes in cyclic gas exchange (both cyclic and discontinuous) in several other insect species were therefore substantiated. Interspecific mass-scaling of metabolic rate (ca. 0.466-0.573, excluding and including phylogenetic non-independence, respectively) produced an exponent lower than 0.75 (but not distinguishable from it or from 0.67). The increase of metabolic rate with mass was modulated by an increase in burst volume and not by a change in cycle frequency, in keeping with investigations of species showing discontinuous gas exchange. These findings are discussed in the context of the emerging macrophysiological metabolic theory of ecology.
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Integrating Cellular Metabolism into a Multiscale Whole-Body Model
Krauss, Markus; Schaller, Stephan; Borchers, Steffen; Findeisen, Rolf; Lippert, Jörg; Kuepfer, Lars
2012-01-01
Cellular metabolism continuously processes an enormous range of external compounds into endogenous metabolites and is as such a key element in human physiology. The multifaceted physiological role of the metabolic network fulfilling the catalytic conversions can only be fully understood from a whole-body perspective where the causal interplay of the metabolic states of individual cells, the surrounding tissue and the whole organism are simultaneously considered. We here present an approach relying on dynamic flux balance analysis that allows the integration of metabolic networks at the cellular scale into standardized physiologically-based pharmacokinetic models at the whole-body level. To evaluate our approach we integrated a genome-scale network reconstruction of a human hepatocyte into the liver tissue of a physiologically-based pharmacokinetic model of a human adult. The resulting multiscale model was used to investigate hyperuricemia therapy, ammonia detoxification and paracetamol-induced toxication at a systems level. The specific models simultaneously integrate multiple layers of biological organization and offer mechanistic insights into pathology and medication. The approach presented may in future support a mechanistic understanding in diagnostics and drug development. PMID:23133351
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Cohen, M. J.; Reijo, C. J.; Hensley, R. T.
2017-12-01
Riverine processing of nutrients and carbon is a local process, subject to heterogeneity in sediment, biotic, insolation, and flow velocity drivers. Measurements at the reach scale aggregate across riverscapes, limiting their utility for enumerating these drivers, and thus for scaling to river networks. Using a combination of in situ sensors that sample water chemistry at high temporal resolution and open benthic chambers that isolate the biogeochemical impacts of a small footprint of benthic surface area, we explored controls on metabolism and nutrient cycling. We specifically sought to answer two questions. First, what are the controls on primary production, with a particular emphasis on the relative roles of light vs. nutrient limitation? Second, what are the pathways of nutrient retention, and do the reaction kinetics of these different pathways differ? We demonstrate the considerable utility of these benthic chambers, reasoning that they provide experimental units for river processes that are not attainable at the reach or network scale. Specifically, in addition to their ability to sample the heterogeneity of the river bed as well as observe nutrient depletion to create concentrations well below ambient levels, they enable manipulative experiments (e.g., nutrient enrichment, light reduction, grazer adjustments) while retaining key elements of the natural system. Across several of Florida's spring-fed river sites, our results strongly support the primacy of light limitation of primary production, with very little evidence of any incremental effects of nutrient enrichment. Nutrient depletion assays further support the dominance of two N retention mechanisms (denitrification and assimilation), the kinetics of which differ markedly, with denitrification exhibiting nearly first-order reactions, and assimilation following zero-order or Michaelis-Menten kinetics over the range of observed concentrations. This latter result helps explain the absence of strong
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New paradigms for metabolic modeling of human cells
DEFF Research Database (Denmark)
Mardinoglu, Adil; Nielsen, Jens
2015-01-01
review recent work on reconstruction of GEMs for human cell/tissue types and cancer, and the use of GEMs for identification of metabolic changes occurring in response to disease development. We further discuss how GEMs can be used for the development of efficient therapeutic strategies. Finally......, challenges in integration of cell/tissue models for simulation of whole body functions as well as integration of GEMs with other biological networks for generating complete cell/tissue models are presented.......Abnormalities in cellular functions are associated with the progression of human diseases, often resulting in metabolic reprogramming. GEnome-scale metabolic Models (GEMs) have enabled studying global metabolic reprogramming in connection with disease development in a systematic manner. Here we...
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Falk, C.; And Others
The development of the Maslowian Scale, a method of revealing a picture of one's needs and concerns based on Abraham Maslow's levels of self-actualization, is described. This paper also explains how the scale is supported by the theories of L. Kohlberg, C. Rogers, and T. Rusk. After a literature search, a list of statements was generated…
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Reimonn, Thomas M; Park, Seo-Young; Agarabi, Cyrus D; Brorson, Kurt A; Yoon, Seongkyu
2016-09-01
Genome-scale flux balance analysis (FBA) is a powerful systems biology tool to characterize intracellular reaction fluxes during cell cultures. FBA estimates intracellular reaction rates by optimizing an objective function, subject to the constraints of a metabolic model and media uptake/excretion rates. A dynamic extension to FBA, dynamic flux balance analysis (DFBA), can calculate intracellular reaction fluxes as they change during cell cultures. In a previous study by Read et al. (2013), a series of informed amino acid supplementation experiments were performed on twelve parallel murine hybridoma cell cultures, and this data was leveraged for further analysis (Read et al., Biotechnol Prog. 2013;29:745-753). In order to understand the effects of media changes on the model murine hybridoma cell line, a systems biology approach is applied in the current study. Dynamic flux balance analysis was performed using a genome-scale mouse metabolic model, and multivariate data analysis was used for interpretation. The calculated reaction fluxes were examined using partial least squares and partial least squares discriminant analysis. The results indicate media supplementation increases product yield because it raises nutrient levels extending the growth phase, and the increased cell density allows for greater culture performance. At the same time, the directed supplementation does not change the overall metabolism of the cells. This supports the conclusion that product quality, as measured by glycoform assays, remains unchanged because the metabolism remains in a similar state. Additionally, the DFBA shows that metabolic state varies more at the beginning of the culture but less by the middle of the growth phase, possibly due to stress on the cells during inoculation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1163-1173, 2016. © 2016 American Institute of Chemical Engineers.
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Directory of Open Access Journals (Sweden)
Kim Hyun
2011-12-01
Full Text Available Abstract Background Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. Results We herein introduce a framework for network modularization and Bayesian network analysis (FMB to investigate organism’s metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. Conclusions After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis.
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Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup
2011-01-01
Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism's metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis.
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Dynamics of Storage Carbohydrates Metabolism in Saccharomyces cerevisiae
Suarez-Mendez, C.A.
2015-01-01
Production of chemicals via biotechnological routes are becoming rapidly an alternative to oil-based processes. Several microorganisms including yeast, bacteria, fungi and algae can transform feedstocks into high-value molecules at industrial scale. Improvement of the bioprocess performance is a key factor for making this technology economically feasible. Despite the vast knowledge on microbial metabolism, some gaps still remain open. In Saccharomyces cerevisiae, metabolism of storage carbohy...
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Causality violations in Lovelock theories
Brustein, Ram; Sherf, Yotam
2018-04-01
Higher-derivative gravity theories, such as Lovelock theories, generalize Einstein's general relativity (GR). Modifications to GR are expected when curvatures are near Planckian and appear in string theory or supergravity. But can such theories describe gravity on length scales much larger than the Planck cutoff length scale? Here we find causality constraints on Lovelock theories that arise from the requirement that the equations of motion (EOM) of perturbations be hyperbolic. We find a general expression for the "effective metric" in field space when Lovelock theories are perturbed around some symmetric background solution. In particular, we calculate explicitly the effective metric for a general Lovelock theory perturbed around cosmological Friedman-Robertson-Walker backgrounds and for some specific cases when perturbed around Schwarzschild-like solutions. For the EOM to be hyperbolic, the effective metric needs to be Lorentzian. We find that, unlike for GR, the effective metric is generically not Lorentzian when the Lovelock modifications are significant. So, we conclude that Lovelock theories can only be considered as perturbative extensions of GR and not as truly modified theories of gravity. We compare our results to those in the literature and find that they agree with and reproduce the results of previous studies.
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DEFF Research Database (Denmark)
Brochado, Ana Rita
processes. Metabolism is an extensively studied and characterised subcellular system, for which several modeling approaches have been proposed over the last 20 years. Nowadays, stoichiometric modeling of metabolism is done at the genome scale and it has diverse applications, many of them for helping....... This chapter aims at providing the reader with relevant state-of-the-art information concerning Systems Biology, Genome-Scale Metabolic Modeling and Metabolic Engineering. Particular attention is given to the yeast Saccharomyces cerevisiae, the eukaryotic model organism used thought the thesis.......A holistic view of the cell is fundamental for gaining insights into genotype to phenotype relationships. Systems Biology is a discipline within Biology, which uses such holistic approach by focusing on the development and application of tools for studying the structure and dynamics of cellular...
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Directory of Open Access Journals (Sweden)
M.F. Holovko
2017-12-01
Full Text Available The scaled particle theory is developed for the description of thermodynamical properties of a mixture of hard spheres and hard spherocylinders. Analytical expressions for free energy, pressure and chemical potentials are derived. From the minimization of free energy, a nonlinear integral equation for the orientational singlet distribution function is formulated. An isotropic-nematic phase transition in this mixture is investigated from the bifurcation analysis of this equation. It is shown that with an increase of concentration of hard spheres, the total packing fraction of a mixture on phase boundaries slightly increases. The obtained results are compared with computer simulations data.
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Smith, Robert W; van Rosmalen, Rik P; Martins Dos Santos, Vitor A P; Fleck, Christian
2018-06-19
Models of metabolism are often used in biotechnology and pharmaceutical research to identify drug targets or increase the direct production of valuable compounds. Due to the complexity of large metabolic systems, a number of conclusions have been drawn using mathematical methods with simplifying assumptions. For example, constraint-based models describe changes of internal concentrations that occur much quicker than alterations in cell physiology. Thus, metabolite concentrations and reaction fluxes are fixed to constant values. This greatly reduces the mathematical complexity, while providing a reasonably good description of the system in steady state. However, without a large number of constraints, many different flux sets can describe the optimal model and we obtain no information on how metabolite levels dynamically change. Thus, to accurately determine what is taking place within the cell, finer quality data and more detailed models need to be constructed. In this paper we present a computational framework, DMPy, that uses a network scheme as input to automatically search for kinetic rates and produce a mathematical model that describes temporal changes of metabolite fluxes. The parameter search utilises several online databases to find measured reaction parameters. From this, we take advantage of previous modelling efforts, such as Parameter Balancing, to produce an initial mathematical model of a metabolic pathway. We analyse the effect of parameter uncertainty on model dynamics and test how recent flux-based model reduction techniques alter system properties. To our knowledge this is the first time such analysis has been performed on large models of metabolism. Our results highlight that good estimates of at least 80% of the reaction rates are required to accurately model metabolic systems. Furthermore, reducing the size of the model by grouping reactions together based on fluxes alters the resulting system dynamics. The presented pipeline automates the
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Modifications of Einstein's theory of gravity at large distances
2015-01-01
In the last few years modified gravity theories have been proposed as extensions of Einstein's theory of gravity. Their main motivation is to explain the latest cosmological and astrophysical data on dark energy and dark matter. The study of general relativity at small scales has already produced important results (cf e.g. LNP 863 Quantum Gravity and Quantum Cosmology) while its study at large scales is challenging because recent and upcoming observational results will provide important information on the validity of these modified theories. In this volume, various aspects of modified gravity at large scales will be discussed: high-curvature gravity theories; general scalar-tensor theories; Galileon theories and their cosmological applications; F(R) gravity theories; massive, new massive and topologically massive gravity; Chern-Simons modifications of general relativity (including holographic variants) and higher-spin gravity theories, to name but a few of the most important recent developments. Edite...
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International Nuclear Information System (INIS)
Maggiore, Michele; Riotto, Antonio
2010-01-01
A classic method for computing the mass function of dark matter halos is provided by excursion set theory, where density perturbations evolve stochastically with the smoothing scale, and the problem of computing the probability of halo formation is mapped into the so-called first-passage time problem in the presence of a barrier. While the full dynamical complexity of halo formation can only be revealed through N-body simulations, excursion set theory provides a simple analytic framework for understanding various aspects of this complex process. In this series of papers we propose improvements of both technical and conceptual aspects of excursion set theory, and we explore up to which point the method can reproduce quantitatively the data from N-body simulations. In Paper I of the series, we show how to derive excursion set theory from a path integral formulation. This allows us both to derive rigorously the absorbing barrier boundary condition, that in the usual formulation is just postulated, and to deal analytically with the non-Markovian nature of the random walk. Such a non-Markovian dynamics inevitably enters when either the density is smoothed with filters such as the top-hat filter in coordinate space (which is the only filter associated with a well-defined halo mass) or when one considers non-Gaussian fluctuations. In these cases, beside 'Markovian' terms, we find 'memory' terms that reflect the non-Markovianity of the evolution with the smoothing scale. We develop a general formalism for evaluating perturbatively these non-Markovian corrections, and in this paper we perform explicitly the computation of the halo mass function for Gaussian fluctuations, to first order in the non-Markovian corrections due to the use of a top-hat filter in coordinate space. In Paper II of this series we propose to extend excursion set theory by treating the critical threshold for collapse as a stochastic variable, which better captures some of the dynamical complexity of the
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Eringen, A Cemal
1999-01-01
Microcontinuum field theories constitute an extension of classical field theories -- of elastic bodies, deformations, electromagnetism, and the like -- to microscopic spaces and short time scales. Material bodies are here viewed as collections of large numbers of deformable particles, much as each volume element of a fluid in statistical mechanics is viewed as consisting of a large number of small particles for which statistical laws are valid. Classical continuum theories are valid when the characteristic length associated with external forces or stimuli is much larger than any internal scale of the body under consideration. When the characteristic lengths are comparable, however, the response of the individual constituents becomes important, for example, in considering the fluid or elastic properties of blood, porous media, polymers, liquid crystals, slurries, and composite materials. This volume is concerned with the kinematics of microcontinua. It begins with a discussion of strain, stress tensors, balanc...