CoRoT-2b: a Tidally Inflated, Young Exoplanet?

NASA Astrophysics Data System (ADS)

Guillot, Tristan; Havel, M.

2009-09-01

CoRoT-2b is among the most anomalously large transiting exoplanet known. Due to its large mass (3.3 Mjup), its large radius ( 1.5 Rjup) cannot be explained by standard evolution models. Recipes that work for other anomalously large exoplanets (e.g. HD209458b), such as invoking kinetic energy transport in the planetary interior or increased opacities, clearly fail for CoRoT-2b. Interestingly, the planet's parent star is an active star with a large fraction (7 to 20%) of spots and a rapid rotation (4.5 days). We first model the star's evolution to accurately constrain the planetary parameters. We find that the stellar activity has little influence on the star's evolution and inferred parameters. However, stellar evolution models point towards two kind of solutions for the star-planet system: (i) a very young system (20-40 Ma) with a star still undergoing pre-main sequence contraction, and a planet which could have a radius as low as 1.4 Rjup, or (ii) a young main-sequence star (40 to 500 Ma) with a planet that is slightly more inflated ( 1.5 Rjup). In either case, planetary evolution models require a significant added internal energy to explain the inferred planet size: from a minimum of 3x1028 erg/s in case (i), to up to 1.5x1029 erg/s in case (ii). We find that evolution models consistently including planet/star tides are able to reproduce the inferred radius but only for a short period of time ( 10 Ma). This points towards a young age for the star/planet system and dissipation by tides due to either circularization or synchronization of the planet. Additional observations of the star (infrared excess due to disk?) and of the planet (precise Rossiter effect, IR secondary eclispe) would be highly valuable to understand the early evolution of star-exoplanet systems.

Mesoscale analysis of failure in quasi-brittle materials: comparison between lattice model and acoustic emission data.

PubMed

Grégoire, David; Verdon, Laura; Lefort, Vincent; Grassl, Peter; Saliba, Jacqueline; Regoin, Jean-Pierre; Loukili, Ahmed; Pijaudier-Cabot, Gilles

2015-10-25

The purpose of this paper is to analyse the development and the evolution of the fracture process zone during fracture and damage in quasi-brittle materials. A model taking into account the material details at the mesoscale is used to describe the failure process at the scale of the heterogeneities. This model is used to compute histograms of the relative distances between damaged points. These numerical results are compared with experimental data, where the damage evolution is monitored using acoustic emissions. Histograms of the relative distances between damage events in the numerical calculations and acoustic events in the experiments exhibit good agreement. It is shown that the mesoscale model provides relevant information from the point of view of both global responses and the local failure process. © 2015 The Authors. International Journal for Numerical and Analytical Methods in Geomechanics published by John Wiley & Sons Ltd.

Fingering in a channel and tripolar Loewner evolutions.

PubMed

Durán, Miguel A; Vasconcelos, Giovani L

2011-11-01

A class of Laplacian growth models in the channel geometry is studied using the formalism of tripolar Loewner evolutions, in which three points, namely, the channel corners and the point at infinity, are kept fixed. Initially, the problem of fingered growth, where growth takes place only at the tips of slitlike fingers, is revisited and a class of exact solutions of the corresponding Loewner equation is presented for the case of stationary driving functions. A model for interface growth is then formulated in terms of a generalized tripolar Loewner equation and several examples are presented. It is shown that the growing interface evolves into a steadily moving finger and that tip competition arises for nonsymmetric initial configurations with multiple tips.

Fingering in a channel and tripolar Loewner evolutions

NASA Astrophysics Data System (ADS)

Durán, Miguel A.; Vasconcelos, Giovani L.

2011-11-01

A class of Laplacian growth models in the channel geometry is studied using the formalism of tripolar Loewner evolutions, in which three points, namely, the channel corners and the point at infinity, are kept fixed. Initially, the problem of fingered growth, where growth takes place only at the tips of slitlike fingers, is revisited and a class of exact solutions of the corresponding Loewner equation is presented for the case of stationary driving functions. A model for interface growth is then formulated in terms of a generalized tripolar Loewner equation and several examples are presented. It is shown that the growing interface evolves into a steadily moving finger and that tip competition arises for nonsymmetric initial configurations with multiple tips.

Application of biomarkers in cancer risk management: evaluation from stochastic clonal evolutionary and dynamic system optimization points of view.

PubMed

Li, Xiaohong; Blount, Patricia L; Vaughan, Thomas L; Reid, Brian J

2011-02-01

Aside from primary prevention, early detection remains the most effective way to decrease mortality associated with the majority of solid cancers. Previous cancer screening models are largely based on classification of at-risk populations into three conceptually defined groups (normal, cancer without symptoms, and cancer with symptoms). Unfortunately, this approach has achieved limited successes in reducing cancer mortality. With advances in molecular biology and genomic technologies, many candidate somatic genetic and epigenetic "biomarkers" have been identified as potential predictors of cancer risk. However, none have yet been validated as robust predictors of progression to cancer or shown to reduce cancer mortality. In this Perspective, we first define the necessary and sufficient conditions for precise prediction of future cancer development and early cancer detection within a simple physical model framework. We then evaluate cancer risk prediction and early detection from a dynamic clonal evolution point of view, examining the implications of dynamic clonal evolution of biomarkers and the application of clonal evolution for cancer risk management in clinical practice. Finally, we propose a framework to guide future collaborative research between mathematical modelers and biomarker researchers to design studies to investigate and model dynamic clonal evolution. This approach will allow optimization of available resources for cancer control and intervention timing based on molecular biomarkers in predicting cancer among various risk subsets that dynamically evolve over time.

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

PubMed

Bednar, David; Beerens, Koen; Sebestova, Eva; Bendl, Jaroslav; Khare, Sagar; Chaloupkova, Radka; Prokop, Zbynek; Brezovsky, Jan; Baker, David; Damborsky, Jiri

2015-11-01

There is great interest in increasing proteins' stability to enhance their utility as biocatalysts, therapeutics, diagnostics and nanomaterials. Directed evolution is a powerful, but experimentally strenuous approach. Computational methods offer attractive alternatives. However, due to the limited reliability of predictions and potentially antagonistic effects of substitutions, only single-point mutations are usually predicted in silico, experimentally verified and then recombined in multiple-point mutants. Thus, substantial screening is still required. Here we present FireProt, a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt's reliability and applicability was demonstrated by validating its predictions against 656 mutations from the ProTherm database. We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and γ-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased (ΔTm = 24°C and 21°C) by constructing and characterizing only a handful of multiple-point mutants. FireProt can be applied to any protein for which a tertiary structure and homologous sequences are available, and will facilitate the rapid development of robust proteins for biomedical and biotechnological applications.

Winnerless competition principle and prediction of the transient dynamics in a Lotka-Volterra model

NASA Astrophysics Data System (ADS)

Afraimovich, Valentin; Tristan, Irma; Huerta, Ramon; Rabinovich, Mikhail I.

2008-12-01

Predicting the evolution of multispecies ecological systems is an intriguing problem. A sufficiently complex model with the necessary predicting power requires solutions that are structurally stable. Small variations of the system parameters should not qualitatively perturb its solutions. When one is interested in just asymptotic results of evolution (as time goes to infinity), then the problem has a straightforward mathematical image involving simple attractors (fixed points or limit cycles) of a dynamical system. However, for an accurate prediction of evolution, the analysis of transient solutions is critical. In this paper, in the framework of the traditional Lotka-Volterra model (generalized in some sense), we show that the transient solution representing multispecies sequential competition can be reproducible and predictable with high probability.

Winnerless competition principle and prediction of the transient dynamics in a Lotka-Volterra model.

PubMed

Afraimovich, Valentin; Tristan, Irma; Huerta, Ramon; Rabinovich, Mikhail I

2008-12-01

Predicting the evolution of multispecies ecological systems is an intriguing problem. A sufficiently complex model with the necessary predicting power requires solutions that are structurally stable. Small variations of the system parameters should not qualitatively perturb its solutions. When one is interested in just asymptotic results of evolution (as time goes to infinity), then the problem has a straightforward mathematical image involving simple attractors (fixed points or limit cycles) of a dynamical system. However, for an accurate prediction of evolution, the analysis of transient solutions is critical. In this paper, in the framework of the traditional Lotka-Volterra model (generalized in some sense), we show that the transient solution representing multispecies sequential competition can be reproducible and predictable with high probability.

Interdependency enriches the spatial reciprocity in prisoner's dilemma game on weighted networks

NASA Astrophysics Data System (ADS)

Meng, Xiaokun; Sun, Shiwen; Li, Xiaoxuan; Wang, Li; Xia, Chengyi; Sun, Junqing

2016-01-01

To model the evolution of cooperation under the realistic scenarios, we propose an interdependent network-based game model which simultaneously considers the difference of individual roles in the spatial prisoner's dilemma game. In our model, the system is composed of two lattices on which an agent designated as a cooperator or defector will be allocated, meanwhile each agent will be endowed as a specific weight taking from three typical distributions on one lattice (i.e., weighted lattice), and set to be 1.0 on the other one (i.e., un-weighted or standard lattice). In addition, the interdependency will be built through the utility coupling between point-to-point partners. Extensive simulations indicate that the cooperation will be continuously elevated for the weighted lattice as the utility coupling strength (α) increases; while the cooperation will take on a nontrivial evolution on the standard lattice as α varies, and will be still greatly promoted when compared to the case of α = 0. At the same time, the full T - K phase diagrams are also explored to illustrate the evolutionary behaviors, and it is powerfully shown that the interdependency drives the defectors to survive within the narrower range, but individual weighting of utility will further broaden the coexistence space of cooperators and defectors, which renders the nontrivial evolution of cooperation in our model. Altogether, the current consequences about the evolution of cooperation will be helpful for us to provide the insights into the prevalent cooperation phenomenon within many real-world systems.

Nonequilibrium dynamics of the O( N ) model on dS3 and AdS crunches

NASA Astrophysics Data System (ADS)

Kumar, S. Prem; Vaganov, Vladislav

2018-03-01

We study the nonperturbative quantum evolution of the interacting O( N ) vector model at large- N , formulated on a spatial two-sphere, with time dependent couplings which diverge at finite time. This model - the so-called "E-frame" theory, is related via a conformal transformation to the interacting O( N ) model in three dimensional global de Sitter spacetime with time independent couplings. We show that with a purely quartic, relevant deformation the quantum evolution of the E-frame model is regular even when the classical theory is rendered singular at the end of time by the diverging coupling. Time evolution drives the E-frame theory to the large- N Wilson-Fisher fixed point when the classical coupling diverges. We study the quantum evolution numerically for a variety of initial conditions and demonstrate the finiteness of the energy at the classical "end of time". With an additional (time dependent) mass deformation, quantum backreaction lowers the mass, with a putative smooth time evolution only possible in the limit of infinite quartic coupling. We discuss the relevance of these results for the resolution of crunch singularities in AdS geometries dual to E-frame theories with a classical gravity dual.

Six-vertex model and Schramm-Loewner evolution.

PubMed

Kenyon, Richard; Miller, Jason; Sheffield, Scott; Wilson, David B

2017-05-01

Square ice is a statistical mechanics model for two-dimensional ice, widely believed to have a conformally invariant scaling limit. We associate a Peano (space-filling) curve to a square ice configuration, and more generally to a so-called six-vertex model configuration, and argue that its scaling limit is a space-filling version of the random fractal curve SLE_{κ}, Schramm-Loewner evolution with parameter κ, where 4<κ≤12+8sqrt[2]. For square ice, κ=12. At the "free-fermion point" of the six-vertex model, κ=8+4sqrt[3]. These unusual values lie outside the classical interval 2≤κ≤8.

Slow relaxation of cascade-induced defects in Fe

DOE PAGES

Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.; ...

2015-02-17

On-the-fly kinetic Monte Carlo (KMC) simulations are performed to investigate slow relaxation of non-equilibrium systems. Point defects induced by 25 keV cascades in α -Fe are shown to lead to a characteristic time-evolution, described by the replenish and relax mechanism. Then, we produce an atomistically-based assessment of models proposed to explain the slow structural relaxation by focusing on the aggregation of 50 vacancies and 25 self-interstital atoms (SIA) in 10-lattice-parameter α-Fe boxes, two processes that are closely related to cascade annealing and exhibit similar time signature. Four atomistic effects explain the timescales involved in the evolution: defect concentration heterogeneities, concentration-enhancedmore » mobility, cluster-size dependent bond energies and defect-induced pressure. In conclusion, these findings suggest that the two main classes of models to explain slow structural relaxation, the Eyring model and the Gibbs model, both play a role to limit the rate of relaxation of these simple point-defect systems.« less

Modeling Evolution on Nearly Neutral Network Fitness Landscapes

NASA Astrophysics Data System (ADS)

Yakushkina, Tatiana; Saakian, David B.

2017-08-01

To describe virus evolution, it is necessary to define a fitness landscape. In this article, we consider the microscopic models with the advanced version of neutral network fitness landscapes. In this problem setting, we suppose a fitness difference between one-point mutation neighbors to be small. We construct a modification of the Wright-Fisher model, which is related to ordinary infinite population models with nearly neutral network fitness landscape at the large population limit. From the microscopic models in the realistic sequence space, we derive two versions of nearly neutral network models: with sinks and without sinks. We claim that the suggested model describes the evolutionary dynamics of RNA viruses better than the traditional Wright-Fisher model with few sequences.

Coarse pointing mechanism assembly for satellite interlink experiment

NASA Technical Reports Server (NTRS)

Maeusli, P. A.; Ivorra, M. T.; Gass, V.; Berthoud, J. F.

1996-01-01

Since 1975, MECANEX S.A. has been manufacturing components for solar array drives and mechanisms used in space applications. In 1991, work was started in an early phase C (Engineering Model) on a Coarse Pointing Mechanism Assembly (CPMA) for the Semiconductor-laser Inter-satellite Link EXperiment (SILEX). This paper deals with the history, the evolution, and the lessons learned from taking over a pre-design in 1991 to the delivery of last flight models (FM 5 & 6) in 1995.

Modeling the Evolution of a Science Project in Software-Reliant System Acquisition Programs

DTIC Science & Technology

2013-07-24

might: • Limit worker burnout • Perform better regarding schedule 10 Software Technology Conference April 10, 2013 © 2013 Carnegie Mellon...University The Evolution of a Science Project Key Preliminary Findings -3 The tipping point contributes to the “90% Done” Syndrome Percentage...worker burnout - SP User Satisfaction SP increasing satisfaction indicated satisfaction + + B3 Moderating User Satisfaction overage switch demand switch

Modelling the morphodynamics and co-evolution of coast and estuarine environments

NASA Astrophysics Data System (ADS)

Morris, Chloe; Coulthard, Tom; Parsons, Daniel R.; Manson, Susan; Barkwith, Andrew

2017-04-01

The morphodynamics of coast and estuarine environments are known to be sensitive to environmental change and sea-level rise. However, whilst these systems have received considerable individual research attention, how they interact and co-evolve is relatively understudied. These systems are intrinsically linked and it is therefore advantageous to study them holistically in order to build a more comprehensive understanding of their behaviour and to inform sustainable management over the long term. Complex environments such as these are often studied using numerical modelling techniques. Inherent from the limited research in this area, existing models are currently not capable of simulating dynamic coast-estuarine interactions. A new model is being developed through coupling the one-line Coastline Evolution Model (CEM) with CAESAR-Lisflood (C-L), a hydrodynamic Landscape Evolution Model. It is intended that the eventual model be used to advance the understanding of these systems and how they may evolve over the mid to long term in response to climate change. In the UK, the Holderness Coast, Humber Estuary and Spurn Point system offers a diverse and complex case study for this research. Holderness is one of the fastest eroding coastlines in Europe and research suggests that the large volumes of material removed from its cliffs are responsible for the formation of the Spurn Point feature and for the Holocene infilling of the Humber Estuary. Marine, fluvial and coastal processes are continually reshaping this system and over the next century, it is predicted that climate change could lead to increased erosion along the coast and supply of material to the Humber Estuary and Spurn Point. How this manifests will be hugely influential to the future morphology of these systems and the existence of Spurn Point. Progress to date includes a new version of the CEM that has been prepared for integration into C-L and includes an improved graphical user interface and more complex geomorphological processes. Preliminary results from simulations of the Holderness Coast and Spurn Point support findings of other authors, who suggest that changes to the wave climate influences sediment transport patterns in the nearshore zone. The angle of wave approach to the Holderness shows particular significance compared to the height of waves, with an optimum volume of material transported at 42 degrees. Further applications and results of this new model will be presented and discussed.

A dynamical system approach to Bianchi III cosmology for Hu-Sawicki type f( R) gravity

NASA Astrophysics Data System (ADS)

Banik, Sebika Kangsha; Banik, Debika Kangsha; Bhuyan, Kalyan

2018-02-01

The cosmological dynamics of spatially homogeneous but anisotropic Bianchi type-III space-time is investigated in presence of a perfect fluid within the framework of Hu-Sawicki model. We use the dynamical system approach to perform a detailed analysis of the cosmological behaviour of this model for the model parameters n=1, c_1=1, determining all the fixed points, their stability and corresponding cosmological evolution. We have found stable fixed points with de Sitter solution along with unstable radiation like fixed points. We have identified a matter like point which act like an unstable spiral and when the initial conditions of a trajectory are very close to this point, it stabilizes at a stable accelerating point. Thus, in this model, the universe can naturally approach to a phase of accelerated expansion following a radiation or a matter dominated phase. It is also found that the isotropisation of this model is affected by the spatial curvature and that all the isotropic fixed points are found to be spatially flat.

Some insights on the dust properties of nearby galaxies, as seen with Herschel

NASA Astrophysics Data System (ADS)

Galliano, Frédéric

2017-12-01

Nearby galaxies are particularly relevant laboratories to study dust evolution due to the diversity of physical conditions they harbor and to the wealth of data at our disposal. In this paper, we review several recent advances in this field, mainly based on Herschel observations. We first discuss the problems linked with our ignorance of grain emissivities, and show that it can be constrained in some cases. New models are starting to incorporate these constraints. We then present methodological issues encountered when fitting spectral energy distributions, leading to biases in derived dust properties, and some attempts to solve them. Subsequently, we review studies scrutinizing dust evolution: (i) from a global point of view, inferring long term cosmic dust evolution; (ii) from a local point of view, looking for indices of dust processing in the ISM.

Asymptotic stability of spectral-based PDF modeling for homogeneous turbulent flows

NASA Astrophysics Data System (ADS)

Campos, Alejandro; Duraisamy, Karthik; Iaccarino, Gianluca

2015-11-01

Engineering models of turbulence, based on one-point statistics, neglect spectral information inherent in a turbulence field. It is well known, however, that the evolution of turbulence is dictated by a complex interplay between the spectral modes of velocity. For example, for homogeneous turbulence, the pressure-rate-of-strain depends on the integrated energy spectrum weighted by components of the wave vectors. The Interacting Particle Representation Model (IPRM) (Kassinos & Reynolds, 1996) and the Velocity/Wave-Vector PDF model (Van Slooten & Pope, 1997) emulate spectral information in an attempt to improve the modeling of turbulence. We investigate the evolution and asymptotic stability of the IPRM using three different approaches. The first approach considers the Lagrangian evolution of individual realizations (idealized as particles) of the stochastic process defined by the IPRM. The second solves Lagrangian evolution equations for clusters of realizations conditional on a given wave vector. The third evolves the solution of the Eulerian conditional PDF corresponding to the aforementioned clusters. This last method avoids issues related to discrete particle noise and slow convergence associated with Lagrangian particle-based simulations.

INFRARED TWO-COLOR DIAGRAMS FOR AGB STARS, POST-AGB STARS, AND PLANETARY NEBULAE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suh, Kyung-Won, E-mail: kwsuh@chungbuk.ac.kr

2015-08-01

We present various infrared two-color diagrams (2CDs) for asymptotic giant branch (AGB) stars, post-AGB stars, and Planetary Nebulae (PNe) and investigate possible evolutionary tracks. We use catalogs from the available literature for the sample of 4903 AGB stars (3373 O-rich; 1168 C-rich; 362 S-type), 660 post-AGB stars (326 post-AGB; 334 pre-PN), and 1510 PNe in our Galaxy. For each object in the catalog, we cross-identify the IRAS, AKARI, Midcourse Space Experiment, and 2MASS counterparts. The IR 2CDs can provide useful information about the structure and evolution of the dust envelopes as well as the central stars. To find possible evolutionarymore » tracks from AGB stars to PNe on the 2CDs, we investigate spectral evolution of post-AGB stars by making simple but reasonable assumptions on the evolution of the central star and dust shell. We perform radiative transfer model calculations for the detached dust shells around evolving central stars in the post-AGB phase. We find that the theoretical dust shell model tracks using dust opacity functions of amorphous silicate and amorphous carbon roughly coincide with the densely populated observed points of AGB stars, post-AGB stars, and PNe on various IR 2CDs. Even though some discrepancies are inevitable, the end points of the theoretical post-AGB model tracks generally converge in the region of the observed points of PNe on most 2CDs.« less

Evolution of the Orszag-Tang vortex system in a compressible medium. II - Supersonic flow

NASA Technical Reports Server (NTRS)

Picone, J. Michael; Dahlburg, Russell B.

1991-01-01

A study is presented on the effect of embedded supersonic flows and the resulting emerging shock waves on phenomena associated with MHD turbulence, including reconnection, the formation of current sheets and vortex structures, and the evolution of spatial and temporal correlations among physical variables. A two-dimensional model problem, the Orszag-Tang (1979) vortex system, is chosen, which involves decay from nonrandom initial conditions. The system is doubly periodic, and the initial conditions consist of single-mode solenoidal velocity and magnetic fields, each containing X points and O points. The initial mass density is flat, and the initial pressure fluctuations are incompressible, balancing the local forces for a magnetofluid of unit mass density. Results on the evolution of the local structure of the flow field, the global properties of the system, and spectral correlations are presented. The important dynamical properties and observational consequences of embedded supersonic regions and emerging shocks in the Orszag-Tang model of an MHD system undergoing reconnection are discussed. Conclusions are drawn regarding the effects of local supersonic regions on MHD turbulence.

Corneal changes induced by laser ablation: study of the visual-quality evolution by a customized eye model

NASA Astrophysics Data System (ADS)

Ortiz, D.; Anera, R. G.; Saiz, J. M.; Jiménez, J. R.; Moreno, F.; Jiménez Del Barco, L.; González, F.

2006-11-01

This study focuses on the changes induced in both the asphericity and homogeneity of the cornea for a group of myopic eyes undergoing LASIK surgery. Eyes were characterized by a Kooijman-based customized eye model in which changes were introduced in the form of Gaussian-distributed refractive-index variations of given correlation length for the inhomogeneities and in the form of an expression, based on the modified Munnerlyn's paraxial formula, for the post-LASIK asphericity. Visual quality was evaluated in terms of the Modulation Transfer Function and the Point-Spread Function. The results show that, on average, the evolution of visual acuity is consistent with the change in corneal asphericity, while the evolution of contrast sensitivity requires a loss in corneal homogeneity in order to be explained. By including both effects in the model, the overall model performance in predicting visual quality is improved.

Glassy Dynamics in the Adaptive Immune Response Prevents Autoimmune Disease

NASA Astrophysics Data System (ADS)

Sun, Jun; Deem, Michael

2006-03-01

The immune system normally protects the human host against death by infection. However, when an immune response is mistakenly directed at self antigens, autoimmune disease can occur. We describe a model of protein evolution to simulate the dynamics of the adaptive immune response to antigens. Computer simulations of the dynamics of antibody evolution show that different evolutionary mechanisms, namely gene segment swapping and point mutation, lead to different evolved antibody binding affinities. Although a combination of gene segment swapping and point mutation can yield a greater affinity to a specific antigen than point mutation alone, the antibodies so evolved are highly cross-reactive and would cause autoimmune disease, and this is not the chosen dynamics of the immune system. We suggest that in the immune system a balance has evolved between binding affinity and specificity in the mechanism for searching the amino acid sequence space of antibodies. Our model predicts that chronic infection may lead to autoimmune disease as well due to cross-reactivity and suggests a broad distribution for the time of onset of autoimmune disease due to chronic exposure. The slow search of antibody sequence space by point mutation leads to the broad of distribution times.

Tumor evolution: Linear, branching, neutral or punctuated?☆

PubMed Central

Davis, Alexander; Gao, Ruli; Navin, Nicholas

2017-01-01

Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of how this genetic diversity emerges over time remains limited. A central challenge in studying tumor evolution is the difficulty in collecting longitudinal samples from cancer patients. Consequently, most studies have inferred tumor evolution from single time-point samples, providing very indirect information. These data have led to several competing models of tumor evolution: linear, branching, neutral and punctuated. Each model makes different assumptions regarding the timing of mutations and selection of clones, and therefore has different implications for the diagnosis and therapeutic treatment of cancer patients. Furthermore, emerging evidence suggests that models may change during tumor progression or operate concurrently for different classes of mutations. Finally, we discuss data that supports the theory that most human tumors evolve from a single cell in the normal tissue. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby. PMID:28110020

Estimation of main diversification time-points of hantaviruses using phylogenetic analyses of complete genomes.

PubMed

Castel, Guillaume; Tordo, Noël; Plyusnin, Alexander

2017-04-02

Because of the great variability of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. Intriguing questions remain about the timescale of the diversification events that influenced this evolution. In this paper we attempted to estimate the first ever timing of hantavirus diversification based on thirty five available complete genomes representing five major groups of hantaviruses and the assumption of co-speciation of hantaviruses with their respective mammal hosts. Phylogenetic analyses were used to estimate the main diversification points during hantavirus evolution in mammals while host diversification was mostly estimated from independent calibrators taken from fossil records. Our results support an earlier developed hypothesis of co-speciation of known hantaviruses with their respective mammal hosts and hence a common ancestor for all hantaviruses carried by placental mammals. Copyright © 2017 Elsevier B.V. All rights reserved.

Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.

PubMed

Rubin, Ilan N; Doebeli, Michael

2017-12-21

Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into the evolutionary dynamics, effectively guaranteeing eventual branching. Large mutations allow the second order disruptive selection to dominate the first order selection toward phenotypic heterogeneity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rate and State Friction Relation for Nanoscale Contacts: Thermally Activated Prandtl-Tomlinson Model with Chemical Aging

NASA Astrophysics Data System (ADS)

Tian, Kaiwen; Goldsby, David L.; Carpick, Robert W.

2018-05-01

Rate and state friction (RSF) laws are widely used empirical relationships that describe macroscale to microscale frictional behavior. They entail a linear combination of the direct effect (the increase of friction with sliding velocity due to the reduced influence of thermal excitations) and the evolution effect (the change in friction with changes in contact "state," such as the real contact area or the degree of interfacial chemical bonds). Recent atomic force microscope (AFM) experiments and simulations found that nanoscale single-asperity amorphous silica-silica contacts exhibit logarithmic aging (increasing friction with time) over several decades of contact time, due to the formation of interfacial chemical bonds. Here we establish a physically based RSF relation for such contacts by combining the thermally activated Prandtl-Tomlinson (PTT) model with an evolution effect based on the physics of chemical aging. This thermally activated Prandtl-Tomlinson model with chemical aging (PTTCA), like the PTT model, uses the loading point velocity for describing the direct effect, not the tip velocity (as in conventional RSF laws). Also, in the PTTCA model, the combination of the evolution and direct effects may be nonlinear. We present AFM data consistent with the PTTCA model whereby in aging tests, for a given hold time, static friction increases with the logarithm of the loading point velocity. Kinetic friction also increases with the logarithm of the loading point velocity at sufficiently high velocities, but at a different increasing rate. The discrepancy between the rates of increase of static and kinetic friction with velocity arises from the fact that appreciable aging during static contact changes the energy landscape. Our approach extends the PTT model, originally used for crystalline substrates, to amorphous materials. It also establishes how conventional RSF laws can be modified for nanoscale single-asperity contacts to provide a physically based friction relation for nanoscale contacts that exhibit chemical bond-induced aging, as well as other aging mechanisms with similar physical characteristics.

Complete tidal evolution of Pluto-Charon

NASA Astrophysics Data System (ADS)

Cheng, W. H.; Lee, Man Hoi; Peale, S. J.

2014-05-01

Both Pluto and its satellite Charon have rotation rates synchronous with their orbital mean motion. This is the theoretical end point of tidal evolution where transfer of angular momentum has ceased. Here we follow Pluto’s tidal evolution from an initial state having the current total angular momentum of the system but with Charon in an eccentric orbit with semimajor axis a≈4RP (where RP is the radius of Pluto), consistent with its impact origin. Two tidal models are used, where the tidal dissipation function Q∝1/frequency and Q = constant, where details of the evolution are strongly model dependent. The inclusion of the gravitational harmonic coefficient C22 of both bodies in the analysis allows smooth, self consistent evolution to the dual synchronous state, whereas its omission frustrates successful evolution in some cases. The zonal harmonic J2 can also be included, but does not cause a significant effect on the overall evolution. The ratio of dissipation in Charon to that in Pluto controls the behavior of the orbital eccentricity, where a judicious choice leads to a nearly constant eccentricity until the final approach to dual synchronous rotation. The tidal models are complete in the sense that every nuance of tidal evolution is realized while conserving total angular momentum-including temporary capture into spin-orbit resonances as Charon’s spin decreases and damped librations about the same.

Real-time evolution of non-Gaussian cumulants in the QCD critical regime

NASA Astrophysics Data System (ADS)

Mukherjee, Swagato; Venugopalan, Raju; Yin, Yi

2015-09-01

We derive a coupled set of equations that describe the nonequilibrium evolution of cumulants of critical fluctuations for spacetime trajectories on the crossover side of the QCD phase diagram. In particular, novel expressions are obtained for the nonequilibrium evolution of non-Gaussian skewness and kurtosis cumulants. UBy utilizing a simple model of the spacetime evolution of a heavy-ion collision, we demonstrate that, depending on the relaxation rate of critical fluctuations, skewness and kurtosis can differ significantly in magnitude as well as in sign from equilibrium expectations. Memory effects are important and shown to persist even for trajectories that skirt the edge of the critical regime. We use phenomenologically motivated parametrizations of freeze-out curves and of the beam-energy dependence of the net baryon chemical potential to explore the implications of our model study for the critical-point search in heavy-ion collisions.

Real time evolution of non-Gaussian cumulants in the QCD critical regime

DOE PAGES

Mukherjee, Swagato; Venugopalan, Raju; Yin, Yi

2015-09-23

In this study, we derive a coupled set of equations that describe the nonequilibrium evolution of cumulants of critical fluctuations for spacetime trajectories on the crossover side of the QCD phase diagram. In particular, novel expressions are obtained for the nonequilibrium evolution of non-Gaussian skewness and kurtosis cumulants. UBy utilizing a simple model of the spacetime evolution of a heavy-ion collision, we demonstrate that, depending on the relaxation rate of critical fluctuations, skewness and kurtosis can differ significantly in magnitude as well as in sign from equilibrium expectations. Memory effects are important and shown to persist even for trajectories thatmore » skirt the edge of the critical regime. We use phenomenologically motivated parametrizations of freeze-out curves and of the beam-energy dependence of the net baryon chemical potential to explore the implications of our model study for the critical-point search in heavy-ion collisions.« less

[Identification of coupling relationship between urbanization and ecological environment in Jilin from entropy change perspective].

PubMed

Sun, Ping-Jun; Xiu, Chun-Liang; Zhang, Tian-Jiao

2014-03-01

By using the entropy change equation of the second law of thermodynamics, entropy method and PSE model, this article made an analysis on coupling relationship between urbanization and ecological environment in Jilin Province from 2001 to 2011. In the study period, the urbanization development had been out of normal evolution track: The economic urbanization and space urbanization dominated the whole urbanization process, while population urbanization was neglected too seriously, with an apparent characteristic of extensive and inefficient input of resources (especially land resource). According to the levels of ecological environment on the basis of PSE model, not only the pressure index, sensitivity index and the elasticity index, but also the comprehensive index showed considerable growth with obvious stage characteristics: ascending-descending-ascending. The total entropy values of the urbanization were less than zero during the time, which meant an unstable rising curve. While the total trophy values of the ecological environment varied below and above zero, and 2003, 2006, 2010 and 2011 were the "turning points", reflecting the instability of the ecological environment. The coupling total entropy values between urbanization and ecological environment had the same characteristics with the ecological environment: the same "turning points" and shape of the curve, in which, the "turning points" corresponded to the type of antagonistic evolution pattern, while the rest of years responded to the type of coordination evolution pattern.

Arctic melt ponds and bifurcations in the climate system

NASA Astrophysics Data System (ADS)

Sudakov, I.; Vakulenko, S. A.; Golden, K. M.

2015-05-01

Understanding how sea ice melts is critical to climate projections. In the Arctic, melt ponds that develop on the surface of sea ice floes during the late spring and summer largely determine their albedo - a key parameter in climate modeling. Here we explore the possibility of a conceptual sea ice climate model passing through a bifurcation point - an irreversible critical threshold as the system warms, by incorporating geometric information about melt pond evolution. This study is based on a bifurcation analysis of the energy balance climate model with ice-albedo feedback as the key mechanism driving the system to bifurcation points.

Anisotropic Bianchi type-III model in Palatini f (R) gravity

NASA Astrophysics Data System (ADS)

Banik, Debika Kangsha; Banik, Sebika Kangsha; Bhuyan, Kalyan

2017-03-01

We derive exact solutions for anisotropic Bianchi type-III cosmological model in the Palatini formalism of f (R) gravity using Dynamical System Approach. For the f (R) of the form f(R) =R-β /Rn and f(R) =R+α Rm , we have found the fixed points describing the radiation-dominated, matter dominated and de Sitter evolution periods. Fixed points have also been found which have non-vanishing shear playing a very significant role in describing the anisotropy present in the early universe. In addition, we have also found that the spatial curvature affect isotropisation of this cosmological model.

A non-equilibrium neutral model for analysing cultural change.

PubMed

Kandler, Anne; Shennan, Stephen

2013-08-07

Neutral evolution is a frequently used model to analyse changes in frequencies of cultural variants over time. Variants are chosen to be copied according to their relative frequency and new variants are introduced by a process of random mutation. Here we present a non-equilibrium neutral model which accounts for temporally varying population sizes and mutation rates and makes it possible to analyse the cultural system under consideration at any point in time. This framework gives an indication whether observed changes in the frequency distributions of a set of cultural variants between two time points are consistent with the random copying hypothesis. We find that the likelihood of the existence of the observed assemblage at the end of the considered time period (expressed by the probability of the observed number of cultural variants present in the population during the whole period under neutral evolution) is a powerful indicator of departures from neutrality. Further, we study the effects of frequency-dependent selection on the evolutionary trajectories and present a case study of change in the decoration of pottery in early Neolithic Central Europe. Based on the framework developed we show that neutral evolution is not an adequate description of the observed changes in frequency. Copyright © 2013 Elsevier Ltd. All rights reserved.

Center manifolds for a class of degenerate evolution equations and existence of small-amplitude kinetic shocks

NASA Astrophysics Data System (ADS)

Pogan, Alin; Zumbrun, Kevin

2018-06-01

We construct center manifolds for a class of degenerate evolution equations including the steady Boltzmann equation and related kinetic models, establishing in the process existence and behavior of small-amplitude kinetic shock and boundary layers. Notably, for Boltzmann's equation, we show that elements of the center manifold decay in velocity at near-Maxwellian rate, in accord with the formal Chapman-Enskog picture of near-equilibrium flow as evolution along the manifold of Maxwellian states, or Grad moment approximation via Hermite polynomials in velocity. Our analysis is from a classical dynamical systems point of view, with a number of interesting modifications to accommodate ill-posedness of the underlying evolution equation.

Microphysical Processes Affecting the Pinatubo Volcanic Plume

NASA Technical Reports Server (NTRS)

Hamill, Patrick; Houben, Howard; Young, Richard; Turco, Richard; Zhao, Jingxia

1996-01-01

In this paper we consider microphysical processes which affect the formation of sulfate particles and their size distribution in a dispersing cloud. A model for the dispersion of the Mt. Pinatubo volcanic cloud is described. We then consider a single point in the dispersing cloud and study the effects of nucleation, condensation and coagulation on the time evolution of the particle size distribution at that point.

Effects of income redistribution on the evolution of cooperation in spatial public goods games

NASA Astrophysics Data System (ADS)

Pei, Zhenhua; Wang, Baokui; Du, Jinming

2017-01-01

Income redistribution is the transfer of income from some individuals to others directly or indirectly by means of social mechanisms, such as taxation, public services and so on. Employing a spatial public goods game, we study the influence of income redistribution on the evolution of cooperation. Two kinds of evolutionary models are constructed, which describe local and global redistribution of income respectively. In the local model, players have to pay part of their income after each PGG and the accumulated income is redistributed to the members. While in the global model, all the players pay part of their income after engaging in all the local PGGs, which are centred on himself and his nearest neighbours, and the accumulated income is redistributed to the whole population. We show that the cooperation prospers significantly with increasing income expenditure proportion in the local redistribution of income, while in the global model the situation is opposite. Furthermore, the cooperation drops dramatically from the maximum curvature point of income expenditure proportion. In particular, the intermediate critical points are closely related to the renormalized enhancement factors.

Computational evolution: taking liberties.

PubMed

Correia, Luís

2010-09-01

Evolution has, for a long time, inspired computer scientists to produce computer models mimicking its behavior. Evolutionary algorithm (EA) is one of the areas where this approach has flourished. EAs have been used to model and study evolution, but they have been especially developed for their aptitude as optimization tools for engineering. Developed models are quite simple in comparison with their natural sources of inspiration. However, since EAs run on computers, we have the freedom, especially in optimization models, to test approaches both realistic and outright speculative, from the biological point of view. In this article, we discuss different common evolutionary algorithm models, and then present some alternatives of interest. These include biologically inspired models, such as co-evolution and, in particular, symbiogenetics and outright artificial operators and representations. In each case, the advantages of the modifications to the standard model are identified. The other area of computational evolution, which has allowed us to study basic principles of evolution and ecology dynamics, is the development of artificial life platforms for open-ended evolution of artificial organisms. With these platforms, biologists can test theories by directly manipulating individuals and operators, observing the resulting effects in a realistic way. An overview of the most prominent of such environments is also presented. If instead of artificial platforms we use the real world for evolving artificial life, then we are dealing with evolutionary robotics (ERs). A brief description of this area is presented, analyzing its relations to biology. Finally, we present the conclusions and identify future research avenues in the frontier of computation and biology. Hopefully, this will help to draw the attention of more biologists and computer scientists to the benefits of such interdisciplinary research.

Monte Carlo calculations of lunar regolith thickness distributions.

NASA Technical Reports Server (NTRS)

Oberbeck, V. R.; Quaide, W. L.; Mahan, M.; Paulson, J.

1973-01-01

It is pointed out that none of the existing models of lunar regolith evolution take into account the relationship between regolith thickness, crater shape, and volume of debris ejected. The results of a Monte Carlo computer simulation of regolith evolution are presented. The simulation was designed to consider the full effect of the buffering regolith through calculation of the amount of debris produced by any given crater as a function of the amount of debris present at the site of the crater at the time of crater formation. The method is essentially an improved version of the Oberbeck and Quaide (1968) model.

Evolution families of conformal mappings with fixed points and the Löwner-Kufarev equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goryainov, V V

2015-01-31

The paper is concerned with evolution families of conformal mappings of the unit disc to itself that fix an interior point and a boundary point. Conditions are obtained for the evolution families to be differentiable, and an existence and uniqueness theorem for an evolution equation is proved. A convergence theorem is established which describes the topology of locally uniform convergence of evolution families in terms of infinitesimal generating functions. The main result in this paper is the embedding theorem which shows that any conformal mapping of the unit disc to itself with two fixed points can be embedded into a differentiable evolution familymore » of such mappings. This result extends the range of the parametric method in the theory of univalent functions. In this way the problem of the mutual change of the derivative at an interior point and the angular derivative at a fixed point on the boundary is solved for a class of mappings of the unit disc to itself. In particular, the rotation theorem is established for this class of mappings. Bibliography: 27 titles.« less

Two-point spectral model for variable density homogeneous turbulence

NASA Astrophysics Data System (ADS)

Pal, Nairita; Kurien, Susan; Clark, Timothy; Aslangil, Denis; Livescu, Daniel

2017-11-01

We present a comparison between a two-point spectral closure model for buoyancy-driven variable density homogeneous turbulence, with Direct Numerical Simulation (DNS) data of the same system. We wish to understand how well a suitable spectral model might capture variable density effects and the transition to turbulence from an initially quiescent state. Following the BHRZ model developed by Besnard et al. (1990), the spectral model calculation computes the time evolution of two-point correlations of the density fluctuations with the momentum and the specific-volume. These spatial correlations are expressed as function of wavenumber k and denoted by a (k) and b (k) , quantifying mass flux and turbulent mixing respectively. We assess the accuracy of the model, relative to a full DNS of the complete hydrodynamical equations, using a and b as metrics. Work at LANL was performed under the auspices of the U.S. DOE Contract No. DE-AC52-06NA25396.

Dynamics of symmetry breaking during quantum real-time evolution in a minimal model system.

PubMed

Heyl, Markus; Vojta, Matthias

2014-10-31

One necessary criterion for the thermalization of a nonequilibrium quantum many-particle system is ergodicity. It is, however, not sufficient in cases where the asymptotic long-time state lies in a symmetry-broken phase but the initial state of nonequilibrium time evolution is fully symmetric with respect to this symmetry. In equilibrium, one particular symmetry-broken state is chosen as a result of an infinitesimal symmetry-breaking perturbation. From a dynamical point of view the question is: Can such an infinitesimal perturbation be sufficient for the system to establish a nonvanishing order during quantum real-time evolution? We study this question analytically for a minimal model system that can be associated with symmetry breaking, the ferromagnetic Kondo model. We show that after a quantum quench from a completely symmetric state the system is able to break its symmetry dynamically and discuss how these features can be observed experimentally.

Multi-agent fare optimization model of two modes problem and its analysis based on edge of chaos

NASA Astrophysics Data System (ADS)

Li, Xue-yan; Li, Xue-mei; Li, Xue-wei; Qiu, He-ting

2017-03-01

This paper proposes a new framework of fare optimization & game model for studying the competition between two travel modes (high speed railway and civil aviation) in which passengers' group behavior is taken into consideration. The small-world network is introduced to construct the multi-agent model of passengers' travel mode choice. The cumulative prospect theory is adopted to depict passengers' bounded rationality, the heterogeneity of passengers' reference point is depicted using the idea of group emotion computing. The conceptions of "Langton parameter" and "evolution entropy" in the theory of "edge of chaos" are introduced to create passengers' "decision coefficient" and "evolution entropy of travel mode choice" which are used to quantify passengers' group behavior. The numerical simulation and the analysis of passengers' behavior show that (1) the new model inherits the features of traditional model well and the idea of self-organizing traffic flow evolution fully embodies passengers' bounded rationality, (2) compared with the traditional model (logit model), when passengers are in the "edge of chaos" state, the total profit of the transportation system is higher.

Evolution of dispersal in spatially and temporally variable environments: The importance of life cycles.

PubMed

Massol, François; Débarre, Florence

2015-07-01

Spatiotemporal variability of the environment is bound to affect the evolution of dispersal, and yet model predictions strongly differ on this particular effect. Recent studies on the evolution of local adaptation have shown that the life cycle chosen to model the selective effects of spatiotemporal variability of the environment is a critical factor determining evolutionary outcomes. Here, we investigate the effect of the order of events in the life cycle on the evolution of unconditional dispersal in a spatially heterogeneous, temporally varying landscape. Our results show that the occurrence of intermediate singular strategies and disruptive selection are conditioned by the temporal autocorrelation of the environment and by the life cycle. Life cycles with dispersal of adults versus dispersal of juveniles, local versus global density regulation, give radically different evolutionary outcomes that include selection for total philopatry, evolutionary bistability, selection for intermediate stable states, and evolutionary branching points. Our results highlight the importance of accounting for life-cycle specifics when predicting the effects of the environment on evolutionarily selected trait values, such as dispersal, as well as the need to check the robustness of model conclusions against modifications of the life cycle. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

The Dynamics of a Viscous Gas Ring around a Kerr Black Hole

NASA Astrophysics Data System (ADS)

Riffert, H.

2000-01-01

The dynamics of a rotationally symmetric viscous gas ring around a Kerr black hole is calculated in the thin-disk approximation. An evolution equation for the surface density Σ(t,r) is derived, which is the relativistic extension of a classical equation obtained by R. Lüst. A singular point appears at the radius of the last stable circular orbit r=rc. The nature of this point is investigated, and it turns out that the solution is always bounded at rc, and no boundary condition can be obtained at this radius. A unique solution of an initial value problem requires a matching condition at rc which follows from the flow structure between rc and the horizon. In the model presented here, the density in this domain is zero, and the resulting boundary condition leads to a vanishing shear stress at r=rc, which is the condition used in the standard stationary thin-disk model of Novikov & Thorne. Numerical solutions of the evolution equation are presented for two different angular momenta of the black hole. The time evolution of the resulting accretion rate depends strongly on this angular momentum.

On an application of Tikhonov's fixed point theorem to a nonlocal Cahn-Hilliard type system modeling phase separation

NASA Astrophysics Data System (ADS)

Colli, Pierluigi; Gilardi, Gianni; Sprekels, Jürgen

2016-06-01

This paper investigates a nonlocal version of a model for phase separation on an atomic lattice that was introduced by P. Podio-Guidugli (2006) [36]. The model consists of an initial-boundary value problem for a nonlinearly coupled system of two partial differential equations governing the evolution of an order parameter ρ and the chemical potential μ. Singular contributions to the local free energy in the form of logarithmic or double-obstacle potentials are admitted. In contrast to the local model, which was studied by P. Podio-Guidugli and the present authors in a series of recent publications, in the nonlocal case the equation governing the evolution of the order parameter contains in place of the Laplacian a nonlocal expression that originates from nonlocal contributions to the free energy and accounts for possible long-range interactions between the atoms. It is shown that just as in the local case the model equations are well posed, where the technique of proving existence is entirely different: it is based on an application of Tikhonov's fixed point theorem in a rather unusual separable and reflexive Banach space.

A conformal approach for the analysis of the non-linear stability of radiation cosmologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luebbe, Christian, E-mail: c.luebbe@ucl.ac.uk; Department of Mathematics, University of Leicester, University Road, LE1 8RH; Valiente Kroon, Juan Antonio, E-mail: j.a.valiente-kroon@qmul.ac.uk

2013-01-15

The conformal Einstein equations for a trace-free (radiation) perfect fluid are derived in terms of the Levi-Civita connection of a conformally rescaled metric. These equations are used to provide a non-linear stability result for de Sitter-like trace-free (radiation) perfect fluid Friedman-Lemaitre-Robertson-Walker cosmological models. The solutions thus obtained exist globally towards the future and are future geodesically complete. - Highlights: Black-Right-Pointing-Pointer We study the Einstein-Euler system in General Relativity using conformal methods. Black-Right-Pointing-Pointer We analyze the structural properties of the associated evolution equations. Black-Right-Pointing-Pointer We establish the non-linear stability of pure radiation cosmological models.

An idealised study for the long term evolution of crescentic bars

NASA Astrophysics Data System (ADS)

Chen, W. L.; Dodd, N.; Tiessen, M. C. H.; Calvete, D.

2018-01-01

An idealised study that identifies the mechanisms in the long term evolution of crescentic bar systems in nature is presented. Growth to finite amplitude (i.e., equilibration, sometimes referred to as saturation) and higher harmonic interaction are hypothesised to be the leading nonlinear effects in long-term evolution of these systems. These nonlinear effects are added to a linear stability model and used to predict crescentic bar development along a beach in Duck, North Carolina (USA) over a 2-month period. The equilibration prolongs the development of bed patterns, thus allowing the long term evolution. Higher harmonic interaction enables the amplitude to be transferred from longer to shorter lengthscales, which leads to the dominance of shorter lengthscales in latter post-storm stages, as observed at Duck. The comparison with observations indicates the importance of higher harmonic interaction in the development of nearshore crescentic bar systems in nature. Additionally, it is concluded that these nonlinear effects should be included in models simulating the development of different bed patterns, and that this points a way forward for long-term morphodynamical modelling in general.

Progenitors of Core-Collapse Supernovae

NASA Astrophysics Data System (ADS)

Hirschi, R.; Arnett, D.; Cristini, A.; Georgy, C.; Meakin, C.; Walkington, I.

2017-02-01

Massive stars have a strong impact on their surroundings, in particular when they produce a core-collapse supernova at the end of their evolution. In these proceedings, we review the general evolution of massive stars and their properties at collapse as well as the transition between massive and intermediate-mass stars. We also summarise the effects of metallicity and rotation. We then discuss some of the major uncertainties in the modelling of massive stars, with a particular emphasis on the treatment of convection in 1D stellar evolution codes. Finally, we present new 3D hydrodynamic simulations of convection in carbon burning and list key points to take from 3D hydrodynamic studies for the development of new prescriptions for convective boundary mixing in 1D stellar evolution codes.

General phase transition models for vehicular traffic with point constraints on the flow

NASA Astrophysics Data System (ADS)

Dal Santo, E.; Rosini, M. D.; Dymski, N.; Benyahia, M.

2017-12-01

We generalize the phase transition model studied in [R. Colombo. Hyperbolic phase transition in traffic flow.\\ SIAM J.\\ Appl.\\ Math., 63(2):708-721, 2002], that describes the evolution of vehicular traffic along a one-lane road. Two different phases are taken into account, according to whether the traffic is low or heavy. The model is given by a scalar conservation law in the \\emph{free-flow} phase and by a system of two conservation laws in the \\emph{congested} phase. In particular, we study the resulting Riemann problems in the case a local point constraint on the flux of the solutions is enforced.

The MV model of the color glass condensate for a finite number of sources including Coulomb interactions

DOE PAGES

McLerran, Larry; Skokov, Vladimir V.

2016-09-19

We modify the McLerran–Venugopalan model to include only a finite number of sources of color charge. In the effective action for such a system of a finite number of sources, there is a point-like interaction and a Coulombic interaction. The point interaction generates the standard fluctuation term in the McLerran–Venugopalan model. The Coulomb interaction generates the charge screening originating from well known evolution in x. Such a model may be useful for computing angular harmonics of flow measured in high energy hadron collisions for small systems. In this study we provide a basic formulation of the problem on a lattice.

Chemical evolution in spiral and irregular galaxies

NASA Technical Reports Server (NTRS)

Torres-Peimbert, S.

1986-01-01

A brief review of models of chemical evolution of the interstellar medium in our galaxy and other galaxies is presented. These models predict the time variation and radial dependence of chemical composition in the gas as function of the input parameters; initial mass function, stellar birth rate, chemical composition of mass lost by stars during their evolution (yields), and the existence of large scale mass flows, like infall from the halo, outflow to the intergalactic medium or radial flows within a galaxy. At present there is a considerable wealth of observational data on the composition of HII regions in spiral and irregular galaxies to constrain the models. Comparisons are made between theory and the observed physical conditions. In particular, studies of helium, carbon, nitrogen and oxygen abundances are reviewed. In many molecular clouds the information we have on the amount of H2 is derived from the observed CO column density, and a standard CO/H2 ratio derived for the solar neighborhood. Chemical evolution models and the observed variations in O/H and N/O values, point out the need to include these results in a CO/H2 relation that should be, at least, a function of the O/H ratio. This aspect is also discussed.

Multiresponse modeling of variably saturated flow and isotope tracer transport for a hillslope experiment at the Landscape Evolution Observatory

NASA Astrophysics Data System (ADS)

Scudeler, Carlotta; Pangle, Luke; Pasetto, Damiano; Niu, Guo-Yue; Volkmann, Till; Paniconi, Claudio; Putti, Mario; Troch, Peter

2016-10-01

This paper explores the challenges of model parameterization and process representation when simulating multiple hydrologic responses from a highly controlled unsaturated flow and transport experiment with a physically based model. The experiment, conducted at the Landscape Evolution Observatory (LEO), involved alternate injections of water and deuterium-enriched water into an initially very dry hillslope. The multivariate observations included point measures of water content and tracer concentration in the soil, total storage within the hillslope, and integrated fluxes of water and tracer through the seepage face. The simulations were performed with a three-dimensional finite element model that solves the Richards and advection-dispersion equations. Integrated flow, integrated transport, distributed flow, and distributed transport responses were successively analyzed, with parameterization choices at each step supported by standard model performance metrics. In the first steps of our analysis, where seepage face flow, water storage, and average concentration at the seepage face were the target responses, an adequate match between measured and simulated variables was obtained using a simple parameterization consistent with that from a prior flow-only experiment at LEO. When passing to the distributed responses, it was necessary to introduce complexity to additional soil hydraulic parameters to obtain an adequate match for the point-scale flow response. This also improved the match against point measures of tracer concentration, although model performance here was considerably poorer. This suggests that still greater complexity is needed in the model parameterization, or that there may be gaps in process representation for simulating solute transport phenomena in very dry soils.

Rapid evolution of cis-regulatory sequences via local point mutations

NASA Technical Reports Server (NTRS)

Stone, J. R.; Wray, G. A.

2001-01-01

Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.

Sensitivity of WallDYN material migration modeling to uncertainties in mixed-material surface binding energies

DOE PAGES

Nichols, J. H.; Jaworski, M. A.; Schmid, K.

2017-03-09

The WallDYN package has recently been applied to a number of tokamaks to self-consistently model the evolution of mixed-material plasma facing surfaces. A key component of the WallDYN model is the concentration-dependent surface sputtering rate, calculated using SDTRIM.SP. This modeled sputtering rate is strongly influenced by the surface binding energies (SBEs) of the constituent materials, which are well known for pure elements but often are poorly constrained for mixed-materials. This work examines the sensitivity of WallDYN surface evolution calculations to different models for mixed-material SBEs, focusing on the carbon/lithium/oxygen/deuterium system present in NSTX. A realistic plasma background is reconstructed frommore » a high density, H-mode NSTX discharge, featuring an attached outer strike point with local density and temperature of 4 × 10 20 m -3 and 4 eV, respectively. It is found that various mixed-material SBE models lead to significant qualitative and quantitative changes in the surface evolution profile at the outer divertor, with the highest leverage parameter being the C-Li binding model. Uncertainties of order 50%, appearing on time scales relevant to tokamak experiments, highlight the importance of choosing an appropriate mixed-material sputtering representation when modeling the surface evolution of plasma facing components. Lastly, these results are generalized to other fusion-relevant materials with different ranges of SBEs.« less

Sensitivity of WallDYN material migration modeling to uncertainties in mixed-material surface binding energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nichols, J. H.; Jaworski, M. A.; Schmid, K.

The WallDYN package has recently been applied to a number of tokamaks to self-consistently model the evolution of mixed-material plasma facing surfaces. A key component of the WallDYN model is the concentration-dependent surface sputtering rate, calculated using SDTRIM.SP. This modeled sputtering rate is strongly influenced by the surface binding energies (SBEs) of the constituent materials, which are well known for pure elements but often are poorly constrained for mixed-materials. This work examines the sensitivity of WallDYN surface evolution calculations to different models for mixed-material SBEs, focusing on the carbon/lithium/oxygen/deuterium system present in NSTX. A realistic plasma background is reconstructed frommore » a high density, H-mode NSTX discharge, featuring an attached outer strike point with local density and temperature of 4 × 10 20 m -3 and 4 eV, respectively. It is found that various mixed-material SBE models lead to significant qualitative and quantitative changes in the surface evolution profile at the outer divertor, with the highest leverage parameter being the C-Li binding model. Uncertainties of order 50%, appearing on time scales relevant to tokamak experiments, highlight the importance of choosing an appropriate mixed-material sputtering representation when modeling the surface evolution of plasma facing components. Lastly, these results are generalized to other fusion-relevant materials with different ranges of SBEs.« less

On Mathematical Anti-Evolutionism

NASA Astrophysics Data System (ADS)

Rosenhouse, Jason

2016-03-01

The teaching of evolution in American high schools has long been a source of controversy. The past decade has seen an important shift in the rhetoric of anti-evolutionists, toward arguments of a strongly mathematical character. These mathematical arguments, while different in their specifics, follow the same general program and rely on the same underlying model of evolution. We shall discuss the nature and history of this program and model and describe general reasons for skepticism with regard to any anti-evolutionary arguments based upon them. We shall then survey the major arguments used by anti-evolutionists, to show how our general considerations make it possible to quickly identify their weakest points.

Dynamical Models of Elliptical Galaxies in z=0.5 Clusters. II. Mass-to-Light Ratio Evolution without Fundamental Plane Assumptions

NASA Astrophysics Data System (ADS)

van der Marel, Roeland P.; van Dokkum, Pieter G.

2007-10-01

We study the mass-to-light ratio (M/L) evolution of early-type galaxies using dynamical modeling of resolved internal kinematics. This makes fewer assumptions than fundamental plane (FP) studies and provides a powerful new approach for studying galaxy evolution. We focus on the sample of 25 galaxies in clusters at z~0.5 modeled in Paper I. For comparison, we compile and homogenize M/L literature data for 60 nearby galaxies that were modeled in comparable detail. The nearby sample obeys log(M/L)B=Z+Slog(σeff/200 km s-1), where Z=0.896+/-0.010, S=0.992+/-0.054, and σeff is the effective velocity dispersion. The z~0.5 sample follows a similar relation, but with lower zero point. The implied M/L evolution is Δlog(M/L)/Δz=-0.457+/-0.046(random)+/-0.078(systematic), consistent with passive evolution following high-redshift formation. This agrees with the FP results for this sample by van Dokkum & van der Marel, and confirms that FP evolution tracks M/L evolution, which is an important verification of the assumptions that underlie FP studies. However, while we find more FP evolution for galaxies of low σeff (or low mass), the dynamical M/L evolution shows little correlation with σeff. We argue that this difference can be plausibly attributed to a combination of two effects: (1) evolution in structural galaxy properties other than M/L, and (2) the neglect of rotational support in studies of FP evolution. The results leave the question open as to whether the low-mass galaxies in the sample have younger populations than the high-mass galaxies. This highlights the general importance in the study of population ages for complementing dynamical measurements with broadband colors or spectroscopic population diagnostics.

Random genetic drift, natural selection, and noise in human cranial evolution.

PubMed

Roseman, Charles C

2016-08-01

This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Breakdown simulations in a focused microwave beam within the simplified model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Semenov, V. E.; Rakova, E. I.; Glyavin, M. Yu.

2016-07-15

The simplified model is proposed to simulate numerically air breakdown in a focused microwave beam. The model is 1D from the mathematical point of view, but it takes into account the spatial non-uniformity of microwave field amplitude along the beam axis. The simulations are completed for different frequencies and different focal lengths of microwave beams. The results demonstrate complicated regimes of the breakdown evolution which represents a series of repeated ionization waves. These waves start at the focal point and propagate towards incident microwave radiation. The ionization wave parameters vary during propagation. At relatively low frequencies, the propagation regime ofmore » subsequent waves can also change qualitatively. Each next ionization wave is less pronounced than the previous one, and the breakdown evolution approaches the steady state with relatively small plasma density. The ionization wave parameters are sensitive to the weak source of external ionization, but the steady state is independent on such a source. As the beam focal length decreases, the stationary plasma density increases and the onset of the steady state occurs faster.« less

Chewing on the trees: Constraints and adaptation in the evolution of the primate mandible.

PubMed

Meloro, Carlo; Cáceres, Nilton Carlos; Carotenuto, Francesco; Sponchiado, Jonas; Melo, Geruza Leal; Passaro, Federico; Raia, Pasquale

2015-07-01

Chewing on different food types is a demanding biological function. The classic assumption in studying the shape of feeding apparatuses is that animals are what they eat, meaning that adaptation to different food items accounts for most of their interspecific variation. Yet, a growing body of evidence points against this concept. We use the primate mandible as a model structure to investigate the complex interplay among shape, size, diet, and phylogeny. We find a weak but significant impact of diet on mandible shape variation in primates as a whole but not in anthropoids and catarrhines as tested in isolation. These clades mainly exhibit allometric shape changes, which are unrelated to diet. Diet is an important factor in the diversification of strepsirrhines and platyrrhines and a phylogenetic signal is detected in all primate clades. Peaks in morphological disparity occur during the Oligocene (between 37 and 25 Ma) supporting the notion that an adaptive radiation characterized the evolution of South American monkeys. In all primate clades, the evolution of mandible size is faster than its shape pointing to a strong effect of allometry on ecomorphological diversification in this group. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Oparin's coacervates as an important milestone in chemical evolution

NASA Astrophysics Data System (ADS)

Kolb, Vera M.

2015-09-01

Although Oparin's coacervate model for the origin of life by chemical evolution is almost 100 years old, it is still valid. However, the structure of his originally proposed coacervate is not considered prebiotic, based on some recent developments in prebiotic chemistry. We have remedied this deficiency of the Oparin's model, by substituting his coacervate with a prebiotically feasible one. Oparin's coacervates are aqueous structures, but have a boundary with the rest of the aqueous medium. They exhibit properties of self-replication, and provide a path to a primitive metabolism, via chemical competition and thus a primitive selection. Thus, coacervates are good models for proto-cells. We review here some salient points of Oparin's model and address also some philosophical views on the beginning of natural selection in primitive chemical systems.

The Path of the Blind Watchmaker: A Model of Evolution

DTIC Science & Technology

2011-04-06

computational biology has now reached the point that astronomy reached when it began to look backward in time to the Big Bang. Our goal is look backward in...treatment. We claim that computational biology has now reached the point that astronomy reached when it began to look backward in time to the Big...evolutionary process itself, in fact, created it. When astronomy reached a critical mass of theory, technology, and observational data, astronomers

Spherically symmetric Einstein-aether perfect fluid models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coley, Alan A.; Latta, Joey; Leon, Genly

We investigate spherically symmetric cosmological models in Einstein-aether theory with a tilted (non-comoving) perfect fluid source. We use a 1+3 frame formalism and adopt the comoving aether gauge to derive the evolution equations, which form a well-posed system of first order partial differential equations in two variables. We then introduce normalized variables. The formalism is particularly well-suited for numerical computations and the study of the qualitative properties of the models, which are also solutions of Horava gravity. We study the local stability of the equilibrium points of the resulting dynamical system corresponding to physically realistic inhomogeneous cosmological models and astrophysicalmore » objects with values for the parameters which are consistent with current constraints. In particular, we consider dust models in (β−) normalized variables and derive a reduced (closed) evolution system and we obtain the general evolution equations for the spatially homogeneous Kantowski-Sachs models using appropriate bounded normalized variables. We then analyse these models, with special emphasis on the future asymptotic behaviour for different values of the parameters. Finally, we investigate static models for a mixture of a (necessarily non-tilted) perfect fluid with a barotropic equations of state and a scalar field.« less

The evolution of music in comparative perspective.

PubMed

Fitch, W Tecumseh

2005-12-01

In this paper, I briefly review some comparative data that provide an empirical basis for research on the evolution of music making in humans. First, a brief comparison of music and language leads to discussion of design features of music, suggesting a deep connection between the biology of music and language. I then selectively review data on animal "music." Examining sound production in animals, we find examples of repeated convergent evolution or analogy (the evolution of vocal learning of complex songs in birds, whales, and seals). A fascinating but overlooked potential homology to instrumental music is provided by manual percussion in African apes. Such comparative behavioral data, combined with neuroscientific and developmental data, provide an important starting point for any hypothesis about how or why human music evolved. Regarding these functional and phylogenetic questions, I discuss some previously proposed functions of music, including Pinker's "cheesecake" hypothesis; Darwin's and others' sexual selection model; Dunbar's group "grooming" hypothesis; and Trehub's caregiving model. I conclude that only the last hypothesis receives strong support from currently available data. I end with a brief synopsis of Darwin's model of a songlike musical "protolanguage," concluding that Darwin's model is consistent with much of the available evidence concerning the evolution of both music and language. There is a rich future for empirical investigations of the evolution of music, both in investigations of individual differences among humans, and in interspecific investigations of musical abilities in other animals, especially those of our ape cousins, about which we know little.

A Monte Carlo model for 3D grain evolution during welding

NASA Astrophysics Data System (ADS)

Rodgers, Theron M.; Mitchell, John A.; Tikare, Veena

2017-09-01

Welding is one of the most wide-spread processes used in metal joining. However, there are currently no open-source software implementations for the simulation of microstructural evolution during a weld pass. Here we describe a Potts Monte Carlo based model implemented in the SPPARKS kinetic Monte Carlo computational framework. The model simulates melting, solidification and solid-state microstructural evolution of material in the fusion and heat-affected zones of a weld. The model does not simulate thermal behavior, but rather utilizes user input parameters to specify weld pool and heat-affect zone properties. Weld pool shapes are specified by Bézier curves, which allow for the specification of a wide range of pool shapes. Pool shapes can range from narrow and deep to wide and shallow representing different fluid flow conditions within the pool. Surrounding temperature gradients are calculated with the aide of a closest point projection algorithm. The model also allows simulation of pulsed power welding through time-dependent variation of the weld pool size. Example simulation results and comparisons with laboratory weld observations demonstrate microstructural variation with weld speed, pool shape, and pulsed-power.

Radial restricted solid-on-solid and etching interface-growth models

NASA Astrophysics Data System (ADS)

Alves, Sidiney G.

2018-03-01

An approach to generate radial interfaces is presented. A radial network recursively obtained is used to implement discrete model rules designed originally for the investigation in flat substrates. I used the restricted solid-on-solid and etching models as to test the proposed scheme. The results indicate the Kardar, Parisi, and Zhang conjecture is completely verified leading to a good agreement between the interface radius fluctuation distribution and the Gaussian unitary ensemble. The evolution of the radius agrees well with the generalized conjecture, and the two-point correlation function exhibits also a good agreement with the covariance of the Airy2 process. The approach can be used to investigate radial interfaces evolution for many other classes of universality.

Radial restricted solid-on-solid and etching interface-growth models.

PubMed

Alves, Sidiney G

2018-03-01

An approach to generate radial interfaces is presented. A radial network recursively obtained is used to implement discrete model rules designed originally for the investigation in flat substrates. I used the restricted solid-on-solid and etching models as to test the proposed scheme. The results indicate the Kardar, Parisi, and Zhang conjecture is completely verified leading to a good agreement between the interface radius fluctuation distribution and the Gaussian unitary ensemble. The evolution of the radius agrees well with the generalized conjecture, and the two-point correlation function exhibits also a good agreement with the covariance of the Airy_{2} process. The approach can be used to investigate radial interfaces evolution for many other classes of universality.

An overview of structurally complex network-based modeling of public opinion in the “We the Media” era

NASA Astrophysics Data System (ADS)

Wang, Guanghui; Wang, Yufei; Liu, Yijun; Chi, Yuxue

2018-05-01

As the transmission of public opinion on the Internet in the “We the Media” era tends to be supraterritorial, concealed and complex, the traditional “point-to-surface” transmission of information has been transformed into “point-to-point” reciprocal transmission. A foundation for studies of the evolution of public opinion and its transmission on the Internet in the “We the Media” era can be laid by converting the massive amounts of fragmented information on public opinion that exists on “We the Media” platforms into structurally complex networks of information. This paper describes studies of structurally complex network-based modeling of public opinion on the Internet in the “We the Media” era from the perspective of the development and evolution of complex networks. The progress that has been made in research projects relevant to the structural modeling of public opinion on the Internet is comprehensively summarized. The review considers aspects such as regular grid-based modeling of the rules that describe the propagation of public opinion on the Internet in the “We the Media” era, social network modeling, dynamic network modeling, and supernetwork modeling. Moreover, an outlook for future studies that address complex network-based modeling of public opinion on the Internet is put forward as a summary from the perspective of modeling conducted using the techniques mentioned above.

Physical properties of PNe: what IFU spectrographs can do?

NASA Astrophysics Data System (ADS)

Costa, R.; Lago, P. J. A.; Faes, D., M.

2014-04-01

Structure, kinematics and physical parameters of planetary nebulae are related to their progenitor stars. A better understanding of these properties is essential to improve the knowledge of the late stages of evolution of intermediate-mass stars, as well as to better understand the chemical enrichment mechanisms that feed the interstellar medium with the nucleosynthesis yields from such stars. Integral Field Unit (IFU) spectrographs can provide valuable information from these objects, mapping such properties point-to-point over the projected nebulae. In this communication we present the results of a survey of physical properties for southern PNe. We have used IFU spectroscopy in order to derive the angular distribution of electron densities and ionic abundances, and also to map the ionization profiles. The aim is to characterize their physical properties and structures, and results can be used in morpho-kinematical models (such as SHAPE) or in photoionization models (such as CLOUDY) to describe in detail the 3D structure and evolution of these objects.

Effect of nickel on point defects diffusion in Fe – Ni alloys

DOE PAGES

Anento, Napoleon; Serra, Anna; Osetsky, Yury N.

2017-05-05

Iron-Nickel alloys are perspective alloys as nuclear energy structural materials because of their good radiation damage tolerance and mechanical properties. Understanding of experimentally observed features such as the effect of Ni content to radiation defects evolution is essential for developing predictive models of radiation. Recently an atomic-scale modelling study has revealed one particular mechanism of Ni effect related to the reduced mobility of clusters of interstitial atoms in Fe-Ni alloys. In this paper we present results of the microsecond-scale molecular dynamics study of point defects, i.e. vacancies and self-interstitial atoms, diffusion in Fe-Ni alloys. It is found that the additionmore » of Ni atoms affects diffusion processes: diffusion of vacancies is enhanced in the presence of Ni, whereas diffusion of interstitials is reduced and these effects increase at high Ni concentration and low temperature. As a result, the role of Ni solutes in radiation damage evolution in Fe-Ni alloys is discussed.« less

Extant-only comparative methods fail to recover the disparity preserved in the bird fossil record.

PubMed

Mitchell, Jonathan S

2015-09-01

Most extant species are in clades with poor fossil records, and recent studies of comparative methods show they have low power to infer even highly simplified models of trait evolution without fossil data. Birds are a well-studied radiation, yet their early evolutionary patterns are still contentious. The fossil record suggests that birds underwent a rapid ecological radiation after the end-Cretaceous mass extinction, and several smaller, subsequent radiations. This hypothesized series of repeated radiations from fossil data is difficult to test using extant data alone. By uniting morphological and phylogenetic data on 604 extant genera of birds with morphological data on 58 species of extinct birds from 50 million years ago, the "halfway point" of avian evolution, I have been able to test how well extant-only methods predict the diversity of fossil forms. All extant-only methods underestimate the disparity, although the ratio of within- to between-clade disparity does suggest high early rates. The failure of standard models to predict high early disparity suggests that recent radiations are obscuring deep time patterns in the evolution of birds. Metrics from different models can be used in conjunction to provide more valuable insights than simply finding the model with the highest relative fit. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Effect of impurity doping on tunneling conductance in AB-stacked bi-layer graphene: A tight-binding study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rout, G. C., E-mail: siva1987@iopb.res.in, E-mail: skp@iopb.res.in, E-mail: gcr@iopb.res.in; Sahu, Sivabrata; Panda, S. K.

2016-04-13

We report here a microscopic tight-binding model calculation for AB-stacked bilayer graphene in presence of biasing potential between the two layers and the impurity effects to study the evolution of the total density of states with special emphasis on opening of band gap near Dirac point. We have calculated the electron Green’s functions for both the A and B sub-lattices by Zubarev technique. The imaginary part of the Green’s function gives the partial and total density of states of electrons. The density of states are computed numerically for 1000 × 1000 grid points of the electron momentum. The evolution ofmore » the opening of band gap near van-Hove singularities as well as near Dirac point is investigated by varying the different interlayer hoppings and the biasing potentials. The inter layer hopping splits the density of states at van-Hove singularities and produces a V-shaped gap near Dirac point. Further the biasing potential introduces a U shaped gap near Dirac point with a density minimum at the applied potential(i.e. at V/2).« less

On the evolution of the Universe

NASA Astrophysics Data System (ADS)

Kondratenko, P. O.

2014-12-01

In this paper a model of creation and evolution of the universe in which the laws of physics are performed. The model implies that our Universe is a part of a Super-Universe as a separate layer in the fiber space, and the information communication exists between adjacent layers through the single point. During the formation of Super-Universe it was filled first a one-dimensional World of Field-time, then a two-dimensional (1+1) World was filled with energy and Planck's particles which carry the electric and magnetic charges. Completion of two-dimensional world filling leads to a "transfusion" of energy into the neighboring three-dimensional World which presents a world of known quarks which have the fractional electric charges, color charges, and spins. The next step is a "transfusion" of energy into the four-dimensional (3+1) World and the birth of the particles of this World. Evolution of this World has a completion by the brane creation of five-dimensional World. This evolution is accompanying by the birth of the entire set of stable and unstable heavy nuclei and atoms. A filling of each new layer at the fiber space does not bring the entropy into this space (i.e. cold and completely deterministic start of evolution). The proposed model supports the anthropic principle in the Universe.

A new f(R) model in the light of local gravity test and late-time cosmology

NASA Astrophysics Data System (ADS)

Nautiyal, Akhilesh; Panda, Sukanta; Patel, Avani

We propose a new model of f(R) gravity containing Arctan function in the Lagrangian. We show here that this model satisfies fifth force constraint unlike a similar model in 2013 by Kruglov. In addition to this, we carry out the fixed point analysis as well as comment on the existence of curvature singularity in this model. The cosmological evolution for this f(R) gravity model is also analyzed in the Friedmann-Robertson-Walker (FRW) background. To understand observational significance of the model, cosmological parameters are obtained numerically and compared with those of Lambda cold dark matter (ΛCDM) model. We also scrutinize the model with supernova data. We apply Om diagnostic given by Sahni et al. in 2008 to the model. Using this diagnostic, we detect the distinction between cosmic evolution caused by the f(R) model and ΛCDM. We find best-fit parameter values of the model using baryon acoustic oscillations data.

The Nature of Culture: an eight-grade model for the evolution and expansion of cultural capacities in hominins and other animals.

PubMed

Haidle, Miriam Noël; Bolus, Michael; Collard, Mark; Conard, Nicholas; Garofoli, Duilio; Lombard, Marlize; Nowell, April; Tennie, Claudio; Whiten, Andrew

2015-07-20

Tracing the evolution of human culture through time is arguably one of the most controversial and complex scholarly endeavors, and a broad evolutionary analysis of how symbolic, linguistic, and cultural capacities emerged and developed in our species is lacking. Here we present a model that, in broad terms, aims to explain the evolution and portray the expansion of human cultural capacities (the EECC model), that can be used as a point of departure for further multidisciplinary discussion and more detailed investigation. The EECC model is designed to be flexible, and can be refined to accommodate future archaeological, paleoanthropological, genetic or evolutionary psychology/behavioral analyses and discoveries. Our proposed concept of cultural behavior differentiates between empirically traceable behavioral performances and behavioral capacities that are theoretical constructs. Based largely on archaeological data (the 'black box' that most directly opens up hominin cultural evolution), and on the extension of observable problem-solution distances, we identify eight grades of cultural capacity. Each of these grades is considered within evolutionary-biological and historical-social trajectories. Importantly, the model does not imply an inevitable progression, but focuses on expansion of cultural capacities based on the integration of earlier achievements. We conclude that there is not a single cultural capacity or a single set of abilities that enabled human culture; rather, several grades of cultural capacity in animals and hominins expanded during our evolution to shape who we are today.

Strategy evolution driven by switching probabilities in structured multi-agent systems

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Chen, Zengqiang; Li, Zhiqi

2017-10-01

Evolutionary mechanism driving the commonly seen cooperation among unrelated individuals is puzzling. Related models for evolutionary games on graphs traditionally assume that players imitate their successful neighbours with higher benefits. Notably, an implicit assumption here is that players are always able to acquire the required pay-off information. To relax this restrictive assumption, a contact-based model has been proposed, where switching probabilities between strategies drive the strategy evolution. However, the explicit and quantified relation between a player's switching probability for her strategies and the number of her neighbours remains unknown. This is especially a key point in heterogeneously structured system, where players may differ in the numbers of their neighbours. Focusing on this, here we present an augmented model by introducing an attenuation coefficient and evaluate its influence on the evolution dynamics. Results show that the individual influence on others is negatively correlated with the contact numbers specified by the network topologies. Results further provide the conditions under which the coexisting strategies can be calculated analytically.

Outer boundary as arrested history in general relativity

NASA Astrophysics Data System (ADS)

Lau, Stephen R.

2002-06-01

We present explicit outer boundary conditions for the canonical variables of general relativity. The conditions are associated with the causal evolution of a finite Cauchy domain, a so-called quasilocal boost, and they suggest a consistent scheme for modelling such an evolution numerically. The scheme involves a continuous boost in the spacetime orthogonal complement ⊥Tp(B) of the tangent space Tp(B) belonging to each point p on the system boundary B. We show how the boost rate may be computed numerically via equations similar to those appearing in canonical investigations of black-hole thermodynamics (although here holding at an outer two-surface rather than the bifurcate two-surface of a Killing horizon). We demonstrate the numerical scheme on a model example, the quasilocal boost of a spherical three-ball in Minkowski spacetime. Developing our general formalism with recent hyperbolic formulations of the Einstein equations in mind, we use Anderson and York's 'Einstein-Christoffel' hyperbolic system as the evolution equations for our numerical simulation of the model.

Cancer in light of experimental evolution.

PubMed

Sprouffske, Kathleen; Merlo, Lauren M F; Gerrish, Philip J; Maley, Carlo C; Sniegowski, Paul D

2012-09-11

Cancer initiation, progression, and the emergence of therapeutic resistance are evolutionary phenomena of clonal somatic cell populations. Studies in microbial experimental evolution and the theoretical work inspired by such studies are yielding deep insights into the evolutionary dynamics of clonal populations, yet there has been little explicit consideration of the relevance of this rapidly growing field to cancer biology. Here, we examine how the understanding of mutation, selection, and spatial structure in clonal populations that is emerging from experimental evolution may be applicable to cancer. Along the way, we discuss some significant ways in which cancer differs from the model systems used in experimental evolution. Despite these differences, we argue that enhanced prediction and control of cancer may be possible using ideas developed in the context of experimental evolution, and we point out some prospects for future research at the interface between these traditionally separate areas. Copyright © 2012 Elsevier Ltd. All rights reserved.

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

PubMed Central

Pankey, M. Sabrina; Minin, Vladimir N.; Imholte, Greg C.; Suchard, Marc A.; Oakley, Todd H.

2014-01-01

Despite contingency in life’s history, the similarity of evolutionarily convergent traits may represent predictable solutions to common conditions. However, the extent to which overall gene expression levels (transcriptomes) underlying convergent traits are themselves convergent remains largely unexplored. Here, we show strong statistical support for convergent evolutionary origins and massively parallel evolution of the entire transcriptomes in symbiotic bioluminescent organs (bacterial photophores) from two divergent squid species. The gene expression similarities are so strong that regression models of one species’ photophore can predict organ identity of a distantly related photophore from gene expression levels alone. Our results point to widespread parallel changes in gene expression evolution associated with convergent origins of complex organs. Therefore, predictable solutions may drive not only the evolution of novel, complex organs but also the evolution of overall gene expression levels that underlie them. PMID:25336755

Cancer in Light of Experimental Evolution

PubMed Central

Sprouffske, Kathleen; Merlo, Lauren M.F.; Gerrish, Philip J.; Maley, Carlo C.; Sniegowski, Paul D.

2012-01-01

Cancer initiation, progression, and the emergence of therapeutic resistance are evolutionary phenomena of clonal somatic cell populations. Studies in microbial experimental evolution and the theoretical work inspired by such studies are yielding deep insights into the evolutionary dynamics of clonal populations, yet there has been little explicit consideration of the relevance of this rapidly growing field to cancer biology. Here, we examine how the understanding of mutation, selection, and spatial structure in clonal populations that is emerging from experimental evolution may be applicable to cancer. Along the way, we discuss some significant ways in which cancer differs from the model systems used in experimental evolution. Despite these differences, we argue that enhanced prediction and control of cancer may be possible using ideas developed in the context of experimental evolution, and we point out some prospects for future research at the interface between these traditionally separate areas. PMID:22975007

Inactivation of tumor suppressor genes and cancer therapy: An evolutionary game theory approach.

PubMed

Khadem, Heydar; Kebriaei, Hamed; Veisi, Zahra

2017-06-01

Inactivation of alleles in tumor suppressor genes (TSG) is one of the important issues resulting in evolution of cancerous cells. In this paper, the evolution of healthy, one and two missed allele cells is modeled using the concept of evolutionary game theory and replicator dynamics. The proposed model also takes into account the interaction rates of the cells as designing parameters of the system. Different combinations of the equilibrium points of the parameterized nonlinear system is studied and categorized into some cases. In each case, the interaction rates' values are suggested in a way that the equilibrium points of the replicator dynamics are located on an appropriate region of the state space. Based on the suggested interaction rates, it is proved that the system doesn't have any undesirable interior equilibrium point as well. Therefore, the system will converge to the desirable region, where there is a scanty level of cancerous cells. In addition, the proposed conditions for interaction rates guarantee that, when a trajectory of the system reaches the boundaries, then it will stay there forever which is a desirable property since the equilibrium points have been already located on the boundaries, appropriately. The simulation results show the effectiveness of the suggestions in the elimination of the cancerous cells in different scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Towards physical principles of biological evolution

NASA Astrophysics Data System (ADS)

Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

2018-03-01

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice for adequate modeling of the biological level of complexity, and new developments within physics itself are likely to be required.

A mathematical model of “Gone with the Wind”

NASA Astrophysics Data System (ADS)

Rinaldi, Sergio; Della Rossa, Fabio; Landi, Pietro

2013-08-01

We develop a mathematical model for mimicking the love story between Scarlett and Rhett described in “Gone with the Wind”. In line with tradition in classical physics, the model is composed of two Ordinary Differential Equations, one for Scarlett and one for Rhett, which encapsulate their main psycho-physical characteristics. The two lovers are described as so-called insecure individuals because they respond very strongly to small involvements of the partner but then attenuate their reaction when the pressure exerted by the partner becomes too high. These characteristics of Scarlett and Rhett clearly emerge during the first part of the film and are sufficient to develop a model that perfectly predicts the complex evolution and the dramatic end of the love story. Since the predicted evolution of the romantic relationship is a direct consequence of the characters of the two individuals, the agreement between the model and the film supports the high credibility of the story. Although credibility of a fictitious story is not necessary from a purely artistic point of view, in most cases it is very appreciated, at the point of being essential in making the film popular. In conclusion, we can say that we have explained with a scientific approach why “Gone with the Wind” has become one of the most successful films of all times.

Stability and bifurcation in a model for the dynamics of stem-like cells in leukemia under treatment

NASA Astrophysics Data System (ADS)

Rǎdulescu, I. R.; Cândea, D.; Halanay, A.

2012-11-01

A mathematical model for the dynamics of leukemic cells during treatment is introduced. Delay differential equations are used to model cells' evolution and are based on the Mackey-Glass approach, incorporating Goldie-Coldman law. Since resistance is propagated by cells that have the capacity of self-renewal, a population of stem-like cells is studied. Equilibrium points are calculated and their stability properties are investigated.

Role of Grain Boundaries under Long-Time Radiation

NASA Astrophysics Data System (ADS)

Zhu, Yichao; Luo, Jing; Guo, Xu; Xiang, Yang; Chapman, Stephen Jonathan

2018-06-01

Materials containing a high proportion of grain boundaries offer significant potential for the development of radiation-resistant structural materials. However, a proper understanding of the connection between the radiation-induced microstructural behavior of a grain boundary and its impact at long natural time scales is still missing. In this Letter, point defect absorption at interfaces is summarized by a jump Robin-type condition at a coarse-grained level, wherein the role of interface microstructure is effectively taken into account. Then a concise formula linking the sink strength of a polycrystalline aggregate with its grain size is introduced and is well compared with experimental observation. Based on the derived model, a coarse-grained formulation incorporating the coupled evolution of grain boundaries and point defects is proposed, so as to underpin the study of long-time morphological evolution of grains induced by irradiation. Our simulation results suggest that the presence of point defect sources within a grain further accelerates its shrinking process, and radiation tends to trigger the extension of twin boundary sections.

Implementation and application of a gradient enhanced crystal plasticity model

NASA Astrophysics Data System (ADS)

Soyarslan, C.; Perdahcıoǧlu, E. S.; Aşık, E. E.; van den Boogaard, A. H.; Bargmann, S.

2017-10-01

A rate-independent crystal plasticity model is implemented in which description of the hardening of the material is given as a function of the total dislocation density. The evolution of statistically stored dislocations (SSDs) is described using a saturating type evolution law. The evolution of geometrically necessary dislocations (GNDs) on the other hand is described using the gradient of the plastic strain tensor in a non-local manner. The gradient of the incremental plastic strain tensor is computed explicitly during an implicit FE simulation after each converged step. Using the plastic strain tensor stored as state variables at each integration point and an efficient numerical algorithm to find the gradients, the GND density is obtained. This results in a weak coupling of the equilibrium solution and the gradient enhancement. The algorithm is applied to an academic test problem which considers growth of a cylindrical void in a single crystal matrix.

Nonlinear viscosity in brane-world cosmology with a Gauss–Bonnet term

NASA Astrophysics Data System (ADS)

Debnath, P. S.; Beesham, A.; Paul, B. C.

2018-06-01

Cosmological solutions are obtained with nonlinear bulk viscous cosmological fluid in the Randall–Sundrum type II (RS) brane-world model with or without Gauss–Bonnet (GB) terms. To describe such a viscous fluid, we consider the nonlinear transport equation which may be used far from equilibrium during inflation or reheating. Cosmological models are explored for both (i) power law and (ii) exponential evolution of the early universe in the presence of an imperfect fluid described by the non-linear Israel and Stewart theory (nIS). We obtain analytic solutions and the complex field equations are also analyzed numerically to study the evolution of the universe. The stability analysis of the equilibrium points of the dynamical system associated with the evolution of the nonlinear bulk viscous fluid in the RS Brane in the presence (or absence) of a GB term are also studied.

From Particles and Point Clouds to Voxel Models: High Resolution Modeling of Dynamic Landscapes in Open Source GIS

NASA Astrophysics Data System (ADS)

Mitasova, H.; Hardin, E. J.; Kratochvilova, A.; Landa, M.

2012-12-01

Multitemporal data acquired by modern mapping technologies provide unique insights into processes driving land surface dynamics. These high resolution data also offer an opportunity to improve the theoretical foundations and accuracy of process-based simulations of evolving landforms. We discuss development of new generation of visualization and analytics tools for GRASS GIS designed for 3D multitemporal data from repeated lidar surveys and from landscape process simulations. We focus on data and simulation methods that are based on point sampling of continuous fields and lead to representation of evolving surfaces as series of raster map layers or voxel models. For multitemporal lidar data we present workflows that combine open source point cloud processing tools with GRASS GIS and custom python scripts to model and analyze dynamics of coastal topography (Figure 1) and we outline development of coastal analysis toolbox. The simulations focus on particle sampling method for solving continuity equations and its application for geospatial modeling of landscape processes. In addition to water and sediment transport models, already implemented in GIS, the new capabilities under development combine OpenFOAM for wind shear stress simulation with a new module for aeolian sand transport and dune evolution simulations. Comparison of observed dynamics with the results of simulations is supported by a new, integrated 2D and 3D visualization interface that provides highly interactive and intuitive access to the redesigned and enhanced visualization tools. Several case studies will be used to illustrate the presented methods and tools and demonstrate the power of workflows built with FOSS and highlight their interoperability.Figure 1. Isosurfaces representing evolution of shoreline and a z=4.5m contour between the years 1997-2011at Cape Hatteras, NC extracted from a voxel model derived from series of lidar-based DEMs.

A stochastic model for tumor geometry evolution during radiation therapy in cervical cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yifang; Lee, Chi-Guhn; Chan, Timothy C. Y., E-mail: tcychan@mie.utoronto.ca

2014-02-15

Purpose: To develop mathematical models to predict the evolution of tumor geometry in cervical cancer undergoing radiation therapy. Methods: The authors develop two mathematical models to estimate tumor geometry change: a Markov model and an isomorphic shrinkage model. The Markov model describes tumor evolution by investigating the change in state (either tumor or nontumor) of voxels on the tumor surface. It assumes that the evolution follows a Markov process. Transition probabilities are obtained using maximum likelihood estimation and depend on the states of neighboring voxels. The isomorphic shrinkage model describes tumor shrinkage or growth in terms of layers of voxelsmore » on the tumor surface, instead of modeling individual voxels. The two proposed models were applied to data from 29 cervical cancer patients treated at Princess Margaret Cancer Centre and then compared to a constant volume approach. Model performance was measured using sensitivity and specificity. Results: The Markov model outperformed both the isomorphic shrinkage and constant volume models in terms of the trade-off between sensitivity (target coverage) and specificity (normal tissue sparing). Generally, the Markov model achieved a few percentage points in improvement in either sensitivity or specificity compared to the other models. The isomorphic shrinkage model was comparable to the Markov approach under certain parameter settings. Convex tumor shapes were easier to predict. Conclusions: By modeling tumor geometry change at the voxel level using a probabilistic model, improvements in target coverage and normal tissue sparing are possible. Our Markov model is flexible and has tunable parameters to adjust model performance to meet a range of criteria. Such a model may support the development of an adaptive paradigm for radiation therapy of cervical cancer.« less

3D microstructural evolution of primary recrystallization and grain growth in cold rolled single-phase aluminum alloys

NASA Astrophysics Data System (ADS)

Adam, Khaled; Zöllner, Dana; Field, David P.

2018-04-01

Modeling the microstructural evolution during recrystallization is a powerful tool for the profound understanding of alloy behavior and for use in optimizing engineering properties through annealing. In particular, the mechanical properties of metallic alloys are highly dependent upon evolved microstructure and texture from the softening process. In the present work, a Monte Carlo (MC) Potts model was used to model the primary recrystallization and grain growth in cold rolled single-phase Al alloy. The microstructural representation of two kinds of dislocation densities, statistically stored dislocations and geometrically necessary dislocations were quantified based on the ViscoPlastic Fast Fourier transform method. This representation was then introduced into the MC Potts model to identify the favorable sites for nucleation where orientation gradients and entanglements of dislocations are high. Additionally, in situ observations of non-isothermal microstructure evolution for single-phase aluminum alloy 1100 were made to validate the simulation. The influence of the texture inhomogeneity is analyzed from a theoretical point of view using an orientation distribution function for deformed and evolved texture.

Lithologic Effects on Landscape Response to Base Level Changes: A Modeling Study in the Context of the Eastern Jura Mountains, Switzerland

NASA Astrophysics Data System (ADS)

Yanites, Brian J.; Becker, Jens K.; Madritsch, Herfried; Schnellmann, Michael; Ehlers, Todd A.

2017-11-01

Landscape evolution is a product of the forces that drive geomorphic processes (e.g., tectonics and climate) and the resistance to those processes. The underlying lithology and structural setting in many landscapes set the resistance to erosion. This study uses a modified version of the Channel-Hillslope Integrated Landscape Development (CHILD) landscape evolution model to determine the effect of a spatially and temporally changing erodibility in a terrain with a complex base level history. Specifically, our focus is to quantify how the effects of variable lithology influence transient base level signals. We set up a series of numerical landscape evolution models with increasing levels of complexity based on the lithologic variability and base level history of the Jura Mountains of northern Switzerland. The models are consistent with lithology (and therewith erodibility) playing an important role in the transient evolution of the landscape. The results show that the erosion rate history at a location depends on the rock uplift and base level history, the range of erodibilities of the different lithologies, and the history of the surface geology downstream from the analyzed location. Near the model boundary, the history of erosion is dominated by the base level history. The transient wave of incision, however, is quite variable in the different model runs and depends on the geometric structure of lithology used. It is thus important to constrain the spatiotemporal erodibility patterns downstream of any given point of interest to understand the evolution of a landscape subject to variable base level in a quantitative framework.

Random unitary evolution model of quantum Darwinism with pure decoherence

NASA Astrophysics Data System (ADS)

Balanesković, Nenad

2015-10-01

We study the behavior of Quantum Darwinism [W.H. Zurek, Nat. Phys. 5, 181 (2009)] within the iterative, random unitary operations qubit-model of pure decoherence [J. Novotný, G. Alber, I. Jex, New J. Phys. 13, 053052 (2011)]. We conclude that Quantum Darwinism, which describes the quantum mechanical evolution of an open system S from the point of view of its environment E, is not a generic phenomenon, but depends on the specific form of input states and on the type of S-E-interactions. Furthermore, we show that within the random unitary model the concept of Quantum Darwinism enables one to explicitly construct and specify artificial input states of environment E that allow to store information about an open system S of interest with maximal efficiency.

Non-Lipschitzian dynamics for neural net modelling

NASA Technical Reports Server (NTRS)

Zak, Michail

1989-01-01

Failure of the Lipschitz condition in unstable equilibrium points of dynamical systems leads to a multiple-choice response to an initial deterministic input. The evolution of such systems is characterized by a special type of unpredictability measured by unbounded Liapunov exponents. Possible relation of these systems to future neural networks is discussed.

Long-Term Evolution of a Long-Term Evolution Model

DTIC Science & Technology

2011-01-01

equations for the movement of the dune toe yD and the berm crest location yB are dyD/dt=(qw-qo)/DD and dyB/dt=-(qw-qo)/(DB+DC) respectively, where qw...and sand properties, yB and yD = distances to the seaward end of the berm and the dune toe , respectively, with the y-axis pointing offshore, y50...relative to mean sea level, MSL); zD = dune toe elevation (with respect to MSL); T = swash period (taken to be the same as the wave period); and Cs

Dynamical Galam model

NASA Astrophysics Data System (ADS)

Cheon, Taksu; Galam, Serge

2018-06-01

We introduce a model of temporal evolution of political opinions which amounts to a dynamical extension of Galam model in which the proportions of inflexibles are treated as dynamical variables. We find that the critical value of inflexibles in the original Galam model now turns into a fixed point of the system whose stability controls the phase trajectory of the political opinions. The appearance of two phases is found, in which majority-preserving and regime-changing limit cycles are respectively dominant, and the phase transition between them is observed.

The development and application of landscape evolution models to coupled coast-estuarine environments

NASA Astrophysics Data System (ADS)

Morris, Chloe; Coulthard, Tom; Parsons, Daniel R.; Manson, Susan; Barkwith, Andrew

2017-04-01

Landscape Evolution Models (LEMs) are proven to be useful tools in understanding the morphodynamics of coast and estuarine systems. However, perhaps owing to the lack of research in this area, current models are not capable of simulating the dynamic interactions between these systems and their co-evolution at the meso-scale. Through a novel coupling of numerical models, this research is designed to explore coupled coastal-estuarine interactions, controls on system behaviour and the influence that environmental change could have. This will contribute to the understanding of the morphodynamics of these systems and how they may behave and evolve over the next century in response to climate changes, with the aim of informing management practices. This goal is being achieved through the modification and coupling of the one-line Coastline Evolution Model (CEM) with the hydrodynamic LEM CAESAR-Lisflood (C-L). The major issues faced with coupling these programs are their differing complexities and the limited graphical visualisations produced by the CEM that hinder the dissemination of results. The work towards overcoming these issues and reported here, include a new version of the CEM that incorporates a range of more complex geomorphological processes and boasts a graphical user interface that guides users through model set-up and projects a live output during model runs. The improved version is a stand-alone tool that can be used for further research projects and for teaching purposes. A sensitivity analysis using the Morris method has been completed to identify which key variables, including wave climate, erosion and weathering values, dominate the control of model behaviour. The model is being applied and tested using the evolution of the Holderness Coast, Humber Estuary and Spurn Point on the east coast of England (UK), which possess diverse geomorphologies and complex, co-evolving sediment pathways. Simulations using the modified CEM are currently being completed to ascertain the processes influential to the morphodynamics and evolution of these systems; presently this includes increasing sea levels and changing wave climate patterns. Outputs and findings from these runs will be presented and discussed, with the aid of the improved graphical visualisations and animations that illustrate the evolution of simulated environments.

Biological signatures of dynamic river networks from a coupled landscape evolution and neutral community model

NASA Astrophysics Data System (ADS)

Stokes, M.; Perron, J. T.

2017-12-01

Freshwater systems host exceptionally species-rich communities whose spatial structure is dictated by the topology of the river networks they inhabit. Over geologic time, river networks are dynamic; drainage basins shrink and grow, and river capture establishes new connections between previously separated regions. It has been hypothesized that these changes in river network structure influence the evolution of life by exchanging and isolating species, perhaps boosting biodiversity in the process. However, no general model exists to predict the evolutionary consequences of landscape change. We couple a neutral community model of freshwater organisms to a landscape evolution model in which the river network undergoes drainage divide migration and repeated river capture. Neutral community models are macro-ecological models that include stochastic speciation and dispersal to produce realistic patterns of biodiversity. We explore the consequences of three modes of speciation - point mutation, time-protracted, and vicariant (geographic) speciation - by tracking patterns of diversity in time and comparing the final result to an equilibrium solution of the neutral model on the final landscape. Under point mutation, a simple model of stochastic and instantaneous speciation, the results are identical to the equilibrium solution and indicate the dominance of the species-area relationship in forming patterns of diversity. The number of species in a basin is proportional to its area, and regional species richness reaches its maximum when drainage area is evenly distributed among sub-basins. Time-protracted speciation is also modeled as a stochastic process, but in order to produce more realistic rates of diversification, speciation is not assumed to be instantaneous. Rather, each new species must persist for a certain amount of time before it is considered to be established. When vicariance (geographic speciation) is included, there is a transient signature of increased regional diversity after river capture. The results indicate that the mode of speciation and the rate of speciation relative to the rate of divide migration determine the evolutionary signature of river capture.

Full velocity difference model for a car-following theory.

PubMed

Jiang, R; Wu, Q; Zhu, Z

2001-07-01

In this paper, we present a full velocity difference model for a car-following theory based on the previous models in the literature. To our knowledge, the model is an improvement over the previous ones theoretically, because it considers more aspects in car-following process than others. This point is verified by numerical simulation. Then we investigate the property of the model using both analytic and numerical methods, and find that the model can describe the phase transition of traffic flow and estimate the evolution of traffic congestion.

A new molecular evolution model for limited insertion independent of substitution.

PubMed

Lèbre, Sophie; Michel, Christian J

2013-10-01

We recently introduced a new molecular evolution model called the IDIS model for Insertion Deletion Independent of Substitution [13,14]. In the IDIS model, the three independent processes of substitution, insertion and deletion of residues have constant rates. In order to control the genome expansion during evolution, we generalize here the IDIS model by introducing an insertion rate which decreases when the sequence grows and tends to 0 for a maximum sequence length nmax. This new model, called LIIS for Limited Insertion Independent of Substitution, defines a matrix differential equation satisfied by a vector P(t) describing the sequence content in each residue at evolution time t. An analytical solution is obtained for any diagonalizable substitution matrix M. Thus, the LIIS model gives an expression of the sequence content vector P(t) in each residue under evolution time t as a function of the eigenvalues and the eigenvectors of matrix M, the residue insertion rate vector R, the total insertion rate r, the initial and maximum sequence lengths n0 and nmax, respectively, and the sequence content vector P(t0) at initial time t0. The derivation of the analytical solution is much more technical, compared to the IDIS model, as it involves Gauss hypergeometric functions. Several propositions of the LIIS model are derived: proof that the IDIS model is a particular case of the LIIS model when the maximum sequence length nmax tends to infinity, fixed point, time scale, time step and time inversion. Using a relation between the sequence length l and the evolution time t, an expression of the LIIS model as a function of the sequence length l=n(t) is obtained. Formulas for 'insertion only', i.e. when the substitution rates are all equal to 0, are derived at evolution time t and sequence length l. Analytical solutions of the LIIS model are explicitly derived, as a function of either evolution time t or sequence length l, for two classical substitution matrices: the 3-parameter symmetric substitution matrix [12] (LIIS-SYM3) and the HKY asymmetric substitution matrix[9] (LIIS-HKY). An evaluation of the LIIS model (precisely, LIIS-HKY) based on four statistical analyses of the GC content in complete genomes of four prokaryotic taxonomic groups, namely Chlamydiae, Crenarchaeota, Spirochaetes and Thermotogae, shows the expected improvement from the theory of the LIIS model compared to the IDIS model. Copyright © 2013 Elsevier Inc. All rights reserved.

Vortex motion in doubly connected domains

NASA Astrophysics Data System (ADS)

Zannetti, L.; Gallizio, F.; Ottino, G. M.

The unsteady two-dimensional rotational flow past doubly connected domains is analytically addressed. By concentrating the vorticity in point vortices, the flow is modelled as a potential flow with point singularities. The dependence of the complex potential on time is defined according to the Kelvin theorem. The general case of non-null circulations around the solid bodies is discussed. Vortex shedding and time evolution of the circulation past a two-element airfoil and past a two-bladed Darrieus turbine are presented as physically coherent examples.

A process model for the heat-affected zone microstructure evolution in duplex stainless steel weldments: Part I. the model

NASA Astrophysics Data System (ADS)

Hemmer, H.; Grong, Ø.

1999-11-01

The present investigation is concerned with modeling of the microstructure evolution in duplex stainless steels under thermal conditions applicable to welding. The important reactions that have been modeled are the dissolution of austenite during heating, subsequent grain growth in the delta ferrite regime, and finally, the decomposition of the delta ferrite to austenite during cooling. As a starting point, a differential formulation of the underlying diffusion problem is presented, based on the internal-state variable approach. These solutions are later manipulated and expressed in terms of the Scheil integral in the cases where the evolution equation is separable or can be made separable by a simple change of variables. The models have then been applied to describe the heat-affected zone microstructure evolution during both thick-plate and thin-plate welding of three commercial duplex stainless steel grades: 2205, 2304, and 2507. The results may conveniently be presented in the form of novel process diagrams, which display contours of constant delta ferrite grain size along with information about dissolution and reprecipitation of austenite for different combinations of weld input energy and peak temperature. These diagrams are well suited for quantitative readings and illustrate, in a condensed manner, the competition between the different variables that lead to structural changes during welding of duplex stainless steels.

Transition from regular to irregular reflection of cylindrical converging shock waves over convex obstacles

NASA Astrophysics Data System (ADS)

Vignati, F.; Guardone, A.

2017-11-01

An analytical model for the evolution of regular reflections of cylindrical converging shock waves over circular-arc obstacles is proposed. The model based on the new (local) parameter, the perceived wedge angle, which substitutes the (global) wedge angle of planar surfaces and accounts for the time-dependent curvature of both the shock and the obstacle at the reflection point, is introduced. The new model compares fairly well with numerical results. Results from numerical simulations of the regular to Mach transition—eventually occurring further downstream along the obstacle—point to the perceived wedge angle as the most significant parameter to identify regular to Mach transitions. Indeed, at the transition point, the value of the perceived wedge angle is between 39° and 42° for all investigated configurations, whereas, e.g., the absolute local wedge angle varies in between 10° and 45° in the same conditions.

A physical model for strain accumulation in the San Francisco Bay region: Stress evolution since 1838

USGS Publications Warehouse

Pollitz, F.; Bakun, W.H.; Nyst, M.

2004-01-01

Understanding of the behavior of plate boundary zones has progressed to the point where reasonably comprehensive physical models can predict their evolution. The San Andreas fault system in the San Francisco Bay region (SFBR) is dominated by a few major faults whose behavior over about one earthquake cycle is fairly well understood. By combining the past history of large ruptures on SFBR faults with a recently proposed physical model of strain accumulation in the SFBR, we derive the evolution of regional stress from 1838 until the present. This effort depends on (1) an existing compilation of the source properties of historic and contemporary SFBR earthquakes based on documented shaking, geodetic data, and seismic data (Bakun, 1999) and (2) a few key parameters of a simple regional viscoelastic coupling model constrained by recent GPS data (Pollitz and Nyst, 2004). Although uncertainties abound in the location, magnitude, and fault geometries of historic ruptures and the physical model relies on gross simplifications, the resulting stress evolution model is sufficiently detailed to provide a useful window into the past stress history. In the framework of Coulomb failure stress, we find that virtually all M ??? 5.8 earthquakes prior to 1906 and M ??? 5.5 earthquakes after 1906 are consistent with stress triggering from previous earthquakes. These events systematically lie in zones of predicted stress concentration elevated 5-10 bars above the regional average. The SFBR is predicted to have emerged from the 1906 "shadow" in about 1980, consistent with the acceleration in regional seismicity at that time. The stress evolution model may be a reliable indicator of the most likely areas to experience M ??? 5.5 shocks in the future.

Phylogenetic comparative methods on phylogenetic networks with reticulations.

PubMed

Bastide, Paul; Solís-Lemus, Claudia; Kriebel, Ricardo; Sparks, K William; Ané, Cécile

2018-04-25

The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

Probabilistic seismic hazard in the San Francisco Bay area based on a simplified viscoelastic cycle model of fault interactions

USGS Publications Warehouse

Pollitz, F.F.; Schwartz, D.P.

2008-01-01

We construct a viscoelastic cycle model of plate boundary deformation that includes the effect of time-dependent interseismic strain accumulation, coseismic strain release, and viscoelastic relaxation of the substrate beneath the seismogenic crust. For a given fault system, time-averaged stress changes at any point (not on a fault) are constrained to zero; that is, kinematic consistency is enforced for the fault system. The dates of last rupture, mean recurrence times, and the slip distributions of the (assumed) repeating ruptures are key inputs into the viscoelastic cycle model. This simple formulation allows construction of stress evolution at all points in the plate boundary zone for purposes of probabilistic seismic hazard analysis (PSHA). Stress evolution is combined with a Coulomb failure stress threshold at representative points on the fault segments to estimate the times of their respective future ruptures. In our PSHA we consider uncertainties in a four-dimensional parameter space: the rupture peridocities, slip distributions, time of last earthquake (for prehistoric ruptures) and Coulomb failure stress thresholds. We apply this methodology to the San Francisco Bay region using a recently determined fault chronology of area faults. Assuming single-segment rupture scenarios, we find that fature rupture probabilities of area faults in the coming decades are the highest for the southern Hayward, Rodgers Creek, and northern Calaveras faults. This conclusion is qualitatively similar to that of Working Group on California Earthquake Probabilities, but the probabilities derived here are significantly higher. Given that fault rupture probabilities are highly model-dependent, no single model should be used to assess to time-dependent rupture probabilities. We suggest that several models, including the present one, be used in a comprehensive PSHA methodology, as was done by Working Group on California Earthquake Probabilities.

Individual-based models for adaptive diversification in high-dimensional phenotype spaces.

PubMed

Ispolatov, Iaroslav; Madhok, Vaibhav; Doebeli, Michael

2016-02-07

Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state before diversification occurs, as exemplified by the concept of evolutionary branching points in adaptive dynamics theory. Recent results indicate that adaptive dynamics may often not converge to equilibrium points and instead generate complicated trajectories if evolution takes place in high-dimensional phenotype spaces. Even though some analytical results on diversification in complex phenotype spaces are available, to study this problem in general we need to reconstruct individual-based models from the adaptive dynamics generating the non-equilibrium dynamics. Here we first provide a method to construct individual-based models such that they faithfully reproduce the given adaptive dynamics attractor without diversification. We then show that a propensity to diversify can be introduced by adding Gaussian competition terms that generate frequency dependence while still preserving the same adaptive dynamics. For sufficiently strong competition, the disruptive selection generated by frequency-dependence overcomes the directional evolution along the selection gradient and leads to diversification in phenotypic directions that are orthogonal to the selection gradient. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Monte Carlo model for 3D grain evolution during welding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodgers, Theron M.; Mitchell, John A.; Tikare, Veena

Welding is one of the most wide-spread processes used in metal joining. However, there are currently no open-source software implementations for the simulation of microstructural evolution during a weld pass. Here we describe a Potts Monte Carlo based model implemented in the SPPARKS kinetic Monte Carlo computational framework. The model simulates melting, solidification and solid-state microstructural evolution of material in the fusion and heat-affected zones of a weld. The model does not simulate thermal behavior, but rather utilizes user input parameters to specify weld pool and heat-affect zone properties. Weld pool shapes are specified by Bezier curves, which allow formore » the specification of a wide range of pool shapes. Pool shapes can range from narrow and deep to wide and shallow representing different fluid flow conditions within the pool. Surrounding temperature gradients are calculated with the aide of a closest point projection algorithm. Furthermore, the model also allows simulation of pulsed power welding through time-dependent variation of the weld pool size. Example simulation results and comparisons with laboratory weld observations demonstrate microstructural variation with weld speed, pool shape, and pulsed-power.« less

A Monte Carlo model for 3D grain evolution during welding

DOE PAGES

Rodgers, Theron M.; Mitchell, John A.; Tikare, Veena

2017-08-04

Welding is one of the most wide-spread processes used in metal joining. However, there are currently no open-source software implementations for the simulation of microstructural evolution during a weld pass. Here we describe a Potts Monte Carlo based model implemented in the SPPARKS kinetic Monte Carlo computational framework. The model simulates melting, solidification and solid-state microstructural evolution of material in the fusion and heat-affected zones of a weld. The model does not simulate thermal behavior, but rather utilizes user input parameters to specify weld pool and heat-affect zone properties. Weld pool shapes are specified by Bezier curves, which allow formore » the specification of a wide range of pool shapes. Pool shapes can range from narrow and deep to wide and shallow representing different fluid flow conditions within the pool. Surrounding temperature gradients are calculated with the aide of a closest point projection algorithm. Furthermore, the model also allows simulation of pulsed power welding through time-dependent variation of the weld pool size. Example simulation results and comparisons with laboratory weld observations demonstrate microstructural variation with weld speed, pool shape, and pulsed-power.« less

Organizational models of emergency psychiatric intervention: state of the art.

PubMed

Barra, A; Daini, S; Tonioni, F; Bria, P

2007-01-01

Authors outline the differences between medical and psychiatric definition of emergency and analyze different organizational models of psychiatric intervention in Emergency Room. The historical evolution changed these models, and the relation with services for acute and subacute patients in hospital and community services. The Italian reform model is compared with the slow deinstitutionalization of psychiatry in other countries. Critical points in Italian emergency organization after the Psychiatric Reform are pointed out: low number of beds for acute patients, difficulties and delays in transfer from Emergency Room to GHPW (General Hospital Psychiatric Ward), waiting lists for voluntary treatments. To overcome some of these problems, the Authors propose that even in hospitals without psychiatric ward, a small unit of short psychiatric observation be implemented, for voluntary treatments, before transfer to other institutions.

Division of labour and the evolution of multicellularity

PubMed Central

Ispolatov, Iaroslav; Ackermann, Martin; Doebeli, Michael

2012-01-01

Understanding the emergence and evolution of multicellularity and cellular differentiation is a core problem in biology. We develop a quantitative model that shows that a multicellular form emerges from genetically identical unicellular ancestors when the compartmentalization of poorly compatible physiological processes into component cells of an aggregate produces a fitness advantage. This division of labour between the cells in the aggregate occurs spontaneously at the regulatory level owing to mechanisms present in unicellular ancestors and does not require any genetic predisposition for a particular role in the aggregate or any orchestrated cooperative behaviour of aggregate cells. Mathematically, aggregation implies an increase in the dimensionality of phenotype space that generates a fitness landscape with new fitness maxima, in which the unicellular states of optimized metabolism become fitness saddle points. Evolution of multicellularity is modelled as evolution of a hereditary parameter: the propensity of cells to stick together, which determines the fraction of time a cell spends in the aggregate form. Stickiness can increase evolutionarily owing to the fitness advantage generated by the division of labour between cells in an aggregate. PMID:22158952

Critical zone evolution and the origins of organised complexity in watersheds

NASA Astrophysics Data System (ADS)

Harman, C.; Troch, P. A.; Pelletier, J.; Rasmussen, C.; Chorover, J.

2012-04-01

The capacity of the landscape to store and transmit water is the result of a historical trajectory of landscape, soil and vegetation development, much of which is driven by hydrology itself. Progress in geomorphology and pedology has produced models of surface and sub-surface evolution in soil-mantled uplands. These dissected, denuding modeled landscapes are emblematic of the kinds of dissipative self-organized flow structures whose hydrologic organization may also be understood by low-dimensional hydrologic models. They offer an exciting starting-point for examining the mapping between the long-term controls on landscape evolution and the high-frequency hydrologic dynamics. Here we build on recent theoretical developments in geomorphology and pedology to try to understand how the relative rates of erosion, sediment transport and soil development in a landscape determine catchment storage capacity and the relative dominance of runoff process, flow pathways and storage-discharge relationships. We do so by using a combination of landscape evolution models, hydrologic process models and data from a variety of sources, including the University of Arizona Critical Zone Observatory. A challenge to linking the landscape evolution and hydrologic model representations is the vast differences in the timescales implicit in the process representations. Furthermore the vast array of processes involved makes parameterization of such models an enormous challenge. The best data-constrained geomorphic transport and soil development laws only represent hydrologic processes implicitly, through the transport and weathering rate parameters. In this work we propose to avoid this problem by identifying the relationship between the landscape and soil evolution parameters and macroscopic climate and geological controls. These macroscopic controls (such as the aridity index) have two roles: 1) they express the water and energy constraints on the long-term evolution of the landscape system, and 2) they bound the range of plausible short-term hydroclimatic regimes that may drive a particular landscape's hydrologic dynamics. To ensure that the hydrologic dynamics implicit in the evolutionary parameters are compatible with the dynamics observed in the hydrologic modeling, a set of consistency checks based on flow process dominance are developed.

Bouc-Wen hysteresis model identification using Modified Firefly Algorithm

NASA Astrophysics Data System (ADS)

Zaman, Mohammad Asif; Sikder, Urmita

2015-12-01

The parameters of Bouc-Wen hysteresis model are identified using a Modified Firefly Algorithm. The proposed algorithm uses dynamic process control parameters to improve its performance. The algorithm is used to find the model parameter values that results in the least amount of error between a set of given data points and points obtained from the Bouc-Wen model. The performance of the algorithm is compared with the performance of conventional Firefly Algorithm, Genetic Algorithm and Differential Evolution algorithm in terms of convergence rate and accuracy. Compared to the other three optimization algorithms, the proposed algorithm is found to have good convergence rate with high degree of accuracy in identifying Bouc-Wen model parameters. Finally, the proposed method is used to find the Bouc-Wen model parameters from experimental data. The obtained model is found to be in good agreement with measured data.

Participation costs can suppress the evolution of upstream reciprocity.

PubMed

Peña, Jorge; Pestelacci, Enea; Berchtold, André; Tomassini, Marco

2011-03-21

Indirect reciprocity, one of the many mechanisms proposed to explain the evolution of cooperation, is the idea that altruistic actions can be rewarded by third parties. Upstream or generalized reciprocity is one type of indirect reciprocity in which individuals help someone if they have been helped by somebody else in the past. Although empirically found to be at work in humans, the evolution of upstream reciprocity is difficult to explain from a theoretical point of view. A recent model of upstream reciprocity, first proposed by Nowak and Roch (2007) and further analyzed by Iwagami and Masuda (2010), shows that while upstream reciprocity alone does not lead to the evolution of cooperation, it can act in tandem with mechanisms such as network reciprocity and increase the total level of cooperativity in the population. We argue, however, that Nowak and Roch's model systematically leads to non-uniform interaction rates, where more cooperative individuals take part in more games than less cooperative ones. As a result, the critical benefit-to-cost ratios derived under this model in previous studies are not invariant with respect to the addition of participation costs. We show that accounting for these costs can hinder and even suppress the evolution of upstream reciprocity, both for populations with non-random encounters and graph-structured populations. Copyright © 2011 Elsevier Ltd. All rights reserved.

Notes from 1999 on computational algorithm of the Local Wave-Vector (LWV) model for the dynamical evolution of the second-rank velocity correlation tensor starting from the mean-flow-coupled Navier-Stokes equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zemach, Charles; Kurien, Susan

These notes present an account of the Local Wave Vector (LWV) model of a turbulent flow defined throughout physical space. The previously-developed Local Wave Number (LWN) model is taken as a point of departure. Some general properties of turbulent fields and appropriate notation are given first. The LWV model is presently restricted to incompressible flows and the incompressibility assumption is introduced at an early point in the discussion. The assumption that the turbulence is homogeneous is also introduced early on. This assumption can be relaxed by generalizing the space diffusion terms of LWN, but the present discussion is focused onmore » a modeling of homogeneous turbulence.« less

Modeling Day-to-day Flow Dynamics on Degradable Transport Network

PubMed Central

Gao, Bo; Zhang, Ronghui; Lou, Xiaoming

2016-01-01

Stochastic link capacity degradations are common phenomena in transport network which can cause travel time variations and further can affect travelers’ daily route choice behaviors. This paper formulates a deterministic dynamic model, to capture the day-to-day (DTD) flow evolution process in the presence of degraded link capacity degradations. The aggregated network flow dynamics are driven by travelers’ study of uncertain travel time and their choice of risky routes. This paper applies the exponential-smoothing filter to describe travelers’ study of travel time variations, and meanwhile formulates risk attitude parameter updating equation to reflect travelers’ endogenous risk attitude evolution schema. In addition, this paper conducts theoretical analyses to investigate several significant mathematical characteristics implied in the proposed DTD model, including fixed point existence, uniqueness, stability and irreversibility. Numerical experiments are used to demonstrate the effectiveness of the DTD model and verify some important dynamic system properties. PMID:27959903

Coronal loop hydrodynamics. The solar flare observed on November 12, 1980 revisited: The UV line emission

NASA Astrophysics Data System (ADS)

Betta, R. M.; Peres, G.; Reale, F.; Serio, S.

2001-12-01

We revisit a well-studied solar flare whose X-ray emission originating from a simple loop structure was observed by most of the instruments on board SMM on November 12, 1980. The X-ray emission of this flare, as observed with the XRP, was successfully modeled previously. Here we include a detailed modeling of the transition region and we compare the hydrodynamic results with the UVSP observations in two EUV lines, measured in areas smaller than the XRP rasters, covering only some portions of the flaring loop (the top and the foot-points). The single loop hydrodynamic model, which fits well the evolution of coronal lines (those observed with the XRP and the Fe XXI 1354.1 Å line observed with the UVSP) fails to model the flux level and evolution of the O V 1371.3 Åline.

Model for nucleon valence structure functions at all x, all p ⊥ and all Q 2 from the correspondence between QCD and DTU

NASA Astrophysics Data System (ADS)

Cohen-Tannoudji, G.; El Hassouni, A.; Mantrach, A.; Oudrhiri-Safiani, E. G.

1982-09-01

We propose a simple parametrization of the nucleon valence structure functions at all x, all p ⊥ and all Q 2. We use the DTU parton model to fix the parametrization at a reference point ( Q {0/2}=3 GeV2) and we mimic the QCD evolution by replacing the dimensioned parameters of the DTU parton model by functions depending on Q 2. Excellent agreement is obtained with existing data.

Approximating basins of attraction for dynamical systems via stable radial bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cavoretto, R.; De Rossi, A.; Perracchione, E.

2016-06-08

In applied sciences it is often required to model and supervise temporal evolution of populations via dynamical systems. In this paper, we focus on the problem of approximating the basins of attraction of such models for each stable equilibrium point. We propose to reconstruct the basins via an implicit interpolant using stable radial bases, obtaining the surfaces by partitioning the phase space into disjoint regions. An application to a competition model presenting jointly three stable equilibria is considered.

NUMERICAL MODELING OF THE COAGULATION AND POROSITY EVOLUTION OF DUST AGGREGATES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okuzumi, Satoshi; Sakagami, Masa-aki; Tanaka, Hidekazu, E-mail: satoshi.okuzumi@ax2.ecs.kyoto-u.ac.j

2009-12-20

Porosity evolution of dust aggregates is crucial in understanding dust evolution in protoplanetary disks. In this study, we present useful tools to study the coagulation and porosity evolution of dust aggregates. First, we present a new numerical method for simulating dust coagulation and porosity evolution as an extension of the conventional Smoluchowski equation. This method follows the evolution of the mean porosity for each aggregate mass simultaneously with the evolution of the mass distribution function. This method reproduces the results of previous Monte Carlo simulations with much less computational expense. Second, we propose a new collision model for porous dustmore » aggregates on the basis of our N-body experiments on aggregate collisions. As the first step, we focus on 'hit-and-stick' collisions, which involve neither compression nor fragmentation of aggregates. We first obtain empirical data on porosity changes between the classical limits of ballistic cluster-cluster and particle-cluster aggregation. Using the data, we construct a recipe for the porosity change due to general hit-and-stick collisions as well as formulae for the aerodynamical and collisional cross sections. Our collision model is thus more realistic than a previous model of Ormel et al. based on the classical aggregation limits only. Simple coagulation simulations using the extended Smoluchowski method show that our collision model explains the fractal dimensions of porous aggregates observed in a full N-body simulation and a laboratory experiment. By contrast, similar simulations using the collision model of Ormel et al. result in much less porous aggregates, meaning that this model underestimates the porosity increase upon unequal-sized collisions. Besides, we discover that aggregates at the high-mass end of the distribution can have a considerably small aerodynamical cross section per unit mass compared with aggregates of lower masses. This occurs when aggregates drift under uniform acceleration (e.g., gravity) and their collision is induced by the difference in their terminal velocities. We point out an important implication of this discovery for dust growth in protoplanetary disks.« less

Modeling thermal spike driven reactions at low temperature and application to zirconium carbide radiation damage

NASA Astrophysics Data System (ADS)

Ulmer, Christopher J.; Motta, Arthur T.

2017-11-01

The development of TEM-visible damage in materials under irradiation at cryogenic temperatures cannot be explained using classical rate theory modeling with thermally activated reactions since at low temperatures thermal reaction rates are too low. Although point defect mobility approaches zero at low temperature, the thermal spikes induced by displacement cascades enable some atom mobility as it cools. In this work a model is developed to calculate "athermal" reaction rates from the atomic mobility within the irradiation-induced thermal spikes, including both displacement cascades and electronic stopping. The athermal reaction rates are added to a simple rate theory cluster dynamics model to allow for the simulation of microstructure evolution during irradiation at cryogenic temperatures. The rate theory model is applied to in-situ irradiation of ZrC and compares well at cryogenic temperatures. The results show that the addition of the thermal spike model makes it possible to rationalize microstructure evolution in the low temperature regime.

Degeneration of the Y chromosome in evolutionary aging models

NASA Astrophysics Data System (ADS)

Lobo, M. P.; Onody, R. N.

2005-06-01

The Y chromosomes are genetically degenerated and do not recombine with their matching partners X. Recombination of XX pairs is pointed out as the key factor for the Y chromosome degeneration. However, there is an additional evolutionary force driving sex-chromosomes evolution. Here we show this mechanism by means of two different evolutionary models, in which sex chromosomes with non-recombining XX and XY pairs of chromosomes is considered. Our results show three curious effects. First, we observed that even when both XX and XY pairs of chromosomes do not recombine, the Y chromosomes still degenerate. Second, the accumulation of mutations on Y chromosomes followed a completely different pattern then those accumulated on X chromosomes. And third, the models may differ with respect to sexual proportion. These findings suggest that a more primeval mechanism rules the evolution of Y chromosomes due exclusively to the sex-chromosomes asymmetry itself, i.e., the fact that Y chromosomes never experience female bodies. Over aeons, natural selection favored X chromosomes spontaneously, even if at the very beginning of evolution, both XX and XY pairs of chromosomes did not recombine.

The evolution of massive stars including mass loss - Presupernova models and explosion

NASA Technical Reports Server (NTRS)

Woosley, S. E.; Langer, Norbert; Weaver, Thomas A.

1993-01-01

The evolution of massive stars of 35, 40, 60, and 85 solar masses is followed through all stages of nuclear burning to the point of Fe core collapse. Critical nuclear reaction and mass-loss rates are varied. Efficient mass loss during the Wolf-Rayet (WR) stage is likely to lead to final masses as small as 4 solar masses. For a reasonable parameterization of the mass loss, there may be convergence of all WR stars, both single and in binaries, to a narrow band of small final masses. Our representative model, a 4.25 solar-mass WR presupernova derived from a 60 solar mass star, is followed through a simulated explosion, and its explosive nucleosynthesis and light curve are determined. Its properties are similar to those observed in Type Ib supernovae. The effects of the initial mass and mass loss on the presupernova structure of small mass WR models is also explored. Important properties of the presupernova star and its explosion can only be obtained by following the complete evolution starting on the main sequence.

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Noise effect in metabolic networks

NASA Astrophysics Data System (ADS)

Li, Zheng-Yan; Xie, Zheng-Wei; Chen, Tong; Ouyang, Qi

2009-12-01

Constraint-based models such as flux balance analysis (FBA) are a powerful tool to study biological metabolic networks. Under the hypothesis that cells operate at an optimal growth rate as the result of evolution and natural selection, this model successfully predicts most cellular behaviours in growth rate. However, the model ignores the fact that cells can change their cellular metabolic states during evolution, leaving optimal metabolic states unstable. Here, we consider all the cellular processes that change metabolic states into a single term 'noise', and assume that cells change metabolic states by randomly walking in feasible solution space. By simulating a state of a cell randomly walking in the constrained solution space of metabolic networks, we found that in a noisy environment cells in optimal states tend to travel away from these points. On considering the competition between the noise effect and the growth effect in cell evolution, we found that there exists a trade-off between these two effects. As a result, the population of the cells contains different cellular metabolic states, and the population growth rate is at suboptimal states.

Evolution of opinions on social networks in the presence of competing committed groups.

PubMed

Xie, Jierui; Emenheiser, Jeffrey; Kirby, Matthew; Sreenivasan, Sameet; Szymanski, Boleslaw K; Korniss, Gyorgy

2012-01-01

Public opinion is often affected by the presence of committed groups of individuals dedicated to competing points of view. Using a model of pairwise social influence, we study how the presence of such groups within social networks affects the outcome and the speed of evolution of the overall opinion on the network. Earlier work indicated that a single committed group within a dense social network can cause the entire network to quickly adopt the group's opinion (in times scaling logarithmically with the network size), so long as the committed group constitutes more than about 10% of the population (with the findings being qualitatively similar for sparse networks as well). Here we study the more general case of opinion evolution when two groups committed to distinct, competing opinions A and B, and constituting fractions pA and pB of the total population respectively, are present in the network. We show for stylized social networks (including Erdös-Rényi random graphs and Barabási-Albert scale-free networks) that the phase diagram of this system in parameter space (pA,pB) consists of two regions, one where two stable steady-states coexist, and the remaining where only a single stable steady-state exists. These two regions are separated by two fold-bifurcation (spinodal) lines which meet tangentially and terminate at a cusp (critical point). We provide further insights to the phase diagram and to the nature of the underlying phase transitions by investigating the model on infinite (mean-field limit), finite complete graphs and finite sparse networks. For the latter case, we also derive the scaling exponent associated with the exponential growth of switching times as a function of the distance from the critical point.

Evolution of Opinions on Social Networks in the Presence of Competing Committed Groups

PubMed Central

Xie, Jierui; Emenheiser, Jeffrey; Kirby, Matthew; Sreenivasan, Sameet; Szymanski, Boleslaw K.; Korniss, Gyorgy

2012-01-01

Public opinion is often affected by the presence of committed groups of individuals dedicated to competing points of view. Using a model of pairwise social influence, we study how the presence of such groups within social networks affects the outcome and the speed of evolution of the overall opinion on the network. Earlier work indicated that a single committed group within a dense social network can cause the entire network to quickly adopt the group's opinion (in times scaling logarithmically with the network size), so long as the committed group constitutes more than about of the population (with the findings being qualitatively similar for sparse networks as well). Here we study the more general case of opinion evolution when two groups committed to distinct, competing opinions and , and constituting fractions and of the total population respectively, are present in the network. We show for stylized social networks (including Erdös-Rényi random graphs and Barabási-Albert scale-free networks) that the phase diagram of this system in parameter space consists of two regions, one where two stable steady-states coexist, and the remaining where only a single stable steady-state exists. These two regions are separated by two fold-bifurcation (spinodal) lines which meet tangentially and terminate at a cusp (critical point). We provide further insights to the phase diagram and to the nature of the underlying phase transitions by investigating the model on infinite (mean-field limit), finite complete graphs and finite sparse networks. For the latter case, we also derive the scaling exponent associated with the exponential growth of switching times as a function of the distance from the critical point. PMID:22448238

The Impact of Mutation and Gene Conversion on the Local Diversification of Antigen Genes in African Trypanosomes

PubMed Central

Gjini, Erida; Haydon, Daniel T.; Barry, J. David; Cobbold, Christina A.

2012-01-01

Patterns of genetic diversity in parasite antigen gene families hold important information about their potential to generate antigenic variation within and between hosts. The evolution of such gene families is typically driven by gene duplication, followed by point mutation and gene conversion. There is great interest in estimating the rates of these processes from molecular sequences for understanding the evolution of the pathogen and its significance for infection processes. In this study, a series of models are constructed to investigate hypotheses about the nucleotide diversity patterns between closely related gene sequences from the antigen gene archive of the African trypanosome, the protozoan parasite causative of human sleeping sickness in Equatorial Africa. We use a hidden Markov model approach to identify two scales of diversification: clustering of sequence mismatches, a putative indicator of gene conversion events with other lower-identity donor genes in the archive, and at a sparser scale, isolated mismatches, likely arising from independent point mutations. In addition to quantifying the respective probabilities of occurrence of these two processes, our approach yields estimates for the gene conversion tract length distribution and the average diversity contributed locally by conversion events. Model fitting is conducted using a Bayesian framework. We find that diversifying gene conversion events with lower-identity partners occur at least five times less frequently than point mutations on variant surface glycoprotein (VSG) pairs, and the average imported conversion tract is between 14 and 25 nucleotides long. However, because of the high diversity introduced by gene conversion, the two processes have almost equal impact on the per-nucleotide rate of sequence diversification between VSG subfamily members. We are able to disentangle the most likely locations of point mutations and conversions on each aligned gene pair. PMID:22735079

Optimized growth and reorientation of anisotropic material based on evolution equations

NASA Astrophysics Data System (ADS)

Jantos, Dustin R.; Junker, Philipp; Hackl, Klaus

2018-07-01

Modern high-performance materials have inherent anisotropic elastic properties. The local material orientation can thus be considered to be an additional design variable for the topology optimization of structures containing such materials. In our previous work, we introduced a variational growth approach to topology optimization for isotropic, linear-elastic materials. We solved the optimization problem purely by application of Hamilton's principle. In this way, we were able to determine an evolution equation for the spatial distribution of density mass, which can be evaluated in an iterative process within a solitary finite element environment. We now add the local material orientation described by a set of three Euler angles as additional design variables into the three-dimensional model. This leads to three additional evolution equations that can be separately evaluated for each (material) point. Thus, no additional field unknown within the finite element approach is needed, and the evolution of the spatial distribution of density mass and the evolution of the Euler angles can be evaluated simultaneously.

Quasi-brittle damage modeling based on incremental energy relaxation combined with a viscous-type regularization

NASA Astrophysics Data System (ADS)

Langenfeld, K.; Junker, P.; Mosler, J.

2018-05-01

This paper deals with a constitutive model suitable for the analysis of quasi-brittle damage in structures. The model is based on incremental energy relaxation combined with a viscous-type regularization. A similar approach—which also represents the inspiration for the improved model presented in this paper—was recently proposed in Junker et al. (Contin Mech Thermodyn 29(1):291-310, 2017). Within this work, the model introduced in Junker et al. (2017) is critically analyzed first. This analysis leads to an improved model which shows the same features as that in Junker et al. (2017), but which (i) eliminates unnecessary model parameters, (ii) can be better interpreted from a physics point of view, (iii) can capture a fully softened state (zero stresses), and (iv) is characterized by a very simple evolution equation. In contrast to the cited work, this evolution equation is (v) integrated fully implicitly and (vi) the resulting time-discrete evolution equation can be solved analytically providing a numerically efficient closed-form solution. It is shown that the final model is indeed well-posed (i.e., its tangent is positive definite). Explicit conditions guaranteeing this well-posedness are derived. Furthermore, by additively decomposing the stress rate into deformation- and purely time-dependent terms, the functionality of the model is explained. Illustrative numerical examples confirm the theoretical findings.

Evolution of the lunar highland crust

NASA Technical Reports Server (NTRS)

Taylor, S. R.; Bence, A. E.

1975-01-01

The evolution of three distinct element associations in the lunar highland crust is discussed in terms of the Taylor-Jakes model which involves melting of most of the moon during accretion. Sources for (1) high Ca, Al, Sr, Eu, (2) high Mg and Cr, and (3) high K, REE, Zr, Hf, Nb are suggested. Bombardment by large projectiles during the differentiation process causes melting and mixing, which produces a wide range of compositions in the crust. The formation of dunite, troctolite, high-, medium-, and low-K Fra Mauro basalts, and rocks close to the olivine-spinel-plagioclase peritectic point is considered.

Tipping Points in Resource Abundance Drive Irreversible Changes in Community Structure.

PubMed

Haney, Seth D; Siepielski, Adam M

2018-05-01

Global climate change has made what were seemingly extraordinary environmental conditions, such as prolonged droughts, commonplace. One consequence of extreme environmental change is concomitant changes in resource abundance. How will such extreme resource changes impact biodiversity? We developed a trait-based consumer-resource model to examine how resource abundance affects the potential for adaptive evolution and coexistence among competitors. We found that moderate changes in resource abundance have little effect on trait evolution. However, when resource scarcities were sufficiently extreme, a critical transition-a tipping point-occurred, which caused consumer traits to diverge and restructured the community in a way that outlasted the scarcity. Therefore, even though traits can evolve in response to minor resource fluctuations, large environmental shifts may be necessary for producing long-lasting impacts on community structure. These results may also help to illuminate patterns of stasis frequently observed in nature, despite the considerable evidence demonstrating rapid evolutionary change.

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

PubMed Central

Chan, Yvonne H.; Venev, Sergey V.; Zeldovich, Konstantin B.; Matthews, C. Robert

2017-01-01

Sequence divergence of orthologous proteins enables adaptation to environmental stresses and promotes evolution of novel functions. Limits on evolution imposed by constraints on sequence and structure were explored using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Fitness effects of point mutations in three phylogenetically divergent IGPS proteins during adaptation to temperature stress were probed by auxotrophic complementation of yeast with prokaryotic, thermophilic IGPS. Analysis of beneficial mutations pointed to an unexpected, long-range allosteric pathway towards the active site of the protein. Significant correlations between the fitness landscapes of distant orthologues implicate both sequence and structure as primary forces in defining the TIM barrel fitness landscape and suggest that fitness landscapes can be translocated in sequence space. Exploration of fitness landscapes in the context of a protein fold provides a strategy for elucidating the sequence-structure-fitness relationships in other common motifs. PMID:28262665

Quantum speed limit for arbitrary initial states

PubMed Central

Zhang, Ying-Jie; Han, Wei; Xia, Yun-Jie; Cao, Jun-Peng; Fan, Heng

2014-01-01

The minimal time a system needs to evolve from an initial state to its one orthogonal state is defined as the quantum speed limit time, which can be used to characterize the maximal speed of evolution of a quantum system. This is a fundamental question of quantum physics. We investigate the generic bound on the minimal evolution time of the open dynamical quantum system. This quantum speed limit time is applicable to both mixed and pure initial states. We then apply this result to the damped Jaynes-Cummings model and the Ohimc-like dephasing model starting from a general time-evolution state. The bound of this time-dependent state at any point in time can be found. For the damped Jaynes-Cummings model, when the system starts from the excited state, the corresponding bound first decreases and then increases in the Markovian dynamics. While in the non-Markovian regime, the speed limit time shows an interesting periodic oscillatory behavior. For the case of Ohimc-like dephasing model, this bound would be gradually trapped to a fixed value. In addition, the roles of the relativistic effects on the speed limit time for the observer in non-inertial frames are discussed. PMID:24809395

G-bounce

DOE Office of Scientific and Technical Information (OSTI.GOV)

Easson, Damien A.; Sawicki, Ignacy; Vikman, Alexander, E-mail: easson@asu.edu, E-mail: ignacy.sawicki@uni-heidelberg.de, E-mail: alexander.vikman@cern.ch

2011-11-01

We present a wide class of models which realise a bounce in a spatially flat Friedmann universe in standard General Relativity. The key ingredient of the theories we consider is a noncanonical, minimally coupled scalar field belonging to the class of theories with Kinetic Gravity Braiding / Galileon-like self-couplings. In these models, the universe smoothly evolves from contraction to expansion, suffering neither from ghosts nor gradient instabilities around the turning point. The end-point of the evolution can be a standard radiation-domination era or an inflationary phase. We formulate necessary restrictions for Lagrangians needed to obtain a healthy bounce and illustratemore » our results with phase portraits for simple systems including the recently proposed Galilean Genesis scenario.« less

Molecular Evolution and Mosaicism of Leptospiral Outer Membrane Proteins Involves Horizontal DNA Transfer

PubMed Central

Haake, David A.; Suchard, Marc A.; Kelley, Melissa M.; Dundoo, Manjula; Alt, David P.; Zuerner, Richard L.

2004-01-01

Leptospires belong to a genus of parasitic bacterial spirochetes that have adapted to a broad range of mammalian hosts. Mechanisms of leptospiral molecular evolution were explored by sequence analysis of four genes shared by 38 strains belonging to the core group of pathogenic Leptospira species: L. interrogans, L. kirschneri, L. noguchii, L. borgpetersenii, L. santarosai, and L. weilii. The 16S rRNA and lipL32 genes were highly conserved, and the lipL41 and ompL1 genes were significantly more variable. Synonymous substitutions are distributed throughout the ompL1 gene, whereas nonsynonymous substitutions are clustered in four variable regions encoding surface loops. While phylogenetic trees for the 16S, lipL32, and lipL41 genes were relatively stable, 8 of 38 (20%) ompL1 sequences had mosaic compositions consistent with horizontal transfer of DNA between related bacterial species. A novel Bayesian multiple change point model was used to identify the most likely sites of recombination and to determine the phylogenetic relatedness of the segments of the mosaic ompL1 genes. Segments of the mosaic ompL1 genes encoding two of the surface-exposed loops were likely acquired by horizontal transfer from a peregrine allele of unknown ancestry. Identification of the most likely sites of recombination with the Bayesian multiple change point model, an approach which has not previously been applied to prokaryotic gene sequence analysis, serves as a model for future studies of recombination in molecular evolution of genes. PMID:15090524

Experimental evolution in biofilm populations

PubMed Central

Steenackers, Hans P.; Parijs, Ilse; Foster, Kevin R.; Vanderleyden, Jozef

2016-01-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. PMID:26895713

Evolution of functional specialization and division of labor.

PubMed

Rueffler, Claus; Hermisson, Joachim; Wagner, Günter P

2012-02-07

Division of labor among functionally specialized modules occurs at all levels of biological organization in both animals and plants. Well-known examples include the evolution of specialized enzymes after gene duplication, the evolution of specialized cell types, limb diversification in arthropods, and the evolution of specialized colony members in many taxa of marine invertebrates and social insects. Here, we identify conditions favoring the evolution of division of labor by means of a general mathematical model. Our starting point is the assumption that modules contribute to two different biological tasks and that the potential of modules to contribute to these tasks is traded off. Our results are phrased in terms of properties of performance functions that map the phenotype of modules to measures of performance. We show that division of labor is favored by three factors: positional effects that predispose modules for one of the tasks, accelerating performance functions, and synergistic interactions between modules. If modules can be lost or damaged, selection for robustness can counteract selection for functional specialization. To illustrate our theory we apply it to the evolution of specialized enzymes coded by duplicated genes.

Experimental evolution in biofilm populations.

PubMed

Steenackers, Hans P; Parijs, Ilse; Dubey, Akanksha; Foster, Kevin R; Vanderleyden, Jozef

2016-05-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. © FEMS 2016.

Multiple Active Contours Guided by Differential Evolution for Medical Image Segmentation

PubMed Central

Cruz-Aceves, I.; Avina-Cervantes, J. G.; Lopez-Hernandez, J. M.; Rostro-Gonzalez, H.; Garcia-Capulin, C. H.; Torres-Cisneros, M.; Guzman-Cabrera, R.

2013-01-01

This paper presents a new image segmentation method based on multiple active contours guided by differential evolution, called MACDE. The segmentation method uses differential evolution over a polar coordinate system to increase the exploration and exploitation capabilities regarding the classical active contour model. To evaluate the performance of the proposed method, a set of synthetic images with complex objects, Gaussian noise, and deep concavities is introduced. Subsequently, MACDE is applied on datasets of sequential computed tomography and magnetic resonance images which contain the human heart and the human left ventricle, respectively. Finally, to obtain a quantitative and qualitative evaluation of the medical image segmentations compared to regions outlined by experts, a set of distance and similarity metrics has been adopted. According to the experimental results, MACDE outperforms the classical active contour model and the interactive Tseng method in terms of efficiency and robustness for obtaining the optimal control points and attains a high accuracy segmentation. PMID:23983809

Evolution of Extragalactic Radio Sources and Quasar/Galaxy Unification

NASA Astrophysics Data System (ADS)

Onah, C. I.; Ubachukwu, A. A.; Odo, F. C.; Onuchukwu, C. C.

2018-04-01

We use a large sample of radio sources to investigate the effects of evolution, luminosity selection and radio source orientation in explaining the apparent deviation of observed angular size - redshift (θ - z) relation of extragalactic radio sources (EGRSs) from the standard model. We have fitted the observed θ - z data with standard cosmological models based on a flat universe (Ω0 = 1). The size evolution of EGRSs has been described as luminosity, temporal and orientation-dependent in the form DP,z,Φ ≍ P±q(1 + z)-m sinΦ, with q=0.3, Φ=59°, m=-0.26 for radio galaxies and q=-0.5, Φ=33°, m=3.1 for radio quasars respectively. Critical points of luminosity, logPcrit=26.33 WHz-1 and logDc=2.51 kpc (316.23 kpc) of the present sample of radio sources were also observed. All the results were found to be consistent with the popular quasar/galaxy unification scheme.

Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens

PubMed Central

Gallie, Jenna; Libby, Eric; Bertels, Frederic; Remigi, Philippe; Jendresen, Christian B.; Ferguson, Gayle C.; Desprat, Nicolas; Buffing, Marieke F.; Sauer, Uwe; Beaumont, Hubertus J. E.; Martinussen, Jan; Kilstrup, Mogens; Rainey, Paul B.

2015-01-01

Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF), while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON). This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution. PMID:25763575

Geometry in a dynamical system without space: Hyperbolic Geometry in Kuramoto Oscillator Systems

NASA Astrophysics Data System (ADS)

Engelbrecht, Jan; Chen, Bolun; Mirollo, Renato

Kuramoto oscillator networks have the special property that their time evolution is constrained to lie on 3D orbits of the Möbius group acting on the N-fold torus TN which explains the N - 3 constants of motion discovered by Watanabe and Strogatz. The dynamics for phase models can be further reduced to 2D invariant sets in T N - 1 which have a natural geometry equivalent to the unit disk Δ with hyperbolic metric. We show that the classic Kuramoto model with order parameter Z1 (the first moment of the oscillator configuration) is a gradient flow in this metric with a unique fixed point on each generic 2D invariant set, corresponding to the hyperbolic barycenter of an oscillator configuration. This gradient property makes the dynamics especially easy to analyze. We exhibit several new families of Kuramoto oscillator models which reduce to gradient flows in this metric; some of these have a richer fixed point structure including non-hyperbolic fixed points associated with fixed point bifurcations. Work Supported by NSF DMS 1413020.

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.

PubMed

Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A; Catenacci, Daniel V T; Hudson, Richard R; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

2015-11-24

The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 "polymorphic" SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors.

A simple and general method for solving detailed chemical evolution with delayed production of iron and other chemical elements

NASA Astrophysics Data System (ADS)

Vincenzo, F.; Matteucci, F.; Spitoni, E.

2017-04-01

We present a theoretical method for solving the chemical evolution of galaxies by assuming an instantaneous recycling approximation for chemical elements restored by massive stars and the delay time distribution formalism for delayed chemical enrichment by Type Ia Supernovae. The galaxy gas mass assembly history, together with the assumed stellar yields and initial mass function, represents the starting point of this method. We derive a simple and general equation, which closely relates the Laplace transforms of the galaxy gas accretion history and star formation history, which can be used to simplify the problem of retrieving these quantities in the galaxy evolution models assuming a linear Schmidt-Kennicutt law. We find that - once the galaxy star formation history has been reconstructed from our assumptions - the differential equation for the evolution of the chemical element X can be suitably solved with classical methods. We apply our model to reproduce the [O/Fe] and [Si/Fe] versus [Fe/H] chemical abundance patterns as observed at the solar neighbourhood by assuming a decaying exponential infall rate of gas and different delay time distributions for Type Ia Supernovae; we also explore the effect of assuming a non-linear Schmidt-Kennicutt law, with the index of the power law being k = 1.4. Although approximate, we conclude that our model with the single-degenerate scenario for Type Ia Supernovae provides the best agreement with the observed set of data. Our method can be used by other complementary galaxy stellar population synthesis models to predict also the chemical evolution of galaxies.

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

PubMed Central

Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A.; Catenacci, Daniel V. T.; Hudson, Richard R.; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

2015-01-01

The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 “polymorphic” SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors. PMID:26561581

GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites.

PubMed

Leinweber, Matthias; Fober, Thomas; Freisleben, Bernd

2018-01-01

In this paper, we present a novel approach to solve the labeled point cloud superpositioning problem for performing structural comparisons of protein binding sites. The solution is based on a parallel evolution strategy that operates on large populations and runs on GPU hardware. The proposed evolution strategy reduces the likelihood of getting stuck in a local optimum of the multimodal real-valued optimization problem represented by labeled point cloud superpositioning. The performance of the GPU-based parallel evolution strategy is compared to a previously proposed CPU-based sequential approach for labeled point cloud superpositioning, indicating that the GPU-based parallel evolution strategy leads to qualitatively better results and significantly shorter runtimes, with speed improvements of up to a factor of 1,500 for large populations. Binary classification tests based on the ATP, NADH, and FAD protein subsets of CavBase, a database containing putative binding sites, show average classification rate improvements from about 92 percent (CPU) to 96 percent (GPU). Further experiments indicate that the proposed GPU-based labeled point cloud superpositioning approach can be superior to traditional protein comparison approaches based on sequence alignments.

Simple point vortex model for the relaxation of 2D superfluid turbulence in a Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Kim, Joon Hyun; Kwon, Woo Jin; Shin, Yong-Il

2016-05-01

In a recent experiment, it was found that the dissipative evolution of a corotating vortex pair in a trapped Bose-Einstein condensate is well described by a point vortex model with longitudinal friction on the vortex motion and the thermal friction coefficient was determined as a function of sample temperature. In this poster, we present a numerical study on the relaxation of 2D superfluid turbulence based on the dissipative point vortex model. We consider a homogeneous system in a cylindrical trap having randomly distributed vortices and implement the vortex-antivortex pair annihilation by removing a pair when its separation becomes smaller than a certain threshold value. We characterize the relaxation of the turbulent vortex states with the decay time required for the vortex number to be reduced to a quarter of initial number. We find the vortex decay time is inversely proportional to the thermal friction coefficient. In particular, we observe the decay times obtained from this work show good quantitative agreement with the experimental results in, indicating that in spite of its simplicity, the point vortex model reasonably captures the physics in the relaxation dynamics of the real system.

On the optically thick winds of Wolf-Rayet stars

NASA Astrophysics Data System (ADS)

Gräfener, G.; Owocki, S. P.; Grassitelli, L.; Langer, N.

2017-12-01

Context. The classical Wolf-Rayet (WR) phase is believed to mark the end stage of the evolution of massive stars with initial masses higher than 25M⊙. Stars in this phase expose their stripped cores with the products of H- or He-burning at their surface. They develop strong, optically thick stellar winds that are important for the mechanical and chemical feedback of massive stars, and that determine whether the most massive stars end their lives as neutron stars or black holes. The winds of WR stars are currently not well understood, and their inclusion in stellar evolution models relies on uncertain empirical mass-loss relations. Aims: We investigate theoretically the mass-loss properties of H-free WR stars of the nitrogen sequence (WN stars). Methods: We connected stellar structure models for He stars with wind models for optically thick winds and assessed the degree to which these two types of models can simultaneously fulfil their respective sonic-point conditions. Results: Fixing the outer wind law and terminal wind velocity ν∞, we obtain unique solutions for the mass-loss rates of optically thick, radiation-driven winds of WR stars in the phase of core He-burning. The resulting mass-loss relations as a function of stellar parameters agree well with previous empirical relations. Furthermore, we encounter stellar mass limits below which no continuous solutions exist. While these mass limits agree with observations of WR stars in the Galaxy, they contradict observations in the LMC. Conclusions: While our results in particular confirm the slope of often-used empirical mass-loss relations, they imply that only part of the observed WN population can be understood in the framework of the standard assumptions of a smooth transonic flow and compact stellar core. This means that alternative approaches such as a clumped and inflated wind structure or deviations from the diffusion limit at the sonic point may have to be invoked. Qualitatively, the existence of mass limits for the formation of WR-type winds may be relevant for the non-detection of low-mass WR stars in binary systems, which are believed to be progenitors of Type Ib/c supernovae. The sonic-point conditions derived in this work may provide a possibility to include optically thick winds in stellar evolution models in a more physically motivated form than in current models.

Hyperextended Cosmological Perturbation Theory: Predicting Nonlinear Clustering Amplitudes

NASA Astrophysics Data System (ADS)

Scoccimarro, Román; Frieman, Joshua A.

1999-07-01

We consider the long-standing problem of predicting the hierarchical clustering amplitudes Sp in the strongly nonlinear regime of gravitational evolution. N-body results for the nonlinear evolution of the bispectrum (the Fourier transform of the three-point density correlation function) suggest a physically motivated Ansatz that yields the strongly nonlinear behavior of the skewness, S3, starting from leading-order perturbation theory. When generalized to higher order (p>3) polyspectra or correlation functions, this Ansatz leads to a good description of nonlinear amplitudes in the strongly nonlinear regime for both scale-free and cold dark matter models. Furthermore, these results allow us to provide a general fitting formula for the nonlinear evolution of the bispectrum that interpolates between the weakly and strongly nonlinear regimes, analogous to previous expressions for the power spectrum.

The Brownian mean field model

NASA Astrophysics Data System (ADS)

Chavanis, Pierre-Henri

2014-05-01

We discuss the dynamics and thermodynamics of the Brownian mean field (BMF) model which is a system of N Brownian particles moving on a circle and interacting via a cosine potential. It can be viewed as the canonical version of the Hamiltonian mean field (HMF) model. The BMF model displays a second order phase transition from a homogeneous phase to an inhomogeneous phase below a critical temperature T c = 1 / 2. We first complete the description of this model in the mean field approximation valid for N → +∞. In the strong friction limit, the evolution of the density towards the mean field Boltzmann distribution is governed by the mean field Smoluchowski equation. For T < T c , this equation describes a process of self-organization from a non-magnetized (homogeneous) phase to a magnetized (inhomogeneous) phase. We obtain an analytical expression for the temporal evolution of the magnetization close to T c . Then, we take fluctuations (finite N effects) into account. The evolution of the density is governed by the stochastic Smoluchowski equation. From this equation, we derive a stochastic equation for the magnetization and study its properties both in the homogenous and inhomogeneous phase. We show that the fluctuations diverge at the critical point so that the mean field approximation ceases to be valid. Actually, the limits N → +∞ and T → T c do not commute. The validity of the mean field approximation requires N( T - T c ) → +∞ so that N must be larger and larger as T approaches T c . We show that the direction of the magnetization changes rapidly close to T c while its amplitude takes a long time to relax. We also indicate that, for systems with long-range interactions, the lifetime of metastable states scales as e N except close to a critical point. The BMF model shares many analogies with other systems of Brownian particles with long-range interactions such as self-gravitating Brownian particles, the Keller-Segel model describing the chemotaxis of bacterial populations, the Kuramoto model describing the collective synchronization of coupled oscillators, the Desai-Zwanzig model, and the models describing the collective motion of social organisms such as bird flocks or fish schools.

Numerical-experimental investigation of load paths in DP800 dual phase steel during Nakajima test

NASA Astrophysics Data System (ADS)

Bergs, Thomas; Nick, Matthias; Feuerhack, Andreas; Trauth, Daniel; Klocke, Fritz

2018-05-01

Fuel efficiency requirements demand lightweight construction of vehicle body parts. The usage of advanced high strength steels permits a reduction of sheet thickness while still maintaining the overall strength required for crash safety. However, damage, internal defects (voids, inclusions, micro fractures), microstructural defects (varying grain size distribution, precipitates on grain boundaries, anisotropy) and surface defects (micro fractures, grooves) act as a concentration point for stress and consequently as an initiation point for failure both during deep drawing and in service. Considering damage evolution in the design of car body deep drawing processes allows for a further reduction in material usage and therefore body weight. Preliminary research has shown that a modification of load paths in forming processes can help mitigate the effects of damage on the material. This paper investigates the load paths in Nakajima tests of a DP800 dual phase steel to research damage in deep drawing processes. Investigation is done via a finite element model using experimentally validated material data for a DP800 dual phase steel. Numerical simulation allows for the investigation of load paths with respect to stress states, strain rates and temperature evolution, which cannot be easily observed in physical experiments. Stress triaxiality and the Lode parameter are used to describe the stress states. Their evolution during the Nakajima tests serves as an indicator for damage evolution. The large variety of sheet metal forming specific load paths in Nakajima tests allows a comprehensive evaluation of damage for deep drawing. The results of the numerical simulation conducted in this project and further physical experiments will later be used to calibrate a damage model for simulation of deep drawing processes.

Mechanical model for filament buckling and growth by phase ordering.

PubMed

Rey, Alejandro D; Abukhdeir, Nasser M

2008-02-05

A mechanical model of open filament shape and growth driven by phase ordering is formulated. For a given phase-ordering driving force, the model output is the filament shape evolution and the filament end-point kinematics. The linearized model for the slope of the filament is the Cahn-Hilliard model of spinodal decomposition, where the buckling corresponds to concentration fluctuations. Two modes are predicted: (i) sequential growth and buckling and (ii) simultaneous buckling and growth. The relation among the maximum buckling rate, filament tension, and matrix viscosity is given. These results contribute to ongoing work in smectic A filament buckling.

Physical properties of the WR stars in Westerlund 1

NASA Astrophysics Data System (ADS)

Rosslowe, C. K.; Crowther, P. A.; Clark, J. S.; Negueruela, I.

The Westerlund 1 (Wd1) cluster hosts a rich and varied collection of massive stars. Its dynamical youth and the absence of ongoing star formation indicate a coeval population. As such, the simultaneous presence of both late-type supergiants and Wolf-Rayet stars has defied explanation in the context of single-star evolution. Observational evidence points to a high binary fraction, hence this stellar population offers a robust test for stellar models accounting for both single-star and binary evolution. We present an optical to near-IR (VLT & NTT) spectroscopic analysis of 22 WR stars in Wd 1, delivering physical properties for the WR stars. We discuss how these differ from the Galactic field population, and how they may be reconciled with the predictions of single and binary evolutionary models.

Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.

PubMed

Arenas, Miguel

2015-04-01

NGS technologies present a fast and cheap generation of genomic data. Nevertheless, ancestral genome inference is not so straightforward due to complex evolutionary processes acting on this material such as inversions, translocations, and other genome rearrangements that, in addition to their implicit complexity, can co-occur and confound ancestral inferences. Recently, models of genome evolution that accommodate such complex genomic events are emerging. This letter explores these novel evolutionary models and proposes their incorporation into robust statistical approaches based on computer simulations, such as approximate Bayesian computation, that may produce a more realistic evolutionary analysis of genomic data. Advantages and pitfalls in using these analytical methods are discussed. Potential applications of these ancestral genomic inferences are also pointed out.

An evolving effective stress approach to anisotropic distortional hardening

DOE PAGES

Lester, B. T.; Scherzinger, W. M.

2018-03-11

A new yield surface with an evolving effective stress definition is proposed for consistently and efficiently describing anisotropic distortional hardening. Specifically, a new internal state variable is introduced to capture the thermodynamic evolution between different effective stress definitions. The corresponding yield surface and evolution equations of the internal variables are derived from thermodynamic considerations enabling satisfaction of the second law. A closest point projection return mapping algorithm for the proposed model is formulated and implemented for use in finite element analyses. Finally, select constitutive and larger scale boundary value problems are solved to explore the capabilities of the model andmore » examine the impact of distortional hardening on constitutive and structural responses. Importantly, these simulations demonstrate the tractability of the proposed formulation in investigating large-scale problems of interest.« less

An evolving effective stress approach to anisotropic distortional hardening

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lester, B. T.; Scherzinger, W. M.

A new yield surface with an evolving effective stress definition is proposed for consistently and efficiently describing anisotropic distortional hardening. Specifically, a new internal state variable is introduced to capture the thermodynamic evolution between different effective stress definitions. The corresponding yield surface and evolution equations of the internal variables are derived from thermodynamic considerations enabling satisfaction of the second law. A closest point projection return mapping algorithm for the proposed model is formulated and implemented for use in finite element analyses. Finally, select constitutive and larger scale boundary value problems are solved to explore the capabilities of the model andmore » examine the impact of distortional hardening on constitutive and structural responses. Importantly, these simulations demonstrate the tractability of the proposed formulation in investigating large-scale problems of interest.« less

Atmospheric Modeling Using Accelerometer Data During Mars Atmosphere and Volatile Evolution (MAVEN) Flight Operations

NASA Technical Reports Server (NTRS)

Tolson, Robert H.; Lugo, Rafael A.; Baird, Darren T.; Cianciolo, Alicia D.; Bougher, Stephen W.; Zurek, Richard M.

2017-01-01

The Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft is a NASA orbiter designed to explore the Mars upper atmosphere, typically from 140 to 160 km altitude. In addition to the nominal science mission, MAVEN has performed several Deep Dip campaigns in which the orbit's closest point of approach, also called periapsis, was lowered to an altitude range of 115 to 135 km. MAVEN accelerometer data were used during mission operations to estimate atmospheric parameters such as density, scale height, along-track gradients, and wave structures. Density and scale height estimates were compared against those obtained from the Mars Global Reference Atmospheric Model and used to aid the MAVEN navigation team in planning maneuvers to raise and lower periapsis during Deep Dip operations. This paper describes the processes used to reconstruct atmosphere parameters from accelerometers data and presents the results of their comparison to model and navigation-derived values.

[The history of development of evolutionary methods in St. Petersburg school of computer simulation in biology].

PubMed

Menshutkin, V V; Kazanskiĭ, A B; Levchenko, V F

2010-01-01

The history of rise and development of evolutionary methods in Saint Petersburg school of biological modelling is traced and analyzed. Some pioneering works in simulation of ecological and evolutionary processes, performed in St.-Petersburg school became an exemplary ones for many followers in Russia and abroad. The individual-based approach became the crucial point in the history of the school as an adequate instrument for construction of models of biological evolution. This approach is natural for simulation of the evolution of life-history parameters and adaptive processes in populations and communities. In some cases simulated evolutionary process was used for solving a reverse problem, i. e., for estimation of uncertain life-history parameters of population. Evolutionary computations is one more aspect of this approach application in great many fields. The problems and vistas of ecological and evolutionary modelling in general are discussed.

Constraints and entropy in a model of network evolution

NASA Astrophysics Data System (ADS)

Tee, Philip; Wakeman, Ian; Parisis, George; Dawes, Jonathan; Kiss, István Z.

2017-11-01

Barabási-Albert's "Scale Free" model is the starting point for much of the accepted theory of the evolution of real world communication networks. Careful comparison of the theory with a wide range of real world networks, however, indicates that the model is in some cases, only a rough approximation to the dynamical evolution of real networks. In particular, the exponent γ of the power law distribution of degree is predicted by the model to be exactly 3, whereas in a number of real world networks it has values between 1.2 and 2.9. In addition, the degree distributions of real networks exhibit cut offs at high node degree, which indicates the existence of maximal node degrees for these networks. In this paper we propose a simple extension to the "Scale Free" model, which offers better agreement with the experimental data. This improvement is satisfying, but the model still does not explain why the attachment probabilities should favor high degree nodes, or indeed how constraints arrive in non-physical networks. Using recent advances in the analysis of the entropy of graphs at the node level we propose a first principles derivation for the "Scale Free" and "constraints" model from thermodynamic principles, and demonstrate that both preferential attachment and constraints could arise as a natural consequence of the second law of thermodynamics.

On Religion and Language Evolutions Seen Through Mathematical and Agent Based Models

NASA Astrophysics Data System (ADS)

Ausloos, M.

Religions and languages are social variables, like age, sex, wealth or political opinions, to be studied like any other organizational parameter. In fact, religiosity is one of the most important sociological aspects of populations. Languages are also obvious characteristics of the human species. Religions, languages appear though also disappear. All religions and languages evolve and survive when they adapt to the society developments. On the other hand, the number of adherents of a given religion, or the number of persons speaking a language is not fixed in time, - nor space. Several questions can be raised. E.g. from a oscopic point of view : How many religions/languages exist at a given time? What is their distribution? What is their life time? How do they evolve? From a "microscopic" view point: can one invent agent based models to describe oscopic aspects? Do simple evolution equations exist? How complicated must be a model? These aspects are considered in the present note. Basic evolution equations are outlined and critically, though briefly, discussed. Similarities and differences between religions and languages are summarized. Cases can be illustrated with historical facts and data. It is stressed that characteristic time scales are different. It is emphasized that "external fields" are historically very relevant in the case of religions, rending the study more " interesting" within a mechanistic approach based on parity and symmetry of clusters concepts. Yet the modern description of human societies through networks in reported simulations is still lacking some mandatory ingredients, i.e. the non scalar nature of the nodes, and the non binary aspects of nodes and links, though for the latter this is already often taken into account, including directions. From an analytical point of view one can consider a population independently of the others. It is intuitively accepted, but also found from the statistical analysis of the frequency distribution that an attachment process is the primary cause of the distribution evolution in the number of adepts: usually the initial religion/language is that of the mother. However later on, changes can occur either due to "heterogeneous agent interaction" processes or due to "external field" constraints, - or both. In so doing one has to consider competition-like processes, in a general environment with different rates of reproduction. More general equations are thus proposed for future work.

A novel method of multi-scale simulation of macro-scale deformation and microstructure evolution on metal forming

NASA Astrophysics Data System (ADS)

Huang, Shiquan; Yi, Youping; Li, Pengchuan

2011-05-01

In recent years, multi-scale simulation technique of metal forming is gaining significant attention for prediction of the whole deformation process and microstructure evolution of product. The advances of numerical simulation at macro-scale level on metal forming are remarkable and the commercial FEM software, such as Deform2D/3D, has found a wide application in the fields of metal forming. However, the simulation method of multi-scale has little application due to the non-linearity of microstructure evolution during forming and the difficulty of modeling at the micro-scale level. This work deals with the modeling of microstructure evolution and a new method of multi-scale simulation in forging process. The aviation material 7050 aluminum alloy has been used as example for modeling of microstructure evolution. The corresponding thermal simulated experiment has been performed on Gleeble 1500 machine. The tested specimens have been analyzed for modeling of dislocation density, nucleation and growth of recrystallization(DRX). The source program using cellular automaton (CA) method has been developed to simulate the grain nucleation and growth, in which the change of grain topology structure caused by the metal deformation was considered. The physical fields at macro-scale level such as temperature field, stress and strain fields, which can be obtained by commercial software Deform 3D, are coupled with the deformed storage energy at micro-scale level by dislocation model to realize the multi-scale simulation. This method was explained by forging process simulation of the aircraft wheel hub forging. Coupled the results of Deform 3D with CA results, the forging deformation progress and the microstructure evolution at any point of forging could be simulated. For verifying the efficiency of simulation, experiments of aircraft wheel hub forging have been done in the laboratory and the comparison of simulation and experiment result has been discussed in details.

Global regularizing flows with topology preservation for active contours and polygons.

PubMed

Sundaramoorthi, Ganesh; Yezzi, Anthony

2007-03-01

Active contour and active polygon models have been used widely for image segmentation. In some applications, the topology of the object(s) to be detected from an image is known a priori, despite a complex unknown geometry, and it is important that the active contour or polygon maintain the desired topology. In this work, we construct a novel geometric flow that can be added to image-based evolutions of active contours and polygons in order to preserve the topology of the initial contour or polygon. We emphasize that, unlike other methods for topology preservation, the proposed geometric flow continually adjusts the geometry of the original evolution in a gradual and graceful manner so as to prevent a topology change long before the curve or polygon becomes close to topology change. The flow also serves as a global regularity term for the evolving contour, and has smoothness properties similar to curvature flow. These properties of gradually adjusting the original flow and global regularization prevent geometrical inaccuracies common with simple discrete topology preservation schemes. The proposed topology preserving geometric flow is the gradient flow arising from an energy that is based on electrostatic principles. The evolution of a single point on the contour depends on all other points of the contour, which is different from traditional curve evolutions in the computer vision literature.

Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

PubMed Central

Bastolla, Ugo

2014-01-01

The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change. PMID:24970217

Cosmic CARNage I: on the calibration of galaxy formation models

NASA Astrophysics Data System (ADS)

Knebe, Alexander; Pearce, Frazer R.; Gonzalez-Perez, Violeta; Thomas, Peter A.; Benson, Andrew; Asquith, Rachel; Blaizot, Jeremy; Bower, Richard; Carretero, Jorge; Castander, Francisco J.; Cattaneo, Andrea; Cora, Sofía A.; Croton, Darren J.; Cui, Weiguang; Cunnama, Daniel; Devriendt, Julien E.; Elahi, Pascal J.; Font, Andreea; Fontanot, Fabio; Gargiulo, Ignacio D.; Helly, John; Henriques, Bruno; Lee, Jaehyun; Mamon, Gary A.; Onions, Julian; Padilla, Nelson D.; Power, Chris; Pujol, Arnau; Ruiz, Andrés N.; Srisawat, Chaichalit; Stevens, Adam R. H.; Tollet, Edouard; Vega-Martínez, Cristian A.; Yi, Sukyoung K.

2018-04-01

We present a comparison of nine galaxy formation models, eight semi-analytical, and one halo occupation distribution model, run on the same underlying cold dark matter simulation (cosmological box of comoving width 125h-1 Mpc, with a dark-matter particle mass of 1.24 × 109h-1M⊙) and the same merger trees. While their free parameters have been calibrated to the same observational data sets using two approaches, they nevertheless retain some `memory' of any previous calibration that served as the starting point (especially for the manually tuned models). For the first calibration, models reproduce the observed z = 0 galaxy stellar mass function (SMF) within 3σ. The second calibration extended the observational data to include the z = 2 SMF alongside the z ˜ 0 star formation rate function, cold gas mass, and the black hole-bulge mass relation. Encapsulating the observed evolution of the SMF from z = 2 to 0 is found to be very hard within the context of the physics currently included in the models. We finally use our calibrated models to study the evolution of the stellar-to-halo mass (SHM) ratio. For all models, we find that the peak value of the SHM relation decreases with redshift. However, the trends seen for the evolution of the peak position as well as the mean scatter in the SHM relation are rather weak and strongly model dependent. Both the calibration data sets and model results are publicly available.

A maximally particle-hole asymmetric spectrum emanating from a semi-Dirac point.

PubMed

Quan, Yundi; Pickett, Warren E

2018-02-21

Tight binding models have proven an effective means of revealing Dirac (massless) dispersion, flat bands (infinite mass), and intermediate cases such as the semi-Dirac (sD) dispersion. This approach is extended to a three band model that yields, with chosen parameters in a two-band limit, a closed line with maximally asymmetric particle-hole dispersion: infinite mass holes, zero mass particles. The model retains the sD points for a general set of parameters. Adjacent to this limiting case, hole Fermi surfaces are tiny and needle-like. A pair of large electron Fermi surfaces at low doping merge and collapse at half filling to a flat (zero energy) closed contour with infinite mass along the contour and enclosing no carriers on either side, while the hole Fermi surface has shrunk to a point at zero energy, also containing no carriers. The tight binding model is used to study several characteristics of the dispersion and density of states. The model inspired generalization of sD dispersion to a general  ±[Formula: see text] form, for which analysis reveals that both n and m must be odd to provide a diabolical point with topological character. Evolution of the Hofstadter spectrum of this three band system with interband coupling strength is presented and discussed.

A maximally particle-hole asymmetric spectrum emanating from a semi-Dirac point

NASA Astrophysics Data System (ADS)

Quan, Yundi; Pickett, Warren E.

2018-02-01

Tight binding models have proven an effective means of revealing Dirac (massless) dispersion, flat bands (infinite mass), and intermediate cases such as the semi-Dirac (sD) dispersion. This approach is extended to a three band model that yields, with chosen parameters in a two-band limit, a closed line with maximally asymmetric particle-hole dispersion: infinite mass holes, zero mass particles. The model retains the sD points for a general set of parameters. Adjacent to this limiting case, hole Fermi surfaces are tiny and needle-like. A pair of large electron Fermi surfaces at low doping merge and collapse at half filling to a flat (zero energy) closed contour with infinite mass along the contour and enclosing no carriers on either side, while the hole Fermi surface has shrunk to a point at zero energy, also containing no carriers. The tight binding model is used to study several characteristics of the dispersion and density of states. The model inspired generalization of sD dispersion to a general  ± \\sqrt{k_x2n +k_y2m} form, for which analysis reveals that both n and m must be odd to provide a diabolical point with topological character. Evolution of the Hofstadter spectrum of this three band system with interband coupling strength is presented and discussed.

Criticality of the random field Ising model in and out of equilibrium: A nonperturbative functional renormalization group description

NASA Astrophysics Data System (ADS)

Balog, Ivan; Tarjus, Gilles; Tissier, Matthieu

2018-03-01

We show that, contrary to previous suggestions based on computer simulations or erroneous theoretical treatments, the critical points of the random-field Ising model out of equilibrium, when quasistatically changing the applied source at zero temperature, and in equilibrium are not in the same universality class below some critical dimension dD R≈5.1 . We demonstrate this by implementing a nonperturbative functional renormalization group for the associated dynamical field theory. Above dD R, the avalanches, which characterize the evolution of the system at zero temperature, become irrelevant at large distance, and hysteresis and equilibrium critical points are then controlled by the same fixed point. We explain how to use computer simulation and finite-size scaling to check the correspondence between in and out of equilibrium criticality in a far less ambiguous way than done so far.

Time-dependent probability density functions and information geometry in stochastic logistic and Gompertz models

NASA Astrophysics Data System (ADS)

Tenkès, Lucille-Marie; Hollerbach, Rainer; Kim, Eun-jin

2017-12-01

A probabilistic description is essential for understanding growth processes in non-stationary states. In this paper, we compute time-dependent probability density functions (PDFs) in order to investigate stochastic logistic and Gompertz models, which are two of the most popular growth models. We consider different types of short-correlated multiplicative and additive noise sources and compare the time-dependent PDFs in the two models, elucidating the effects of the additive and multiplicative noises on the form of PDFs. We demonstrate an interesting transition from a unimodal to a bimodal PDF as the multiplicative noise increases for a fixed value of the additive noise. A much weaker (leaky) attractor in the Gompertz model leads to a significant (singular) growth of the population of a very small size. We point out the limitation of using stationary PDFs, mean value and variance in understanding statistical properties of the growth in non-stationary states, highlighting the importance of time-dependent PDFs. We further compare these two models from the perspective of information change that occurs during the growth process. Specifically, we define an infinitesimal distance at any time by comparing two PDFs at times infinitesimally apart and sum these distances in time. The total distance along the trajectory quantifies the total number of different states that the system undergoes in time, and is called the information length. We show that the time-evolution of the two models become more similar when measured in units of the information length and point out the merit of using the information length in unifying and understanding the dynamic evolution of different growth processes.

Identifying musical pieces from fMRI data using encoding and decoding models.

PubMed

Hoefle, Sebastian; Engel, Annerose; Basilio, Rodrigo; Alluri, Vinoo; Toiviainen, Petri; Cagy, Maurício; Moll, Jorge

2018-02-02

Encoding models can reveal and decode neural representations in the visual and semantic domains. However, a thorough understanding of how distributed information in auditory cortices and temporal evolution of music contribute to model performance is still lacking in the musical domain. We measured fMRI responses during naturalistic music listening and constructed a two-stage approach that first mapped musical features in auditory cortices and then decoded novel musical pieces. We then probed the influence of stimuli duration (number of time points) and spatial extent (number of voxels) on decoding accuracy. Our approach revealed a linear increase in accuracy with duration and a point of optimal model performance for the spatial extent. We further showed that Shannon entropy is a driving factor, boosting accuracy up to 95% for music with highest information content. These findings provide key insights for future decoding and reconstruction algorithms and open new venues for possible clinical applications.

Impact of different policies on unhealthy dietary behaviors in an urban adult population: an agent-based simulation model.

PubMed

Zhang, Donglan; Giabbanelli, Philippe J; Arah, Onyebuchi A; Zimmerman, Frederick J

2014-07-01

Unhealthy eating is a complex-system problem. We used agent-based modeling to examine the effects of different policies on unhealthy eating behaviors. We developed an agent-based simulation model to represent a synthetic population of adults in Pasadena, CA, and how they make dietary decisions. Data from the 2007 Food Attitudes and Behaviors Survey and other empirical studies were used to calibrate the parameters of the model. Simulations were performed to contrast the potential effects of various policies on the evolution of dietary decisions. Our model showed that a 20% increase in taxes on fast foods would lower the probability of fast-food consumption by 3 percentage points, whereas improving the visibility of positive social norms by 10%, either through community-based or mass-media campaigns, could improve the consumption of fruits and vegetables by 7 percentage points and lower fast-food consumption by 6 percentage points. Zoning policies had no significant impact. Interventions emphasizing healthy eating norms may be more effective than directly targeting food prices or regulating local food outlets. Agent-based modeling may be a useful tool for testing the population-level effects of various policies within complex systems.

Sediment Dynamics in Shallow Tidal Landscapes: The Role of Wind Waves and Tidal Currents

NASA Astrophysics Data System (ADS)

Carniello, L.; D'Alpaos, A.

2014-12-01

A precise description of sediment dynamics (resuspension and re-distribution of sediments) is crucial when investigating the long term evolution of the different morphological entities characterizing tidal landscapes. It has been demonstrated that wind waves are the main responsible for sediment resuspension in shallow micro-tidal lagoons where tidal currents, which produce shear stresses large enough to carry sediments into suspension only within the main channels, are mainly responsible for sediment redistribution. A mathematical model has been developed to describe sediment entrainment, transport and deposition due to the combined effect of tidal currents and wind waves in shallow lagoons considering both cohesive and non-cohesive sediments. The model was calibrated and tested using both in situ point observations and turbidity maps obtained analyzing satellite images. Once calibrated the model can integrate the high temporal resolution of point observations with the high spatial resolution of remote sensing, overcoming the intrinsic limitation of these two types of observations. The model was applied to the specific test case of the Venice lagoon simulating an entire year (2005) which was shown to be a "representative" year for wind and tide characteristics. The time evolution of the computed total bottom shear stresses (BSS) and suspended sediment concentration (SSC) was analyzed on the basis of a "Peaks Over Threshold" method once a critical value for shear stress and turbidity were chosen. The analyses of the numerical results enabled us to demonstrate that resuspension events can be modeled as marked Poisson processes: interarrival time, intensity of peak excesses and duration being exponentially distributed random variable. The probability distributions of the interarrival time of overthreshold exceedances in both BSS and SSC as well as their intensity and duration can be used in long-term morphodynamic studies to generate synthetic series statistically equivalent to real sequences through which MonteCarlo realizations of relevant morphological evolutions can be computed.

Computational modelling of mesoscale dislocation patterning and plastic deformation of single crystals

NASA Astrophysics Data System (ADS)

Xia, Shengxu; El-Azab, Anter

2015-07-01

We present a continuum dislocation dynamics model that predicts the formation of dislocation cell structure in single crystals at low strains. The model features a set of kinetic equations of the curl type that govern the space and time evolution of the dislocation density in the crystal. These kinetic equations are coupled to stress equilibrium and deformation kinematics using the eigenstrain approach. A custom finite element method has been developed to solve the coupled system of equations of dislocation kinetics and crystal mechanics. The results show that, in general, dislocations self-organize in patterns under their mutual interactions. However, the famous dislocation cell structure has been found to form only when cross slip is implemented in the model. Cross slip is also found to lower the yield point, increase the hardening rate, and sustain an increase in the dislocation density over the hardening regime. Analysis of the cell structure evolution reveals that the average cell size decreases with the applied stress, which is consistent with the similitude principle.

On the acoustics of ancient Greek and Roman theaters.

PubMed

Farnetani, Andrea; Prodi, Nicola; Pompoli, Roberto

2008-09-01

The interplay of architecture and acoustics is remarkable in ancient Greek and Roman theaters. Frequently they are nowadays lively performance spaces and the knowledge of the sound field inside them is still an issue of relevant importance. Even if the transition from Greek to Roman theaters can be described with a great architectural detail, a comprehensive and objective approach to the two types of spaces from the acoustical point of view is available at present only as a computer model study [P. Chourmouziadou and J. Kang, "Acoustic evolution of ancient Greek and Roman theaters," Appl. Acoust. 69, re (2007)]. This work addresses the same topic from the experimental point of view, and its aim is to provide a basis to the acoustical evolution from Greek to Roman theater design. First, by means of in situ and scale model measurements, the most important features of the sound field in ancient theaters are clarified and discussed. Then it has been possible to match quantitatively the role of some remarkable architectural design variables with acoustics, and it is seen how this criterion can be used effectively to define different groups of ancient theaters. Finally some more specific wave phenomena are addressed and discussed.

An Extended Objective Evaluation of the 29-km Eta Model for Weather Support to the United States Space Program

NASA Technical Reports Server (NTRS)

Nutter, Paul; Manobianco, John

1998-01-01

This report describes the Applied Meteorology Unit's objective verification of the National Centers for Environmental Prediction 29-km eta model during separate warm and cool season periods from May 1996 through January 1998. The verification of surface and upper-air point forecasts was performed at three selected stations important for 45th Weather Squadron, Spaceflight Meteorology Group, and National Weather Service, Melbourne operational weather concerns. The statistical evaluation identified model biases that may result from inadequate parameterization of physical processes. Since model biases are relatively small compared to the random error component, most of the total model error results from day-to-day variability in the forecasts and/or observations. To some extent, these nonsystematic errors reflect the variability in point observations that sample spatial and temporal scales of atmospheric phenomena that cannot be resolved by the model. On average, Meso-Eta point forecasts provide useful guidance for predicting the evolution of the larger scale environment. A more substantial challenge facing model users in real time is the discrimination of nonsystematic errors that tend to inflate the total forecast error. It is important that model users maintain awareness of ongoing model changes. Such changes are likely to modify the basic error characteristics, particularly near the surface.

Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

PubMed Central

Obbard, Darren J.; Maclennan, John; Kim, Kang-Wook; Rambaut, Andrew; O’Grady, Patrick M.; Jiggins, Francis M.

2012-01-01

An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25–40 Ma) is closer to being compatible with independent fossil-derived dates (20–50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available. PMID:22683811

Topology of quantum discord

NASA Astrophysics Data System (ADS)

Nguyen, Nga T. T.; Joynt, Robert

2017-04-01

Quantum discord is an important measure of quantum correlations that can serve as a resource for certain types of quantum information processing. Like entanglement, discord is subject to destruction by external noise. The routes by which this destruction can take place depends on the shape of the hypersurface of zero discord C in the space of generalized Bloch vectors. For 2 qubits, we show that with a few points subtracted, this hypersurface is a simply-connected 9-dimensional manifold embedded in a 15-dimensional background space. We do this by constructing an explicit homeomorphism from a known manifold to the subtracted version of C . We also construct a coordinate map on C that can be used for integration or other purposes. This topological characterization of C has important implications for the classification of the possible time evolutions of discord in physical models. The classification for discord contrasts sharply with the possible evolutions of entanglement. We classify the possible joint evolutions of entanglement and discord. There are 9 allowed categories: 6 categories for a Markovian process and 3 categories for a non-Markovian process, respectively. We illustrate these conclusions with an anisotropic XY spin model. All 9 categories can be obtained by adjusting parameters in this model.

MAGNETIC FLUX TRANSPORT AND THE LONG-TERM EVOLUTION OF SOLAR ACTIVE REGIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ugarte-Urra, Ignacio; Upton, Lisa; Warren, Harry P.

2015-12-20

With multiple vantage points around the Sun, Solar Terrestrial Relations Observatory (STEREO) and Solar Dynamics Observatory imaging observations provide a unique opportunity to view the solar surface continuously. We use He ii 304 Å data from these observatories to isolate and track ten active regions and study their long-term evolution. We find that active regions typically follow a standard pattern of emergence over several days followed by a slower decay that is proportional in time to the peak intensity in the region. Since STEREO does not make direct observations of the magnetic field, we employ a flux-luminosity relationship to infermore » the total unsigned magnetic flux evolution. To investigate this magnetic flux decay over several rotations we use a surface flux transport model, the Advective Flux Transport model, that simulates convective flows using a time-varying velocity field and find that the model provides realistic predictions when information about the active region's magnetic field strength and distribution at peak flux is available. Finally, we illustrate how 304 Å images can be used as a proxy for magnetic flux measurements when magnetic field data is not accessible.« less

Simplified stock markets described by number operators

NASA Astrophysics Data System (ADS)

Bagarello, F.

2009-06-01

In this paper we continue our systematic analysis of the operatorial approach previously proposed in an economical context and we discuss a mixed toy model of a simplified stock market, i.e. a model in which the price of the shares is given as an input. We deduce the time evolution of the portfolio of the various traders of the market, as well as of other observable quantities. As in a previous paper, we solve the equations of motion by means of a fixed point like approximation.

Spatiotemporal correlation buildup after an interaction quench in the Luttinger model

NASA Astrophysics Data System (ADS)

Abeling, Nils O.; Kehrein, Stefan

We study the evolution of density-density correlations at different times and distances in the exactly solvable Luttinger model after a sudden quench from the ground state. We discuss the difference between correlations and susceptibilities, and how these results can be interpreted from the point of view of Lieb-Robinson bounds. For the correlation functions we specifically show that pre-quench entanglement in the ground state leads to algebraically decaying long distance tails outside the light cone.

Assessment of Groundwater Susceptibility to Non-Point Source Contaminants Using Three-Dimensional Transient Indexes.

PubMed

Zhang, Yong; Weissmann, Gary S; Fogg, Graham E; Lu, Bingqing; Sun, HongGuang; Zheng, Chunmiao

2018-06-05

Groundwater susceptibility to non-point source contamination is typically quantified by stable indexes, while groundwater quality evolution (or deterioration globally) can be a long-term process that may last for decades and exhibit strong temporal variations. This study proposes a three-dimensional (3- d ), transient index map built upon physical models to characterize the complete temporal evolution of deep aquifer susceptibility. For illustration purposes, the previous travel time probability density (BTTPD) approach is extended to assess the 3- d deep groundwater susceptibility to non-point source contamination within a sequence stratigraphic framework observed in the Kings River fluvial fan (KRFF) aquifer. The BTTPD, which represents complete age distributions underlying a single groundwater sample in a regional-scale aquifer, is used as a quantitative, transient measure of aquifer susceptibility. The resultant 3- d imaging of susceptibility using the simulated BTTPDs in KRFF reveals the strong influence of regional-scale heterogeneity on susceptibility. The regional-scale incised-valley fill deposits increase the susceptibility of aquifers by enhancing rapid downward solute movement and displaying relatively narrow and young age distributions. In contrast, the regional-scale sequence-boundary paleosols within the open-fan deposits "protect" deep aquifers by slowing downward solute movement and displaying a relatively broad and old age distribution. Further comparison of the simulated susceptibility index maps to known contaminant distributions shows that these maps are generally consistent with the high concentration and quick evolution of 1,2-dibromo-3-chloropropane (DBCP) in groundwater around the incised-valley fill since the 1970s'. This application demonstrates that the BTTPDs can be used as quantitative and transient measures of deep aquifer susceptibility to non-point source contamination.

Tracking the origin and divergence of cholinesterases and neuroligins: the evolution of synaptic proteins.

PubMed

Lenfant, Nicolas; Hotelier, Thierry; Bourne, Yves; Marchot, Pascale; Chatonnet, Arnaud

2014-07-01

A cholinesterase activity can be found in all kingdoms of living organism, yet cholinesterases involved in cholinergic transmission appeared only recently in the animal phylum. Among various proteins homologous to cholinesterases, one finds neuroligins. These proteins, with an altered catalytic triad and no known hydrolytic activity, display well-identified cell adhesion properties. The availability of complete genomes of a few metazoans provides opportunities to evaluate when these two protein families emerged during evolution. In bilaterian animals, acetylcholinesterase co-localizes with proteins of cholinergic synapses while neuroligins co-localize and may interact with proteins of excitatory glutamatergic or inhibitory GABAergic/glycinergic synapses. To compare evolution of the cholinesterases and neuroligins with other proteins involved in the architecture and functioning of synapses, we devised a method to search for orthologs of these partners in genomes of model organisms representing distinct stages of metazoan evolution. Our data point to a progressive recruitment of synaptic components during evolution. This finding may shed light on the common or divergent developmental regulation events involved into the setting and maintenance of the cholinergic versus glutamatergic and GABAergic/glycinergic synapses.

Superposition and alignment of labeled point clouds.

PubMed

Fober, Thomas; Glinca, Serghei; Klebe, Gerhard; Hüllermeier, Eyke

2011-01-01

Geometric objects are often represented approximately in terms of a finite set of points in three-dimensional euclidean space. In this paper, we extend this representation to what we call labeled point clouds. A labeled point cloud is a finite set of points, where each point is not only associated with a position in three-dimensional space, but also with a discrete class label that represents a specific property. This type of model is especially suitable for modeling biomolecules such as proteins and protein binding sites, where a label may represent an atom type or a physico-chemical property. Proceeding from this representation, we address the question of how to compare two labeled points clouds in terms of their similarity. Using fuzzy modeling techniques, we develop a suitable similarity measure as well as an efficient evolutionary algorithm to compute it. Moreover, we consider the problem of establishing an alignment of the structures in the sense of a one-to-one correspondence between their basic constituents. From a biological point of view, alignments of this kind are of great interest, since mutually corresponding molecular constituents offer important information about evolution and heredity, and can also serve as a means to explain a degree of similarity. In this paper, we therefore develop a method for computing pairwise or multiple alignments of labeled point clouds. To this end, we proceed from an optimal superposition of the corresponding point clouds and construct an alignment which is as much as possible in agreement with the neighborhood structure established by this superposition. We apply our methods to the structural analysis of protein binding sites.

The Deformations of Carbon Nanotubes under Cutting.

PubMed

Deng, Jue; Wang, Chao; Guan, Guozhen; Wu, Hao; Sun, Hong; Qiu, Longbin; Chen, Peining; Pan, Zhiyong; Sun, Hao; Zhang, Bo; Che, Renchao; Peng, Huisheng

2017-08-22

The determination of structural evolution at the atomic level is essential to understanding the intrinsic physics and chemistries of nanomaterials. Mechanochemistry represents a promising method to trace structural evolution, but conventional mechanical tension generates random breaking points, which makes it unavailable for effective analysis. It remains difficult to find an appropriate model to study shear deformations. Here, we synthesize high-modulus carbon nanotubes that can be cut precisely, and the structural evolution is efficiently investigated through a combination of geometry phase analysis and first-principles calculations. The lattice fluctuation depends on the anisotropy, chirality, curvature, and slicing rate. The strain distribution further reveals a plastic breaking mechanism for the conjugated carbon atoms under cutting. The resulting sliced carbon nanotubes with controllable sizes and open ends are promising for various applications, for example, as an anode material for lithium-ion batteries.

A transverse separate-spin-evolution streaming instability

NASA Astrophysics Data System (ADS)

Iqbal, Z.; Andreev, Pavel A.; Murtaza, G.

2018-05-01

By using the separate spin evolution quantum hydrodynamical model, the instability of transverse mode due to electron streaming in a partially spin polarized magnetized degenerate plasma is studied. The electron spin polarization gives birth to a new spin-dependent wave (i.e., separate spin evolution streaming driven ordinary wave) in the real wave spectrum. It is shown that the spin polarization and streaming speed significantly affect the frequency of this new mode. Analyzing growth rate, it is found that the electron spin effects reduce the growth rate and shift the threshold of instability as well as its termination point towards higher values. Additionally, how the other parameters like electron streaming and Fermi pressure influence the growth rate is also investigated. Current study can help towards better understanding of the existence of new waves and streaming instability in the astrophysical plasmas.

The structure of common-envelope remnants

NASA Astrophysics Data System (ADS)

Hall, Philip D.

2015-05-01

We investigate the structure and evolution of the remnants of common-envelope evolution in binary star systems. In a common-envelope phase, two stars become engulfed in a gaseous envelope and, under the influence of drag forces, spiral to smaller separations. They may merge to form a single star or the envelope may be ejected to leave the stars in a shorter period orbit. This process explains the short orbital periods of many observed binary systems, such as cataclysmic variables and low-mass X-ray binary systems. Despite the importance of these systems, and of common-envelope evolution to their formation, it remains poorly understood. Specifically, we are unable to confidently predict the outcome of a common-envelope phase from the properties at its onset. After presenting a review of work on stellar evolution, binary systems, common-envelope evolution and the computer programs used, we describe the results of three computational projects on common-envelope evolution. Our work specifically relates to the methods and prescriptions which are used for predicting the outcome. We use the Cambridge stellar-evolution code STARS to produce detailed models of the structure and evolution of remnants of common-envelope evolution. We compare different assumptions about the uncertain end-of-common envelope structure and envelope mass of remnants which successfully eject their common envelopes. In the first project, we use detailed remnant models to investigate whether planetary nebulae are predicted after common-envelope phases initiated by low-mass red giants. We focus on the requirement that a remnant evolves rapidly enough to photoionize the nebula and compare the predictions for different ideas about the structure at the end of a common-envelope phase. We find that planetary nebulae are possible for some prescriptions for the end-of-common envelope structure. In our second contribution, we compute a large set of single-star models and fit new formulae to the core radii of evolved stars. These formulae can be used to better compute the outcome of common-envelope evolution with rapid evolution codes. We find that the new formulae are necessary for accurate predictions of the properties of post-common envelope systems. Finally, we use detailed remnant models of massive stars to investigate whether hydrogen may be retained after a common-envelope phase to the point of core-collapse and so be observable in supernovae. We find that this is possible and thus common-envelope evolution may contribute to the formation of Type IIb supernovae.

Space-time evolution of a growth fold (Betic Cordillera, Spain). Evidences from 3D geometrical modelling

NASA Astrophysics Data System (ADS)

Martin-Rojas, Ivan; Alfaro, Pedro; Estévez, Antonio

2014-05-01

We present a study that encompasses several software tools (iGIS©, ArcGIS©, Autocad©, etc.) and data (geological mapping, high resolution digital topographic data, high resolution aerial photographs, etc.) to create a detailed 3D geometric model of an active fault propagation growth fold. This 3D model clearly shows structural features of the analysed fold, as well as growth relationships and sedimentary patterns. The results obtained permit us to discuss the kinematics and structural evolution of the fold and the fault in time and space. The study fault propagation fold is the Crevillente syncline. This fold represents the northern limit of the Bajo Segura Basin, an intermontane basin in the Eastern Betic Cordillera (SE Spain) developed from upper Miocene on. 3D features of the Crevillente syncline, including growth pattern, indicate that limb rotation and, consequently, fault activity was higher during Messinian than during Tortonian; consequently, fault activity was also higher. From Pliocene on our data point that limb rotation and fault activity steadies or probably decreases. This in time evolution of the Crevillente syncline is not the same all along the structure; actually the 3D geometric model indicates that observed lateral heterogeneity is related to along strike variation of fault displacement.

STELLAR POPULATIONS AND EVOLUTION OF EARLY-TYPE CLUSTER GALAXIES: CONSTRAINTS FROM OPTICAL IMAGING AND SPECTROSCOPY OF z = 0.5-0.9 GALAXY CLUSTERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jorgensen, Inger; Chiboucas, Kristin, E-mail: ijorgensen@gemini.edu, E-mail: kchiboucas@gemini.edu

2013-03-15

We present an analysis of stellar populations and evolutionary history of galaxies in three similarly rich galaxy clusters MS0451.6-0305 (z = 0.54), RXJ0152.7-1357 (z = 0.83), and RXJ1226.9+3332 (z = 0.89). Our analysis is based on high signal-to-noise ground-based optical spectroscopy and Hubble Space Telescope imaging for a total of 17-34 members in each cluster. Using the dynamical masses together with the effective radii and the velocity dispersions, we find no indication of evolution of sizes or velocity dispersions with redshift at a given galaxy mass. We establish the Fundamental Plane (FP) and scaling relations between absorption line indices andmore » velocity dispersions. We confirm that the FP is steeper at z Almost-Equal-To 0.86 compared to the low-redshift FP, indicating that under the assumption of passive evolution the formation redshift, z{sub form}, depends on the galaxy velocity dispersion (or alternatively mass). At a velocity dispersion of {sigma} = 125 km s{sup -1} (Mass = 10{sup 10.55} M{sub Sun }) we find z{sub form} = 1.24 {+-} 0.05, while at {sigma} = 225 km s{sup -1} (Mass = 10{sup 11.36} M{sub Sun }) the formation redshift is z{sub form} = 1.95{sup +0.3}{sub -0.2}, for a Salpeter initial mass function. The three clusters follow similar scaling relations between absorption line indices and velocity dispersions as those found for low-redshift galaxies. The zero point offsets for the Balmer lines depend on cluster redshifts. However, the offsets indicate a slower evolution, and therefore higher formation redshift, than the zero point differences found from the FP, if interpreting the data using a passive evolution model. Specifically, the strength of the higher order Balmer lines H{delta} and H{gamma} implies z{sub form} > 2.8. The scaling relations for the metal indices in general show small and in some cases insignificant zero point offsets, favoring high formation redshifts for a passive evolution model. Based on the absorption line indices and recent stellar population models from Thomas et al., we find that MS0451.6-0305 has a mean metallicity [M/H] approximately 0.2 dex below that of the other clusters and our low-redshift sample. We confirm our previous result that RXJ0152.7-1357 has a mean abundance ratio [{alpha}/Fe] approximately 0.3 dex higher than that of the other clusters. The differences in [M/H] and [{alpha}/Fe] between the high-redshift clusters and the low-redshift sample are inconsistent with a passive evolution scenario for early-type cluster galaxies over the redshift interval studied. Low-level star formation may be able to bring the metallicity of MS0451.6-0305 in agreement with the low-redshift sample, while we speculate whether galaxy mergers can lead to sufficiently large changes in the abundance ratios for the RXJ0152.7-1357 galaxies to allow them to reach the low-redshift sample values in the time available.« less

Quantum ratchet effect in a time non-uniform double-kicked model

NASA Astrophysics Data System (ADS)

Chen, Lei; Wang, Zhen-Yu; Hui, Wu; Chu, Cheng-Yu; Chai, Ji-Min; Xiao, Jin; Zhao, Yu; Ma, Jin-Xiang

2017-07-01

The quantum ratchet effect means that the directed transport emerges in a quantum system without a net force. The delta-kicked model is a quantum Hamiltonian model for the quantum ratchet effect. This paper investigates the quantum ratchet effect based on a time non-uniform double-kicked model, in which two flashing potentials alternately act on a particle with a homogeneous initial state of zero momentum, while the intervals between adjacent actions are not equal. The evolution equation of the state of the particle is derived from its Schrödinger equation, and the numerical method to solve the evolution equation is pointed out. The results show that quantum resonances can induce the ratchet effect in this time non-uniform double-kicked model under certain conditions; some quantum resonances, which cannot induce the ratchet effect in previous models, can induce the ratchet effect in this model, and the strengths of the ratchet effect in this model are stronger than those in previous models under certain conditions. These results enrich people’s understanding of the delta-kicked model, and provides a new optional scheme to control the quantum transport of cold atoms in experiment.

3 Lectures: "Lagrangian Models", "Numerical Transport Schemes", and "Chemical and Transport Models"

NASA Technical Reports Server (NTRS)

Douglass, A.

2005-01-01

The topics for the three lectures for the Canadian Summer School are Lagrangian Models, numerical transport schemes, and chemical and transport models. In the first lecture I will explain the basic components of the Lagrangian model (a trajectory code and a photochemical code), the difficulties in using such a model (initialization) and show some applications in interpretation of aircraft and satellite data. If time permits I will show some results concerning inverse modeling which is being used to evaluate sources of tropospheric pollutants. In the second lecture I will discuss one of the core components of any grid point model, the numerical transport scheme. I will explain the basics of shock capturing schemes, and performance criteria. I will include an example of the importance of horizontal resolution to polar processes. We have learned from NASA's global modeling initiative that horizontal resolution matters for predictions of the future evolution of the ozone hole. The numerical scheme will be evaluated using performance metrics based on satellite observations of long-lived tracers. The final lecture will discuss the evolution of chemical transport models over the last decade. Some of the problems with assimilated winds will be demonstrated, using satellite data to evaluate the simulations.

The Biological Big Bang model for the major transitions in evolution.

PubMed

Koonin, Eugene V

2007-08-20

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal. I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB). A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis.

The Biological Big Bang model for the major transitions in evolution

PubMed Central

Koonin, Eugene V

2007-01-01

Background Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal. Hypothesis I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB). Conclusion A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis. Reviewers This article was reviewed by William Martin, Sergei Maslov, and Leonid Mirny. PMID:17708768

Stable long-time semiclassical description of zero-point energy in high-dimensional molecular systems.

PubMed

Garashchuk, Sophya; Rassolov, Vitaly A

2008-07-14

Semiclassical implementation of the quantum trajectory formalism [J. Chem. Phys. 120, 1181 (2004)] is further developed to give a stable long-time description of zero-point energy in anharmonic systems of high dimensionality. The method is based on a numerically cheap linearized quantum force approach; stabilizing terms compensating for the linearization errors are added into the time-evolution equations for the classical and nonclassical components of the momentum operator. The wave function normalization and energy are rigorously conserved. Numerical tests are performed for model systems of up to 40 degrees of freedom.

Late-time behaviour of the tilted Bianchi type VIh models

NASA Astrophysics Data System (ADS)

Hervik, S.; van den Hoogen, R. J.; Lim, W. C.; Coley, A. A.

2007-08-01

We study tilted perfect fluid cosmological models with a constant equation of state parameter in spatially homogeneous models of Bianchi type VIh using dynamical systems methods and numerical experimentation, with an emphasis on their future asymptotic evolution. We determine all of the equilibrium points of the type VIh state space (which correspond to exact self-similar solutions of the Einstein equations, some of which are new), and their stability is investigated. We find that there are vacuum plane-wave solutions that act as future attractors. In the parameter space, a 'loophole' is shown to exist in which there are no stable equilibrium points. We then show that a Hopf-bifurcation can occur resulting in a stable closed orbit (which we refer to as the Mussel attractor) corresponding to points both inside the loophole and points just outside the loophole; in the former case the closed curves act as late-time attractors while in the latter case these attracting curves will co-exist with attracting equilibrium points. In the special Bianchi type III case, centre manifold theory is required to determine the future attractors. Comprehensive numerical experiments are carried out to complement and confirm the analytical results presented. We note that the Bianchi type VIh case is of particular interest in that it contains many different subcases which exhibit many of the different possible future asymptotic behaviours of Bianchi cosmological models.

Time evolution of gamma rays from supernova remnants

NASA Astrophysics Data System (ADS)

Gaggero, Daniele; Zandanel, Fabio; Cristofari, Pierre; Gabici, Stefano

2018-04-01

We present a systematic phenomenological study focused on the time evolution of the non-thermal radiation - from radio waves to gamma rays - emitted by typical supernova remnants via hadronic and leptonic mechanisms, for two classes of progenitors: thermonuclear and core-collapse. To this aim, we develop a numerical tool designed to model the evolution of the cosmic ray spectrum inside a supernova remnant, and compute the associated multi-wavelength emission. We demonstrate the potential of this tool in the context of future population studies based on large collection of high-energy gamma-ray data. We discuss and explore the relevant parameter space involved in the problem, and focus in particular on their impact on the maximum energy of accelerated particles, in order to study the effectiveness and duration of the PeVatron phase. We outline the crucial role of the ambient medium through which the shock propagates during the remnant evolution. In particular, we point out the role of dense clumps in creating a significant hardening in the hadronic gamma-ray spectrum.

Sensitivity, optimal scaling and minimum roundoff errors in flexible structure models

NASA Technical Reports Server (NTRS)

Skelton, Robert E.

1987-01-01

Traditional modeling notions presume the existence of a truth model that relates the input to the output, without advanced knowledge of the input. This has led to the evolution of education and research approaches (including the available control and robustness theories) that treat the modeling and control design as separate problems. The paper explores the subtleties of this presumption that the modeling and control problems are separable. A detailed study of the nature of modeling errors is useful to gain insight into the limitations of traditional control and identification points of view. Modeling errors need not be small but simply appropriate for control design. Furthermore, the modeling and control design processes are inevitably iterative in nature.

Cosmological models with running cosmological term and decaying dark matter

NASA Astrophysics Data System (ADS)

Szydłowski, Marek; Stachowski, Aleksander

2017-03-01

We investigate the dynamics of the generalized ΛCDM model, which the Λ term is running with the cosmological time. On the example of the model Λ(t) =Λbare + α2/t2 we show the existence of a mechanism of the modification of the scaling law for energy density of dark matter: ρdm ∝a - 3 + λ(t). We use an approach developed by Urbanowski in which properties of unstable vacuum states are analyzed from the point of view of the quantum theory of unstable states. We discuss the evolution of Λ(t) term and pointed out that during the cosmic evolution there is a long phase in which this term is approximately constant. We also present the statistical analysis of both the Λ(t) CDM model with dark energy and decaying dark matter and the ΛCDM standard cosmological model. We use data such as Planck, SNIa, BAO, H(z) and AP test. While for the former we find the best fit value of the parameter Ωα2,0 is negative (energy transfer is from the dark matter to dark energy sector) and the parameter Ωα2,0 belongs to the interval (- 0 . 000040 , - 0 . 000383) at 2- σ level. The decaying dark matter causes to lowering a mass of dark matter particles which are lighter than CDM particles and remain relativistic. The rate of the process of decaying matter is estimated. Our model is consistent with the decaying mechanism producing unstable particles (e.g. sterile neutrinos) for which α2 is negative.

What do Simulations Predict for the Galaxy Stellar Mass Function and its Evolution in Different Environments?

NASA Astrophysics Data System (ADS)

Vulcani, Benedetta; De Lucia, Gabriella; Poggianti, Bianca M.; Bundy, Kevin; More, Surhud; Calvi, Rosa

2014-06-01

We present a comparison between the observed galaxy stellar mass function and the one predicted from the De Lucia & Blaizot semi-analytic model applied to the Millennium Simulation, for cluster satellites and galaxies in the field (meant as a wide portion of the sky, including all environments), in the local universe (z ~ 0.06), and at intermediate redshift (z ~ 0.6), with the aim to shed light on the processes which regulate the mass distribution in different environments. While the mass functions in the field and in its finer environments (groups, binary, and single systems) are well matched in the local universe down to the completeness limit of the observational sample, the model overpredicts the number of low-mass galaxies in the field at z ~ 0.6 and in clusters at both redshifts. Above M * = 1010.25 M ⊙, it reproduces the observed similarity of the cluster and field mass functions but not the observed evolution. Our results point out two shortcomings of the model: an incorrect treatment of cluster-specific environmental effects and an overefficient galaxy formation at early times (as already found by, e.g., Weinmann et al.). Next, we consider only simulations. Also using the Guo et al. model, we find that the high-mass end of the mass functions depends on halo mass: only very massive halos host massive galaxies, with the result that their mass function is flatter. Above M * = 109.4 M ⊙, simulations show an evolution in the number of the most massive galaxies in all environments. Mass functions obtained from the two prescriptions are different, however, results are qualitatively similar, indicating that the adopted methods to model the evolution of central and satellite galaxies still have to be better implemented in semi-analytic models.

Analytic Evolution of Singular Distribution Amplitudes in QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tandogan Kunkel, Asli

2014-08-01

Distribution amplitudes (DAs) are the basic functions that contain information about the quark momentum. DAs are necessary to describe hard exclusive processes in quantum chromodynamics. We describe a method of analytic evolution of DAs that have singularities such as nonzero values at the end points of the support region, jumps at some points inside the support region and cusps. We illustrate the method by applying it to the evolution of a at (constant) DA, antisymmetric at DA, and then use the method for evolution of the two-photon generalized distribution amplitude. Our approach to DA evolution has advantages over the standardmore » method of expansion in Gegenbauer polynomials [1, 2] and over a straightforward iteration of an initial distribution with evolution kernel. Expansion in Gegenbauer polynomials requires an infinite number of terms in order to accurately reproduce functions in the vicinity of singular points. Straightforward iteration of an initial distribution produces logarithmically divergent terms at each iteration. In our method the logarithmic singularities are summed from the start, which immediately produces a continuous curve. Afterwards, in order to get precise results, only one or two iterations are needed.« less

Method for discovering relationships in data by dynamic quantum clustering

DOEpatents

Weinstein, Marvin; Horn, David

2017-05-09

Data clustering is provided according to a dynamical framework based on quantum mechanical time evolution of states corresponding to data points. To expedite computations, we can approximate the time-dependent Hamiltonian formalism by a truncated calculation within a set of Gaussian wave-functions (coherent states) centered around the original points. This allows for analytic evaluation of the time evolution of all such states, opening up the possibility of exploration of relationships among data-points through observation of varying dynamical-distances among points and convergence of points into clusters. This formalism may be further supplemented by preprocessing, such as dimensional reduction through singular value decomposition and/or feature filtering.

Method for discovering relationships in data by dynamic quantum clustering

DOEpatents

Weinstein, Marvin; Horn, David

2014-10-28

Data clustering is provided according to a dynamical framework based on quantum mechanical time evolution of states corresponding to data points. To expedite computations, we can approximate the time-dependent Hamiltonian formalism by a truncated calculation within a set of Gaussian wave-functions (coherent states) centered around the original points. This allows for analytic evaluation of the time evolution of all such states, opening up the possibility of exploration of relationships among data-points through observation of varying dynamical-distances among points and convergence of points into clusters. This formalism may be further supplemented by preprocessing, such as dimensional reduction through singular value decomposition and/or feature filtering.

Equilibrium points of the tilted perfect fluid Bianchi VIh state space

NASA Astrophysics Data System (ADS)

Apostolopoulos, Pantelis S.

2005-05-01

We present the full set of evolution equations for the spatially homogeneous cosmologies of type VIh filled with a tilted perfect fluid and we provide the corresponding equilibrium points of the resulting dynamical state space. It is found that only when the group parameter satisfies h > -1 a self-similar solution exists. In particular we show that for h > -{1/9} there exists a self-similar equilibrium point provided that γ ∈ ({2(3+sqrt{-h})/5+3sqrt{-h}},{3/2}) whereas for h < -{frac 19} the state parameter belongs to the interval γ ∈(1,{2(3+sqrt{-h})/5+3sqrt{-h}}). This family of new exact self-similar solutions belongs to the subclass nαα = 0 having non-zero vorticity. In both cases the equilibrium points have a six-dimensional stable manifold and may act as future attractors at least for the models satisfying nαα = 0. Also we give the exact form of the self-similar metrics in terms of the state and group parameter. As an illustrative example we provide the explicit form of the corresponding self-similar radiation model (γ = {frac 43}), parametrised by the group parameter h. Finally we show that there are no tilted self-similar models of type III and irrotational models of type VIh.

Learning and Transition of Symbols: Towards a Dynamical Model of a Symbolic Individual

NASA Astrophysics Data System (ADS)

Hashimoto, Takashi; Masumi, Akira

The remarkable feature of linguistic communications is the use of symbols for transmitting information and mutual understanding. Deacon (1997) pointed out that humans are symbolic species, namely, we show symbolic cognitive activities such as learning, formation, and manipulation of symbols. In research into the origin and the evolution of language, we should elucidate the emerging process of such symbolic cognitive activities.

Calling in Sick: Impacts of Fever on Intra-Urban Human Mobility

DTIC Science & Technology

2016-07-13

Disease manifestations can significantly alter behavior in human and non-human animal hosts [1], leading to important consequences for the ecology of both...due to illness is a case in point. Such effects have potentially broad significance throughout epidemiology, ecology , and evolution. Hypothesized...goals and the nested relationships among our models [35]. 6 Ethics approval The procedures for enrollment of participants, dengue diagnosis

Examples of equilibrium and non-equilibrium behavior in evolutionary systems

NASA Astrophysics Data System (ADS)

Soulier, Arne

With this thesis, we want to shed some light into the darkness of our understanding of simply defined statistical mechanics systems and the surprisingly complex dynamical behavior they exhibit. We will do so by presenting in turn one equilibrium and then one non-equilibrium system with evolutionary dynamics. In part 1, we will present the seceder-model, a newly developed system that cannot equilibrate. We will then study several properties of the system and obtain an idea of the richness of the dynamics of the seceder model, which is particular impressive given the minimal amount of modeling necessary in its setup. In part 2, we will present extensions to the directed polymer in random media problem on a hypercube and its connection to the Eigen model of evolution. Our main interest will be the influence of time-dependent and time-independent changes in the fitness landscape viewed by an evolving population. This part contains the equilibrium dynamics. The stochastic models and the topic of evolution and non-equilibrium in general will allow us to point out similarities to the various lines of thought in game theory.

Unparticle dark energy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, D.-C.; Stojkovic, Dejan; Dutta, Sourish

2009-09-15

We examine a dark energy model where a scalar unparticle degree of freedom plays the role of quintessence. In particular, we study a model where the unparticle degree of freedom has a standard kinetic term and a simple mass potential, the evolution is slowly rolling and the field value is of the order of the unparticle energy scale ({lambda}{sub u}). We study how the evolution of w depends on the parameters B (a function of unparticle scaling dimension d{sub u}), the initial value of the field {phi}{sub i} (or equivalently, {lambda}{sub u}) and the present matter density {omega}{sub m0}. Wemore » use observational data from type Ia supernovae, baryon acoustic oscillations and the cosmic microwave background to constrain the model parameters and find that these models are not ruled out by the observational data. From a theoretical point of view, unparticle dark energy model is very attractive, since unparticles (being bound states of fundamental fermions) are protected from radiative corrections. Further, coupling of unparticles to the standard model fields can be arbitrarily suppressed by raising the fundamental energy scale M{sub F}, making the unparticle dark energy model free of most of the problems that plague conventional scalar field quintessence models.« less

Data Assimilation Methods on a Non-conservative Adaptive Mesh

NASA Astrophysics Data System (ADS)

Guider, Colin Thomas; Rabatel, Matthias; Carrassi, Alberto; Jones, Christopher K. R. T.

2017-04-01

Adaptive mesh methods are used to model a wide variety of physical phenomena. Some of these models, in particular those of sea ice movement, are particularly interesting in that they use a remeshing process to remove and insert mesh points at various points in their evolution. This presents a challenge in developing compatible data assimilation schemes, as the dimension of the state space we wish to estimate can change over time when these remeshings occur. In this work, we first describe a remeshing scheme for an adaptive mesh in one dimension. We then develop advanced data assimilation methods that are appropriate for such a moving and remeshed grid. We hope to extend these techniques to two-dimensional models, like the Lagrangian sea ice model neXtSIM te{ns}. \\bibitem{ns} P. Rampal, S. Bouillon, E. Ólason, and M. Morlighem. ne{X}t{SIM}: a new {L}agrangian sea ice model. {The Cryosphere}, 10 (3): 1055-1073, 2016.

Post-Fukushima Energy and Nuclear Policy Evolution

NASA Astrophysics Data System (ADS)

Masuda, Tatsuo

2014-07-01

The Fukushima nuclear disaster should be marked as a point of departure towards energy policy evolution needed in the 21st century. Japan had cast off the skin after the oil shocks of the 1970s, where energy efficiency and saving played a critical role. Japan might have looked very different without these innovative policies. The post-Fukushima Japan faces multiple challenges, each of which constitutes a daunting task for policymakers such as surging LNG import costs and nuclear restarting. However, overcoming these problems one by one is not enough. Intensifying climate impact alerts us to the arrival of a historical inflection point requiring a radical shift in energy model worldwide, where Japan will be best suited to take the lead in view of its energy history and technology. The on-going effort after Fukushima to renew her energy and nuclear policy is suggestive of her potential to develop an innovative energy model by casting off the skin again. Asia will become the "problem centre" of the world if it may fail to address global environmental problems deriving from the heavy use of energy (about 46% of world's energy used by Asia alone in 2035). If successful, on the contrary, Asia will become the "solution centre" benefiting the global community. Asia is too big to fail as the whole world will be badly affected. The new energy model of Japan will serve as "public goods" for Asian countries in developing their new energy model towards sustainable future.

On a quantum mechanical system theory of the origin of life: from the Stapp-model to the origin of natural symbols

NASA Astrophysics Data System (ADS)

Balázs, András

2016-01-01

The Heisenberg-James-Stapp (quantum mechanical) mind model is surveyed and criticized briefly. The criticism points out that the model, while being essentially consistent concerning (human) consciousness, fundamentally lacks the evolutional point of view both onto- and phylogenetically. Ethology and other than Jamesian psychology is quoted and a quantum mechanical theoretical scheme is suggested to essentially extend Stapp's frame in an evolutionary context. It is proposed that its central supposition, spontaneous quantum measurement can be better utilized in an investigation of the origin of the "subjective" process, having come about concomitantly with the chemistry of the origin of life. We dwell on its applicability at this latter process, at its heart standing, it is supposed, the endophysical nonlinear "self-measurement" of (quantum mechanically describable) matter, and so our investigation is extended to this primeval phenomenon. It is suggested that the life phenomenon is an indirect C* → (W*) → C* quantum algebraic process transition, where the (W*) system would represent the living state. Summarized also are our previous results on an internalized, "reversed", time process, introduced originally by Gunji, which is subordinated to the external "forwards" time evolution, driving towards symmetry by gradual space-mappings, where the original splitting-up must have come about in a spontaneous symmetry breaking nonlinear "self-measurement" of matter in an endophysical World.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parada, Javiera; Richer, Harvey; Heyl, Jeremy

Blue stragglers (BSS) are stars whose position in the color–magnitude diagram (CMD) places them above the main sequence (MS) turn-off (TO) point of a star cluster. Using data from the core of 47 Tuc in the ultraviolet (UV), we have identified various stellar populations in the CMD, and used their radial distributions to study the evolution and origin of BSS, and obtain a dynamical estimate of the mass of BSS systems. When we separate the BSS into two samples by their magnitude, we find that the bright BSS show a much more centrally concentrated radial distribution and thus higher massmore » estimate (over twice the TO mass for these BSS systems), suggesting an origin involving triple or multiple stellar systems. In contrast, the faint BSS are less concentrated, with a radial distribution similar to the MS binaries, pointing to the MS binaries as the likely progenitors of these BSS. Putting our data together with available photometric data in the visible and using MESA evolutionary models, we calculate the expected number of stars in each evolutionary stage for the normal evolution of stars and the number of stars coming from the evolution of BSS. The results indicate that BSS have a post-MS evolution comparable to that of a normal star of the same mass and a MS BSS lifetime of about 200–300 Myr. We also find that the excess population of asymptotic giant branch stars in 47 Tuc is due to evolved BSS.« less

What If We Had A Magnetograph at Lagrangian L5?

NASA Technical Reports Server (NTRS)

Pevtsov, Alexei A.; Bertello, Luca; MacNeice, Peter; Petrie, Gordon

2016-01-01

Synoptic Carrington charts of magnetic field are routinely used as an input for modelings of solar wind and other aspects of space weather forecast. However, these maps are constructed using only the observations from the solar hemisphere facing Earth. The evolution of magnetic flux on the "farside" of the Sun, which may affect the topology of coronal field in the "nearside," is largely ignored. It is commonly accepted that placing a magnetograph in Lagrangian L5 point would improve the space weather forecast. However, the quantitative estimates of anticipated improvements have been lacking. We use longitudinal magnetograms from the Synoptic Optical Long-term Investigations of the Sun (SOLIS) to investigate how adding data from L5 point would affect the outcome of two major models used in space weather forecast.

The fluid mechanics of thrombus formation

NASA Technical Reports Server (NTRS)

1972-01-01

Experimental data are presented for the growth of thrombi (blood clots) in a stagnation point flow of fresh blood. Thrombus shape, size and structure are shown to depend on local flow conditions. The evolution of a thrombus is described in terms of a physical model that includes platelet diffusion, a platelet aggregation mechanism, and diffusion and convection of the chemical species responsible for aggregation. Diffusion-controlled and convection-controlled regimes are defined by flow parameters and thrombus location, and the characteristic growth pattern in each regime is explained. Quantitative comparisons with an approximate theoretical model are presented, and a more general model is formulated.

Two Androdioecious and One Dioecious New Species of Pristionchus (Nematoda: Diplogastridae): New Reference Points for the Evolution of Reproductive Mode

PubMed Central

Kanzaki, Natsumi; Ragsdale, Erik J.; Herrmann, Matthias; Susoy, Vladislav

2013-01-01

Rhabditid nematodes are one of a few animal taxa in which androdioecious reproduction, involving hermaphrodites and males, is found. In the genus Pristionchus, several cases of androdioecy are known, including the model species P. pacificus. A comprehensive understanding of the evolution of reproductive mode depends on dense taxon sampling and careful morphological and phylogenetic reconstruction. In this article, two new androdioecious species, P. boliviae n. sp. and P. mayeri n. sp., and one gonochoristic outgroup, P. atlanticus n. sp., are described on morphological, molecular, and biological evidence. Their phylogenetic relationships are inferred from 26 ribosomal protein genes and a partial SSU rRNA gene. Based on current representation, the new androdioecious species are sister taxa, indicating either speciation from an androdioecious ancestor or rapid convergent evolution in closely related species. Male sexual characters distinguish the new species, and new characters for six closely related Pristionchus species are presented. Male papillae are unusually variable in P. boliviae n. sp. and P. mayeri n. sp., consistent with the predictions of “selfing syndrome.” Description and phylogeny of new androdioecious species, supported by fuller outgroup representation, establish new reference points for mechanistic studies in the Pristionchus system by expanding its comparative context. PMID:24115783

Impacts of the Detection of Cassiopeia A Point Source.

PubMed

Umeda; Nomoto; Tsuruta; Mineshige

2000-05-10

Very recently the Chandra first light observation discovered a point-like source in the Cassiopeia A supernova remnant. This detection was subsequently confirmed by the analyses of the archival data from both ROSAT and Einstein observations. Here we compare the results from these observations with the scenarios involving both black holes (BHs) and neutron stars (NSs). If this point source is a BH, we offer as a promising model a disk-corona type model with a low accretion rate in which a soft photon source at approximately 0.1 keV is Comptonized by higher energy electrons in the corona. If it is an NS, the dominant radiation observed by Chandra most likely originates from smaller, hotter regions of the stellar surface, but we argue that it is still worthwhile to compare the cooler component from the rest of the surface with cooling theories. We emphasize that the detection of this point source itself should potentially provide enormous impacts on the theories of supernova explosion, progenitor scenario, compact remnant formation, accretion to compact objects, and NS thermal evolution.

General aspects of Gauss-Bonnet models without potential in dimension four

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santillán, Osvaldo P., E-mail: firenzecita@hotmail.com

In the present work, the isotropic and homogenous solutions with spatial curvature k =0 of four dimensional Gauss-Bonnet models are characterized. The main assumption is that the scalar field φ which is coupled to the Gauss-Bonnet term has no potential [1]–[2]. Some singular and some eternal solutions are described. The evolution of the universe is given in terms of a curve γ=( H (φ), φ) which is the solution of a polynomial equation P ( H {sup 2}, φ)=0 with φ dependent coefficients. In addition, it is shown that the initial conditions in these models put several restrictions on themore » evolution. For instance, an universe initially contracting will be contracting always for future times and an universe that is expanding was always expanding at past times. Thus, there are no cyclic cosmological solutions for this model. These results are universal, that is, independent on the form of the coupling f (φ) between the scalar field and the Gauss-Bonnet term. In addition, a proof that at a turning point φ-dot →0 a singularity necessarily emerges is presented, except for some specific choices of the coupling. This is valid unless the Hubble constant H → 0 at this point. This proof is based on the Raychaudhuri equation for the model. The description presented here is in part inspired in the works [3]–[4]. However, the mathematical methods that are implemented are complementary of those in these references, and they may be helpful for study more complicated situations in a future.« less

Metabolically Coupled Replicator Systems: Overview of an RNA-world model concept of prebiotic evolution on mineral surfaces.

PubMed

Czárán, Tamás; Könnyű, Balázs; Szathmáry, Eörs

2015-09-21

Metabolically Coupled Replicator Systems (MCRS) are a family of models implementing a simple, physico-chemically and ecologically feasible scenario for the first steps of chemical evolution towards life. Evolution in an abiotically produced RNA-population sets in as soon as any one of the RNA molecules become autocatalytic by engaging in template directed self-replication from activated monomers, and starts increasing exponentially. Competition for the finite external supply of monomers ignites selection favouring RNA molecules with catalytic activity helping self-replication by any possible means. One way of providing such autocatalytic help is to become a replicase ribozyme. An additional way is through increasing monomer supply by contributing to monomer synthesis from external resources, i.e., by evolving metabolic enzyme activity. Retroevolution may build up an increasingly autotrophic, cooperating community of metabolic ribozymes running an increasingly complicated and ever more efficient metabolism. Maintaining such a cooperating community of metabolic replicators raises two serious ecological problems: one is keeping the system coexistent in spite of the different replicabilities of the cooperating replicators; the other is constraining parasitism, i.e., keeping "cheaters" in check. Surface-bound MCRS provide an automatic solution to both problems: coexistence and parasite resistance are the consequences of assuming the local nature of metabolic interactions. In this review we present an overview of results published in previous articles, showing that these effects are, indeed, robust in different MCRS implementations, by considering different environmental setups and realistic chemical details in a few different models. We argue that the MCRS model framework naturally offers a suitable starting point for the future modelling of membrane evolution and extending the theory to cover the emergence of the first protocell in a self-consistent manner. The coevolution of metabolic, genetic and membrane functions is hypothesized to follow the progressive sequestration scenario, the conceptual blueprint for the earliest steps of protocell evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Explaining Leibniz equivalence as difference of non-inertial appearances: Dis-solution of the Hole Argument and physical individuation of point-events

NASA Astrophysics Data System (ADS)

Lusanna, Luca; Pauri, Massimo

"The last remnant of physical objectivity of space-time" is disclosed in the case of a continuous family of spatially non-compact models of general relativity (GR). The physical individuation of point-events is furnished by the autonomous degrees of freedom of the gravitational field (viz., the Dirac observables) which represent-as it were-the ontic part of the metric field. The physical role of the epistemic part (viz. the gauge variables) is likewise clarified as embodying the unavoidable non-inertial aspects of GR. At the end the philosophical import of the Hole Argument is substantially weakened and in fact the Argument itself dissolved, while a specific four-dimensional holistic and structuralist view of space-time (called point-structuralism) emerges, including elements common to the tradition of both substantivalism and relationism. The observables of our models undergo real temporal change: this gives new evidence to the fact that statements like the frozen-time character of evolution, as other ontological claims about GR, are model dependent.

Effect of Interfacial Turbulence and Accommodation Coefficient on CFD Predictions of Pressurization and Pressure Control in Cryogenic Storage Tank

NASA Technical Reports Server (NTRS)

Kassemi, Mohammad; Kartuzova, Olga; Hylton, Sonya

2015-01-01

Laminar models agree closely with the pressure evolution and vapor phase temperature stratification but under-predict liquid temperatures. Turbulent SST k-w and k-e models under-predict the pressurization rate and extent of stratification in the vapor but represent liquid temperature distributions fairly well. These conclusions seem to equally apply to large cryogenic tank simulations as well as small scale simulant fluid pressurization cases. Appropriate turbulent models that represent both interfacial and bulk vapor phase turbulence with greater fidelity are needed. Application of LES models to the tank pressurization problem can serve as a starting point.

Impact of Different Policies on Unhealthy Dietary Behaviors in an Urban Adult Population: An Agent-Based Simulation Model

PubMed Central

Giabbanelli, Philippe J.; Arah, Onyebuchi A.; Zimmerman, Frederick J.

2014-01-01

Objectives. Unhealthy eating is a complex-system problem. We used agent-based modeling to examine the effects of different policies on unhealthy eating behaviors. Methods. We developed an agent-based simulation model to represent a synthetic population of adults in Pasadena, CA, and how they make dietary decisions. Data from the 2007 Food Attitudes and Behaviors Survey and other empirical studies were used to calibrate the parameters of the model. Simulations were performed to contrast the potential effects of various policies on the evolution of dietary decisions. Results. Our model showed that a 20% increase in taxes on fast foods would lower the probability of fast-food consumption by 3 percentage points, whereas improving the visibility of positive social norms by 10%, either through community-based or mass-media campaigns, could improve the consumption of fruits and vegetables by 7 percentage points and lower fast-food consumption by 6 percentage points. Zoning policies had no significant impact. Conclusions. Interventions emphasizing healthy eating norms may be more effective than directly targeting food prices or regulating local food outlets. Agent-based modeling may be a useful tool for testing the population-level effects of various policies within complex systems. PMID:24832414

Caesium-137 and strontium-90 temporal series in the Tagus River: experimental results and a modelling study.

PubMed

Miró, Conrado; Baeza, Antonio; Madruga, María J; Periañez, Raul

2012-11-01

The objective of this work consisted of analysing the spatial and temporal evolution of two radionuclide concentrations in the Tagus River. Time-series analysis techniques and numerical modelling have been used in this study. (137)Cs and (90)Sr concentrations have been measured from 1994 to 1999 at several sampling points in Spain and Portugal. These radionuclides have been introduced into the river by the liquid releases from several nuclear power plants in Spain, as well as from global fallout. Time-series analysis techniques have allowed the determination of radionuclide transit times along the river, and have also pointed out the existence of temporal cycles of radionuclide concentrations at some sampling points, which are attributed to water management in the reservoirs placed along the Tagus River. A stochastic dispersion model, in which transport with water, radioactive decay and water-sediment interactions are solved through Monte Carlo methods, has been developed. Model results are, in general, in reasonable agreement with measurements. The model has finally been applied to the calculation of mean ages of radioactive content in water and sediments in each reservoir. This kind of model can be a very useful tool to support the decision-making process after an eventual emergency situation. Copyright © 2012 Elsevier Ltd. All rights reserved.

A New Framework For The Evolution of Terrestrial Planets: Bi-stability, Stochastic Effects, and the Non-Uniqueness of Tectonic States

NASA Astrophysics Data System (ADS)

Weller, M. B.; Lenardic, A.

2017-12-01

Of all the Solar System bodies, the Earth is the only one for which significant observation and constraints are accessible such that they can be used to discriminate between competing models of Earth's tectonic evolution. Therefore, it is a natural tendency to use these observations to inform more general models of planetary evolution. Yet, our understating of Earth's evolution is far from complete. Geodynamic and geochemical evidence suggests that plate tectonics may not have operated on the early Earth, with both the timing of its onset and the length of its activity far from certain. In recent years, the potential of tectonic bi-stability (multiple stable, energetically allowed solutions) has been shown to be dynamically viable, both from analytical analysis and through numeric experiments in two and three dimensions. The indication is that multiple tectonic modes may operate on a single planetary body at different times within its temporal evolution. Further, there exists the potential that feedback mechanisms between the internal dynamics and surface processes (e.g., surface temperature changes driven by long term climate evolution), acting at different thermal evolution times, can cause terrestrial worlds to alternate between multiple tectonic states over giga-year timescales. Implied here is that terrestrial planets have the potential to migrate through tectonic regimes at similar `thermal evolutionary times' - points were planets have a similar bulk mantle temperature and energies -, but at very different `temporal times' - time since planetary formation. It can then be shown that identical planets at similar stages of their evolution may exhibit different tectonic regimes due to random fluctuations. A new framework of planetary evolution that moves toward probabilistic arguments based on general physical principals, as opposed to particular rheologies, and incorporates the potential of tectonic regime transitions and multiple tectonics states being viable at equivalent physical and chemical conditions, will be discussed.

Statistical dynamics of religion evolutions

NASA Astrophysics Data System (ADS)

Ausloos, M.; Petroni, F.

2009-10-01

A religion affiliation can be considered as a “degree of freedom” of an agent on the human genre network. A brief review is given on the state of the art in data analysis and modelization of religious “questions” in order to suggest and if possible initiate further research, after using a “statistical physics filter”. We present a discussion of the evolution of 18 so-called religions, as measured through their number of adherents between 1900 and 2000. Some emphasis is made on a few cases presenting a minimum or a maximum in the investigated time range-thereby suggesting a competitive ingredient to be considered, besides the well accepted “at birth” attachment effect. The importance of the “external field” is still stressed through an Avrami late stage crystal growth-like parameter. The observed features and some intuitive interpretations point to opinion based models with vector, rather than scalar, like agents.

On building a memory evolutive system for application to learning and cognition modeling.

PubMed

de Lima do Rego Monteiro, Julio; Kogler, Joao Eduardo; Ribeiro, Joao Henrique Ranhel; Netto, Marcio Lobo

2010-01-01

We address here aspects of the implementation of a memory evolutive system (MES), based on the model proposed by A. Ehresmann and J. Vanbremeersch (2007), by means of a simulated network of spiking neurons with time dependent plasticity. We point out the advantages and challenges of applying category theory for the representation of cognition, by using the MES architecture. Then we discuss the issues concerning the minimum requirements that an artificial neural network (ANN) should fulfill in order that it would be capable of expressing the categories and mappings between them, underlying the MES. We conclude that a pulsed ANN based on Izhikevich's formal neuron with STDP (spike time-dependent plasticity) has sufficient dynamical properties to achieve these requirements, provided it can cope with the topological requirements. Finally, we present some perspectives of future research concerning the proposed ANN topology.

Model of climate evolution based on continental drift and polar wandering

NASA Technical Reports Server (NTRS)

Donn, W. L.; Shaw, D. M.

1977-01-01

The thermodynamic meteorologic model of Adem is used to trace the evolution of climate from Triassic to present time by applying it to changing geography as described by continental drift and polar wandering. Results show that the gross changes of climate in the Northern Hemisphere can be fully explained by the strong cooling in high latitudes as continents moved poleward. High-latitude mean temperatures in the Northern Hemisphere dropped below the freezing point 10 to 15 m.y. ago, thereby accounting for the late Cenozoic glacial age. Computed meridional temperature gradients for the Northern Hemisphere steepened from 20 to 40 C over the 200-m.y. period, an effect caused primarily by the high-latitude temperature decrease. The primary result of the work is that the cooling that has occurred since the warm Mesozoic period and has culminated in glaciation is explainable wholly by terrestrial processes.

Evolution of male strategies with sex-ratio-dependent pay-offs: connecting pair bonds with grandmothering.

PubMed

Loo, Sara L; Hawkes, Kristen; Kim, Peter S

2017-09-19

Men's provisioning of mates and offspring has been central to ideas about human evolution because paternal provisioning is absent in our closest evolutionary cousins, the great apes, and is widely assumed to result in pair bonding, which distinguishes us from them. Yet mathematical modelling has shown that paternal care does not readily spread in populations where competition for multiple mates is the common male strategy. Here we add to models that point to the mating sex ratio as an explanation for pairing as pay-offs to mate guarding rise with a male-biased sex ratio. This is of interest for human evolution because our grandmothering life history shifts the mating sex ratio from female- to male-biased. Using a difference equation model, we explore the relative pay-offs for three competing male strategies (dependant care, multiple mating, mate guarding) in response to changing adult sex ratios. When fertile females are abundant, multiple mating prevails. As they become scarce, mate guarding triumphs. The threshold for this shift depends on guarding efficiency. Combined with mating sex ratios of hunter-gatherer and chimpanzee populations, these results strengthen the hypothesis that the evolution of our grandmothering life history propelled the shift to pair bonding in the human lineage.This article is part of the themed issue 'Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies'. © 2017 The Author(s).

Can the History of Science Contribute to Modelling in Physics Teaching?

NASA Astrophysics Data System (ADS)

Machado, Juliana; Braga, Marco Antônio Barbosa

2016-10-01

A characterization of the modelling process in science is proposed for science education, based on Mario Bunge's ideas about the construction of models in science. Galileo's Dialogues are analysed as a potentially fruitful starting point to implement strategies aimed at modelling in the classroom in the light of that proposal. It is argued that a modelling process for science education can be conceived as the evolution from phenomenological approaches towards more representational ones, emphasizing the role of abstraction and idealization in model construction. The shift of reference of theories—from sensible objects to conceptual objects—and the black-box models construction process, which are both explicitly presented features in Galileo's Dialogues, are indicated as highly relevant aspects for modelling in science education.

Local and global bifurcations in an economic growth model with endogenous labour supply and multiplicative external habits

NASA Astrophysics Data System (ADS)

Gori, Luca; Sodini, Mauro

2014-03-01

This paper analyses the mathematical properties of an economic growth model with overlapping generations, endogenous labour supply, and multiplicative external habits. The dynamics of the economy is characterised by a two-dimensional map describing the time evolution of capital and labour supply. We show that if the relative importance of external habits in the utility function is sufficiently high, multiple (determinate or indeterminate) fixed points and poverty traps can exist. In addition, periodic or quasiperiodic behaviour and/or coexistence of attractors may occur.

Stochastic effects in hybrid inflation

NASA Astrophysics Data System (ADS)

Martin, Jérôme; Vennin, Vincent

2012-02-01

Hybrid inflation is a two-field model where inflation ends due to an instability. In the neighborhood of the instability point, the potential is very flat and the quantum fluctuations dominate over the classical motion of the inflaton and waterfall fields. In this article, we study this regime in the framework of stochastic inflation. We numerically solve the two coupled Langevin equations controlling the evolution of the fields and compute the probability distributions of the total number of e-folds and of the inflation exit point. Then, we discuss the physical consequences of our results, in particular, the question of how the quantum diffusion can affect the observable predictions of hybrid inflation.

Breakup of a thin drop under a stagnation point flow

NASA Astrophysics Data System (ADS)

Hooshanginejad, Alireza; Lee, Sungyon; Shelley, Michael

2017-11-01

Recent studies by Hooshanginejad and Lee (2017) have demonstrated complex depinning behaviors of a partially wetting droplet under wind. Motivated by this study, we examine the coupled evolution of a 2D thin drop and external wind, when it is initially held against a fast stagnation point flow. Our drop lubrication model employs the potential flow and Prandtl boundary layer theory for outer flow to compute the internal drop flow corresponding to drop deformations. Furthermore, both the analytical and numerical steady state solutions provide a partial prediction for the drop's final shape and help identify the range of droplet sizes that undergo a breakup for the given flow condition.

Berkeley's New Approach to Global Engagement: Early and Current Efforts to Become More International. Research & Occasional Paper Series: CSHE.12.15

ERIC Educational Resources Information Center

Dirks, Nicholas B.; Gilman, Nils

2015-01-01

This essay discusses past and current thinking about the globalization of higher education (from a U.S. point of view in particular) and a new model we are attempting to develop at the University of California, Berkeley. This essay begins with a brief narrative of the historical evolution of efforts to internationalize education, from the…

Minimization principles for the coupled problem of Darcy-Biot-type fluid transport in porous media linked to phase field modeling of fracture

NASA Astrophysics Data System (ADS)

Miehe, Christian; Mauthe, Steffen; Teichtmeister, Stephan

2015-09-01

This work develops new minimization and saddle point principles for the coupled problem of Darcy-Biot-type fluid transport in porous media at fracture. It shows that the quasi-static problem of elastically deforming, fluid-saturated porous media is related to a minimization principle for the evolution problem. This two-field principle determines the rate of deformation and the fluid mass flux vector. It provides a canonically compact model structure, where the stress equilibrium and the inverse Darcy's law appear as the Euler equations of a variational statement. A Legendre transformation of the dissipation potential relates the minimization principle to a characteristic three field saddle point principle, whose Euler equations determine the evolutions of deformation and fluid content as well as Darcy's law. A further geometric assumption results in modified variational principles for a simplified theory, where the fluid content is linked to the volumetric deformation. The existence of these variational principles underlines inherent symmetries of Darcy-Biot theories of porous media. This can be exploited in the numerical implementation by the construction of time- and space-discrete variational principles, which fully determine the update problems of typical time stepping schemes. Here, the proposed minimization principle for the coupled problem is advantageous with regard to a new unconstrained stable finite element design, while space discretizations of the saddle point principles are constrained by the LBB condition. The variational principles developed provide the most fundamental approach to the discretization of nonlinear fluid-structure interactions, showing symmetric systems in algebraic update procedures. They also provide an excellent starting point for extensions towards more complex problems. This is demonstrated by developing a minimization principle for a phase field description of fracture in fluid-saturated porous media. It is designed for an incorporation of alternative crack driving forces, such as a convenient criterion in terms of the effective stress. The proposed setting provides a modeling framework for the analysis of complex problems such as hydraulic fracture. This is demonstrated by a spectrum of model simulations.

Is the standard model saved asymptotically by conformal symmetry?

NASA Astrophysics Data System (ADS)

Gorsky, A.; Mironov, A.; Morozov, A.; Tomaras, T. N.

2015-03-01

It is pointed out that the top-quark and Higgs masses and the Higgs VEV with great accuracy satisfy the relations 4 m {/H 2} = 2 m {/T 2} = v 2, which are very special and reminiscent of analogous ones at Argyres-Douglas points with enhanced conformal symmetry. Furthermore, the RG evolution of the corresponding Higgs self-interaction and Yukawa couplings λ(0) = 1/8 and y(0) = 1 leads to the free-field stable point in the pure scalar sector at the Planck scale, also suggesting enhanced conformal symmetry. Thus, it is conceivable that the Standard Model is the low-energy limit of a distinct special theory with (super?) conformal symmetry at the Planck scale. In the context of such a "scenario," one may further speculate that the Higgs particle is the Goldstone boson of (partly) spontaneously broken conformal symmetry. This would simultaneously resolve the hierarchy and Landau pole problems in the scalar sector and would provide a nearly flat potential with two almost degenerate minima at the electroweak and Planck scales.

Evolution, the loss of diversity and the role of trade-offs.

PubMed

Best, Alex; Bowers, Roger; White, Andy

2015-06-01

We investigate how the loss of previously evolved diversity in host resistance to disease is dependent on the complexity of the underlying evolutionary trade-off. Working within the adaptive dynamics framework, using graphical tools (pairwise invasion plots, PIPs; trait evolution plots, TEPs) and algebraic analysis we consider polynomial trade-offs of increasing degree. Our focus is on the evolutionary trajectory of the dimorphic population after it has been attracted to an evolutionary branching point. We show that for sufficiently complex trade-offs (here, polynomials of degree three or higher) the resulting invasion boundaries can form closed 'oval' areas of invadability and strategy coexistence. If no attracting singular strategies exist within this region, then the population is destined to evolve outside of the region of coexistence, resulting in the loss of one strain. In particular, the loss of diversity in this model always occurs in such a way that the remaining strain is not attracted back to the branching point but to an extreme of the trade-off, meaning the diversity is lost forever. We also show similar results for a non-polynomial but complex trade-off, and for a different eco-evolutionary model. Our work further highlights the importance of trade-offs to evolutionary behaviour. Copyright © 2015 Elsevier Inc. All rights reserved.

An evolutionary resolution of manipulation conflict.

PubMed

González-Forero, Mauricio

2014-07-01

Individuals can manipulate the behavior of social partners. However, manipulation may conflict with the fitness interests of the manipulated individuals. Manipulated individuals can then be favored to resist manipulation, possibly reducing or eliminating the manipulated behavior in the long run. I use a mathematical model to show that conflicts where manipulation and resistance coevolve can disappear as a result of the coevolutionary process. I find that while manipulated individuals are selected to resist, they can simultaneously be favored to express the manipulated behavior at higher efficiency (i.e., providing increasing fitness effects to recipients of the manipulated behavior). Efficiency can increase to a point at which selection for resistance disappears. This process yields an efficient social behavior that is induced by social partners, and over which the inducing and induced individuals are no longer in conflict. A necessary factor is costly inefficiency. I develop the model to address the evolution of advanced eusociality via maternal manipulation (AEMM). The model predicts AEMM to be particularly likely in taxa with ancestrally imperfect resistance to maternal manipulation. Costly inefficiency occurs if the cost of delayed dispersal is larger than the benefit of exploiting the maternal patch. I discuss broader implications of the process. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Complex systems analysis of series of blackouts: cascading failure, critical points, and self-organization.

PubMed

Dobson, Ian; Carreras, Benjamin A; Lynch, Vickie E; Newman, David E

2007-06-01

We give an overview of a complex systems approach to large blackouts of electric power transmission systems caused by cascading failure. Instead of looking at the details of particular blackouts, we study the statistics and dynamics of series of blackouts with approximate global models. Blackout data from several countries suggest that the frequency of large blackouts is governed by a power law. The power law makes the risk of large blackouts consequential and is consistent with the power system being a complex system designed and operated near a critical point. Power system overall loading or stress relative to operating limits is a key factor affecting the risk of cascading failure. Power system blackout models and abstract models of cascading failure show critical points with power law behavior as load is increased. To explain why the power system is operated near these critical points and inspired by concepts from self-organized criticality, we suggest that power system operating margins evolve slowly to near a critical point and confirm this idea using a power system model. The slow evolution of the power system is driven by a steady increase in electric loading, economic pressures to maximize the use of the grid, and the engineering responses to blackouts that upgrade the system. Mitigation of blackout risk should account for dynamical effects in complex self-organized critical systems. For example, some methods of suppressing small blackouts could ultimately increase the risk of large blackouts.

Effect of surface roughness on contact line dynamics of a thin droplet

NASA Astrophysics Data System (ADS)

Bhattacharjee, Debanik; Soltannia, Babak; Nazaripoor, Hadi; Sadrzadeh, Mohtada

2017-11-01

Any surface possesses inherent roughness. Droplet spreading on a surface is an example of a contact line problem. The tri-phase contact line is prone to stress singularity which can be relieved by using precursor film assumption and disjoining pressure. In this study, an axisymmetric, incompressible, Newtonian droplet spreading on a surface was investigated. An evolution equation which tracks the droplet height over time was obtained considering the lubrication approximation. The nonlinear PDE of evolution equation was solved using finite difference scheme. A simplified Gaussian model was used as a starting point to assess the role of roughness in the dynamics of contact line. The preliminary results revealed that, for both impermeable and permeable surfaces, the apparent contact angle increased in the presence of defects whereas the equilibrium stage remained unaffected. The apparent contact angle, however, was more strongly dependent on the nature and density of defects for impermeable surfaces due to the longer droplet lifetime. Furthermore, random self-affine and non-Gaussian models are employed. The mathematical model results are finally compared with theoretical models like the Cassie-Baxter, Wenzel, and Penetration modes. NSERC.

Kinetics of wealth and the Pareto law

NASA Astrophysics Data System (ADS)

Boghosian, Bruce M.

2014-04-01

An important class of economic models involve agents whose wealth changes due to transactions with other agents. Several authors have pointed out an analogy with kinetic theory, which describes molecules whose momentum and energy change due to interactions with other molecules. We pursue this analogy and derive a Boltzmann equation for the time evolution of the wealth distribution of a population of agents for the so-called Yard-Sale Model of wealth exchange. We examine the solutions to this equation by a combination of analytical and numerical methods and investigate its long-time limit. We study an important limit of this equation for small transaction sizes and derive a partial integrodifferential equation governing the evolution of the wealth distribution in a closed economy. We then describe how this model can be extended to include features such as inflation, production, and taxation. In particular, we show that the model with taxation exhibits the basic features of the Pareto law, namely, a lower cutoff to the wealth density at small values of wealth, and approximate power-law behavior at large values of wealth.

New 3D thermal evolution model for icy bodies application to trans-Neptunian objects

NASA Astrophysics Data System (ADS)

Guilbert-Lepoutre, A.; Lasue, J.; Federico, C.; Coradini, A.; Orosei, R.; Rosenberg, E. D.

2011-05-01

Context. Thermal evolution models have been developed over the years to investigate the evolution of thermal properties based on the transfer of heat fluxes or transport of gas through a porous matrix, among others. Applications of such models to trans-Neptunian objects (TNOs) and Centaurs has shown that these bodies could be strongly differentiated from the point of view of chemistry (i.e. loss of most volatile ices), as well as from physics (e.g. melting of water ice), resulting in stratified internal structures with differentiated cores and potential pristine material close to the surface. In this context, some observational results, such as the detection of crystalline water ice or volatiles, remain puzzling. Aims: In this paper, we would like to present a new fully three-dimensional thermal evolution model. With this model, we aim to improve determination of the temperature distribution inside icy bodies such as TNOs by accounting for lateral heat fluxes, which have been proven to be important for accurate simulations. We also would like to be able to account for heterogeneous boundary conditions at the surface through various albedo properties, for example, that might induce different local temperature distributions. Methods: In a departure from published modeling approaches, the heat diffusion problem and its boundary conditions are represented in terms of real spherical harmonics, increasing the numerical efficiency by roughly an order of magnitude. We then compare this new model and another 3D model recently published to illustrate the advantages and limits of the new model. We try to put some constraints on the presence of crystalline water ice at the surface of TNOs. Results: The results obtained with this new model are in excellent agreement with results obtained by different groups with various models. Small TNOs could remain primitive unless they are formed quickly (less than 2 Myr) or are debris from the disruption of larger bodies. We find that, for large objects with a thermal evolution dominated by the decay of long-lived isotopes (objects with a formation period greater than 2 to 3 Myr), the presence of crystalline water ice would require both a large radius (>300 km) and high density (>1500 kg m-3). In particular, objects with intermediate radii and densities would be an interesting transitory population deserving a detailed study of individual fates.

Alien calculus and a Schwinger-Dyson equation: two-point function with a nonperturbative mass scale

NASA Astrophysics Data System (ADS)

Bellon, Marc P.; Clavier, Pierre J.

2018-02-01

Starting from the Schwinger-Dyson equation and the renormalization group equation for the massless Wess-Zumino model, we compute the dominant nonperturbative contributions to the anomalous dimension of the theory, which are related by alien calculus to singularities of the Borel transform on integer points. The sum of these dominant contributions has an analytic expression. When applied to the two-point function, this analysis gives a tame evolution in the deep euclidean domain at this approximation level, making doubtful the arguments on the triviality of the quantum field theory with positive β -function. On the other side, we have a singularity of the propagator for timelike momenta of the order of the renormalization group invariant scale of the theory, which has a nonperturbative relationship with the renormalization point of the theory. All these results do not seem to have an interpretation in terms of semiclassical analysis of a Feynman path integral.

A novel land surface-hydrologic-sediment dynamics model for stream corridor conservation assessment and its first application

NASA Astrophysics Data System (ADS)

Smithgall, K.; Shen, C.; Langendoen, E. J.; Johnson, P. A.

2015-12-01

Nationally and in the Chesapeake Bay (CB), Stream Corridor restoration costs unsustainable amount of public resources, but decisions are often made with inadequate knowledge of regional-scale system behavior. Bank erosion is a significant issue relevant to sediment and nutrient pollution, aquatic and riparian habitat and stream health. Existing modeling effort either focuses only on reach-scale responses or overly simplifies the descriptions for bank failure mechanics. In this work we present a novel regional-scale processes model integrating hydrology, vegetation dynamics, hydraulics, bank mechanics and sediment transport, based on a coupling between Community Land Model, Process-based Adaptive Watershed Simulator and CONservational Channel Evolution and Pollutant Transport System (CLM + PAWS + CONCEPTS, CPC). We illustrate the feasibility of this modeling platform in a Valley and Ridge basin in Pennsylvania, USA, with channel geometry data collected in 2004 and 2014. The simulations are able to reproduce essential pattern of the observed trends. We study the causes of the noticeable evolution of a relocated channel and the hydrologic controls. Bridging processes on multiple scales, the CPC model creates a new, integrated system that may serve as a confluence point for inter-disciplinary research.

The effect of selection environment on the probability of parallel evolution.

PubMed

Bailey, Susan F; Rodrigue, Nicolas; Kassen, Rees

2015-06-01

Across the great diversity of life, there are many compelling examples of parallel and convergent evolution-similar evolutionary changes arising in independently evolving populations. Parallel evolution is often taken to be strong evidence of adaptation occurring in populations that are highly constrained in their genetic variation. Theoretical models suggest a few potential factors driving the probability of parallel evolution, but experimental tests are needed. In this study, we quantify the degree of parallel evolution in 15 replicate populations of Pseudomonas fluorescens evolved in five different environments that varied in resource type and arrangement. We identified repeat changes across multiple levels of biological organization from phenotype, to gene, to nucleotide, and tested the impact of 1) selection environment, 2) the degree of adaptation, and 3) the degree of heterogeneity in the environment on the degree of parallel evolution at the gene-level. We saw, as expected, that parallel evolution occurred more often between populations evolved in the same environment; however, the extent of parallel evolution varied widely. The degree of adaptation did not significantly explain variation in the extent of parallelism in our system but number of available beneficial mutations correlated negatively with parallel evolution. In addition, degree of parallel evolution was significantly higher in populations evolved in a spatially structured, multiresource environment, suggesting that environmental heterogeneity may be an important factor constraining adaptation. Overall, our results stress the importance of environment in driving parallel evolutionary changes and point to a number of avenues for future work for understanding when evolution is predictable. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Longitudinal change of COPD assessment test (CAT) in a telehealthcare cohort is associated with exacerbation risk.

PubMed

Rassouli, Frank; Baty, Florent; Stolz, Daiana; Albrich, Werner Christian; Tamm, Michael; Widmer, Sandra; Brutsche, Martin Hugo

2017-01-01

There are only scarce data regarding the evolution of the chronic obstructive pulmonary disease (COPD) assessment test (CAT) over time. Our aim was to investigate the evolution of the CAT in a telehealthcare (THC) cohort and to evaluate its potential to predict exacerbations. The CAT was measured weekly over up to 1 year in 40 COPD patients undergoing a THC intervention. The evolution of the CAT was analyzed using linear regression. The association between this evolution and the occurrence of exacerbations was evaluated using the Andersen-Gill formulation of the Cox proportional hazards model for the analysis of recurrent time-to-event data with time-varying predictors. The median CAT at inclusion was 17 (interquartile range 13-22) points. During the study, 25% of patients had a significant negative slope (median -7 points per year [ppy]), 38% were stable (median +0 ppy) and 38% had a significant positive slope (median +6 ppy). The median slope of the CAT in the overall cohort was +1 (interquartile range -3 to +6) ppy. A significant positive association was found between the change in CAT scores and the risk of exacerbations (hazard ratio =1.08, 95% CI: 1.03-1.13; p <0.001). There was an 8% increase of the risk of exacerbation per unit increase in CAT. We detected a significant learning effect in filling out the CAT in 18.4% of patients with a median learning phase of five filled questionnaires. Sixty-three percent of the COPD patients monitored by THC experienced a stable or improved CAT during 1-year follow-up. We found a significant positive association between the evolution of the CAT over time and the risk of exacerbations. In about one-fifth of patients, there was a significant learning effect in filling out the CAT, before reliable results could be obtained. The evolution of the CAT could help to assess the risk for future exacerbations.

Physical scales in the Wigner-Boltzmann equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nedjalkov, M., E-mail: mixi@iue.tuwien.ac.at; Selberherr, S.; Ferry, D.K.

2013-01-15

The Wigner-Boltzmann equation provides the Wigner single particle theory with interactions with bosonic degrees of freedom associated with harmonic oscillators, such as phonons in solids. Quantum evolution is an interplay of two transport modes, corresponding to the common coherent particle-potential processes, or to the decoherence causing scattering due to the oscillators. Which evolution mode will dominate depends on the scales of the involved physical quantities. A dimensionless formulation of the Wigner-Boltzmann equation is obtained, where these scales appear as dimensionless strength parameters. A notion called scaling theorem is derived, linking the strength parameters to the coupling with the oscillators. Itmore » is shown that an increase of this coupling is equivalent to a reduction of both the strength of the electric potential, and the coherence length. Secondly, the existence of classes of physically different, but mathematically equivalent setups of the Wigner-Boltzmann evolution is demonstrated. - Highlights: Black-Right-Pointing-Pointer Dimensionless parameters determine the ratio of quantum or classical WB evolution. Black-Right-Pointing-Pointer The scaling theorem evaluates the decoherence effect due to scattering. Black-Right-Pointing-Pointer Evolution processes are grouped into classes of equivalence.« less

Modeling of Dissipation Element Statistics in Turbulent Non-Premixed Jet Flames

NASA Astrophysics Data System (ADS)

Denker, Dominik; Attili, Antonio; Boschung, Jonas; Hennig, Fabian; Pitsch, Heinz

2017-11-01

The dissipation element (DE) analysis is a method for analyzing and compartmentalizing turbulent scalar fields. DEs can be described by two parameters, namely the Euclidean distance l between their extremal points and the scalar difference in the respective points Δϕ . The joint probability density function (jPDF) of these two parameters P(Δϕ , l) is expected to suffice for a statistical reconstruction of the scalar field. In addition, reacting scalars show a strong correlation with these DE parameters in both premixed and non-premixed flames. Normalized DE statistics show a remarkable invariance towards changes in Reynolds numbers. This feature of DE statistics was exploited in a Boltzmann-type evolution equation based model for the probability density function (PDF) of the distance between the extremal points P(l) in isotropic turbulence. Later, this model was extended for the jPDF P(Δϕ , l) and then adapted for the use in free shear flows. The effect of heat release on the scalar scales and DE statistics is investigated and an extended model for non-premixed jet flames is introduced, which accounts for the presence of chemical reactions. This new model is validated against a series of DNS of temporally evolving jet flames. European Research Council Project ``Milestone''.

Statistical representation of a spray as a point process

NASA Astrophysics Data System (ADS)

Subramaniam, S.

2000-10-01

The statistical representation of a spray as a finite point process is investigated. One objective is to develop a better understanding of how single-point statistical information contained in descriptions such as the droplet distribution function (ddf), relates to the probability density functions (pdfs) associated with the droplets themselves. Single-point statistical information contained in the droplet distribution function (ddf) is shown to be related to a sequence of single surrogate-droplet pdfs, which are in general different from the physical single-droplet pdfs. It is shown that the ddf contains less information than the fundamental single-point statistical representation of the spray, which is also described. The analysis shows which events associated with the ensemble of spray droplets can be characterized by the ddf, and which cannot. The implications of these findings for the ddf approach to spray modeling are discussed. The results of this study also have important consequences for the initialization and evolution of direct numerical simulations (DNS) of multiphase flows, which are usually initialized on the basis of single-point statistics such as the droplet number density in physical space. If multiphase DNS are initialized in this way, this implies that even the initial representation contains certain implicit assumptions concerning the complete ensemble of realizations, which are invalid for general multiphase flows. Also the evolution of a DNS initialized in this manner is shown to be valid only if an as yet unproven commutation hypothesis holds true. Therefore, it is questionable to what extent DNS that are initialized in this manner constitute a direct simulation of the physical droplets. Implications of these findings for large eddy simulations of multiphase flows are also discussed.

Evolutionary Game Model Study of Construction Green Supply Chain Management under the Government Intervention

NASA Astrophysics Data System (ADS)

Xing, Yuanzhi; Deng, Xiaoyi

2017-11-01

The paper first has defined the concepts of green supply chain management and evolution game theory, and pointed out the characteristics of green supply chain management in construction. The main participants and key links of the construction green supply chain management are determined by constructing the organization framework. This paper established the evolutionary game model between construction enterprises and recycling enterprises for the green supply chain closed-loop structure. The waste recycling evolutionary stability equilibrium solution is obtained to explore the principle and effective scope of government policy intervention. This paper put forward the relevant countermeasures to the green supply chain management in construction recycling stage from the government point of view. The conclusion has reference value and guidance to the final product construction enterprises, recycling enterprises and the government during green supply chain.

Relativistic longitudinal self-compression of ultrashort time-domain hollow Gaussian pulses in plasma

NASA Astrophysics Data System (ADS)

Cao, Xiaochao; Fang, Feiyun; Wang, Zhaoying; Lin, Qiang

2017-10-01

We report a study on dynamical evolution of the ultrashort time-domain dark hollow Gaussian (TDHG) pulses beyond the slowly varying envelope approximation in homogenous plasma. Using the complex-source-point model, an analytical formula is proposed for describing TDHG pulses based on the oscillating electric dipoles, which is the exact solution of the Maxwell's equations. The numerical simulations show the relativistic longitudinal self-compression (RSC) due to the relativistic mass variation of moving electrons. The influences of plasma oscillation frequency and collision effect on dynamics of the TDHG pulses in plasma have been considered. Furthermore, we analyze the evolution of instantaneous energy density of the TDHG pulses on axis as well as the off axis condition.

Will there be again a transition from acceleration to deceleration in course of the dark energy evolution of the universe?

NASA Astrophysics Data System (ADS)

Pan, Supriya; Chakraborty, Subenoy

2013-09-01

In this work we consider the evolution of the interactive dark fluids in the background of homogeneous and isotropic FRW model of the universe. The dark fluids consist of a warm dark matter and a dark energy and both are described as perfect fluid with barotropic equation of state. The dark species interact non-gravitationally through an additional term in the energy conservation equations. An autonomous system is formed in the energy density spaces and fixed points are analyzed. A general expression for the deceleration parameter has been obtained and it is possible to have more than one zero of the deceleration parameter. Finally, vanishing of the deceleration parameter has been examined with some examples.

New insights into asteroid 3200 Phaethon's meteor complex

NASA Astrophysics Data System (ADS)

Jakubik, Marian; Neslusan, Lubos

2015-11-01

In this work, we study the meteor complex originating from asteroid 3200 Phaethon. Using a modeling of variety of meteoroid streams and following their dynamical evolution, we confirm the presence of two filaments crossing the Earth observed as Geminid and Daytime Sextantid meteor showers. We use numerical integrations of modeled particles performed for several past perihelion passages of the asteroid considering (i) only the gravity of planets and (2) gravity of planets and the Poynting-Robertson effect. We present the results of comparing our models (predicted showers) with observed showers. We also point out discrepancies, their possible solutions and/or new hypothesis concerning the examined meteor complex.

Neutral Evolution of Duplicated DNA: An Evolutionary Stick-Breaking Process Causes Scale-Invariant Behavior

NASA Astrophysics Data System (ADS)

Massip, Florian; Arndt, Peter F.

2013-04-01

Recently, an enrichment of identical matching sequences has been found in many eukaryotic genomes. Their length distribution exhibits a power law tail raising the question of what evolutionary mechanism or functional constraints would be able to shape this distribution. Here we introduce a simple and evolutionarily neutral model, which involves only point mutations and segmental duplications, and produces the same statistical features as observed for genomic data. Further, we extend a mathematical model for random stick breaking to analytically show that the exponent of the power law tail is -3 and universal as it does not depend on the microscopic details of the model.

Classical integrable defects as quasi Bäcklund transformations

NASA Astrophysics Data System (ADS)

Doikou, Anastasia

2016-10-01

We consider the algebraic setting of classical defects in discrete and continuous integrable theories. We derive the ;equations of motion; on the defect point via the space-like and time-like description. We then exploit the structural similarity of these equations with the discrete and continuous Bäcklund transformations. And although these equations are similar they are not exactly the same to the Bäcklund transformations. We also consider specific examples of integrable models to demonstrate our construction, i.e. the Toda chain and the sine-Gordon model. The equations of the time (space) evolution of the defect (discontinuity) degrees of freedom for these models are explicitly derived.

Variable Cultural Acquisition Costs Constrain Cumulative Cultural Evolution

PubMed Central

Mesoudi, Alex

2011-01-01

One of the hallmarks of the human species is our capacity for cumulative culture, in which beneficial knowledge and technology is accumulated over successive generations. Yet previous analyses of cumulative cultural change have failed to consider the possibility that as cultural complexity accumulates, it becomes increasingly costly for each new generation to acquire from the previous generation. In principle this may result in an upper limit on the cultural complexity that can be accumulated, at which point accumulated knowledge is so costly and time-consuming to acquire that further innovation is not possible. In this paper I first review existing empirical analyses of the history of science and technology that support the possibility that cultural acquisition costs may constrain cumulative cultural evolution. I then present macroscopic and individual-based models of cumulative cultural evolution that explore the consequences of this assumption of variable cultural acquisition costs, showing that making acquisition costs vary with cultural complexity causes the latter to reach an upper limit above which no further innovation can occur. These models further explore the consequences of different cultural transmission rules (directly biased, indirectly biased and unbiased transmission), population size, and cultural innovations that themselves reduce innovation or acquisition costs. PMID:21479170

Continuous and discontinuous phase transitions in the evolution of a polygenic trait under stabilizing selective pressure

NASA Astrophysics Data System (ADS)

Fierro, Annalisa; Cocozza, Sergio; Monticelli, Antonella; Scala, Giovanni; Miele, Gennaro

2017-06-01

The presence of phenomena analogous to phase transition in Statistical Mechanics has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model system, we analyze the evolution of a population of N diploid hermaphrodites in random mating regime. The population evolves under the effect of drift, selective pressure in form of viability on an additive polygenic trait, and mutation. The analysis allows to determine a phase diagram in the plane of mutation rate and strength of selection. The involved pattern of phase transitions is characterized by a line of critical points for weak selective pressure (smaller than a threshold), whereas discontinuous phase transitions, characterized by metastable hysteresis, are observed for strong selective pressure. A finite-size scaling analysis suggests the analogy between our system and the mean-field Ising model for selective pressure approaching the threshold from weaker values. In this framework, the mutation rate, which allows the system to explore the accessible microscopic states, is the parameter controlling the transition from large heterozygosity ( disordered phase) to small heterozygosity ( ordered one).

Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces

NASA Astrophysics Data System (ADS)

Ferrando, N.; Gosálvez, M. A.; Cerdá, J.; Gadea, R.; Sato, K.

2011-03-01

Presently, dynamic surface-based models are required to contain increasingly larger numbers of points and to propagate them over longer time periods. For large numbers of surface points, the octree data structure can be used as a balance between low memory occupation and relatively rapid access to the stored data. For evolution rules that depend on neighborhood states, extended simulation periods can be obtained by using simplified atomistic propagation models, such as the Cellular Automata (CA). This method, however, has an intrinsic parallel updating nature and the corresponding simulations are highly inefficient when performed on classical Central Processing Units (CPUs), which are designed for the sequential execution of tasks. In this paper, a series of guidelines is presented for the efficient adaptation of octree-based, CA simulations of complex, evolving surfaces into massively parallel computing hardware. A Graphics Processing Unit (GPU) is used as a cost-efficient example of the parallel architectures. For the actual simulations, we consider the surface propagation during anisotropic wet chemical etching of silicon as a computationally challenging process with a wide-spread use in microengineering applications. A continuous CA model that is intrinsically parallel in nature is used for the time evolution. Our study strongly indicates that parallel computations of dynamically evolving surfaces simulated using CA methods are significantly benefited by the incorporation of octrees as support data structures, substantially decreasing the overall computational time and memory usage.

Hybrid Self-Adaptive Evolution Strategies Guided by Neighborhood Structures for Combinatorial Optimization Problems.

PubMed

Coelho, V N; Coelho, I M; Souza, M J F; Oliveira, T A; Cota, L P; Haddad, M N; Mladenovic, N; Silva, R C P; Guimarães, F G

2016-01-01

This article presents an Evolution Strategy (ES)--based algorithm, designed to self-adapt its mutation operators, guiding the search into the solution space using a Self-Adaptive Reduced Variable Neighborhood Search procedure. In view of the specific local search operators for each individual, the proposed population-based approach also fits into the context of the Memetic Algorithms. The proposed variant uses the Greedy Randomized Adaptive Search Procedure with different greedy parameters for generating its initial population, providing an interesting exploration-exploitation balance. To validate the proposal, this framework is applied to solve three different [Formula: see text]-Hard combinatorial optimization problems: an Open-Pit-Mining Operational Planning Problem with dynamic allocation of trucks, an Unrelated Parallel Machine Scheduling Problem with Setup Times, and the calibration of a hybrid fuzzy model for Short-Term Load Forecasting. Computational results point out the convergence of the proposed model and highlight its ability in combining the application of move operations from distinct neighborhood structures along the optimization. The results gathered and reported in this article represent a collective evidence of the performance of the method in challenging combinatorial optimization problems from different application domains. The proposed evolution strategy demonstrates an ability of adapting the strength of the mutation disturbance during the generations of its evolution process. The effectiveness of the proposal motivates the application of this novel evolutionary framework for solving other combinatorial optimization problems.

Terrain Dynamics Analysis Using Space-Time Domain Hypersurfaces and Gradient Trajectories Derived From Time Series of 3D Point Clouds

DTIC Science & Technology

2015-08-01

optimized space-time interpolation method. Tangible geospatial modeling system was further developed to support the analysis of changing elevation surfaces...Evolution Mapped by Terrestrial Laser Scanning, talk, AGU Fall 2012 *Hardin E, Mitas L, Mitasova H., Simulation of Wind -Blown Sand for...Geomorphological Applications: A Smoothed Particle Hydrodynamics Approach, GSA 2012 *Russ, E. Mitasova, H., Time series and space-time cube analyses on

Traveling waves in a continuum model of 1D schools

NASA Astrophysics Data System (ADS)

Oza, Anand; Kanso, Eva; Shelley, Michael

2017-11-01

We construct and analyze a continuum model of a 1D school of flapping swimmers. Our starting point is a delay differential equation that models the interaction between a swimmer and its upstream neighbors' wakes, which is motivated by recent experiments in the Applied Math Lab at NYU. We coarse-grain the evolution equations and derive PDEs for the swimmer density and variables describing the upstream wake. We study the equations both analytically and numerically, and find that a uniform density of swimmers destabilizes into a traveling wave. Our model makes a number of predictions about the properties of such traveling waves, and sheds light on the role of hydrodynamics in mediating the structure of swimming schools.

The Impact of Aerosols on Cloud and Precipitation Processes: Cloud-Resolving Model Simulations

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo; Li, Xiaowen; Khain, Alexander; Matsui, Toshihisa; Lang, Stephen; Simpson, Joanne

2012-01-01

Recently, a detailed spectral-bin microphysical scheme was implemented into the Goddard Cumulus Ensemble (GCE) model. Atmospheric aerosols are also described using number density size-distribution functions. A spectral-bin microphysical model is very expensive from a computational point of view and has only been implemented into the 2D version of the GCE at the present time. The model is tested by studying the evolution of deep tropical clouds in the west Pacific warm pool region and summertime convection over a mid-latitude continent with different concentrations of CCN: a low clean concentration and a high dirty concentration. The impact of atmospheric aerosol concentration on cloud and precipitation will be investigated.

The Size Evolution of Passive Galaxies: Observations From the Wide-Field Camera 3 Early Release Science Program

NASA Technical Reports Server (NTRS)

Ryan, R. E., Jr.; Mccarthy, P.J.; Cohen, S. H.; Yan, H.; Hathi, N. P.; Koekemoer, A. M.; Rutkowski, M. J.; Mechtley, M. R.; Windhorst, R. A.; O’Connell, R. W.;

Non-Genomic Origins of Proteins and Metabolism

NASA Technical Reports Server (NTRS)

Pohorille, Andrew

2003-01-01

It is proposed that evolution of inanimate matter to cells endowed with a nucleic acid- based coding of genetic information was preceded by an evolutionary phase, in which peptides not coded by nucleic acids were able to self-organize into networks capable of evolution towards increasing metabolic complexity. Recent findings that truly different, simple peptides (Keefe and Szostak, 2001) can perform the same function (such as ATP binding) provide experimental support for this mechanism of early protobiological evolution. The central concept underlying this mechanism is that the reproduction of cellular functions alone was sufficient for self-maintenance of protocells, and that self- replication of macromolecules was not required at this stage of evolution. The precise transfer of information between successive generations of the earliest protocells was unnecessary and, possibly, undesirable. The key requirement in the initial stage of protocellular evolution was an ability to rapidly explore a large number of protein sequences in order to discover a set of molecules capable of supporting self- maintenance and growth of protocells. Undoubtedly, the essential protocellular functions were carried out by molecules not nearly as efficient or as specific as contemporary proteins. Many, potentially unrelated sequences could have performed each of these functions at an evolutionarily acceptable level. As evolution progressed, however proteins must have performed their functions with increasing efficiency and specificity. This, in turn, put additional constraints on protein sequences and the fraction of proteins capable of performing their functions at the required level decreased. At some point, the likelihood of generating a sufficiently efficient set of proteins through a non-coded synthesis was so small that further evolution was not possible without storing information about the sequences of these proteins. Beyond this point, further evolution required coupling between proteins and informational polymers that is characteristic to all known forms of life. The emergence of such coupling must be postulated in any scenario of the origin of life, no matter whether it starts with RNA or proteins. To examine the evolutionary potential of non-genomic systems, a simple, computationally tractable model, which is still capable of capturing the essential features of the real system, has been studied computationally. Both constructive and destructive processes have been introduced into the model in a stochastic manner. Instead of assuming random reaction sets, only a suite of protobiologically plausible reactions has been considered. Peptides have been explicitly considered as protoenzymes and their catalytic efficiencies have been assigned on the basis of biochemical principles and experimental estimates. Simulations have been carried out using a novel approach (The Next Reaction Method) that is appropriate even for very low concentrations of reactants. Studies have focused on global autocatalytic processes and their diversity.

Non-Dissipative Structural Evolutions in Granular Materials

NASA Astrophysics Data System (ADS)

Pouragha, Mehdi; Wan, Richard

2017-06-01

The structure of the contact network in granular assemblies can evolve due to either dissipative mechanisms such as sliding at contact points, or non-dissipative mechanisms through the phenomenon of contact gain and loss. Being associated with negligible deformations, non-dissipative mechanisms is actually active even in the small strain range of 10-3, especially in the case of densely packed assemblies. Hence, from a constitutive modelling point of view, it is crucial to be able to estimate such non-dissipative evolutions since both elastic and plastic properties of granular assemblies highly depend on contact network characteristics. The current study proposes an analytical scheme that allows us to estimate the non-dissipative contact gain/loss regime in terms of directional changes in the average contact force. The probability distribution of contact forces is used to compute the number of lost contact for each direction. Similarly, the number of newly formed contacts is estimated by considering the probability distribution of the gap between neighbouring particles. Based on the directional contact gain/loss computed, the changes in coordination number and fabric anisotropy can be found which, together with statistical treatments of Love-Weber stress expression, form a complete system of equations describing the evolution of other controlling microvariables. Finally, the results of the calculations have been compared with DEM simulations which verify the accuracy of the proposed scheme.

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) and its successor, APOGEE-2

NASA Astrophysics Data System (ADS)

Majewski, S. R.; APOGEE Team; APOGEE-2 Team

2016-09-01

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) of Sloan Digital Sky Survey III (SDSS-III) has produced a large catalog of high resolution ({R = 22 500}), high quality (S/N > 100), infrared (H-band) spectra for stars throughout all stellar populations of the Milky Way, including in regions veiled by significant dust opacity. APOGEE's half million spectra collected on > 163 000 unique stars, with time series information via repeat visits to each star, are being applied to numerous problems in stellar populations, Galactic astronomy, and stellar astrophysics. From among the early results of the APOGEE project - which span from measurements of Galactic dynamics, to multi-element chemical maps of the disk and bulge, new views of the interstellar medium, explorations of stellar companions, the chemistry of star clusters, and the discovery of rare stellar species - I highlight a few results that demonstrate APOGEE's unique ability to sample and characterize the Galactic disk and bulge. Plans are now under way for an even more ambitious successor to APOGEE: the six-year, dual-hemisphere APOGEE-2 project. Both phases of APOGEE feature a strong focus on targets having asteroseismological measurements from either Kepler or {CoRoT}, from which it is possible to derive relatively precise stellar ages. The combined APOGEE and APOGEE-2 databases of stellar chemistry, dynamics and ages constitute an unusually comprehensive, systematic and homogeneous resource for constraining models of Galactic evolution.

Development and validation of a wear model for the analysis of the wheel profile evolution in railway vehicles

NASA Astrophysics Data System (ADS)

Auciello, J.; Ignesti, M.; Malvezzi, M.; Meli, E.; Rindi, A.

2012-11-01

The numerical wheel wear prediction in railway applications is of great importance for different aspects, such as the safety against vehicle instability and derailment, the planning of wheelset maintenance interventions and the design of an optimal wheel profile from the wear point of view. For these reasons, this paper presents a complete model aimed at the evaluation of the wheel wear and the wheel profile evolution by means of dynamic simulations, organised in two parts which interact with each other mutually: a vehicle's dynamic model and a model for the wear estimation. The first is a 3D multibody model of a railway vehicle implemented in SIMPACK™, a commercial software for the analysis of mechanical systems, where the wheel-rail interaction is entrusted to a C/C++user routine external to SIMPACK, in which the global contact model is implemented. In this regard, the research on the contact points between the wheel and the rail is based on an innovative algorithm developed by the authors in previous works, while normal and tangential forces in the contact patches are calculated according to Hertz's theory and Kalker's global theory, respectively. Due to the numerical efficiency of the global contact model, the multibody vehicle and the contact model interact directly online during the dynamic simulations. The second is the wear model, written in the MATLAB® environment, mainly based on an experimental relationship between the frictional power developed at the wheel-rail interface and the amount of material removed by wear. Starting from a few outputs of the multibody simulations (position of contact points, contact forces and rigid creepages), it evaluates the local variables, such as the contact pressures and local creepages, using a local contact model (Kalker's FASTSIM algorithm). These data are then passed to another subsystem which evaluates, by means of the considered experimental relationship, both the material to be removed and its distribution along the wheel profile, obtaining the correspondent worn wheel geometry. The wheel wear evolution is reproduced by dividing the overall chosen mileage to be simulated in discrete spatial steps: at each step, the dynamic simulations are performed by means of the 3D multibody model keeping the wheel profile constant, while the wheel geometry is updated through the wear model only at the end of the discrete step. Thus, the two parts of the whole model work alternately until the completion of the whole established mileage. Clearly, the choice of an appropriate step length is one of the most important aspects of the procedure and it directly affects the result accuracy and the required computational time to complete the analysis. The whole model has been validated using experimental data relative to tests performed with the ALn 501 'Minuetto' vehicle in service on the Aosta-Pre Saint Didier track; this work has been carried out thanks to a collaboration with Trenitalia S.p.A and Rete Ferroviaria Italiana, which have provided the necessary technical data and experimental results.

Possible impact of global warming on the evolution of hemagglutinins from influenza a viruses.

PubMed

Yan, Shaomin; Wu, Guang

2011-02-01

To determine if global warming has an impact on the evolution of hemagglutinins from influenza A viruses, because both global warming and influenza pandemics/epidemics threaten the world. 4 706 hemagglutinins from influenza A viruses sampled from 1956 to 2009 were converted to a time-series to show their evolutionary process and compared with the global, northern hemisphere and southern hemisphere temperatures, to determine if their trends run in similar or opposite directions. Point-to-point comparisons between temperature and quantified hemagglutinins were performed for all species and for the major prevailing species. The comparisons show that the trends for both hemagglutinin evolution and temperature change run in a similar direction. Global warming has a consistent and progressive impact on the hemagglutinin evolution of influenza A viruses.

The Prosodic Evolution of West Slavic in the Context of the Neo-Acute Stress

ERIC Educational Resources Information Center

Feldstein, Ronald F.

1975-01-01

Because of neo-acute stress--or transferred acute stress--long vowel prosody in West Slavic had a special evolution. Two kinds of long vowel evolution are examined. The nature of transitionality across Slavic territory from tonal opposition to distinctive stress placement is pointed out. (SC)

A New Model for the Seasonal Evolution of Triton

NASA Astrophysics Data System (ADS)

Forget, F.; Decamp, N.; Berthier, J.; Le Guyader, C.

2000-10-01

The seasonal evolution of Triton's surface and atmosphere remains poorly understood. No model [1] has been able to fully reproduce the main characterictics of the Voyager 2 observations in 1989 in combination with the "Global warming" recently inferred from stellar occultations [2]. Within this context, we have developped a new thermal model to study the seasonal nitrogen cycle on Triton. The model is the surface part of a Triton atmosphere General circulation model developped at LMD [3]. The nitrogen cycle was found to be very sensitive to Triton complex seasonal variations of the subsolar point latitude, especially during the current decade (south summer solstice). Since only pre-Voyager formulations were available for such a study, this has motivated some new calculations of Triton's motion based on more recent rotationnal elements combined with a relatively complete dynamic solution [4] adapted to Triton. A new analytic formulation suitable for climate modelling has been derived. On this basis, we wish to suggest a new, realistic scenario to explain Triton's apparence and evolution based on solar-induced variation of the frost albedo. Such variations have been observed in Mars CO2 ice seasonal polar caps [5]. Although they seem to result from complex microphysical behavior, they are likely to occur on Triton since both Triton and Mars polar caps are composed of weakly absorbing ice (N2 or CO2) in vapor pressure equilibrium with the main constituant of the atmosphere. [1] e.g. Hansen and Paige, Icarus 99, 273-288 (1992); Brown and Kirk, J. Geophys. Res. 99, 1965-1981 (1994); Spencer and Moore, Icarus 99, 261-272 (1992). [2] Elliot et al., Nature 393, 765-767 (1998). [3] Forget, Descamp and Hourdin, in ``Pluto and Triton, comparisons and evolution over time", Lowell Observatory's fourth annual workshop, Flagstaff, Arizona. (1999) [4] Le Guyader, Astron. Astrophys. 272, 687-694 (1993). [5] Kieffer et al., J. Geophys. Res. 105, 9653-9700 (2000).

A tectonic model for the Tertiary evolution of strike slip faults and rift basins in SE Asia

NASA Astrophysics Data System (ADS)

Morley, C. K.

2002-04-01

Models for the Tertiary evolution of SE Asia fall into two main types: a pure escape tectonics model with no proto-South China Sea, and subduction of proto-South China Sea oceanic crust beneath Borneo. A related problem is which, if any, of the main strike-slip faults (Mae Ping, Three Pagodas and Aliao Shan-Red River (ASRR)) cross Sundaland to the NW Borneo margin to facilitate continental extrusion? Recent results investigating strike-slip faults, rift basins, and metamorphic core complexes are reviewed and a revised tectonic model for SE Asia proposed. Key points of the new model include: (1) The ASRR shear zone was mainly active in the Eocene-Oligocene in order to link with extension in the South China Sea. The ASRR was less active during the Miocene (tens of kilometres of sinistral displacement), with minor amounts of South China Sea spreading centre extension transferred to the ASRR shear zone. (2) At least three important regions of metamorphic core complex development affected Indochina from the Oligocene-Miocene (Mogok gneiss belt; Doi Inthanon and Doi Suthep; around the ASRR shear zone). Hence, Paleogene crustal thickening, buoyancy-driven crustal collapse, and lower crustal flow are important elements of the Tertiary evolution of Indochina. (3) Subduction of a proto-South China Sea oceanic crust during the Eocene-Early Miocene is necessary to explain the geological evolution of NW Borneo and must be built into any model for the region. (4) The Eocene-Oligocene collision of NE India with Burma activated extrusion tectonics along the Three Pagodas, Mae Ping, Ranong and Klong Marui faults and right lateral motion along the Sumatran subduction zone. (5) The only strike-slip fault link to the NW Borneo margin occurred along the trend of the ASRR fault system, which passes along strike into a right lateral transform system including the Baram line.

Portable open-path optical remote sensing (ORS) Fourier transform infrared (FTIR) instrumentation miniaturization and software for point and click real-time analysis

NASA Astrophysics Data System (ADS)

Zemek, Peter G.; Plowman, Steven V.

2010-04-01

Advances in hardware have miniaturized the emissions spectrometer and associated optics, rendering them easily deployed in the field. Such systems are also suitable for vehicle mounting, and can provide high quality data and concentration information in minutes. Advances in software have accompanied this hardware evolution, enabling the development of portable point-and-click OP-FTIR systems that weigh less than 16 lbs. These systems are ideal for first-responders, military, law enforcement, forensics, and screening applications using optical remote sensing (ORS) methodologies. With canned methods and interchangeable detectors, the new generation of OP-FTIR technology is coupled to the latest forward reference-type model software to provide point-and-click technology. These software models have been established for some time. However, refined user-friendly models that use active, passive, and solar occultation methodologies now allow the user to quickly field-screen and quantify plumes, fence-lines, and combustion incident scenarios in high-temporal-resolution. Synthetic background generation is now redundant as the models use highly accurate instrument line shape (ILS) convolutions and several other parameters, in conjunction with radiative transfer model databases to model a single calibration spectrum to collected sample spectra. Data retrievals are performed directly on single beam spectra using non-linear classical least squares (NLCLS). Typically, the Hitran line database is used to generate the initial calibration spectrum contained within the software.

Characteristic dynamics near two coalescing eigenvalues incorporating continuum threshold effects

NASA Astrophysics Data System (ADS)

Garmon, Savannah; Ordonez, Gonzalo

2017-06-01

It has been reported in the literature that the survival probability P(t) near an exceptional point where two eigenstates coalesce should generally exhibit an evolution P (t ) ˜t2e-Γ t, in which Γ is the decay rate of the coalesced eigenstate; this has been verified in a microwave billiard experiment [B. Dietz et al., Phys. Rev. E 75, 027201 (2007)]. However, the heuristic effective Hamiltonian that is usually employed to obtain this result ignores the possible influence of the continuum threshold on the dynamics. By contrast, in this work we employ an analytical approach starting from the microscopic Hamiltonian representing two simple models in order to show that the continuum threshold has a strong influence on the dynamics near exceptional points in a variety of circumstances. To report our results, we divide the exceptional points in Hermitian open quantum systems into two cases: at an EP2A two virtual bound states coalesce before forming a resonance, anti-resonance pair with complex conjugate eigenvalues, while at an EP2B two resonances coalesce before forming two different resonances. For the EP2B, which is the case studied in the microwave billiard experiment, we verify that the survival probability exhibits the previously reported modified exponential decay on intermediate time scales, but this is replaced with an inverse power law on very long time scales. Meanwhile, for the EP2A the influence from the continuum threshold is so strong that the evolution is non-exponential on all time scales and the heuristic approach fails completely. When the EP2A appears very near the threshold, we obtain the novel evolution P (t ) ˜1 -C1√{t } on intermediate time scales, while further away the parabolic decay (Zeno dynamics) on short time scales is enhanced.

Empirical phylogenies and species abundance distributions are consistent with preequilibrium dynamics of neutral community models with gene flow.

PubMed

Bonnet-Lebrun, Anne-Sophie; Manica, Andrea; Eriksson, Anders; Rodrigues, Ana S L

2017-05-01

Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities-that is with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities-from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in preequilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under preequilibrium conditions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Analysis of Magnitude Correlations in a Self-Similar model of Seismicity

NASA Astrophysics Data System (ADS)

Zambrano, A.; Joern, D.

2017-12-01

A recent model of seismicity that incorporates a self-similar Omori-Utsu relation, which is used to describe the temporal evolution of earthquake triggering, has been shown to provide a more accurate description of seismicity in Southern California when compared to epidemic type aftershock sequence models. Forecasting of earthquakes is an active research area where one of the debated points is whether magnitude correlations of earthquakes exist within real world seismic data. Prior to this work, the analysis of magnitude correlations of the aforementioned self-similar model had not been addressed. Here we present statistical properties of the magnitude correlations for the self-similar model along with an analytical analysis of the branching ratio and criticality parameters.

Electron-density critical points analysis and catastrophe theory to forecast structure instability in periodic solids.

PubMed

Merli, Marcello; Pavese, Alessandro

2018-03-01

The critical points analysis of electron density, i.e. ρ(x), from ab initio calculations is used in combination with the catastrophe theory to show a correlation between ρ(x) topology and the appearance of instability that may lead to transformations of crystal structures, as a function of pressure/temperature. In particular, this study focuses on the evolution of coalescing non-degenerate critical points, i.e. such that ∇ρ(x c ) = 0 and λ 1 , λ 2 , λ 3 ≠ 0 [λ being the eigenvalues of the Hessian of ρ(x) at x c ], towards degenerate critical points, i.e. ∇ρ(x c ) = 0 and at least one λ equal to zero. The catastrophe theory formalism provides a mathematical tool to model ρ(x) in the neighbourhood of x c and allows one to rationalize the occurrence of instability in terms of electron-density topology and Gibbs energy. The phase/state transitions that TiO 2 (rutile structure), MgO (periclase structure) and Al 2 O 3 (corundum structure) undergo because of pressure and/or temperature are here discussed. An agreement of 3-5% is observed between the theoretical model and experimental pressure/temperature of transformation.

Stability of the phase motion in race-track microtrons

NASA Astrophysics Data System (ADS)

Kubyshin, Yu. A.; Larreal, O.; Ramírez-Ros, R.; Seara, T. M.

2017-06-01

We model the phase oscillations of electrons in race-track microtrons by means of an area preserving map with a fixed point at the origin, which represents the synchronous trajectory of a reference particle in the beam. We study the nonlinear stability of the origin in terms of the synchronous phase -the phase of the synchronous particle at the injection. We estimate the size and shape of the stability domain around the origin, whose main connected component is enclosed by an invariant curve. We describe the evolution of the stability domain as the synchronous phase varies. We also clarify the role of the stable and unstable invariant curves of some hyperbolic (fixed or periodic) points.

Crossover from BCS to Bose superconductivity: A functional integral approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Randeria, M.; Sa de Melo, C.A.R.; Engelbrecht, J.R.

1993-04-01

We use a functional integral formulation to study the crossover from cooperative Cooper pairing to the formation and condensation of tightly bound pairs in a 3D continuum model of fermions with attractive interactions. The inadequacy of a saddle point approximation with increasing coupling is pointed out, and the importance of temporal (quantum) fluctuations for normal state properties at intermediate and strong coupling is emphasized. In addition to recovering the Nozieres-Schmitt-Pink interpolation scheme for T{sub c}, and the Leggett variational results for T = 0, we also present results for evolution of the time-dependent Ginzburg-Landau equation and collective mode spectrum asmore » a function of the coupling.« less

Three-Dimensional Structure and Evolution of Extreme-Ultraviolet Bright Points Observed by STEREO/SECCHI/EUVI

NASA Technical Reports Server (NTRS)

Kwon, Ryun Young; Chae, Jongchul; Davila, Joseph M.; Zhang, Jie; Moon, Yong-Jae; Poomvises, Watanachak; Jones, Shaela I.

2012-01-01

We unveil the three-dimensional structure of quiet-Sun EUV bright points and their temporal evolution by applying a triangulation method to time series of images taken by SECCHI/EUVI on board the STEREO twin spacecraft. For this study we examine the heights and lengths as the components of the three-dimensional structure of EUV bright points and their temporal evolutions. Among them we present three bright points which show three distinct changes in the height and length: decreasing, increasing, and steady. We show that the three distinct changes are consistent with the motions (converging, diverging, and shearing, respectively) of their photospheric magnetic flux concentrations. Both growth and shrinkage of the magnetic fluxes occur during their lifetimes and they are dominant in the initial and later phases, respectively. They are all multi-temperature loop systems which have hot loops (approx. 10(exp 6.2) K) overlying cooler ones (approx 10(exp 6.0) K) with cool legs (approx 10(exp 4.9) K) during their whole evolutionary histories. Our results imply that the multi-thermal loop system is a general character of EUV bright points. We conclude that EUV bright points are flaring loops formed by magnetic reconnection and their geometry may represent the reconnected magnetic field lines rather than the separator field lines.

Evidence for Precursors of the Coronal Hole Jets in Solar Bright Points

NASA Astrophysics Data System (ADS)

Bagashvili, Salome R.; Shergelashvili, Bidzina M.; Japaridze, Darejan R.; Kukhianidze, Vasil; Poedts, Stefaan; Zaqarashvili, Teimuraz V.; Khodachenko, Maxim L.; De Causmaecker, Patrick

2018-03-01

A set of 23 observations of coronal jet events that occurred in coronal bright points has been analyzed. The focus was on the temporal evolution of the mean brightness before and during coronal jet events. In the absolute majority of the cases either single or recurrent coronal jets (CJs) were preceded by slight precursor disturbances observed in the mean intensity curves. The key conclusion is that we were able to detect quasi-periodical oscillations with characteristic periods from sub-minute up to 3–4 minute values in the bright point brightness that precedes the jets. Our basic claim is that along with the conventionally accepted scenario of bright-point evolution through new magnetic flux emergence and its reconnection with the initial structure of the bright point and the coronal hole, certain magnetohydrodynamic (MHD) oscillatory and wavelike motions can be excited and these can take an important place in the observed dynamics. These quasi-oscillatory phenomena might play the role of links between different epochs of the coronal jet ignition and evolution. They can be an indication of the MHD wave excitation processes due to the system entropy variations, density variations, or shear flows. It is very likely a sharp outflow velocity transverse gradients at the edges between the open and closed field line regions. We suppose that magnetic reconnections can be the source of MHD waves due to impulsive generation or rapid temperature variations, and shear flow driven nonmodel MHD wave evolution (self-heating and/or overreflection mechanisms).

Quasi-Tangency Points on the Orbits of a Small Body and a Planet at the Low-Velocity Encounter

NASA Astrophysics Data System (ADS)

Emel'yanenko, N. Yu.

2018-03-01

We propose a method for selecting a low-velocity encounter of a small body with a planet from the evolution of the orbital elements. Polar orbital coordinates of the quasi-tangency point on the orbit of a small body are determined. Rectangular heliocentric coordinates of the quasi-tangency point on the orbit of a planet are determined. An algorithm to search for low-velocity encounters in the evolution of the orbital elements of small bodies is described. The low-velocity encounter of comet 39P/Oterma with Jupiter is considered as an example.

Demand modelling of passenger air travel: An analysis and extension, volume 2

NASA Technical Reports Server (NTRS)

Jacobson, I. D.

1978-01-01

Previous intercity travel demand models in terms of their ability to predict air travel in a useful way and the need for disaggregation in the approach to demand modelling are evaluated. The viability of incorporating non-conventional factors (i.e. non-econometric, such as time and cost) in travel demand forecasting models are determined. The investigation of existing models is carried out in order to provide insight into their strong points and shortcomings. The model is characterized as a market segmentation model. This is a consequence of the strengths of disaggregation and its natural evolution to a usable aggregate formulation. The need for this approach both pedagogically and mathematically is discussed. In addition this volume contains two appendices which should prove useful to the non-specialist in the area.

Anomalous scaling in an age-dependent branching model.

PubMed

Keller-Schmidt, Stephanie; Tuğrul, Murat; Eguíluz, Víctor M; Hernández-García, Emilio; Klemm, Konstantin

2015-02-01

We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ(-α). Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)(2). This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.

Mathematical modeling of transformation process of structurally unstable magnetic configurations into structurally stable ones in two-dimensional and three-dimensional geometry

NASA Astrophysics Data System (ADS)

Inovenkov, Igor; Echkina, Eugenia; Ponomarenko, Loubov

Magnetic reconnection is a fundamental process in astrophysical, space and laboratory plasma. In essence, it represents a change of topology of the magnetic field caused by readjustment of the structure of the magnetic field lines. This change leads to release of energy accumulated in the field. We consider transformation process of structurally unstable magnetic configurations into the structurally steady ones from the point of view of the Catastrophe theory. Special attention is paid to modeling of evolution of the structurally unstable three-dimensional magnetic fields.

Two-point coherence of wave packets in turbulent jets

NASA Astrophysics Data System (ADS)

Jaunet, V.; Jordan, P.; Cavalieri, A. V. G.

2017-02-01

An experiment has been performed in order to provide support for wave-packet jet-noise modeling efforts. Recent work has shown that the nonlinear effects responsible for the two-point coherence of wave packets must be correctly accounted for if accurate sound prediction is to be achieved for subsonic turbulent jets. We therefore consider the same Mach 0.4 turbulent jet studied by Cavalieri et al. [Cavalieri et al., J. Fluid Mech. 730, 559 (2013), 10.1017/jfm.2013.346], but this time using two independent but synchronized, time-resolved stereo particle-image velocimetry systems. Each system can be moved independently, allowing simultaneous measurement of velocity in two, axially separated, crossflow planes, enabling eduction of the two-point coherence of wave packets. This and the associated length scales and phase speeds are studied and compared with those of the energy-containing turbulent eddies. The study illustrates how the two-point behavior of wave packets is fundamentally different from that of the more usually studied bulk two-point behavior, suggesting that sound-source modeling efforts should be reconsidered in the framework of wave packets. The study furthermore identifies two families of two-point-coherence behavior, respectively upstream and downstream of the end of the potential core, regions where linear theory is, respectively, successful and unsuccessful in predicting the axial evolution of wave-packets fluctuation energy.

Reverse engineering gene regulatory networks from measurement with missing values.

PubMed

Ogundijo, Oyetunji E; Elmas, Abdulkadir; Wang, Xiaodong

2016-12-01

Gene expression time series data are usually in the form of high-dimensional arrays. Unfortunately, the data may sometimes contain missing values: for either the expression values of some genes at some time points or the entire expression values of a single time point or some sets of consecutive time points. This significantly affects the performance of many algorithms for gene expression analysis that take as an input, the complete matrix of gene expression measurement. For instance, previous works have shown that gene regulatory interactions can be estimated from the complete matrix of gene expression measurement. Yet, till date, few algorithms have been proposed for the inference of gene regulatory network from gene expression data with missing values. We describe a nonlinear dynamic stochastic model for the evolution of gene expression. The model captures the structural, dynamical, and the nonlinear natures of the underlying biomolecular systems. We present point-based Gaussian approximation (PBGA) filters for joint state and parameter estimation of the system with one-step or two-step missing measurements . The PBGA filters use Gaussian approximation and various quadrature rules, such as the unscented transform (UT), the third-degree cubature rule and the central difference rule for computing the related posteriors. The proposed algorithm is evaluated with satisfying results for synthetic networks, in silico networks released as a part of the DREAM project, and the real biological network, the in vivo reverse engineering and modeling assessment (IRMA) network of yeast Saccharomyces cerevisiae . PBGA filters are proposed to elucidate the underlying gene regulatory network (GRN) from time series gene expression data that contain missing values. In our state-space model, we proposed a measurement model that incorporates the effect of the missing data points into the sequential algorithm. This approach produces a better inference of the model parameters and hence, more accurate prediction of the underlying GRN compared to when using the conventional Gaussian approximation (GA) filters ignoring the missing data points.

Fundamentals of continuum mechanics – classical approaches and new trends

NASA Astrophysics Data System (ADS)

Altenbach, H.

2018-04-01

Continuum mechanics is a branch of mechanics that deals with the analysis of the mechanical behavior of materials modeled as a continuous manifold. Continuum mechanics models begin mostly by introducing of three-dimensional Euclidean space. The points within this region are defined as material points with prescribed properties. Each material point is characterized by a position vector which is continuous in time. Thus, the body changes in a way which is realistic, globally invertible at all times and orientation-preserving, so that the body cannot intersect itself and as transformations which produce mirror reflections are not possible in nature. For the mathematical formulation of the model it is also assumed to be twice continuously differentiable, so that differential equations describing the motion may be formulated. Finally, the kinematical relations, the balance equations, the constitutive and evolution equations and the boundary and/or initial conditions should be defined. If the physical fields are non-smooth jump conditions must be taken into account. The basic equations of continuum mechanics are presented following a short introduction. Additionally, some examples of solid deformable continua will be discussed within the presentation. Finally, advanced models of continuum mechanics will be introduced. The paper is dedicated to Alexander Manzhirov’s 60th birthday.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rycroft, Chris H.; Bazant, Martin Z.

An advection-diffusion-limited dissolution model of an object being eroded by a two-dimensional potential flow is presented. By taking advantage of the conformal invariance of the model, a numerical method is introduced that tracks the evolution of the object boundary in terms of a time-dependent Laurent series. Simulations of a variety of dissolving objects are shown, which shrink and collapse to a single point in finite time. The simulations reveal a surprising exact relationship, whereby the collapse point is the root of a non-Analytic function given in terms of the flow velocity and the Laurent series coefficients describing the initial shape.more » This result is subsequently derived using residue calculus. The structure of the non-Analytic function is examined for three different test cases, and a practical approach to determine the collapse point using a generalized Newton-Raphson root-finding algorithm is outlined. These examples also illustrate the possibility that the model breaks down in finite time prior to complete collapse, due to a topological singularity, as the dissolving boundary overlaps itself rather than breaking up into multiple domains (analogous to droplet pinch-off in fluid mechanics). In conclusion, the model raises fundamental mathematical questions about broken symmetries in finite-Time singularities of both continuous and stochastic dynamical systems.« less

Asymmetric collapse by dissolution or melting in a uniform flow

PubMed Central

Bazant, Martin Z.

2016-01-01

An advection–diffusion-limited dissolution model of an object being eroded by a two-dimensional potential flow is presented. By taking advantage of the conformal invariance of the model, a numerical method is introduced that tracks the evolution of the object boundary in terms of a time-dependent Laurent series. Simulations of a variety of dissolving objects are shown, which shrink and collapse to a single point in finite time. The simulations reveal a surprising exact relationship, whereby the collapse point is the root of a non-analytic function given in terms of the flow velocity and the Laurent series coefficients describing the initial shape. This result is subsequently derived using residue calculus. The structure of the non-analytic function is examined for three different test cases, and a practical approach to determine the collapse point using a generalized Newton–Raphson root-finding algorithm is outlined. These examples also illustrate the possibility that the model breaks down in finite time prior to complete collapse, due to a topological singularity, as the dissolving boundary overlaps itself rather than breaking up into multiple domains (analogous to droplet pinch-off in fluid mechanics). The model raises fundamental mathematical questions about broken symmetries in finite-time singularities of both continuous and stochastic dynamical systems. PMID:26997890

Asymmetric collapse by dissolution or melting in a uniform flow

DOE PAGES

Rycroft, Chris H.; Bazant, Martin Z.

2016-01-06

An advection-diffusion-limited dissolution model of an object being eroded by a two-dimensional potential flow is presented. By taking advantage of the conformal invariance of the model, a numerical method is introduced that tracks the evolution of the object boundary in terms of a time-dependent Laurent series. Simulations of a variety of dissolving objects are shown, which shrink and collapse to a single point in finite time. The simulations reveal a surprising exact relationship, whereby the collapse point is the root of a non-Analytic function given in terms of the flow velocity and the Laurent series coefficients describing the initial shape.more » This result is subsequently derived using residue calculus. The structure of the non-Analytic function is examined for three different test cases, and a practical approach to determine the collapse point using a generalized Newton-Raphson root-finding algorithm is outlined. These examples also illustrate the possibility that the model breaks down in finite time prior to complete collapse, due to a topological singularity, as the dissolving boundary overlaps itself rather than breaking up into multiple domains (analogous to droplet pinch-off in fluid mechanics). In conclusion, the model raises fundamental mathematical questions about broken symmetries in finite-Time singularities of both continuous and stochastic dynamical systems.« less

Mean-field approximation for the Sznajd model in complex networks

NASA Astrophysics Data System (ADS)

Araújo, Maycon S.; Vannucchi, Fabio S.; Timpanaro, André M.; Prado, Carmen P. C.

2015-02-01

This paper studies the Sznajd model for opinion formation in a population connected through a general network. A master equation describing the time evolution of opinions is presented and solved in a mean-field approximation. Although quite simple, this approximation allows us to capture the most important features regarding the steady states of the model. When spontaneous opinion changes are included, a discontinuous transition from consensus to polarization can be found as the rate of spontaneous change is increased. In this case we show that a hybrid mean-field approach including interactions between second nearest neighbors is necessary to estimate correctly the critical point of the transition. The analytical prediction of the critical point is also compared with numerical simulations in a wide variety of networks, in particular Barabási-Albert networks, finding reasonable agreement despite the strong approximations involved. The same hybrid approach that made it possible to deal with second-order neighbors could just as well be adapted to treat other problems such as epidemic spreading or predator-prey systems.

Surface structure and structural point defects of liquid and amorphous aluminosilicate nanoparticles.

PubMed

Linh, Nguyen Ngoc; Hoang, Vo Van

2008-07-02

The surface structure of liquid and amorphous aluminosilicate nanoparticles of composition Al(2)O(3)·2SiO(2) has been investigated in a model of different sizes ranging from 2.0 to 5.0 nm with the Born-Mayer type pair potential under non-periodic boundary conditions. Models have been obtained by cooling from the melts at a constant density of 2.6 g cm(-3) via molecular dynamics (MD) simulation. The surface structure has been investigated via the coordination number, bond-angle distributions and structural point defects. Calculations show that surface effects on surface static and thermodynamic properties of models are significant according to the change in the number of Al atoms in the surface layers. Evolution of the local environment of oxygen in the surface shell of nanoparticles upon cooling from the melt toward the glassy state was also found and discussed. In addition, the nanosize dependence of the glass transition temperature was presented.

Surface structure and structural point defects of liquid and amorphous aluminosilicate nanoparticles

NASA Astrophysics Data System (ADS)

Linh, Nguyen Ngoc; Van Hoang, Vo

2008-07-01

The surface structure of liquid and amorphous aluminosilicate nanoparticles of composition Al2O3·2SiO2 has been investigated in a model of different sizes ranging from 2.0 to 5.0 nm with the Born-Mayer type pair potential under non-periodic boundary conditions. Models have been obtained by cooling from the melts at a constant density of 2.6 g cm-3 via molecular dynamics (MD) simulation. The surface structure has been investigated via the coordination number, bond-angle distributions and structural point defects. Calculations show that surface effects on surface static and thermodynamic properties of models are significant according to the change in the number of Al atoms in the surface layers. Evolution of the local environment of oxygen in the surface shell of nanoparticles upon cooling from the melt toward the glassy state was also found and discussed. In addition, the nanosize dependence of the glass transition temperature was presented.

Self-similarity analysis of eubacteria genome based on weighted graph.

PubMed

Qi, Zhao-Hui; Li, Ling; Zhang, Zhi-Meng; Qi, Xiao-Qin

2011-07-07

We introduce a weighted graph model to investigate the self-similarity characteristics of eubacteria genomes. The regular treating in similarity comparison about genome is to discover the evolution distance among different genomes. Few people focus their attention on the overall statistical characteristics of each gene compared with other genes in the same genome. In our model, each genome is attributed to a weighted graph, whose topology describes the similarity relationship among genes in the same genome. Based on the related weighted graph theory, we extract some quantified statistical variables from the topology, and give the distribution of some variables derived from the largest social structure in the topology. The 23 eubacteria recently studied by Sorimachi and Okayasu are markedly classified into two different groups by their double logarithmic point-plots describing the similarity relationship among genes of the largest social structure in genome. The results show that the proposed model may provide us with some new sights to understand the structures and evolution patterns determined from the complete genomes. Copyright © 2011 Elsevier Ltd. All rights reserved.

Quantifying the evolution of flow boiling bubbles by statistical testing and image analysis: toward a general model.

PubMed

Xiao, Qingtai; Xu, Jianxin; Wang, Hua

2016-08-16

A new index, the estimate of the error variance, which can be used to quantify the evolution of the flow patterns when multiphase components or tracers are difficultly distinguishable, was proposed. The homogeneity degree of the luminance space distribution behind the viewing windows in the direct contact boiling heat transfer process was explored. With image analysis and a linear statistical model, the F-test of the statistical analysis was used to test whether the light was uniform, and a non-linear method was used to determine the direction and position of a fixed source light. The experimental results showed that the inflection point of the new index was approximately equal to the mixing time. The new index has been popularized and applied to a multiphase macro mixing process by top blowing in a stirred tank. Moreover, a general quantifying model was introduced for demonstrating the relationship between the flow patterns of the bubble swarms and heat transfer. The results can be applied to investigate other mixing processes that are very difficult to recognize the target.

Restricted Euler dynamics along trajectories of small inertial particles in turbulence

NASA Astrophysics Data System (ADS)

Johnson, Perry; Meneveau, Charles

2016-11-01

The fate of small particles in turbulent flows depends strongly on the surrounding fluid's velocity gradient properties such as rotation and strain-rates. For non-inertial (fluid) particles, the Restricted Euler model provides a simple, low-dimensional dynamical system representation of Lagrangian evolution of velocity gradients in fluid turbulence, at least for short times. Here we derive a new restricted Euler dynamical system for the velocity gradient evolution of inertial particles such as solid particles in a gas or droplets and bubbles in turbulent liquid flows. The model is derived in the limit of small (sub Kolmogorov scale) particles and low Stokes number. The system exhibits interesting fixed points, stability and invariant properties. Comparisons with data from Direct Numerical Simulations show that the model predicts realistic trends such as the tendency of increased straining over rotation along heavy particle trajectories and, for light particles such as bubbles, the tendency of severely reduced self-stretching of strain-rate. Supported by a National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1232825 and by a Grant from The Gulf of Mexico Research Initiative.

Quantifying the evolution of flow boiling bubbles by statistical testing and image analysis: toward a general model

PubMed Central

Xiao, Qingtai; Xu, Jianxin; Wang, Hua

2016-01-01

A new index, the estimate of the error variance, which can be used to quantify the evolution of the flow patterns when multiphase components or tracers are difficultly distinguishable, was proposed. The homogeneity degree of the luminance space distribution behind the viewing windows in the direct contact boiling heat transfer process was explored. With image analysis and a linear statistical model, the F-test of the statistical analysis was used to test whether the light was uniform, and a non-linear method was used to determine the direction and position of a fixed source light. The experimental results showed that the inflection point of the new index was approximately equal to the mixing time. The new index has been popularized and applied to a multiphase macro mixing process by top blowing in a stirred tank. Moreover, a general quantifying model was introduced for demonstrating the relationship between the flow patterns of the bubble swarms and heat transfer. The results can be applied to investigate other mixing processes that are very difficult to recognize the target. PMID:27527065

Evolution of consciousness: Phylogeny, ontogeny, and emergence from general anesthesia

PubMed Central

Mashour, George A.; Alkire, Michael T.

2013-01-01

Are animals conscious? If so, when did consciousness evolve? We address these long-standing and essential questions using a modern neuroscientific approach that draws on diverse fields such as consciousness studies, evolutionary neurobiology, animal psychology, and anesthesiology. We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution. Thus, in agreement with Darwin’s insight and the recent “Cambridge Declaration on Consciousness in Non-Human Animals,” a review of modern scientific data suggests that the differences between species in terms of the ability to experience the world is one of degree and not kind. PMID:23754370

Tidal Interaction among Red Giants Close Binary Systems in APOGEE Database

NASA Astrophysics Data System (ADS)

Sun, Meng; Arras, Phil; Majewski, Steven R.; Troup, Nicholas William; Weinberg, Nevin N.

2017-01-01

Motivated by the newly discovered close binary systems in the Apache Point Observatory Galactic Evolution Experiment (APOGEE-1), the tidal evolution of binaries containing a red giant branch (RGB) star with a stellar or substellar companion was investigated. The tide raised by the companion in the RGB star leads to exchange of angular momentum between the orbit and the stellar spin, causing the orbit to contract. The tidal dissipation rate is computed using turbulent viscosity acting on the equilibrium tidal flow, where careful attention is paid to the effects of reduced viscosity for close-in companions. Evolutionary models for the RGB stars, from the zero-age main sequence to the present, were acquired from the MESA code. "Standard" turbulent viscosity gives rise to such a large orbital decay that many observed systems have decay times much shorter than the RGB evolution time. Several theories for "reduced" turbulent viscosity are investigated, and reduce the number of systems with uncomfortably short decay times.

Research at the Institute of Astronomy and Astrophysics of the Université Libre de Bruxelles

NASA Astrophysics Data System (ADS)

Karinkuzhi, Drisya; Chamel, Nicolas; Goriely, Stéphane; Jorissen, Alain; Pourbaix, Dimitri; Siess, Lionel; Van Eck, Sophie

2018-04-01

Over the years, a coherent research strategy has developed in the field of stellar physics at the Institute of Astronomy and Astrophysics (IAA). It involves observational studies (chemical composition of giant stars, binary properties, tomography of stellar atmospheres) that make use of the large ESO telescopes as well as of other major instruments. The presence of a high-resolution spectrograph on the 3.6-m Devasthal Optical Telescope (DOT) would therefore be highly beneficial to IAA research. These observations are complemented and supported by theoretical studies of mass transfer in binary systems, of standard and non-standard stellar evolution (including the modelling of stellar hydrodynamical nuclear burning for application to certain thermonuclear supernovae) and of nuclear astrophysics (a field in which IAA has been recognized for a long time as an international centre of excellence), including the theory of nucleosynthesis. IAA also addresses the end-points of stellar evolution as it is carrying out research on the compact remnants of stellar evolution of massive stars: neutron stars.

Resolving phylogenetic incongruence to articulate homology and phenotypic evolution: a case study from Nematoda

PubMed Central

Ragsdale, Erik J.; Baldwin, James G.

2010-01-01

Modern morphology-based systematics, including questions of incongruence with molecular data, emphasizes analysis over similarity criteria to assess homology. Yet detailed examination of a few key characters, using new tools and processes such as computerized, three-dimensional ultrastructural reconstruction of cell complexes, can resolve apparent incongruence by re-examining primary homologies. In nematodes of Tylenchomorpha, a parasitic feeding phenotype is thus reconciled with immediate free-living outgroups. Closer inspection of morphology reveals phenotypes congruent with molecular-based phylogeny and points to a new locus of homology in mouthparts. In nematode models, the study of individually homologous cells reveals a conserved modality of evolution among dissimilar feeding apparati adapted to divergent lifestyles. Conservatism of cellular components, consistent with that of other body systems, allows meaningful comparative morphology in difficult groups of microscopic organisms. The advent of phylogenomics is synergistic with morphology in systematics, providing an honest test of homology in the evolution of phenotype. PMID:20106846

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

PubMed Central

McDonald, Bradon R.

2017-01-01

ABSTRACT Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces. Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution. PMID:28588130

TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid

NASA Astrophysics Data System (ADS)

Kononova, Olga; Maksudov, Farkhad; Marx, Kenneth A.; Barsegov, Valeri

2018-01-01

A new computational methodology for the accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and C_α -based coarse-grained structural models of biological particles. The methodology mapped into the software package TensorCalculator was successfully applied to the empty cowpea chlorotic mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid. We found an inhomogeneous stress distribution in various portions of the CCMV structure and stress transfer from one portion of the virus structure to another, which also points to the importance of entropic effects, often ignored in finite element analysis and elastic network modeling. We formulate a criterion for elastic deformation using the first principal stress components. Furthermore, we show that von Mises and Tresca stress tensors can be used to predict the onset of a viral capsid’s mechanical failure, which leads to total structural collapse. TensorCalculator can be used to study stress evolution and dynamics of defects in viral capsids and other large-size protein assemblies.

Surface signature of Mediterranean water eddies in a long-term high-resolution simulation

NASA Astrophysics Data System (ADS)

Ciani, D.; Carton, X.; Barbosa Aguiar, A. C.; Peliz, A.; Bashmachnikov, I.; Ienna, F.; Chapron, B.; Santoleri, R.

2017-12-01

We study the surface signatures of Mediterranean water eddies (Meddies) in the context of a regional, primitive equations model simulation (using the Regional Oceanic Modeling System, ROMS). This model simulation was previously performed to study the mean characteristics and pathways of Meddies during their evolution in the Atlantic Ocean. The advantage of our approach is to take into account different physical mechanisms acting on the evolution of Meddies and their surface signature, having full information on the 3D distribution of all physical variables of interest. The evolution of around 90 long-lived Meddies (whose lifetimes exceeded one year) was investigated. In particular, their surface signature was determined in sea-surface height, temperature and salinity. The Meddy-induced anomalies were studied as a function of the Meddy structure and of the oceanic background. We show that the Meddies can generate positive anomalies in the elevation of the oceanic free-surface and that these anomalies are principally related to the Meddies potential vorticity structure at depth (around 1000 m below the sea-surface). On the contrary, the Meddies thermohaline surface signatures proved to be mostly dominated by local surface conditions and little correlated to the Meddy structure at depth. This work essentially points out that satellite altimetry is the most suitable approach to track subsurface vortices from observations of the sea-surface.

Predicting Galaxy Star Formation Rates via the Co-evolution of Galaxies and Halos

DOE PAGES

Watson, Douglas F.; Hearin, Andrew P.; Berlind, Andreas A.; ...

2014-03-06

In this paper, we test the age matching hypothesis that the star formation rate (SFR) of a galaxy is determined by its dark matter halo formation history, and as such, that more quiescent galaxies reside in older halos. This simple model has been remarkably successful at predicting color-based galaxy statistics at low redshift as measured in the Sloan Digital Sky Survey (SDSS). To further test this method with observations, we present new SDSS measurements of the galaxy two-point correlation function and galaxy-galaxy lensing as a function of stellar mass and SFR, separated into quenched and star forming galaxy samples. Wemore » find that our age matching model is in excellent agreement with these new measurements. We also employ a galaxy group finder and show that our model is able to predict: (1) the relative SFRs of central and satellite galaxies, (2) the SFR-dependence of the radial distribution of satellite galaxy populations within galaxy groups, rich groups, and clusters and their surrounding larger scale environments, and (3) the interesting feature that the satellite quenched fraction as a function of projected radial distance from the central galaxy exhibits an approx r -.15 slope, independent of environment. The accurate prediction for the spatial distribution of satellites is intriguing given the fact that we do not explicitly model satellite-specific processes after infall, and that in our model the virial radius does not mark a special transition region in the evolution of a satellite, contrary to most galaxy evolution models. The success of the model suggests that present-day galaxy SFR is strongly correlated with halo mass assembly history.« less

Dynamical Evolution of an Effective Two-Level System with {\\mathscr{P}}{\\mathscr{T}} Symmetry

NASA Astrophysics Data System (ADS)

Du, Lei; Xu, Zhihao; Yin, Chuanhao; Guo, Liping

2018-05-01

We investigate the dynamics of parity- and time-reversal (PT ) symmetric two-energy-level atoms in the presence of two optical and a radio-frequency (rf) fields. The strength and relative phase of fields can drive the system from unbroken to broken PT symmetric regions. Compared with the Hermitian model, Rabi-type oscillation is still observed, and the oscillation characteristics are also adjusted by the strength and relative phase in the region of unbroken PT symmetry. At exception point (EP), the oscillation breaks down. To better understand the underlying properties we study the effective Bloch dynamics and find the emergence of the z components of the fixed points is the feature of the PT symmetry breaking and the projections in x-y plane can be controlled with high flexibility compared with the standard two-level system with PT symmetry. It helps to study the dynamic behavior of the complex PT symmetric model.

Hydrodynamic-to-ballistic crossover in Dirac materials

NASA Astrophysics Data System (ADS)

Svintsov, D.

2018-03-01

We develop an analytically solvable classical kinetic model of spatially dispersive transport in Dirac materials accounting for strong electron-electron (e-e) and electron-hole (e-h) collisions. We use this model to track the evolution of graphene conductivity and properties of its collective excitations across the hydrodynamic-to-ballistic crossover. We find the relaxation rate of electric current by e-e collisions that is possible due to the lack of Galilean invariance and introduce a universal numerical measure of this noninvariance. We find the two branches of collective excitations in the Dirac fluid: plasmons and electron-hole sound. The sound waves persist at frequencies exceeding the e-e collision frequency, have a small viscous damping at the neutrality point, but acquire large damping due to e-h friction even at slight doping. On the contrary, plasmons acquire strong frictional damping at the neutrality point and become well defined in doped samples.

Bi-SOC-states in one-dimensional random cellular automaton

NASA Astrophysics Data System (ADS)

Czechowski, Zbigniew; Budek, Agnieszka; Białecki, Mariusz

2017-10-01

Two statistically stationary states with power-law scaling of avalanches are found in a simple 1 D cellular automaton. Features of the fixed points, the spiral saddle and the saddle with index 1, are investigated. The migration of states of the automaton between these two self-organized criticality states is demonstrated during evolution of the system in computer simulations. The automaton, being a slowly driven system, can be applied as a toy model of earthquake supercycles.

Configurational entropy of critical earthquake populations

NASA Astrophysics Data System (ADS)

Goltz, C.; Böse, M.

2002-10-01

We present an approach to describe the evolution of distributed seismicity by configurational entropy. We demonstrate the detection of phase transitions in the sense of a critical point phenomenon in a 2D site-percolation model and in temporal and spatial vicinity to the 1992, M7.3 Landers earthquake in Southern California. Our findings support the assumption of intermittent criticality in the Earth's crust. We also address the potential usefulness of the method for earthquake catalogue declustering.

Predicting soil formation on the basis of transport-limited chemical weathering

NASA Astrophysics Data System (ADS)

Yu, Fang; Hunt, Allen Gerhard

2018-01-01

Soil production is closely related to chemical weathering. It has been shown that, under the assumption that chemical weathering is limited by solute transport, the process of soil production is predictable. However, solute transport in soil cannot be described by Gaussian transport. In this paper, we propose an approach based on percolation theory describing non-Gaussian transport of solute to predict soil formation (the net production of soil) by considering both soil production from chemical weathering and removal of soil from erosion. Our prediction shows agreement with observed soil depths in the field. Theoretical soil formation rates are also compared with published rates predicted using soil age-profile thickness (SAST) method. Our formulation can be incorporated directly into landscape evolution models on a point-to-point basis as long as such models account for surface water routing associated with overland flow. Further, our treatment can be scaled-up to address complications associated with continental-scale applications, including those from climate change, such as changes in vegetation, or surface flow organization. The ability to predict soil formation rates has implications for understanding Earth's climate system on account of the relationship to chemical weathering of silicate minerals with the associated drawdown of atmospheric carbon, but it is also important in geomorphology for understanding landscape evolution, including for example, the shapes of hillslopes, and the net transport of sediments to sedimentary basins.

The 2-10 keV unabsorbed luminosity function of AGN from the LSS, CDFS, and COSMOS surveys

NASA Astrophysics Data System (ADS)

Ranalli, P.; Koulouridis, E.; Georgantopoulos, I.; Fotopoulou, S.; Hsu, L.-T.; Salvato, M.; Comastri, A.; Pierre, M.; Cappelluti, N.; Carrera, F. J.; Chiappetti, L.; Clerc, N.; Gilli, R.; Iwasawa, K.; Pacaud, F.; Paltani, S.; Plionis, E.; Vignali, C.

2016-05-01

The XMM-Large scale structure (XMM-LSS), XMM-Cosmological evolution survey (XMM-COSMOS), and XMM-Chandra deep field south (XMM-CDFS) surveys are complementary in terms of sky coverage and depth. Together, they form a clean sample with the least possible variance in instrument effective areas and point spread function. Therefore this is one of the best samples available to determine the 2-10 keV luminosity function of active galactic nuclei (AGN) and their evolution. The samples and the relevant corrections for incompleteness are described. A total of 2887 AGN is used to build the LF in the luminosity interval 1042-1046 erg s-1 and in the redshift interval 0.001-4. A new method to correct for absorption by considering the probability distribution for the column density conditioned on the hardness ratio is presented. The binned luminosity function and its evolution is determined with a variant of the Page-Carrera method, which is improved to include corrections for absorption and to account for the full probability distribution of photometric redshifts. Parametric models, namely a double power law with luminosity and density evolution (LADE) or luminosity-dependent density evolution (LDDE), are explored using Bayesian inference. We introduce the Watanabe-Akaike information criterion (WAIC) to compare the models and estimate their predictive power. Our data are best described by the LADE model, as hinted by the WAIC indicator. We also explore the recently proposed 15-parameter extended LDDE model and find that this extension is not supported by our data. The strength of our method is that it provides unabsorbed, non-parametric estimates, credible intervals for luminosity function parameters, and a model choice based on predictive power for future data. Based on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA member states and NASA.Tables with the samples of the posterior probability distributions are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/590/A80

Considering bioactivity in modelling continental growth and the Earth's evolution

NASA Astrophysics Data System (ADS)

Höning, D.; Spohn, T.

2013-09-01

The complexity of planetary evolution increases with the number of interacting reservoirs. On Earth, even the biosphere is speculated to interact with the interior. It has been argued (e.g., Rosing et al. 2006; Sleep et al, 2012) that the formation of continents could be a consequence of bioactivity harvesting solar energy through photosynthesis to help build the continents and that the mantle should carry a chemical biosignature. Through plate tectonics, the surface biosphere can impact deep subduction zone processes and the interior of the Earth. Subducted sediments are particularly important, because they influence the Earth's interior in several ways, and in turn are strongly influenced by the Earth's biosphere. In our model, we use the assumption that a thick sedimentary layer of low permeability on top of the subducting oceanic crust, caused by a biologically enhanced weathering rate, can suppress shallow dewatering. This in turn leads to greater vailability of water in the source region of andesitic partial melt, resulting in an enhanced rate of continental production and regassing rate into the mantle. Our model includes (i) mantle convection, (ii) continental erosion and production, and (iii) mantle water degassing at mid-ocean ridges and regassing at subduction zones. The mantle viscosity of our model depends on (i) the mantle water concentration and (ii) the mantle temperature, whose time dependency is given by radioactive decay of isotopes in the Earth's mantle. Boundary layer theory yields the speed of convection and the water outgassing rate of the Earth's mantle. Our results indicate that present day values of continental surface area and water content of the Earth's mantle represent an attractor in a phase plane spanned by both parameters. We show that the biologic enhancement of the continental erosion rate is important for the system to reach this fixed point. An abiotic Earth tends to reach an alternative stable fixed point with a smaller continental surface area and dryer mantle. The origin and evolution of life on Earth might be responsible for the rise of continents 3.5 billion years ago.

A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection

DOE PAGES

Plimpton, Steven J.; Sershen, Cheryl L.; May, Elebeoba E.

2015-01-01

This paper describes a method for incorporating a diffusion field modeling oxygen usage and dispersion in a multi-scale model of Mycobacterium tuberculosis (Mtb) infection mediated granuloma formation. We implemented this method over a floating-point field to model oxygen dynamics in host tissue during chronic phase response and Mtb persistence. The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step. Instead, diffusion is modeled by a matrix-based, steady state approximate solution to the diffusion equation. Moreover, presented in figuremore » 1 is the evolution of the diffusion profiles of a containment granuloma over time.« less

Dislocation evolution in 316 L stainless steel during multiaxial ratchetting deformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong Yawei; Kang Guozheng, E-mail: guozhengkang@yahoo.com.cn; Liu Yujie

2012-03-15

Dislocation patterns and their evolutions in 316 L stainless steel during the multiaxial ratchetting deformation were observed by transmission electron microscopy (TEM). The microscopic observations indicate that the dislocation evolution presented during the multiaxial ratchetting with four kinds of multiaxial loading paths is similar to that in the uniaxial case [G. Z. Kang et al., Mater Sci Eng A 527 (2010) 5952]. That is, dislocation networks and dislocation tangles are formed quickly by the multiple-slip and cross-slip of dislocation activated by applied multiaxial stress; and then polarized patterns such as dislocation walls and elongated incipient dislocation cells are formed atmore » the last stage of multiaxial ratchetting. The dislocation patterns evolve more quickly from the modes at low dislocation density to the ones at high density during the multiaxial ratchetting than that in the uniaxial case, and some traces of multiple-slip are observed in the multiaxial ones. The dislocation evolution during the multiaxial ratchetting deformation is summarized by comparing the observed dislocation patterns with those presented in the multiaxial strain-controlled and symmetrical stress-controlled cyclic tests. The multiaxial ratchetting of 316 L stainless steel can be microscopically and qualitatively explained by the observed evolution of dislocation patterns. - Highlights: Black-Right-Pointing-Pointer Dislocation patterns change from lines and nets to tangles, walls and cells. Black-Right-Pointing-Pointer Dislocation patterns evolve quicker in the multiaxial case. Black-Right-Pointing-Pointer Aligned dislocation arrays and some traces of multiple slips are observed. Black-Right-Pointing-Pointer Heterogeneous dislocation patterns result in the multiaxial ratchetting.« less

IMPLICATIONS OF NON-LOCALITY OF TRANSPORT IN GEOMORPHIC TRANSPORT LAWS: HILLSLOPES AND LANDSCAPE EVOLUTION MODELING

NASA Astrophysics Data System (ADS)

Foufoula-Georgiou, E.; Ganti, V. K.; Dietrich, W. E.

2009-12-01

Sediment transport on hillslopes can be thought of as a hopping process, where the sediment moves in a series of jumps. A wide range of processes shape the hillslopes which can move sediment to a large distance in the downslope direction, thus, resulting in a broad-tail in the probability density function (PDF) of hopping lengths. Here, we argue that such a broad-tailed distribution calls for a non-local computation of sediment flux, where the sediment flux is not only a function of local topographic quantities but is an integral flux which takes into account the upslope topographic “memory” of the point of interest. We encapsulate this non-local behavior into a simple fractional diffusive model that involves fractional (non-integer) derivatives. We present theoretical predictions from this nonlocal model and demonstrate a nonlinear dependence of sediment flux on local gradient, consistent with observations. Further, we demonstrate that the non-local model naturally eliminates the scale-dependence exhibited by any local (linear or nonlinear) sediment transport model. An extension to a 2-D framework, where the fractional derivative can be cast into a mixture of directional derivatives, is discussed together with the implications of introducing non-locality into existing landscape evolution models.

Relativistic MHD simulations of collision-induced magnetic dissipation in Poynting-flux-dominated jets/outflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Wei

2015-07-21

The question of the energy composition of the jets/outflows in high-energy astrophysical systems, e.g. GRBs, AGNs, is taken up first: Matter-flux-dominated (MFD), σ < 1, and/or Poynting-flux-dominated (PFD), σ >1? The standard fireball IS model and dissipative photosphere model are MFD, while the ICMART (Internal-Collision-induced MAgnetic Reconnection and Turbulence) model is PFD. Motivated by ICMART model and other relevant problems, such as “jets in a jet” model of AGNs, the author investigates the models from the EMF energy dissipation efficiency, relativistic outflow generation, and σ evolution points of view, and simulates collisions between high-σ blobs to mimic the situation ofmore » the interactions inside the PFD jets/outflows by using a 3D SRMHD code which solves the conservative form of the ideal MHD equations. σ b,f is calculated from the simulation results (threshold = 1). The efficiency obtained from this hybrid method is similar to the efficiency got from the energy evolution of the simulations (35.2%). Efficiency is nearly σ independent, which is also confirmed by the hybrid method. σ b,i - σ b,f provides an interesting linear relationship. Results of several parameter studies of EMF energy dissipation efficiency are shown.« less

Long Term Temporal and Spectral Evolution of Point Sources in Nearby Elliptical Galaxies

NASA Astrophysics Data System (ADS)

Durmus, D.; Guver, T.; Hudaverdi, M.; Sert, H.; Balman, Solen

2016-06-01

We present the results of an archival study of all the point sources detected in the lines of sight of the elliptical galaxies NGC 4472, NGC 4552, NGC 4649, M32, Maffei 1, NGC 3379, IC 1101, M87, NGC 4477, NGC 4621, and NGC 5128, with both the Chandra and XMM-Newton observatories. Specifically, we studied the temporal and spectral evolution of these point sources over the course of the observations of the galaxies, mostly covering the 2000 - 2015 period. In this poster we present the first results of this study, which allows us to further constrain the X-ray source population in nearby elliptical galaxies and also better understand the nature of individual point sources.

The RTOG Outcomes Model: economic end points and measures.

PubMed

Konski, Andre; Watkins-Bruner, Deborah

2004-03-01

Recognising the value added by economic evaluations of clinical trials and the interaction of clinical, humanistic and economic end points, the Radiation Therapy Oncology Group (RTOG) has developed an Outcomes Model that guides the comprehensive assessment of this triad of end points. This paper will focus on the economic component of the model. The Economic Impact Committee was founded in 1994 to study the economic impact of clinical trials of cancer care. A steep learning curve ensued with considerable time initially spent understanding the methodology of economic analysis. Since then, economic analyses have been performed on RTOG clinical trials involving treatments for patients with non-small cell lung cancer, locally-advanced head and neck cancer and prostate cancer. As the care of cancer patients evolves with time, so has the economic analyses performed by the Economic Impact Committee. This paper documents the evolution of the cost-effectiveness analyses of RTOG from performing average cost-utility analysis to more technically sophisticated Monte Carlo simulation of Markov models, to incorporating prospective economic analyses as an initial end point. Briefly, results indicated that, accounting for quality-adjusted survival, concurrent chemotherapy and radiation for the treatment of non-small cell lung cancer, more aggressive radiation fractionation schedules for head and neck cancer and the addition of hormone therapy to radiation for prostate cancer are within the range of economically acceptable recommendations. The RTOG economic analyses have provided information that can further inform clinicians and policy makers of the value added of new or improved treatments.

Modelling of the physico-chemical behaviour of clay minerals with a thermo-kinetic model taking into account particles morphology in compacted material.

NASA Astrophysics Data System (ADS)

Sali, D.; Fritz, B.; Clément, C.; Michau, N.

2003-04-01

Modelling of fluid-mineral interactions is largely used in Earth Sciences studies to better understand the involved physicochemical processes and their long-term effect on the materials behaviour. Numerical models simplify the processes but try to preserve their main characteristics. Therefore the modelling results strongly depend on the data quality describing initial physicochemical conditions for rock materials, fluids and gases, and on the realistic way of processes representations. The current geo-chemical models do not well take into account rock porosity and permeability and the particle morphology of clay minerals. In compacted materials like those considered as barriers in waste repositories, low permeability rocks like mudstones or compacted powders will be used : they contain mainly fine particles and the geochemical models used for predicting their interactions with fluids tend to misjudge their surface areas, which are fundamental parameters in kinetic modelling. The purpose of this study was to improve how to take into account the particles morphology in the thermo-kinetic code KINDIS and the reactive transport code KIRMAT. A new function was integrated in these codes, considering the reaction surface area as a volume depending parameter and the calculated evolution of the mass balance in the system was coupled with the evolution of reactive surface areas. We made application exercises for numerical validation of these new versions of the codes and the results were compared with those of the pre-existing thermo-kinetic code KINDIS. Several points are highlighted. Taking into account reactive surface area evolution during simulation modifies the predicted mass transfers related to fluid-minerals interactions. Different secondary mineral phases are also observed during modelling. The evolution of the reactive surface parameter helps to solve the competition effects between different phases present in the system which are all able to fix the chemical elements mobilised by the water-minerals interaction processes. To validate our model we simulated the compacted bentonite (MX80) studied for engineered barriers for radioactive waste confinement and mainly composed of Na-Ca-montmorillonite. The study of particles morphology and reactive surfaces evolutions reveals that aqueous ions have a complex behaviour, especially when competitions between various mineral phases occur. In that case, our model predicts a preferential precipitation of finest particles, favouring smectites instead of zeolites. This work is a part of a PhD Thesis supported by Andra, the French Radioactive Waste Management Agency.

Exploiting Fast-Variables to Understand Population Dynamics and Evolution

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2018-07-01

We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

Exploiting Fast-Variables to Understand Population Dynamics and Evolution

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2017-11-01

We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

EVOLUTION OF THE CRAB NEBULA IN A LOW ENERGY SUPERNOVA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Haifeng; Chevalier, Roger A., E-mail: hy4px@virginia.edu, E-mail: rac5x@virginia.edu

The nature of the supernova leading to the Crab Nebula has long been controversial because of the low energy that is present in the observed nebula. One possibility is that there is significant energy in extended fast material around the Crab but searches for such material have not led to detections. An electron capture supernova model can plausibly account for the low energy and the observed abundances in the Crab. Here, we examine the evolution of the Crab pulsar wind nebula inside a freely expanding supernova and find that the observed properties are most consistent with a low energy event.more » Both the velocity and radius of the shell material, and the amount of gas swept up by the pulsar wind point to a low explosion energy (∼10{sup 50} erg). We do not favor a model in which circumstellar interaction powers the supernova luminosity near maximum light because the required mass would limit the freely expanding ejecta.« less

Morphogenesis in bat wings: linking development, evolution and ecology.

PubMed

Adams, Rick A

2008-01-01

The evolution of powered flight in mammals required specific developmental shifts from an ancestral limb morphology to one adapted for flight. Through studies of comparative morphogenesis, investigators have quantified points and rates of divergence providing important insights into how wings evolved in mammals. Herein I compare growth,development and skeletogenesis of forelimbs between bats and the more ancestral state provided by the rat (Rattus norvegicus)and quantify growth trajectories that illustrate morphological divergence both developmentally and evolutionarily. In addition, I discuss how wing shape is controlled during morphogenesis by applying multivariate analyses of wing bones and wing membranes and discuss how flight dynamics are stabilized during flight ontogeny. Further, I discuss the development of flight in bats in relation to the ontogenetic niche and how juveniles effect populational foraging patterns. In addition, I provide a hypothetical ontogenetic landscape model that predicts how and when selection is most intense during juvenile morphogenesis and test this model with data from a population of the little brown bat, Myotis lucifugus. (c) 2007 S. Karger AG, Basel

Inhomogeneous screening of gate electric field by interface states in graphene FETs

NASA Astrophysics Data System (ADS)

Singh, Anil Kumar; Gupta, Anjan Kumar

2017-09-01

The electronic states at graphene-SiO2 interface and their inhomogeneity is investigated using the back-gate-voltage dependence of local tunnel spectra acquired with a scanning tunneling microscope. The conductance spectra show two, or occasionally three, minima that evolve along the bias-voltage axis with the back gate voltage. This evolution is modeled using tip-gating and interface states. The energy dependent interface states’ density, Dit(E) , required to model the back-gate evolution of the minima, is found to have significant inhomogeneity in its energy-width. A broad Dit(E) leads to an effect similar to a reduction in the Fermi velocity while the narrow Dit(E) leads to the pinning of the Fermi energy close to the Dirac point, as observed in some places, due to enhanced screening of the gate electric field by the narrow Dit(E) . Finally, this also demonstrates STM as a tool to probe the density of interface states in various 2D Dirac materials.

The correlation function for density perturbations in an expanding universe. IV - The evolution of the correlation function. [galaxy distribution

NASA Technical Reports Server (NTRS)

Mcclelland, J.; Silk, J.

1979-01-01

The evolution of the two-point correlation function for the large-scale distribution of galaxies in an expanding universe is studied on the assumption that the perturbation densities lie in a Gaussian distribution centered on any given mass scale. The perturbations are evolved according to the Friedmann equation, and the correlation function for the resulting distribution of perturbations at the present epoch is calculated. It is found that: (1) the computed correlation function gives a satisfactory fit to the observed function in cosmological models with a density parameter (Omega) of approximately unity, provided that a certain free parameter is suitably adjusted; (2) the power-law slope in the nonlinear regime reflects the initial fluctuation spectrum, provided that the density profile of individual perturbations declines more rapidly than the -2.4 power of distance; and (3) both positive and negative contributions to the correlation function are predicted for cosmological models with Omega less than unity.

X-Ray Probes of Cosmic Star-Formation History

NASA Technical Reports Server (NTRS)

Ghosh, Pranab; White, Nicholas E.

2001-01-01

In a previous paper we point out that the X-ray luminosity L(sub x) of a galaxy is driven by the evolution of its X-ray binary population and that the profile of L(sub x) with redshift can both serve as a diagnostic probe of the Star Formation Rate (SFR) profile and constrain evolutionary models for X-ray binaries. We update our previous work using a suite of more recently developed SFR profiles that span the currently plausible range. The first Chandra deep imaging results on L(sub x)-evolution are beginning to probe the SFR profile of bright spirals and the early results are consistent with predictions based on current SFR models. Using these new SFR profiles the resolution of the "birthrate problem" of lowmass X-ray binaries (LMXBs) and recycled, millisecond pulsars in terms of an evolving global SFR is more complete. We also discuss the possible impact of the variations in the SFR profile of individual galaxies.

Collisional evolution of rotating, non-identical particles. [in Saturn rings

NASA Technical Reports Server (NTRS)

Salo, H.

1987-01-01

Hameen-Anttila's (1984) theory of self-gravitating collisional particle disks is extended to include the effects of particle spin. Equations are derived for the coupled evolution of random velocities and spins, showing that friction and surface irregularity both reduce the local velocity dispersion and transfer significant amounts of random kinetic energy to rotational energy. Results for the equilibrium ratio of rotational energy to random kinetic energy are exact not only for identical nongravitating mass points, but also if finite size, self-gravitating forces, or size distribution are included. The model is applied to the dynamics of Saturn's rings, showing that the inclusion of rotation reduces the geometrical thickness of the layer of cm-sized particles to, at most, about one-half, with large particles being less affected.

Equilibria Configurations for Epitaxial Crystal Growth with Adatoms

NASA Astrophysics Data System (ADS)

Caroccia, Marco; Cristoferi, Riccardo; Dietrich, Laurent

2018-05-01

The behavior of a surface energy F}(E,u)} , where E is a set of finite perimeter and u\\in L^1(partial^{*} E, R_+) , is studied. These energies have been recently considered in the context of materials science to derive a new model in crystal growth that takes into account the effect of atoms, the freely diffusing on the surface (called adatoms), which are responsible for morphological evolution through an attachment and detachment process. Regular critical points, the existence and uniqueness of minimizers are discussed and the relaxation of F in a general setting under the L 1 convergence of sets and the vague convergence of measures is characterized. This is part of an ongoing project aimed at an analytical study of diffuse interface approximations of the associated evolution equations.

Geohistory analysis of the Santa Maria basin, California, and its relationship to tectonic evolution of the continental margin

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCrory, P.A.; Arends, R.G.; Ingle, J.C. Jr.

1991-02-01

The Santa Maria basin of central California is a geologically complex area located along the tectonically active California continental margin. The record of Cenozoic tectonism preserved in Santa Maria strata provides an opportunity to compare the evolution of the region with plate tectonic models for Cenozoic interactions along the margin. Geohistory analysis of Neogene Santa Maria basin strata provides important constraints for hypotheses of the tectonic evolution of the central California margin during its transition from a convergent to a transform plate boundary. Preliminary analyses suggest that the tectonic evolution of the Santa Maria area was dominated by coupling betweenmore » adjacent oceanic plates and the continental margin. This coupling is reflected in the timing of major hiatuses within the basin sedimentary sequence and margin subsidence and uplift which occurred during periods of tectonic plate adjustment. Stratigraphic evidence indicates that the Santa Maria basin originated on the continental shelf in early Miocene time. A component of margin subsidence is postulated to have been caused by cessation of spreading on adjacent offshore microplates approximately 19-18 ma. A sharp reduction in rate of tectonic subsidence in middle Miocene time, observed in the Santa Maria basin both onshore and offshore, was coeval with rotation of crustal blocks as major shearing shifts shoreward. Tectonic uplift of two eastern sites, offshore Point Arguello and near Point Sal, in the late Miocene may have been related to a change to transpressional motion between the Pacific and North American plates, as well as to rotation of the western Transverse Ranges in a restraining geometry.« less

Limits to biodiversity cycles from a unified model of mass-extinction events

NASA Astrophysics Data System (ADS)

Feulner, Georg

2011-04-01

Episodes of species mass extinction dramatically affected the evolution of life on Earth, but their causes remain a source of debate. Even more controversy surrounds the hypothesis of periodicity in the fossil record, with conflicting views still being published in the scientific literature, often even based on the same state-of-the-art datasets. From an empirical point of view, limitations of the currently available data on extinctions and possible causes remain an important issue. From a theoretical point of view, it is likely that a focus on single extinction causes and strong periodic forcings has strongly contributed to this controversy. Here I show that if there is a periodic extinction signal at all, it is much more likely to result from a combination of a comparatively weak periodic cause and various random factors. Tests of this unified model of mass extinctions on the available data show that the model is formally better than a model with random extinction causes only. However, the contribution of the periodic component is small compared to factors such as impacts or volcanic eruptions.

Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity.

PubMed

Bertels, Frederic; Marzel, Alex; Leventhal, Gabriel; Mitov, Venelin; Fellay, Jacques; Günthard, Huldrych F; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Battegay, Manuel; Rauch, Andri; Cavassini, Matthias; Calmy, Alexandra; Bernasconi, Enos; Schmid, Patrick; Scherrer, Alexandra U; Müller, Viktor; Bonhoeffer, Sebastian; Kouyos, Roger; Regoes, Roland R

2018-01-01

Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as "per-parasite pathogenicity". Using viral load and CD4+ T-cell measures from 2014 HIV-1 subtype B-infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence-measured as the rate of decline of CD4+ T cells-and per-parasite pathogenicity are heritable from donor to recipient. We estimated heritability by donor-recipient regressions applied to 196 previously identified transmission pairs, and by phylogenetic mixed models applied to a phylogenetic tree inferred from HIV pol sequences. Regressing the CD4+ T-cell declines and per-parasite pathogenicities of the transmission pairs did not yield heritability estimates significantly different from zero. With the phylogenetic mixed model, however, our best estimate for the heritability of the CD4+ T-cell decline is 17% (5-30%), and that of the per-parasite pathogenicity is 17% (4-29%). Further, we confirm that the set-point viral load is heritable, and estimate a heritability of 29% (12-46%). Interestingly, the pattern of evolution of all these traits differs significantly from neutrality, and is most consistent with stabilizing selection for the set-point viral load, and with directional selection for the CD4+ T-cell decline and the per-parasite pathogenicity. Our analysis shows that the viral genotype affects virulence mainly by modulating the per-parasite pathogenicity, while the indirect effect via the set-point viral load is minor. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Revisiting the diffusion approximation to estimate evolutionary rates of gene family diversification.

PubMed

Gjini, Erida; Haydon, Daniel T; David Barry, J; Cobbold, Christina A

2014-01-21

Genetic diversity in multigene families is shaped by multiple processes, including gene conversion and point mutation. Because multi-gene families are involved in crucial traits of organisms, quantifying the rates of their genetic diversification is important. With increasing availability of genomic data, there is a growing need for quantitative approaches that integrate the molecular evolution of gene families with their higher-scale function. In this study, we integrate a stochastic simulation framework with population genetics theory, namely the diffusion approximation, to investigate the dynamics of genetic diversification in a gene family. Duplicated genes can diverge and encode new functions as a result of point mutation, and become more similar through gene conversion. To model the evolution of pairwise identity in a multigene family, we first consider all conversion and mutation events in a discrete manner, keeping track of their details and times of occurrence; second we consider only the infinitesimal effect of these processes on pairwise identity accounting for random sampling of genes and positions. The purely stochastic approach is closer to biological reality and is based on many explicit parameters, such as conversion tract length and family size, but is more challenging analytically. The population genetics approach is an approximation accounting implicitly for point mutation and gene conversion, only in terms of per-site average probabilities. Comparison of these two approaches across a range of parameter combinations reveals that they are not entirely equivalent, but that for certain relevant regimes they do match. As an application of this modelling framework, we consider the distribution of nucleotide identity among VSG genes of African trypanosomes, representing the most prominent example of a multi-gene family mediating parasite antigenic variation and within-host immune evasion. © 2013 Published by Elsevier Ltd. All rights reserved.

Modelling remediation scenarios in historical mining catchments.

PubMed

Gamarra, Javier G P; Brewer, Paul A; Macklin, Mark G; Martin, Katherine

2014-01-01

Local remediation measures, particularly those undertaken in historical mining areas, can often be ineffective or even deleterious because erosion and sedimentation processes operate at spatial scales beyond those typically used in point-source remediation. Based on realistic simulations of a hybrid landscape evolution model combined with stochastic rainfall generation, we demonstrate that similar remediation strategies may result in differing effects across three contrasting European catchments depending on their topographic and hydrologic regimes. Based on these results, we propose a conceptual model of catchment-scale remediation effectiveness based on three basic catchment characteristics: the degree of contaminant source coupling, the ratio of contaminated to non-contaminated sediment delivery, and the frequency of sediment transport events.

Constructing superconductors by graphene Chern-Simons wormholes

NASA Astrophysics Data System (ADS)

Capozziello, Salvatore; Pincak, Richard; Saridakis, Emmanuel N.

2018-03-01

We propose a new model which simulates the motion of free electrons in graphene by the evolution of strings on manifolds. In this model, molecules which constitute sheets of graphene are polygonal point-like structures which build (N + 1) -dimensional manifolds. By breaking the gravitational-analogue symmetry of graphene sheets, we show that two separated child sheets and a Chern-Simons bridge are produced giving rise to a wormhole. In this structure, free electrons are transmitted from one child sheet to the other producing superconductivity. An analogue between "effective gravitons" and "Cooper pairs" is found. In principle, this phenomenology provides the possibility to construct superconductor structures by using the analogue of cosmological models.

A viable dark fluid model

NASA Astrophysics Data System (ADS)

Elkhateeb, Esraa

2018-01-01

We consider a cosmological model based on a generalization of the equation of state proposed by Nojiri and Odintsov (2004) and Štefančić (2005, 2006). We argue that this model works as a dark fluid model which can interpolate between dust equation of state and the dark energy equation of state. We show how the asymptotic behavior of the equation of state constrained the parameters of the model. The causality condition for the model is also studied to constrain the parameters and the fixed points are tested to determine different solution classes. Observations of Hubble diagram of SNe Ia supernovae are used to further constrain the model. We present an exact solution of the model and calculate the luminosity distance and the energy density evolution. We also calculate the deceleration parameter to test the state of the universe expansion.

Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli.

PubMed

Kisiela, Dagmara I; Radey, Matthew; Paul, Sandip; Porter, Stephen; Polukhina, Kseniya; Tchesnokova, Veronika; Shevchenko, Sofiya; Chan, Diana; Aziz, Maliha; Johnson, Timothy J; Price, Lance B; Johnson, James R; Sokurenko, Evgeni V

2017-07-01

We analyzed the within-household evolution of two household-associated Escherichia coli strains from pandemic clonal group ST131- H 30, using isolates recovered from five individuals within two families, each of which had a distinct strain. Family 1's strain was represented by a urine isolate from the index patient (older sister) with recurrent cystitis and a blood isolate from her younger sister with fatal urosepsis. Family 2's strain was represented by a urine isolate from the index patient (father) with pyelonephritis and renal abscesses, blood and kidney drainage isolates from the daughter with emphysematous pyelonephritis, and urine and fecal isolates from the mother with cystitis. Collectively, the several variants of each family's strain had accumulated a total of 8 (family 1) and 39 (family 2) point mutations; no two isolates were identical. Of the 47 total mutations, 36 resulted in amino acid changes or truncation of coded proteins. Fourteen such mutations (39%) targeted genes encoding transcriptional regulators, and 9 (25%) involved DNA-binding transcription factors (TFs), which significantly exceeded the relative contribution of TF genes to the isolates' genomes (∼6%). At least one-half of the transcriptional regulator mutations were inactivating, based on phenotypic and/or transcriptional analysis. In particular, inactivating mutations in the global regulator LrhA (repressor of type 1 fimbriae and flagella) occurred in the blood isolates from both households and increased the virulence of E. coli strains in a murine sepsis model. The results indicate that E. coli undergoes adaptive evolution between and/or within hosts, generating subpopulations with distinctive phenotypes and virulence potential. IMPORTANCE The clonal evolution of bacterial strains associated with interhost transmission is poorly understood. We characterized the genome sequences of clonal descendants of two Escherichia coli strains, recovered at different time points from multiple individuals within two households who had different types of urinary tract infection. We found evidence that the E. coli strains underwent extensive mutational diversification between and within these individuals, driven disproportionately by inactivation of transcriptional regulators. In urosepsis isolates, the mutations observed in the global regulator LrhA increased bacterial virulence in a murine sepsis model. Our findings help in understanding the adaptive dynamics and strategies of E. coli during short-term natural evolution. Copyright © 2017 American Society for Microbiology.

Reconstruction of DNA sequences using genetic algorithms and cellular automata: towards mutation prediction?

PubMed

Mizas, Ch; Sirakoulis, G Ch; Mardiris, V; Karafyllidis, I; Glykos, N; Sandaltzopoulos, R

2008-04-01

Change of DNA sequence that fuels evolution is, to a certain extent, a deterministic process because mutagenesis does not occur in an absolutely random manner. So far, it has not been possible to decipher the rules that govern DNA sequence evolution due to the extreme complexity of the entire process. In our attempt to approach this issue we focus solely on the mechanisms of mutagenesis and deliberately disregard the role of natural selection. Hence, in this analysis, evolution refers to the accumulation of genetic alterations that originate from mutations and are transmitted through generations without being subjected to natural selection. We have developed a software tool that allows modelling of a DNA sequence as a one-dimensional cellular automaton (CA) with four states per cell which correspond to the four DNA bases, i.e. A, C, T and G. The four states are represented by numbers of the quaternary number system. Moreover, we have developed genetic algorithms (GAs) in order to determine the rules of CA evolution that simulate the DNA evolution process. Linear evolution rules were considered and square matrices were used to represent them. If DNA sequences of different evolution steps are available, our approach allows the determination of the underlying evolution rule(s). Conversely, once the evolution rules are deciphered, our tool may reconstruct the DNA sequence in any previous evolution step for which the exact sequence information was unknown. The developed tool may be used to test various parameters that could influence evolution. We describe a paradigm relying on the assumption that mutagenesis is governed by a near-neighbour-dependent mechanism. Based on the satisfactory performance of our system in the deliberately simplified example, we propose that our approach could offer a starting point for future attempts to understand the mechanisms that govern evolution. The developed software is open-source and has a user-friendly graphical input interface.

Individual variation behind the evolution of cooperation.

PubMed

Barta, Zoltán

2016-02-05

Life on Earth has two remarkable properties. The first is variation: even apart from the vast number of extant species, there are considerable differences between individuals within a single species. The second property is cooperation. It is surprising that until recently the interactions between these two properties have rarely been addressed from an evolutionary point of view. Here, I concentrate on how inter-individual differences influence the evolution of cooperation. First, I deal with cases where individuality is maintained by random processes like mutation or phenotypic noise. Second, I examine when differences in state cause differences in behaviour. Finally, I investigate the effects of individual role specialization. Variation can be important in several ways. Increased random variation can change the expectation about cooperativeness of future partners, altering behaviour in a current relationship. Differences in state may serve as a book-keeping mechanism that is necessary for the evolution of reciprocity. If the cost of cooperation can depend on state then strategic regulation of state makes it possible to coerce partners to cooperate. If conditions force individuals to specialize, cooperation becomes more valuable. My review of theoretical models suggests that variation plays an important role in the evolution of cooperation. © 2016 The Author(s).

Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

2017-02-01

The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

Damage evolution of bi-body model composed of weakly cemented soft rock and coal considering different interface effect.

PubMed

Zhao, Zenghui; Lv, Xianzhou; Wang, Weiming; Tan, Yunliang

2016-01-01

Considering the structure effect of tunnel stability in western mining of China, three typical kinds of numerical model were respectively built as follows based on the strain softening constitutive model and linear elastic-perfectly plastic model for soft rock and interface: R-M, R-C(s)-M and R-C(w)-M. Calculation results revealed that the stress-strain relation and failure characteristics of the three models vary between each other. The combination model without interface or with a strong interface presented continuous failure, while weak interface exhibited 'cut off' effect. Thus, conceptual models of bi-material model and bi-body model were established. Then numerical experiments of tri-axial compression were carried out for the two models. The relationships between stress evolution, failure zone and deformation rate fluctuations as well as the displacement of interface were detailed analyzed. Results show that two breakaway points of deformation rate actually demonstrate the starting and penetration of the main rupture, respectively. It is distinguishable due to the large fluctuation. The bi-material model shows general continuous failure while bi-body model shows 'V' type shear zone in weak body and failure in strong body near the interface due to the interface effect. With the increasing of confining pressure, the 'cut off' effect of weak interface is not obvious. These conclusions lay the theoretical foundation for further development of constitutive model for soft rock-coal combination body.

Contrarian behavior in a complex adaptive system

NASA Astrophysics Data System (ADS)

Liang, Y.; An, K. N.; Yang, G.; Huang, J. P.

2013-01-01

Contrarian behavior is a kind of self-organization in complex adaptive systems (CASs). Here we report the existence of a transition point in a model resource-allocation CAS with contrarian behavior by using human experiments, computer simulations, and theoretical analysis. The resource ratio and system predictability serve as the tuning parameter and order parameter, respectively. The transition point helps to reveal the positive or negative role of contrarian behavior. This finding is in contrast to the common belief that contrarian behavior always has a positive role in resource allocation, say, stabilizing resource allocation by shrinking the redundancy or the lack of resources. It is further shown that resource allocation can be optimized at the transition point by adding an appropriate size of contrarians. This work is also expected to be of value to some other fields ranging from management and social science to ecology and evolution.

Itinerant density wave instabilities at classical and quantum critical points

DOE PAGES

Feng, Yejun; van Wezel, Jasper; Wang, Jiyang; ...

2015-07-27

Charge ordering in metals is a fundamental instability of the electron sea, occurring in a host of materials and often linked to other collective ground states such as superconductivity. What is difficult to parse, however, is whether the charge order originates among the itinerant electrons or whether it arises from the ionic lattice. Here in this study we employ high-resolution X-ray diffraction, combined with high-pressure and low-temperature techniques and theoretical modelling, to trace the evolution of the ordering wavevector Q in charge and spin density wave systems at the approach to both thermal and quantum phase transitions. The non-monotonic behaviourmore » of Q with pressure and the limiting sinusoidal form of the density wave point to the dominant role of the itinerant instability in the vicinity of the critical points, with little influence from the lattice. Fluctuations rather than disorder seem to disrupt coherence.« less

Multi-locus analysis of genomic time series data from experimental evolution.

PubMed

Terhorst, Jonathan; Schlötterer, Christian; Song, Yun S

2015-04-01

Genomic time series data generated by evolve-and-resequence (E&R) experiments offer a powerful window into the mechanisms that drive evolution. However, standard population genetic inference procedures do not account for sampling serially over time, and new methods are needed to make full use of modern experimental evolution data. To address this problem, we develop a Gaussian process approximation to the multi-locus Wright-Fisher process with selection over a time course of tens of generations. The mean and covariance structure of the Gaussian process are obtained by computing the corresponding moments in discrete-time Wright-Fisher models conditioned on the presence of a linked selected site. This enables our method to account for the effects of linkage and selection, both along the genome and across sampled time points, in an approximate but principled manner. We first use simulated data to demonstrate the power of our method to correctly detect, locate and estimate the fitness of a selected allele from among several linked sites. We study how this power changes for different values of selection strength, initial haplotypic diversity, population size, sampling frequency, experimental duration, number of replicates, and sequencing coverage depth. In addition to providing quantitative estimates of selection parameters from experimental evolution data, our model can be used by practitioners to design E&R experiments with requisite power. We also explore how our likelihood-based approach can be used to infer other model parameters, including effective population size and recombination rate. Then, we apply our method to analyze genome-wide data from a real E&R experiment designed to study the adaptation of D. melanogaster to a new laboratory environment with alternating cold and hot temperatures.

Normobaric hyperoxia retards the evolution of ischemic brain tissue toward infarction in a rat model of transient focal cerebral ischemia.

PubMed

Xu, Ji; Zhang, Yuan; Liang, Zhouyuan; Wang, Ting; Li, Weiping; Ren, Lijie; Huang, Shaonong; Liu, Wenlan

2016-01-01

Oxygen therapy has been long considered a logical therapy for ischemic stroke. Our previous studies showed that normobaric hyperoxia (normobaric hyperoxia (NBO), 95% O2 with 5% CO2) treatment during ischemia reduced ischemic neuronal death and cerebromicrovascular injury in animal stroke models. In this study, we studied the effects of NBO on the evolution of ischemic brain tissue to infarction in a rat model of transient focal cerebral ischemia. Male Sprague-Dawley rats were given NBO (95% O2) or normoxia (21% O2) during 90-min filament occlusion of the middle cerebral artery (MCAO), followed by 3 or 22.5 h of reperfusion. 2,3,5-triphenyltetrazolium chloride (TTC) staining was used to evaluate the longitudinal evolution of tissue infarction. Results： In normoxic rats, MCA-supplied cortical and striatal tissue was infarcted after 90-min MCAO with 22.5 h of reperfusion. NBO-treated rats showed a 61.4% reduction in infarct size and tissue infarction mainly occurred in the ischemic striatum. When infarction was assessed at an earlier time point, i.e. at 3 h of reperfusion, normoxic rats showed significantly smaller but mature infarction (no TTC staining, white color), with the infarction mainly occurring in the striatum. Unexpectedly, NBO-treated rats only showed immature lesion (partially stained by TTC, light white color) in the ischemic striatum, indicating that NBO treatment also retarded the process of neuronal death in the ischemic core. Of note, NBO-preserved striatal tissue underwent infarction after prolonged reperfusion. Conclusions： Our results demonstrate that NBO treatment given during cerebral ischemia retards the evolution of ischemic brain tissue toward infarction and NBO-preserved cortical tissue survives better than NBO-preserved striatal tissue during the phase of reperfusion.

Exact solution for a non-Markovian dissipative quantum dynamics.

PubMed

Ferialdi, Luca; Bassi, Angelo

2012-04-27

We provide the exact analytic solution of the stochastic Schrödinger equation describing a harmonic oscillator interacting with a non-Markovian and dissipative environment. This result represents an arrival point in the study of non-Markovian dynamics via stochastic differential equations. It is also one of the few exactly solvable models for infinite-dimensional systems. We compute the Green's function; in the case of a free particle and with an exponentially correlated noise, we discuss the evolution of Gaussian wave functions.

Stability and oscillations in a CML model

NASA Astrophysics Data System (ADS)

Badralexi, Irina; Halanay, Andrei

2017-01-01

We capture the evolution in competition of healthy and leukemic cells in Chronic Myelogenous Leukemia (CML) taking into consideration the response of the immune system. Delay-differential equations in a Mackey-Glass approach are used. We start with the study of stability of the equilibrium points of the system. Conditions on parameters for the local stability are given. Oscillatory behaviors occur naturally in biological phenomena. Thus, we investigate the periodic behavior of solutions and we obtain conditions for periodic solutions to appear through a Hopf bifurcation.

The Harper–Hofstadter Hamiltonian and conical diffraction in photonic lattices with grating assisted tunneling

DOE PAGES

Dubček, Tena; Lelas, Karlo; Jukić, Dario; ...

2015-12-07

Here we propose the realization of a grating assisted tunneling scheme for tunable synthetic magnetic fields in optically induced one- and two-dimensional dielectric photonic lattices. As a signature of the synthetic magnetic fields, we demonstrate conical diffraction patterns in particular realization of these lattices, which possess Dirac points in k-space. Lastly, we compare the light propagation in these realistic (continuous) systems with the evolution in discrete models representing the Harper-Hofstadter Hamiltonian, and obtain excellent agreement.

Polarization singularity indices in Gaussian laser beams

NASA Astrophysics Data System (ADS)

Freund, Isaac

2002-01-01

Two types of point singularities in the polarization of a paraxial Gaussian laser beam are discussed in detail. V-points, which are vector point singularities where the direction of the electric vector of a linearly polarized field becomes undefined, and C-points, which are elliptic point singularities where the ellipse orientations of elliptically polarized fields become undefined. Conventionally, V-points are characterized by the conserved integer valued Poincaré-Hopf index η, with generic value η=±1, while C-points are characterized by the conserved half-integer singularity index IC, with generic value IC=±1/2. Simple algorithms are given for generating V-points with arbitrary positive or negative integer indices, including zero, at arbitrary locations, and C-points with arbitrary positive or negative half-integer or integer indices, including zero, at arbitrary locations. Algorithms are also given for generating continuous lines of these singularities in the plane, V-lines and C-lines. V-points and C-points may be transformed one into another. A topological index based on directly measurable Stokes parameters is used to discuss this transformation. The evolution under propagation of V-points and C-points initially embedded in the beam waist is studied, as is the evolution of V-dipoles and C-dipoles.

Smart sensors and virtual physiology human approach as a basis of personalized therapies in diabetes mellitus.

PubMed

Fernández Peruchena, Carlos M; Prado-Velasco, Manuel

2010-01-01

Diabetes mellitus (DM) has a growing incidence and prevalence in modern societies, pushed by the aging and change of life styles. Despite the huge resources dedicated to improve their quality of life, mortality and morbidity rates, these are still very poor. In this work, DM pathology is revised from clinical and metabolic points of view, as well as mathematical models related to DM, with the aim of justifying an evolution of DM therapies towards the correction of the physiological metabolic loops involved. We analyze the reliability of mathematical models, under the perspective of virtual physiological human (VPH) initiatives, for generating and integrating customized knowledge about patients, which is needed for that evolution. Wearable smart sensors play a key role in this frame, as they provide patient's information to the models.A telehealthcare computational architecture based on distributed smart sensors (first processing layer) and personalized physiological mathematical models integrated in Human Physiological Images (HPI) computational components (second processing layer), is presented. This technology was designed for a renal disease telehealthcare in earlier works and promotes crossroads between smart sensors and the VPH initiative. We suggest that it is able to support a truly personalized, preventive, and predictive healthcare model for the delivery of evolved DM therapies.

Smart Sensors and Virtual Physiology Human Approach as a Basis of Personalized Therapies in Diabetes Mellitus

PubMed Central

Fernández Peruchena, Carlos M; Prado-Velasco, Manuel

2010-01-01

Diabetes mellitus (DM) has a growing incidence and prevalence in modern societies, pushed by the aging and change of life styles. Despite the huge resources dedicated to improve their quality of life, mortality and morbidity rates, these are still very poor. In this work, DM pathology is revised from clinical and metabolic points of view, as well as mathematical models related to DM, with the aim of justifying an evolution of DM therapies towards the correction of the physiological metabolic loops involved. We analyze the reliability of mathematical models, under the perspective of virtual physiological human (VPH) initiatives, for generating and integrating customized knowledge about patients, which is needed for that evolution. Wearable smart sensors play a key role in this frame, as they provide patient’s information to the models. A telehealthcare computational architecture based on distributed smart sensors (first processing layer) and personalized physiological mathematical models integrated in Human Physiological Images (HPI) computational components (second processing layer), is presented. This technology was designed for a renal disease telehealthcare in earlier works and promotes crossroads between smart sensors and the VPH initiative. We suggest that it is able to support a truly personalized, preventive, and predictive healthcare model for the delivery of evolved DM therapies. PMID:21625646

Path-preference cellular-automaton model for traffic flow through transit points and its application to the transcription process in human cells.

PubMed

Ohta, Yoshihiro; Nishiyama, Akinobu; Wada, Yoichiro; Ruan, Yijun; Kodama, Tatsuhiko; Tsuboi, Takashi; Tokihiro, Tetsuji; Ihara, Sigeo

2012-08-01

We all use path routing everyday as we take shortcuts to avoid traffic jams, or by using faster traffic means. Previous models of traffic flow of RNA polymerase II (RNAPII) during transcription, however, were restricted to one dimension along the DNA template. Here we report the modeling and application of traffic flow in transcription that allows preferential paths of different dimensions only restricted to visit some transit points, as previously introduced between the 5' and 3' end of the gene. According to its position, an RNAPII protein molecule prefers paths obeying two types of time-evolution rules. One is an asymmetric simple exclusion process (ASEP) along DNA, and the other is a three-dimensional jump between transit points in DNA where RNAPIIs are staying. Simulations based on our model, and comparison experimental results, reveal how RNAPII molecules are distributed at the DNA-loop-formation-related protein binding sites as well as CTCF insulator proteins (or exons). As time passes after the stimulation, the RNAPII density at these sites becomes higher. Apparent far-distance jumps in one dimension are realized by short-range three-dimensional jumps between DNA loops. We confirm the above conjecture by applying our model calculation to the SAMD4A gene by comparing the experimental results. Our probabilistic model provides possible scenarios for assembling RNAPII molecules into transcription factories, where RNAPII and related proteins cooperatively transcribe DNA.

One-dimensional gravity in infinite point distributions.

PubMed

Gabrielli, A; Joyce, M; Sicard, F

2009-10-01

The dynamics of infinite asymptotically uniform distributions of purely self-gravitating particles in one spatial dimension provides a simple and interesting toy model for the analogous three dimensional problem treated in cosmology. In this paper we focus on a limitation of such models as they have been treated so far in the literature: the force, as it has been specified, is well defined in infinite point distributions only if there is a centre of symmetry (i.e., the definition requires explicitly the breaking of statistical translational invariance). The problem arises because naive background subtraction (due to expansion, or by "Jeans swindle" for the static case), applied as in three dimensions, leaves an unregulated contribution to the force due to surface mass fluctuations. Following a discussion by Kiessling of the Jeans swindle in three dimensions, we show that the problem may be resolved by defining the force in infinite point distributions as the limit of an exponentially screened pair interaction. We show explicitly that this prescription gives a well defined (finite) force acting on particles in a class of perturbed infinite lattices, which are the point processes relevant to cosmological N -body simulations. For identical particles the dynamics of the simplest toy model (without expansion) is equivalent to that of an infinite set of points with inverted harmonic oscillator potentials which bounce elastically when they collide. We discuss and compare with previous results in the literature and present new results for the specific case of this simplest (static) model starting from "shuffled lattice" initial conditions. These show qualitative properties of the evolution (notably its "self-similarity") like those in the analogous simulations in three dimensions, which in turn resemble those in the expanding universe.

NEW TOOLS FOR STREAM MORPHO-DYNAMIC MODELING (Invited)

NASA Astrophysics Data System (ADS)

Tonina, D.; McKean, J. A.; Maturana, O. R.; Luce, C.; Buffington, J. M.

2009-12-01

Morphological evolution of streambeds and sediment transport in streams has been typically studied in long reaches using one-dimensional models, due partly to the lack of accurate and easy-to-acquire river bathymetry. The Experimental Advanced Airborne Research Lidar (EAARL) allows simultaneous surveying in both aquatic and terrestrial domains quickly and remotely. However, its usefulness to define boundary conditions for morpho-dynamic models has not yet been tested. We first evaluated EAARL accuracy and then used the data to model fine sediment transport in gravel bed rivers. A random vertical error, modeled as a Normal distribution with zero mean and 10 cm standard deviation, was introduced to bathymetric point cloud data in an EAARL survey. Comparison of water elevations and velocity and shear stress distributions among simulations with and without these random bathymetric errors showed little effect on model predictions. This result allowed us to use EAARL data to model the effects of chronic and acute loads of fine-grained sediment on riverine ecosystems, river morphology, and bed evolution. The simulations were done with the Multidimensional Surface Water Model System (MD-SWMS, USGS). We added a new sand conservation model and the two-class sediment transport equation of Wilcock and Kenworthy [2002, WRR] to MD-SWMS. Simulations show patterns of fine sediment transport and deposition along meandering and straight stream reaches, and the impact of sudden inputs of fine sediment on salmonid spawning sites. Initial results illustrate the sensitivity of sand transport to flow characteristics. At a base flow of 1 m3/sec, sand moves only a few tens-of-meters from the point source during a 4-month model period. Over the same time interval a constant bankfull flow of 6 m3/sec removes all of the sand from the source area; the sand migrates in distinct waves through the 0.5 km-long model reach and we predict all salmon spawning sites in the reach would be contaminated with sand. Chronic inputs, which may come from human activities, seem to have a more persistent impact on streambed habitat quality than pulsed inputs, which may stem from wild fires and other natural disturbances.

Reduced quasilinear models for energetic particles interaction with Alfvenic eigenmodes

NASA Astrophysics Data System (ADS)

Ghantous, Katy

The Line Broadened Quasilinear (LBQ) and the 1.5D reduced models are able to predict the effect of Alfvenic eigenmodes' interaction with energetic particles in burning plasmas. This interaction can result in energetic-particle losses that can damage the first wall, deteriorate the plasma performance, and even prevent ignition. The 1.5D model assumes a broad spectrum of overlapping modes and, based on analytic expressions for the growth and damping rates, calculates the pressure profiles that the energetic particles relax to upon interacting with the modes. 1.5D is validated with DIII-D experiments and predicted neutron losses consistent with observation. The model is employed to predict alpha-particle fusion-product losses in a large-scale operational parameter-space for burning plasmas. The LBQ model captures the interaction both in the regime of isolated modes as well as in the conventional regime of overlapping modes. Rules were established that allow quasilinear equations to replicate the expected steady-state saturation levels of isolated modes. The fitting formula is improved and the model is benchmarked with a Vlasov code, BOT. The saturation levels are accurately predicted and the mode evolution is well-replicated in the case of steady-state evolution where the collisions are high enough that coherent structures do not form. When the collisionality is low, oscillatory behavior can occur. LBQ can also exhibit non-steady behavior, but the onset of oscillations occurs for much higher collisional rates in BOT than in LBQ. For certain parameters of low collisionality, hole-clump creation and frequency chirping can occur which are not captured by the LBQ model. Also, there are cases of non-steady evolution without chirping which is possible for LBQ to study. However the results are inconclusive since the periods and amplitudes of the oscillations in the mode evolution are not well-replicated. If multiple modes exist, they can grow to the point of overlap which results in two-dimensional diffusion with cross terms. A diffusion scheme is proposed and validated to resolve this dynamics in (Pφ,E) phase-space.

A new kinematic model for the Mesozoic evolution of the Iberia plate

NASA Astrophysics Data System (ADS)

Nirrengarten, Michael; Manatschal, Gianreto; Tugend, Julie; Kusznir, Nick; Sauter, Daniel

2017-04-01

During the Mesozoic Iberia was progressively surrounded by rift systems leading to its transient individualization as a tectonic plate. The kinematic evolution of Iberia prior to oceanic magnetic anomaly C34 ( 83 Ma) is controversial. To date, no kinematic models accounts for the Late Aptian to Albian hyper-extended rift phase observed in the Pyrenees. Consistent isochronal features, such as oceanic magnetic anomalies, representing the backbones of oceanic plate reconstructions are lacking. The only potential candidate, the J-anomaly, located offshore Iberia and Newfoundland has recently been re-interpreted as resulting from polyphased and polygenic magmatic events and does not provide a useful constraint. We use a new reconstruction approach that integrates the spatio-temporal evolution of adjacent hyper-extended rift domains systems to investigate Iberia plate motion during the separation of the super-continent Pangea. The plate modeling is based on careful mapping and restoration of the rift domains with key rift events dated within the study area. The main outcomes of this new model are as follows: 1) A full-fit of the southern North Atlantic 2) Extension on the southern and eastern boundary of Iberia related to the opening of the Central Atlantic 3) Segmentation of the Iberia-Newfoundland rift system by fracture zones prior to a V-shape propagation of mantle exhumation and seafloor spreading 4) No Aptian subduction in the Pyrenean domain and a limited rotation of the Iberia plate 5) The partitioning of deformation between different micro-blocks along the Iberian-Eurasian boundary enabling Late Aptian to Albian extension in the Pyrenees The resulting plate kinematic model for Iberia differs from previous ones on three main points: it does not make use of the J magnetic anomaly because the J anomlay is neither an isochron or a COB marker; the deformation along the Iberian-Eurasian boundary is partitioned between distinct rift systems; and it incorporates extension in the Pyrenees consistent with published geological studies. Nonetheless this model is non-unique and additional observations are needed to further constrain the plate modeling notably by adding new constraints on the rift evolution of the southern and eastern margin of the Iberia plate during the Jurassic.

The Evolution of the Celsius and Kelvin Temperature Scales and the State of the Art

NASA Astrophysics Data System (ADS)

Pellicer, Julio; Amparo Gilabert, M.; Lopez-Baeza, Ernesto

1999-07-01

A physical analysis is given of the evolution undergone by the Celsius and Kelvin temperature scales, from their definition to the present day. It is shown that in the temperature interval between the melting point of ice and the boiling point of water, the Celsius and Kelvin scales, both born centigrade by definition and actually become so afterwards by experimental determination as well, are not so any longer, either by definition or by experimental determination.

An analysis of neural receptive field plasticity by point process adaptive filtering

PubMed Central

Brown, Emery N.; Nguyen, David P.; Frank, Loren M.; Wilson, Matthew A.; Solo, Victor

2001-01-01

Neural receptive fields are plastic: with experience, neurons in many brain regions change their spiking responses to relevant stimuli. Analysis of receptive field plasticity from experimental measurements is crucial for understanding how neural systems adapt their representations of relevant biological information. Current analysis methods using histogram estimates of spike rate functions in nonoverlapping temporal windows do not track the evolution of receptive field plasticity on a fine time scale. Adaptive signal processing is an established engineering paradigm for estimating time-varying system parameters from experimental measurements. We present an adaptive filter algorithm for tracking neural receptive field plasticity based on point process models of spike train activity. We derive an instantaneous steepest descent algorithm by using as the criterion function the instantaneous log likelihood of a point process spike train model. We apply the point process adaptive filter algorithm in a study of spatial (place) receptive field properties of simulated and actual spike train data from rat CA1 hippocampal neurons. A stability analysis of the algorithm is sketched in the Appendix. The adaptive algorithm can update the place field parameter estimates on a millisecond time scale. It reliably tracked the migration, changes in scale, and changes in maximum firing rate characteristic of hippocampal place fields in a rat running on a linear track. Point process adaptive filtering offers an analytic method for studying the dynamics of neural receptive fields. PMID:11593043

Chasing boundaries and cascade effects in a coupled barrier - marshes - lagoon system

NASA Astrophysics Data System (ADS)

Lorenzo Trueba, J.; Mariotti, G.

2015-12-01

Low-lying coasts are often characterized by barriers islands, shore-parallel stretches of sand separated from the mainland by marshes and lagoons. We built an exploratory numerical model to examine the morphological feedbacks within an idealized barrier - marshes -lagoon system and predict its evolution under projected rates of sea level rise and sediment supply to the backbarrier environment. Our starting point is a recently developed morphodynamic model, which couples shoreface evolution and overwash processes in a dynamic framework. As such, the model is able to capture dynamics not reproduced by morphokinematic models, which advect geometries without specific concern to processes. These dynamics include periodic barrier retreat due to time lags in the shoreface response to barrier overwash, height drowning due to insufficient overwash fluxes as sea level rises, and width drowning, which occurs when the shoreface response rate is insufficient to maintain the barrier geometry during overwash-driven landward migration. We extended the model by coupling the barrier model with a model for the evolution of the marsh platform and the boundary between the marsh and the adjacent lagoon. The coupled model explicitly describes marsh edge processes and accounts for the modification of the wave regime associated with lagoon width (fetch). Model results demonstrate that changes in factors that are not typically associated with the dynamics of coastal barriers, such as the lagoon width and the rate of export/import of sediments from and to the lagoon, can lead to previously unidentified complex responses of the coupled system. In particular, a wider lagoon in the backbarrier, and/or a reduction in the supply of muddy sediments to the backbarrier, can increase barrier retreat rates and even trigger barrier drowning. Overall, our findings highlight the importance of incorporating backbarrier dynamics in models that aim at predicting the response of barrier systems.

Star formation with disc accretion and rotation. I. Stars between 2 and 22 M⊙ at solar metallicity

NASA Astrophysics Data System (ADS)

Haemmerlé, L.; Eggenberger, P.; Meynet, G.; Maeder, A.; Charbonnel, C.

2013-09-01

Context. The way angular momentum is built up in stars during their formation process may have an impact on their further evolution. Aims: In the framework of the cold disc accretion scenario, we study how angular momentum builds up inside the star during its formation for the first time and what the consequences are for its evolution on the main sequence (MS). Methods: Computation begins from a hydrostatic core on the Hayashi line of 0.7 M⊙ at solar metallicity (Z = 0.014) rotating as a solid body. Accretion rates depending on the luminosity of the accreting object are considered, which vary between 1.5 × 10-5 and 1.7 × 10-3 M⊙ yr-1. The accreted matter is assumed to have an angular velocity equal to that of the outer layer of the accreting star. Models are computed for a mass-range on the zero-age main sequence (ZAMS) between 2 and 22 M⊙. Results: We study how the internal and surface velocities vary as a function of time during the accretion phase and the evolution towards the ZAMS. Stellar models, whose evolution has been followed along the pre-MS phase, are found to exhibit a shallow gradient of angular velocity on the ZAMS. Typically, the 6 M⊙ model has a core that rotates 50% faster than the surface on the ZAMS. The degree of differential rotation on the ZAMS decreases when the mass increases (for a fixed value of vZAMS/vcrit). The MS evolution of our models with a pre-MS accreting phase show no significant differences with respect to those of corresponding models computed from the ZAMS with an initial solid-body rotation. Interestingly, there exists a maximum surface velocity that can be reached through the present scenario of formation for masses on the ZAMS larger than 8 M⊙. Typically, only stars with surface velocities on the ZAMS lower than about 45% of the critical velocity can be formed for 14 M⊙ models. Reaching higher velocities would require starting from cores that rotate above the critical limit. We find that this upper velocity limit is smaller for higher masses. In contrast, there is no restriction below 8 M⊙, and the whole domain of velocities to the critical point can be reached.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ecker, Christian; Grumiller, Daniel; Stanzer, Philipp

In this paper, we study the time evolution of 2-point functions and entanglement entropy in strongly anisotropic, inhomogeneous and time-dependent N = 4 super Yang-Mills theory in the large N and large ’t Hooft coupling limit using AdS/CFT. On the gravity side this amounts to calculating the length of geodesics and area of extremal surfaces in the dynamical background of two colliding gravitational shockwaves, which we do numerically. We discriminate between three classes of initial conditions corresponding to wide, intermediate and narrow shocks, and show that they exhibit different phenomenology with respect to the nonlocal observables that we determine. Ourmore » results permit to use (holographic) entanglement entropy as an order parameter to distinguish between the two phases of the cross-over from the transparency to the full-stopping scenario in dynamical Yang-Mills plasma formation, which is frequently used as a toy model for heavy ion collisions. The time evolution of entanglement entropy allows to discern four regimes: highly efficient initial growth of entanglement, linear growth, (post) collisional drama and late time (polynomial) fall off. Surprisingly, we found that 2-point functions can be sensitive to the geometry inside the black hole apparent horizon, while we did not find such cases for the entanglement entropy.« less

Multi-angle Spectra Evolution of Ionospheric Turbulence Excited by RF Interactions at HAARP

NASA Astrophysics Data System (ADS)

Sheerin, J. P.; Rayyan, N.; Watkins, B. J.; Watanabe, N.; Golkowski, M.; Bristow, W. A.; Bernhardt, P. A.; Briczinski, S. J., Jr.

2014-12-01

The high power HAARP HF transmitter is employed to generate and study strong Langmuir turbulence (SLT) in the interaction region of overdense ionospheric plasma. Diagnostics included the Modular UHF Ionospheric Radar (MUIR) sited at HAARP, the SuperDARN-Kodiak HF radar, and HF receivers to record stimulated electromagnetic emissions (SEE). Dependence of diagnostic signals on HAARP HF parameters, including pulselength, duty-cycle, aspect angle, and frequency were recorded. Short pulse, low duty cycle experiments demonstrate control of artificial field-aligned irregularities (AFAI) and isolation of ponderomotive effects. For the first time, simultaneous multi-angle radar measurements of plasma line spectra are recorded demonstrating marked dependence on aspect angle with the strongest interaction region observed displaced southward of the HF zenith pointing angle. For a narrow range of HF pointing between Spitze and magnetic zenith, a reduced threshold for AFAI is observed. High time resolution studies of the temporal evolution of the plasma line reveal the appearance of an overshoot effect on ponderomotive timescales. Numerous measurements of the outshifted plasma line are observed. Experimental results are compared to previous high latitude experiments and predictions from recent modeling efforts

Complete solids retention activated sludge process.

PubMed

Amanatidou, E; Samiotis, G; Trikoilidou, E; Pekridis, G; Tsikritzis, L

2016-01-01

In a slaughterhouse's full-scale extended aeration activated sludge wastewater treatment plant (WWTP), operating under complete solids retention time, the evolution of mixed liquor suspended solids (MLSS) and mixed liquor volatile suspended solids (MLVSS) concentration, food to micro-organisms ratio (F/M) and substrate utilization rate (SUR) were studied for over a year. Biomass growth phases in correlation to sludge biological and morphological characteristics were studied. Three distinguished growth phases were observed during the 425 days of monitoring. The imposed operational conditions led the process to extended biomass starvation conditions, minimum F/M, minimum SUR and predator species growth. MLSS and MLVSS reached a stabilization phase (plateau phase) where almost zero sludge accumulation was observed. The concept of degradation of the considered non-biodegradable particulate compounds in influent and in biomass (cell debris) was also studied. Comparison of evolution of observed sludge yields (Yobs) in the WWTP with Yobs predictions by activated sludge models verified the degradation concept for the considered non-biodegradable compounds. Control of the sedimentation process was achieved, by predicting the solids loading rate critical point using state point analysis and stirred/unstirred settling velocity tests and by applying a high return activated sludge rate. The nitrogen gas related sedimentation problems were taken into consideration.

Eclipse-Free-Time Assessment Tool for IRIS

NASA Technical Reports Server (NTRS)

Eagle, David

2012-01-01

IRIS_EFT is a scientific simulation that can be used to perform an Eclipse-Free- Time (EFT) assessment of IRIS (Infrared Imaging Surveyor) mission orbits. EFT is defined to be those time intervals longer than one day during which the IRIS spacecraft is not in the Earth s shadow. Program IRIS_EFT implements a special perturbation of orbital motion to numerically integrate Cowell's form of the system of differential equations. Shadow conditions are predicted by embedding this integrator within Brent s method for finding the root of a nonlinear equation. The IRIS_EFT software models the effects of the following types of orbit perturbations on the long-term evolution and shadow characteristics of IRIS mission orbits. (1) Non-spherical Earth gravity, (2) Atmospheric drag, (3) Point-mass gravity of the Sun, and (4) Point-mass gravity of the Moon. The objective of this effort was to create an in-house computer program that would perform eclipse-free-time analysis. of candidate IRIS spacecraft mission orbits in an accurate and timely fashion. The software is a suite of Fortran subroutines and data files organized as a "computational" engine that is used to accurately predict the long-term orbit evolution of IRIS mission orbits while searching for Earth shadow conditions.

Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks

PubMed Central

Ollivier, Julien F.; Soyer, Orkun S.

2016-01-01

Signalling networks result from combinatorial interactions among many enzymes and scaffolding proteins. These complex systems generate response dynamics that are often essential for correct decision-making in cells. Uncovering biochemical design principles that underpin such response dynamics is a prerequisite to understand evolved signalling networks and to design synthetic ones. Here, we use in silico evolution to explore the possible biochemical design space for signalling networks displaying ultrasensitive and adaptive response dynamics. By running evolutionary simulations mimicking different biochemical scenarios, we find that enzyme sequestration emerges as a key mechanism for enabling such dynamics. Inspired by these findings, and to test the role of sequestration, we design a generic, minimalist model of a signalling cycle, featuring two enzymes and a single scaffolding protein. We show that this simple system is capable of displaying both ultrasensitive and adaptive response dynamics. Furthermore, we find that tuning the concentration or kinetics of the sequestering protein can shift system dynamics between these two response types. These empirical results suggest that enzyme sequestration through scaffolding proteins is exploited by evolution to generate diverse response dynamics in signalling networks and could provide an engineering point in synthetic biology applications. PMID:27163612

Degeneracy between nonadiabatic dark energy models and Λ CDM : Integrated Sachs-Wolfe effect and the cross correlation of CMB with galaxy clustering data

NASA Astrophysics Data System (ADS)

Velten, Hermano; Fazolo, Raquel Emy; von Marttens, Rodrigo; Gomes, Syrios

2018-05-01

As recently pointed out in [Phys. Rev. D 96, 083502 (2017), 10.1103/PhysRevD.96.083502] the evolution of the linear matter perturbations in nonadiabatic dynamical dark energy models is almost indistinguishable (quasidegenerated) to the standard Λ CDM scenario. In this work we extend this analysis to CMB observables in particular the integrated Sachs-Wolfe effect and its cross-correlation with large scale structure. We find that this feature persists for such CMB related observable reinforcing that new probes and analysis are necessary to reveal the nonadiabatic features in the dark energy sector.

Collective firm bankruptcies and phase transition in rating dynamics

NASA Astrophysics Data System (ADS)

Sieczka, P.; Hołyst, J. A.

2009-10-01

We present a simple model of firm rating evolution. We consider two sources of defaults: individual dynamics of economic development and Potts-like interactions between firms. We show that such a defined model leads to phase transition, which results in collective defaults. The existence of the collective phase depends on the mean interaction strength. For small interaction strength parameters, there are many independent bankruptcies of individual companies. For large parameters, there are giant collective defaults of firm clusters. In the case when the individual firm dynamics favors dumping of rating changes, there is an optimal strength of the firm's interactions from the systemic risk point of view. in here

Analysis and application of opinion model with multiple topic interactions.

PubMed

Xiong, Fei; Liu, Yun; Wang, Liang; Wang, Ximeng

2017-08-01

To reveal heterogeneous behaviors of opinion evolution in different scenarios, we propose an opinion model with topic interactions. Individual opinions and topic features are represented by a multidimensional vector. We measure an agent's action towards a specific topic by the product of opinion and topic feature. When pairs of agents interact for a topic, their actions are introduced to opinion updates with bounded confidence. Simulation results show that a transition from a disordered state to a consensus state occurs at a critical point of the tolerance threshold, which depends on the opinion dimension. The critical point increases as the dimension of opinions increases. Multiple topics promote opinion interactions and lead to the formation of macroscopic opinion clusters. In addition, more topics accelerate the evolutionary process and weaken the effect of network topology. We use two sets of large-scale real data to evaluate the model, and the results prove its effectiveness in characterizing a real evolutionary process. Our model achieves high performance in individual action prediction and even outperforms state-of-the-art methods. Meanwhile, our model has much smaller computational complexity. This paper provides a demonstration for possible practical applications of theoretical opinion dynamics.

Dynamic route and departure time choice model based on self-adaptive reference point and reinforcement learning

NASA Astrophysics Data System (ADS)

Li, Xue-yan; Li, Xue-mei; Yang, Lingrun; Li, Jing

2018-07-01

Most of the previous studies on dynamic traffic assignment are based on traditional analytical framework, for instance, the idea of Dynamic User Equilibrium has been widely used in depicting both the route choice and the departure time choice. However, some recent studies have demonstrated that the dynamic traffic flow assignment largely depends on travelers' rationality degree, travelers' heterogeneity and what the traffic information the travelers have. In this paper, we develop a new self-adaptive multi agent model to depict travelers' behavior in Dynamic Traffic Assignment. We use Cumulative Prospect Theory with heterogeneous reference points to illustrate travelers' bounded rationality. We use reinforcement-learning model to depict travelers' route and departure time choosing behavior under the condition of imperfect information. We design the evolution rule of travelers' expected arrival time and the algorithm of traffic flow assignment. Compared with the traditional model, the self-adaptive multi agent model we proposed in this paper can effectively help travelers avoid the rush hour. Finally, we report and analyze the effect of travelers' group behavior on the transportation system, and give some insights into the relation between travelers' group behavior and the performance of transportation system.

Inflection-point inflation in a hyper-charge oriented U ( 1 ) X model

DOE PAGES

Okada, Nobuchika; Okada, Satomi; Raut, Digesh

2017-03-31

Inflection-point inflation is an interesting possibility to realize a successful slow-roll inflation when inflation is driven by a single scalar field with its value during inflation below the Planck mass (ΦI≲M Pl). In order for a renormalization group (RG) improved effective λΦ 4 potential to develop an inflection-point, the running quartic coupling λ(Φ) must exhibit a minimum with an almost vanishing value in its RG evolution, namely λ(Φ I)≃0 and β λ(ΦI)≃0, where β λ is the beta-function of the quartic coupling. Here in this paper, we consider the inflection-point inflation in the context of the minimal gauged U(1) Xmore » extended Standard Model (SM), which is a generalization of the minimal U(1) B$-$L model, and is constructed as a linear combination of the SM U(1) Y and U(1) B$-$L gauge symmetries. We identify the U(1) X Higgs field with the inflaton field. For a successful inflection-point inflation to be consistent with the current cosmological observations, the mass ratios among the U(1) X gauge boson, the right-handed neutrinos and the U(1) X Higgs boson are fixed. Focusing on the case that the extra U(1) X gauge symmetry is mostly aligned along the SM U(1) Y direction, we investigate a consistency between the inflationary predictions and the latest LHC Run-2 results on the search for a narrow resonance with the di-lepton final state.« less

Inflection-point inflation in a hyper-charge oriented U ( 1 ) X model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, Nobuchika; Okada, Satomi; Raut, Digesh

Inflection-point inflation is an interesting possibility to realize a successful slow-roll inflation when inflation is driven by a single scalar field with its value during inflation below the Planck mass (ΦI≲M Pl). In order for a renormalization group (RG) improved effective λΦ 4 potential to develop an inflection-point, the running quartic coupling λ(Φ) must exhibit a minimum with an almost vanishing value in its RG evolution, namely λ(Φ I)≃0 and β λ(ΦI)≃0, where β λ is the beta-function of the quartic coupling. Here in this paper, we consider the inflection-point inflation in the context of the minimal gauged U(1) Xmore » extended Standard Model (SM), which is a generalization of the minimal U(1) B$-$L model, and is constructed as a linear combination of the SM U(1) Y and U(1) B$-$L gauge symmetries. We identify the U(1) X Higgs field with the inflaton field. For a successful inflection-point inflation to be consistent with the current cosmological observations, the mass ratios among the U(1) X gauge boson, the right-handed neutrinos and the U(1) X Higgs boson are fixed. Focusing on the case that the extra U(1) X gauge symmetry is mostly aligned along the SM U(1) Y direction, we investigate a consistency between the inflationary predictions and the latest LHC Run-2 results on the search for a narrow resonance with the di-lepton final state.« less

Modelling of vegetation-driven morphodynamics in braided rivers.

NASA Astrophysics Data System (ADS)

Stecca, Guglielmo; Fedrizzi, Davide; Hicks, Murray; Measures, Richard; Zolezzi, Guido; Bertoldi, Walter; Tal, Michal

2017-04-01

River planform results from the complex interaction between flow, sediment transport and vegetation, and can evolve following a change in these controls. The braided planform of New Zealand's Lower Waitaki River, for instance, is endangered by the action of artificially-introduced alien vegetation, which spread across the braidplain following the reduction in magnitude of floods by hydropower dam construction. This vegetation, by encouraging flow concentration into the main channel, would likely promote a shift towards a single-thread morphology if it was not artificially removed within a central fairway. The purpose of this work is to study the evolution of braided rivers such as the Waitaki under different management scenarios through two-dimensional numerical modelling. The construction of a suitable model represents a task in itself, since a modelling framework coupling all the relevant processes is not yet readily available. Our starting point is the physics-based GIAMT2D numerical model, which solves two-dimensional flow and bedload transport in wet/dry domains, and recently modified by the inclusion of a rule-based bank erosion model. We have further developed this model by adding a vegetation module, which accounts in a simplified manner for time-evolving biomass density, adjusting local flow roughness, critical shear stress for sediment transport, and bank erodibility accordingly. Our goal is to use the model to study decadal-scale evolution of a reach on the Waitaki River and predict planform characteristics under different vegetation management scenarios. Here we present the results of a preliminary application of the model to reproduce the morphodynamic evolution of a braided channel in a set of flume experiments that used alfalfa as vegetation. The experiments began with a braided morphology that spontaneoulsy formed at constant flow over a bed of bare uniform sand. The planform transitioned towards single-thread when this discharge was repeatedly cycled with periods of low flow and vegetation growth.

An adaptive radiation model for the origin of new genefunctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Francino, M. Pilar

2004-10-18

The evolution of new gene functions is one of the keys to evolutionary innovation. Most novel functions result from gene duplication followed by divergence. However, the models hitherto proposed to account for this process are not fully satisfactory. The classic model of neofunctionalization holds that the two paralogous gene copies resulting from a duplication are functionally redundant, such that one of them can evolve under no functional constraints and occasionally acquire a new function. This model lacks a convincing mechanism for the new gene copies to increase in frequency in the population and survive the mutational load expected to accumulatemore » under neutrality, before the acquisition of the rare beneficial mutations that would confer new functionality. The subfunctionalization model has been proposed as an alternative way to generate genes with altered functions. This model also assumes that new paralogous gene copies are functionally redundant and therefore neutral, but it predicts that relaxed selection will affect both gene copies such that some of the capabilities of the parent gene will disappear in one of the copies and be retained in the other. Thus, the functions originally present in a single gene will be partitioned between the two descendant copies. However, although this model can explain increases in gene number, it does not really address the main evolutionary question, which is the development of new biochemical capabilities. Recently, a new concept has been introduced into the gene evolution literature which is most likely to help solve this dilemma. The key point is to allow for a period of natural selection for the duplication per se, before new function evolves, rather than considering gene duplication to be neutral as in the previous models. Here, I suggest a new model that draws on the advantage of postulating selection for gene duplication, and proposes that bursts of adaptive gene amplification in response to specific selection pressures provide the raw material for the evolution of new function.« less

Comparative Validation of Realtime Solar Wind Forecasting Using the UCSD Heliospheric Tomography Model

NASA Technical Reports Server (NTRS)

MacNeice, Peter; Taktakishvili, Alexandra; Jackson, Bernard; Clover, John; Bisi, Mario; Odstrcil, Dusan

2011-01-01

The University of California, San Diego 3D Heliospheric Tomography Model reconstructs the evolution of heliospheric structures, and can make forecasts of solar wind density and velocity up to 72 hours in the future. The latest model version, installed and running in realtime at the Community Coordinated Modeling Center(CCMC), analyzes scintillations of meter wavelength radio point sources recorded by the Solar-Terrestrial Environment Laboratory(STELab) together with realtime measurements of solar wind speed and density recorded by the Advanced Composition Explorer(ACE) Solar Wind Electron Proton Alpha Monitor(SWEPAM).The solution is reconstructed using tomographic techniques and a simple kinematic wind model. Since installation, the CCMC has been recording the model forecasts and comparing them with ACE measurements, and with forecasts made using other heliospheric models hosted by the CCMC. We report the preliminary results of this validation work and comparison with alternative models.

Exactly solvable models of growing interfaces and lattice gases: the Arcetri models, ageing and logarithmic sub-ageing

NASA Astrophysics Data System (ADS)

Durang, Xavier; Henkel, Malte

2017-12-01

Motivated by an analogy with the spherical model of a ferromagnet, the three Arcetri models are defined. They present new universality classes, either for the growth of interfaces, or else for lattice gases. They are distinct from the common Edwards-Wilkinson and Kardar-Parisi-Zhang universality classes. Their non-equilibrium evolution can be studied by the exact computation of their two-time correlators and responses. In both interpretations, the first model has a critical point in any dimension and shows simple ageing at and below criticality. The exact universal exponents are found. The second and third model are solved at zero temperature, in one dimension, where both show logarithmic sub-ageing, of which several distinct types are identified. Physically, the second model describes a lattice gas and the third model describes interface growth. A clear physical picture on the subsequent time and length scales of the sub-ageing process emerges.

Length scale effects and multiscale modeling of thermally induced phase transformation kinetics in NiTi SMA

NASA Astrophysics Data System (ADS)

Frantziskonis, George N.; Gur, Sourav

2017-06-01

Thermally induced phase transformation in NiTi shape memory alloys (SMAs) shows strong size and shape, collectively termed length scale effects, at the nano to micrometer scales, and that has important implications for the design and use of devices and structures at such scales. This paper, based on a recently developed multiscale model that utilizes molecular dynamics (MDs) simulations at small scales and MD-verified phase field (PhF) simulations at larger scales, reports results on specific length scale effects, i.e. length scale effects in martensite phase fraction (MPF) evolution, transformation temperatures (martensite and austenite start and finish) and in the thermally cyclic transformation between austenitic and martensitic phase. The multiscale study identifies saturation points for length scale effects and studies, for the first time, the length scale effect on the kinetics (i.e. developed internal strains) in the B19‧ phase during phase transformation. The major part of the work addresses small scale single crystals in specific orientations. However, the multiscale method is used in a unique and novel way to indirectly study length scale and grain size effects on evolution kinetics in polycrystalline NiTi, and to compare the simulation results to experiments. The interplay of the grain size and the length scale effect on the thermally induced MPF evolution is also shown in this present study. Finally, the multiscale coupling results are employed to improve phenomenological material models for NiTi SMA.

Modelling coastal processes by means of innovative integration of remote sensing and modelling analysis

NASA Astrophysics Data System (ADS)

Taramelli, A.; Zanuttigh, B.; Zucca, F.; Dejana, M.; Valentini, E.

2011-12-01

Coastal marine and inland landforms are dynamic systems undergoing adjustments in form at different time and space scales in response to varying conditions external to the system. Coastal emerged and shallow submerged nearshore areas, affected by short-term perturbations, return to their pre-disturbance morphology and generally reach a dynamic equilibrium. Worldwide in the last century we have experienced in increased coastal inundation, erosion and ecosystem losses. However, erosion can result from a number of other factors, such as altered wind and current patterns, high-energy waves, and reduced fluvial sediment inputs. Direct impacts of human activities, including reclamation of coastal wetlands, deforestation, damming, channelization, diversions of coastal waterways, construction of seawalls and other structures, alter circulation patterns. Also indirect human impacts such as land-uses changes through time (eg. from agricultural to industrial use) have affected coastal ecosystems. The objective of this research is to propose innovative remote sensing applications to monitor specific coastal processes in order to use them within a physical modelling to quantify and model their time evolution. The research was applied in two dynamic and densely populated deltas and coastal areas (the Po and the Plymouth delta) by combining multi-sensor spaceborne remote sensing (SAR and OPTICAL) to physical modelling. The main results are: a) deformation and spatiotemporal variations maps in coastal morphology with a special focus to point out the temporal subsidence evolution, b) inter and intra-annual change detection maps that are both used a to feed a coastal physical modelling (MIKE 21). The basic strategy was to highlight the different components of the coastal system environment through: 1) deformation and spatio-temporal variations maps of coastal morphology, by the use of time-stack from 1992 up today of ESA SAR data (ERS-1/2 and ENVISAT-ASAR sensors) were used to produce deformation maps and to point out the temporal evolution and 2) multitemporal hyperspectral endmembers fractions map of coastal morphology, 3) numerical model well-established through remote sensed based procedures and results in order to produce spatio-temporal scenario in coastal areas. The objective was to locate and characterize important coastal indicators for different regions using multitemporal data from the multi-hyperspectral sensors, as well as topographic elevation, SAR and derived products (eg. coherence) data. The identification of different indicators was based on land spectral properties, topography/landforms (low topography), disturbed areas (agricultural, construction), and vegetation distribution. Moreover, the indicators were assessed at seasonal and interannual time scales over two temporal decades horizons starting from 1990 and 2000.

Nonlinear density wave investigation for an extended car-following model considering driver’s memory and jerk

NASA Astrophysics Data System (ADS)

Jin, Zhizhan; Li, Zhipeng; Cheng, Rongjun; Ge, Hongxia

2018-01-01

Based on the two velocity difference model (TVDM), an extended car-following model is developed to investigate the effect of driver’s memory and jerk on traffic flow in this paper. By using linear stability analysis, the stability conditions are derived. And through nonlinear analysis, the time-dependent Ginzburg-Landau (TDGL) equation and the modified Korteweg-de Vries (mKdV) equation are obtained, respectively. The mKdV equation is constructed to describe the traffic behavior near the critical point. The evolution of traffic congestion and the corresponding energy consumption are discussed. Numerical simulations show that the improved model is found not only to enhance the stability of traffic flow, but also to depress the energy consumption, which are consistent with the theoretical analysis.

The resolved history of galaxy evolution.

PubMed

Brinchmann, Jarle

2002-12-15

We briefly review the study of the evolution of galaxies from an observational point of view, with particular emphasis on the role of the Hubble Space Telescope in probing the evolution of the different morphological types of galaxy. We show how using the stellar mass of galaxies as a tracer of evolution can improve our understanding of the physical process taking place before turning our eyes towards the future and giving an overview of what we can expect from future advances in technology.

Nonlinear evolution of baryon acoustic oscillations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crocce, Martin; Institut de Ciencies de l'Espai, IEEC-CSIC, Campus UAB, Facultat de Ciencies, Torre C5 par-2, Barcelona 08193; Scoccimarro, Roman

2008-01-15

We study the nonlinear evolution of baryon acoustic oscillations in the dark matter power spectrum and the correlation function using renormalized perturbation theory. In a previous paper we showed that renormalized perturbation theory successfully predicts the damping of acoustic oscillations; here we extend our calculation to the enhancement of power due to mode coupling. We show that mode coupling generates additional oscillations that are out of phase with those in the linear spectrum, leading to shifts in the scales of oscillation nodes defined with respect to a smooth spectrum. When Fourier transformed, these out-of-phase oscillations induce percent-level shifts in themore » acoustic peak of the two-point correlation function. We present predictions for these shifts as a function of redshift; these should be considered as a robust lower limit to the more realistic case that includes, in addition, redshift distortions and galaxy bias. We show that these nonlinear effects occur at very large scales, leading to a breakdown of linear theory at scales much larger than commonly thought. We discuss why virialized halo profiles are not responsible for these effects, which can be understood from basic physics of gravitational instability. Our results are in excellent agreement with numerical simulations, and can be used as a starting point for modeling baryon acoustic oscillations in future observations. To meet this end, we suggest a simple physically motivated model to correct for the shifts caused by mode coupling.« less

The dimensionality of stellar chemical space using spectra from the Apache Point Observatory Galactic Evolution Experiment

NASA Astrophysics Data System (ADS)

Price-Jones, Natalie; Bovy, Jo

2018-03-01

Chemical tagging of stars based on their similar compositions can offer new insights about the star formation and dynamical history of the Milky Way. We investigate the feasibility of identifying groups of stars in chemical space by forgoing the use of model derived abundances in favour of direct analysis of spectra. This facilitates the propagation of measurement uncertainties and does not pre-suppose knowledge of which elements are important for distinguishing stars in chemical space. We use ˜16 000 red giant and red clump H-band spectra from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) and perform polynomial fits to remove trends not due to abundance-ratio variations. Using expectation maximized principal component analysis, we find principal components with high signal in the wavelength regions most important for distinguishing between stars. Different subsamples of red giant and red clump stars are all consistent with needing about 10 principal components to accurately model the spectra above the level of the measurement uncertainties. The dimensionality of stellar chemical space that can be investigated in the H band is therefore ≲10. For APOGEE observations with typical signal-to-noise ratios of 100, the number of chemical space cells within which stars cannot be distinguished is approximately 1010±2 × (5 ± 2)n - 10 with n the number of principal components. This high dimensionality and the fine-grained sampling of chemical space are a promising first step towards chemical tagging based on spectra alone.

Damage-based life prediction model for uniaxial low-cycle stress fatigue of super-elastic NiTi shape memory alloy microtubes

NASA Astrophysics Data System (ADS)

Song, Di; Kang, Guozheng; Kan, Qianhua; Yu, Chao; Zhang, Chuanzeng

2015-08-01

Based on the experimental observations for the uniaxial low-cycle stress fatigue failure of super-elastic NiTi shape memory alloy microtubes (Song et al 2015 Smart Mater. Struct. 24 075004) and a new definition of damage variable corresponding to the variation of accumulated dissipation energy, a phenomenological damage model is proposed to describe the damage evolution of the NiTi microtubes during cyclic loading. Then, with a failure criterion of Dc = 1, the fatigue lives of the NiTi microtubes are predicted by the damage-based model, the predicted lives are in good agreement with the experimental ones, and all of the points are located within an error band of 1.5 times.

Large-scale structure from cosmic-string loops in a baryon-dominated universe

NASA Technical Reports Server (NTRS)

Melott, Adrian L.; Scherrer, Robert J.

1988-01-01

The results are presented of a numerical simulation of the formation of large-scale structure in a universe with Omega(0) = 0.2 and h = 0.5 dominated by baryons in which cosmic strings provide the initial density perturbations. The numerical model yields a power spectrum. Nonlinear evolution confirms that the model can account for 700 km/s bulk flows and a strong cluster-cluster correlation, but does rather poorly on smaller scales. There is no visual 'filamentary' structure, and the two-point correlation has too steep a logarithmic slope. The value of G mu = 4 x 10 to the -6th is significantly lower than previous estimates for the value of G mu in baryon-dominated cosmic string models.

The autonomy of biological individuals and artificial models.

PubMed

Moreno, Alvaro; Etxeberria, Arantza; Umerez, Jon

2008-02-01

This paper aims to offer an overview of the meaning of autonomy for biological individuals and artificial models rooted in a specific perspective that pays attention to the historical and structural aspects of its origins and evolution. Taking autopoiesis and the recursivity characteristic of its circular logic as a starting point, we depart from some of its consequences to claim that the theory of autonomy should also take into account historical and structural features. Autonomy should not be considered only in internal or constitutive terms, the largely neglected interactive aspects stemming from it should be equally addressed. Artificial models contribute to get a better understanding of the role of autonomy for life and the varieties of its organization and phenomenological diversity.

THE ROLE OF THE INNER CORONAL NULL POINT IN THE FORMATION AND EVOLUTION OF SOLAR QUIESCENT PROMINENCES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Y. Z., E-mail: yzzhangmail@sohu.com

2015-02-10

Using a 2.5-dimensional MHD simulation, we investigate the role played by the inner coronal null point in the formation and evolution of solar quiescent prominences. The flux rope is characterized by its magnetic fluxes, the toroidal magnetic flux Φ {sub p} and the poloidal flux Φ{sub ψ}. It is found that for a given Φ {sub p}, the catastrophe does not occur in the flux rope system until Φ{sub ψ} increases to a critical point. Moreover, the magnetic flux of the null point is the maximum value of the magnetic flux in the quadrupole background magnetic field, and represented bymore » ψ {sub N}. The results show that the bigger ψ {sub N} usually corresponds to the smaller catastrophic point, the lower magnetic energy of the flux rope system, and the lesser magnetic energy inside the flux rope. Our results confirm that catastrophic disruption of the prominence occurs more easily when there is a bigger ψ {sub N}. However, ψ {sub N} has little influence on the maximum speed of the coronal mass ejections (CMEs) with an erupted prominence. Thus we argue that a topological configuration with the inner coronal null point is a necessary structure for the formation and evolution of solar quiescent prominences. In conclusion, it is easier for the prominences to form and to erupt as a core part of the CMEs in the magnetic structure with a greater ψ {sub N}.« less

"Simulated molecular evolution" or computer-generated artifacts?

PubMed

Darius, F; Rojas, R

1994-11-01

1. The authors define a function with value 1 for the positive examples and 0 for the negative ones. They fit a continuous function but do not deal at all with the error margin of the fit, which is almost as large as the function values they compute. 2. The term "quality" for the value of the fitted function gives the impression that some biological significance is associated with values of the fitted function strictly between 0 and 1, but there is no justification for this kind of interpretation and finding the point where the fit achieves its maximum does not make sense. 3. By neglecting the error margin the authors try to optimize the fitted function using differences in the second, third, fourth, and even fifth decimal place which have no statistical significance. 4. Even if such a fit could profit from more data points, the authors should first prove that the region of interest has some kind of smoothness, that is, that a continuous fit makes any sense at all. 5. "Simulated molecular evolution" is a misnomer. We are dealing here with random search. Since the margin of error is so large, the fitted function does not provide statistically significant information about the points in search space where strings with cleavage sites could be found. This implies that the method is a highly unreliable stochastic search in the space of strings, even if the neural network is capable of learning some simple correlations. 6. Classical statistical methods are for these kind of problems with so few data points clearly superior to the neural networks used as a "black box" by the authors, which in the way they are structured provide a model with an error margin as large as the numbers being computed.7. And finally, even if someone would provide us with a function which separates strings with cleavage sites from strings without them perfectly, so-called simulated molecular evolution would not be better than random selection.Since a perfect fit would only produce exactly ones or zeros,starting a search in a region of space where all strings in the neighborhood get the value zero would not provide any kind of directional information for new iterations. We would just skip from one point to the other in a typical random walk manner.

Constitutive modeling and structural analysis considering simultaneous phase transformation and plastic yield in shape memory alloys

NASA Astrophysics Data System (ADS)

Hartl, D. J.; Lagoudas, D. C.

2009-10-01

The new developments summarized in this work represent both theoretical and experimental investigations of the effects of plastic strain generation in shape memory alloys (SMAs). Based on the results of SMA experimental characterization described in the literature and additional testing described in this work, a new 3D constitutive model is proposed. This phenomenological model captures both the conventional shape memory effects of pseudoelasticity and thermal strain recovery, and additionally considers the initiation and evolution of plastic strains. The model is numerically implemented in a finite element framework using a return mapping algorithm to solve the constitutive equations at each material point. This combination of theory and implementation is unique in its ability to capture the simultaneous evolution of recoverable transformation strains and irrecoverable plastic strains. The consideration of isotropic and kinematic plastic hardening allows the derivation of a theoretical framework capturing the interactions between irrecoverable plastic strain and recoverable strain due to martensitic transformation. Further, the numerical integration of the constitutive equations is formulated such that objectivity is maintained for SMA structures undergoing moderate strains and large displacements. The implemented model has been used to perform 3D analysis of SMA structural components under uniaxial and bending loads, including a case of local buckling behavior. Experimentally validated results considering simultaneous transformation and plasticity in a bending member are provided, illustrating the predictive accuracy of the model and its implementation.

Predicting galaxy star formation rates via the co-evolution of galaxies and haloes

NASA Astrophysics Data System (ADS)

Watson, Douglas F.; Hearin, Andrew P.; Berlind, Andreas A.; Becker, Matthew R.; Behroozi, Peter S.; Skibba, Ramin A.; Reyes, Reinabelle; Zentner, Andrew R.; van den Bosch, Frank C.

2015-01-01

In this paper, we test the age matching hypothesis that the star formation rate (SFR) of a galaxy of fixed stellar mass is determined by its dark matter halo formation history, e.g. more quiescent galaxies reside in older haloes. We present new Sloan Digital Sky Survey measurements of the galaxy two-point correlation function and galaxy-galaxy lensing as a function of stellar mass and SFR, separated into quenched and star-forming galaxy samples to test this simple model. We find that our age matching model is in excellent agreement with these new measurements. We also find that our model is able to predict: (1) the relative SFRs of central and satellite galaxies, (2) the SFR dependence of the radial distribution of satellite galaxy populations within galaxy groups, rich groups, and clusters and their surrounding larger scale environments, and (3) the interesting feature that the satellite quenched fraction as a function of projected radial distance from the central galaxy exhibits an ˜r-.15 slope, independent of environment. These accurate predictions are intriguing given that we do not explicitly model satellite-specific processes after infall, and that in our model the virial radius does not mark a special transition region in the evolution of a satellite. The success of the model suggests that present-day galaxy SFR is strongly correlated with halo mass assembly history.

The dynamics of correlated novelties.

PubMed

Tria, F; Loreto, V; Servedio, V D P; Strogatz, S H

2014-07-31

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called "expanding the adjacent possible". The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution.

The dynamics of correlated novelties

NASA Astrophysics Data System (ADS)

Tria, F.; Loreto, V.; Servedio, V. D. P.; Strogatz, S. H.

2014-07-01

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called ``expanding the adjacent possible''. The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution.

N -loop running should be combined with N -loop matching

NASA Astrophysics Data System (ADS)

Braathen, Johannes; Goodsell, Mark D.; Krauss, Manuel E.; Opferkuch, Toby; Staub, Florian

2018-01-01

We investigate the high-scale behavior of Higgs sectors beyond the Standard Model, pointing out that the proper matching of the quartic couplings before applying the renormalization group equations (RGEs) is of crucial importance for reliable predictions at larger energy scales. In particular, the common practice of leading-order parameters in the RGE evolution is insufficient to make precise statements on a given model's UV behavior, typically resulting in uncertainties of many orders of magnitude. We argue that, before applying N -loop RGEs, a matching should even be performed at N -loop order in contrast to common lore. We show both analytical and numerical results where the impact is sizable for three minimal extensions of the Standard Model: a singlet extension, a second Higgs doublet and finally vector-like quarks. We highlight that the known two-loop RGEs tend to moderate the running of their one-loop counterparts, typically delaying the appearance of Landau poles. For the addition of vector-like quarks we show that the complete two-loop matching and RGE evolution hints at a stabilization of the electroweak vacuum at high energies, in contrast to results in the literature.

Using SDO/AIA to Understand the Thermal Evolution of Solar Prominence Formation

NASA Astrophysics Data System (ADS)

Viall, Nicholeen; M.; Kucera, Therese T.; Karpen, Judith

2016-10-01

In this study, we investigate prominence formation using time series analysis of Solar Dynamics Observatory's Atmospheric Imaging Assembly (SDO/AIA) data. We investigate the thermal properties of forming prominences by analyzing observed light curves using the same technique that we have already successfully applied to active regions to diagnose heating and cooling cycles. This technique tracks the thermal evolution using emission formed at different temperatures, made possible by AIA's different wavebands and high time resolution. We also compute the predicted light curves in the same SDO/AIA channels of a hydrodynamic model of thermal nonequilibrium formation of prominence material, an evaporation-condensation model. In these models of prominence formation, heating at the foot-points of sheared coronal flux-tubes results in evaporation of material of a few MK into the corona followed by catastrophic cooling of the hot material to form cool ( 10,000 K) prominence material. We demonstrate that the SDO/AIA light curves for flux tubes undergoing thermal nonequilibrium vary at different locations along the flux tube, especially in the region where the condensate forms, and we compare the predicted light curves with those observed. Supported by NASA's Living with a Star program.

Type Ia Supernova Explosions from Hybrid Carbon-Oxygen-Neon White Dwarf Progenitors

NASA Astrophysics Data System (ADS)

Willcox, Donald E.; Townsley, Dean M.; Calder, Alan C.; Denissenkov, Pavel A.; Herwig, Falk

2016-11-01

Motivated by recent results in stellar evolution that predict the existence of hybrid white dwarf (WD) stars with a C-O core inside an O-Ne shell, we simulate thermonuclear (Type Ia) supernovae from these hybrid progenitors. We use the FLASH code to perform multidimensional simulations in the deflagration-to-detonation transition (DDT) explosion paradigm. Our hybrid progenitor models were produced with the MESA stellar evolution code and include the effects of the Urca process, and we map the progenitor model to the FLASH grid. We performed a suite of DDT simulations over a range of ignition conditions consistent with the progenitor’s thermal and convective structure assuming multiple ignition points. To compare the results from these hybrid WD stars to previous results from C-O WDs, we construct a set of C-O WD models with similar properties and similarly simulate a suite of explosions. We find that despite significant variability within each suite, trends distinguishing the explosions are apparent in their {}56{Ni} yields and the kinetic properties of the ejecta. We compare our results with other recent work that studies explosions from these hybrid progenitors.

The dynamics of correlated novelties

PubMed Central

Tria, F.; Loreto, V.; Servedio, V. D. P.; Strogatz, S. H.

2014-01-01

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called “expanding the adjacent possible”. The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution. PMID:25080941

The Genetics and Evolution of Human Skin Color: The Case of Desiree's Baby

ERIC Educational Resources Information Center

Schneider, Patricia

2004-01-01

This case explores the genetics and evolution of skin color, using a short story by Kate Chopin called "Desiree's Baby" as a starting point. Students read the story and discuss a series of questions probing the genetics of the family in the tale. Students then read an article about the evolution of skin color and write an essay analyzing the…

Three-dimensional modeling in the study of subsidence in mining Acquaresi (Sardinia South - West) - Francesco Muntoni (1) Teresa Balvis (2) Paolo Bevilacqua (3) (1) Geological, Mining Park of Sardinia - Via Monteverdi, 16 09016 - Iglesias (2) freelance (3) Department of Engineering and Architecture - University of Trieste, Via Valerio 10 - Trieste

NASA Astrophysics Data System (ADS)

Muntoni, F.

2013-12-01

The effects of subsidence and subsequent landslides in mining areas are very frequent, the study examines the proposed mining area of Acquaresi (Sardinia South - West), interested in the years between 1991 and 2003 by major subsidence phenomena and consequent events landslides. The valley of Acquaresi is particularly important, not only for its mines, but also for the aspect related to the geomorphological evolution morphotectonic in the context of Paleozoic lithologies, which have a rectangular structure parallel to the coastline. To make measurements and analysis of the evolution of human morphostructural and throughout the industry, it was considered appropriate to create a three-dimensional model that would allow a synoptic view with the different information available to the industry. E 'was created a model using the points listed extrapolated from the Regional Technical Map scale 1:10,000, the map at scale 1:2000 dell'IGEA and the values of a detailed survey of the study area, measured at a scale 1: 500. How MicroStation CAD software was used, with whom it is made of a TIN high detail taking into account then is, if possible, of quoted points, roads, major infrastructure, contour lines (lines-intermediate-auxiliary), buildings and lines coast. The model was supported and shaped (draping) image obtained by integrating the color orthophotos of the area in 1:10,000 scale of the Autonomous Region of Sardinia and photos to scale 1:2,000 made to run dall'IGEA spa at the last event of the landslide. The use of aerial photographs, a scale similar to that of cartography, has allowed us to achieve excellent results by superimposing the frames of the areas of interest on models made, with views that appear to be consistent with the technical papers, with a maximum error of less than that of the reference mapping. Moreover, to emphasize the tectonic lineations, morphological aspects and changes in landscape and environment, it was considered appropriate to use a three-dimensional model, thanks to software used in this trial, with a high detail 3D visualization. Starting from the Regional Technical Map has been possible to realize the DEM file, then perform an interpolation with a point layer containing elevation values recorded separately and then superimpose the orthophoto to 3D surface. It was also decided to use a terrain model DTM knitted irregular TIN compared to a regular grid pattern GRID, because the first best response to the need to have a shirt that exploited all possible points present and identifiable in the territory. With the use of a TIN was thus possible to insert also the points detected by the GPS in the country to verify the area of detachment of the landslide, thus being able to increase the detail in the area of observation. Getting a noticeable "jump" quality: moving from a two-dimensional to a three-dimensional display. The model thus obtained has allowed a very good point of the area: they are easy to locate the outcrops of the different lithological structures, facilitating the study and evaluation for interventions of recovery.

Insights into mortality patterns and causes of death through a process point of view model

PubMed Central

Anderson, James J.; Li, Ting; Sharrow, David J.

2016-01-01

Process point of view models of mortality, such as the Strehler-Mildvan and stochastic vitality models, represent death in terms of the loss of survival capacity through challenges and dissipation. Drawing on hallmarks of aging, we link these concepts to candidate biological mechanisms through a framework that defines death as challenges to vitality where distal factors defined the age-evolution of vitality and proximal factors define the probability distribution of challenges. To illustrate the process point of view, we hypothesize that the immune system is a mortality nexus, characterized by two vitality streams: increasing vitality representing immune system development and immunosenescence representing vitality dissipation. Proximal challenges define three mortality partitions: juvenile and adult extrinsic mortalities and intrinsic adult mortality. Model parameters, generated from Swedish mortality data (1751-2010), exhibit biologically meaningful correspondences to economic, health and cause-of-death patterns. The model characterizes the 20th century epidemiological transition mainly as a reduction in extrinsic mortality resulting from a shift from high magnitude disease challenges on individuals at all vitality levels to low magnitude stress challenges on low vitality individuals. Of secondary importance, intrinsic mortality was described by a gradual reduction in the rate of loss of vitality presumably resulting from reduction in the rate of immunosenescence. Extensions and limitations of a distal/proximal framework for characterizing more explicit causes of death, e.g. the young adult mortality hump or cancer in old age are discussed. PMID:27885527

A modelling approach to assessing the timescale uncertainties in proxy series with chronological errors

NASA Astrophysics Data System (ADS)

Divine, D.; Godtliebsen, F.; Rue, H.

2012-04-01

Detailed knowledge of past climate variations is of high importance for gaining a better insight into the possible future climate scenarios. The relative shortness of available high quality instrumental climate data conditions the use of various climate proxy archives in making inference about past climate evolution. It, however, requires an accurate assessment of timescale errors in proxy-based paleoclimatic reconstructions. We here propose an approach to assessment of timescale errors in proxy-based series with chronological uncertainties. The method relies on approximation of the physical process(es) forming a proxy archive by a random Gamma process. Parameters of the process are partly data-driven and partly determined from prior assumptions. For a particular case of a linear accumulation model and absolutely dated tie points an analytical solution is found suggesting the Beta-distributed probability density on age estimates along the length of a proxy archive. In a general situation of uncertainties in the ages of the tie points the proposed method employs MCMC simulations of age-depth profiles yielding empirical confidence intervals on the constructed piecewise linear best guess timescale. It is suggested that the approach can be further extended to a more general case of a time-varying expected accumulation between the tie points. The approach is illustrated by using two ice and two lake/marine sediment cores representing the typical examples of paleoproxy archives with age models constructed using tie points of mixed origin.

Pattern recognition tool based on complex network-based approach

NASA Astrophysics Data System (ADS)

Casanova, Dalcimar; Backes, André Ricardo; Martinez Bruno, Odemir

2013-02-01

This work proposed a generalization of the method proposed by the authors: 'A complex network-based approach for boundary shape analysis'. Instead of modelling a contour into a graph and use complex networks rules to characterize it, here, we generalize the technique. This way, the work proposes a mathematical tool for characterization signals, curves and set of points. To evaluate the pattern description power of the proposal, an experiment of plat identification based on leaf veins image are conducted. Leaf vein is a taxon characteristic used to plant identification proposes, and one of its characteristics is that these structures are complex, and difficult to be represented as a signal or curves and this way to be analyzed in a classical pattern recognition approach. Here, we model the veins as a set of points and model as graphs. As features, we use the degree and joint degree measurements in a dynamic evolution. The results demonstrates that the technique has a good power of discrimination and can be used for plant identification, as well as other complex pattern recognition tasks.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Yong; Lii-Rosales, A.; Zhou, Y.

Theory and stochastic lattice-gas modeling is developed for the formation of intercalated metal islands in the gallery between the top layer and the underlying layer at the surface of layered materials. Our model for this process involves deposition of atoms, some fraction of which then enter the gallery through well-separated pointlike defects in the top layer. Subsequently, these atoms diffuse within the subsurface gallery leading to nucleation and growth of intercalated islands nearby the defect point source. For the case of a single point defect, continuum diffusion equation analysis provides insight into the nucleation kinetics. However, complementary tailored lattice-gas modelingmore » produces a more comprehensive and quantitative characterization. We analyze the large spread in nucleation times and positions relative to the defect for the first nucleated island. We also consider the formation of subsequent islands and the evolution of island growth shapes. The shapes reflect in part our natural adoption of a hexagonal close-packed island structure. As a result, motivation and support for the model is provided by scanning tunneling microscopy observations of the formation of intercalated metal islands in highly-ordered pyrolytic graphite at higher temperatures.« less

Representing grounding line migration in synchronous coupling between a marine ice sheet model and a z-coordinate ocean model

NASA Astrophysics Data System (ADS)

Goldberg, D. N.; Snow, K.; Holland, P.; Jordan, J. R.; Campin, J.-M.; Heimbach, P.; Arthern, R.; Jenkins, A.

2018-05-01

Synchronous coupling is developed between an ice sheet model and a z-coordinate ocean model (the MITgcm). A previously-developed scheme to allow continuous vertical movement of the ice-ocean interface of a floating ice shelf ("vertical coupling") is built upon to allow continuous movement of the grounding line, or point of floatation of the ice sheet ("horizontal coupling"). Horizontal coupling is implemented through the maintenance of a thin layer of ocean ( ∼ 1 m) under grounded ice, which is inflated into the real ocean as the ice ungrounds. This is accomplished through a modification of the ocean model's nonlinear free surface evolution in a manner akin to a hydrological model in the presence of steep bathymetry. The coupled model is applied to a number of idealized geometries and shown to successfully represent ocean-forced marine ice sheet retreat while maintaining a continuous ocean circulation.

Analysis of the sensitivity properties of a model of vector-borne bubonic plague.

PubMed

Buzby, Megan; Neckels, David; Antolin, Michael F; Estep, Donald

2008-09-06

Model sensitivity is a key to evaluation of mathematical models in ecology and evolution, especially in complex models with numerous parameters. In this paper, we use some recently developed methods for sensitivity analysis to study the parameter sensitivity of a model of vector-borne bubonic plague in a rodent population proposed by Keeling & Gilligan. The new sensitivity tools are based on a variational analysis involving the adjoint equation. The new approach provides a relatively inexpensive way to obtain derivative information about model output with respect to parameters. We use this approach to determine the sensitivity of a quantity of interest (the force of infection from rats and their fleas to humans) to various model parameters, determine a region over which linearization at a specific parameter reference point is valid, develop a global picture of the output surface, and search for maxima and minima in a given region in the parameter space.

Modelling (18)O2 and (16)O2 unidirectional fluxes in plants. III: fitting of experimental data by a simple model.

PubMed

André, Marcel J

2013-08-01

Photosynthetic assimilation of CO2 in plants results in the balance between the photochemical energy developed by light in chloroplasts, and the consumption of that energy by the oxygenation processes, mainly the photorespiration in C3 plants. The analysis of classical biological models shows the difficulties to bring to fore the oxygenation rate due to the photorespiration pathway. As for other parameters, the most important key point is the estimation of the electron transport rate (ETR or J), i.e. the flux of biochemical energy, which is shared between the reductive and oxidative cycles of carbon. The only reliable method to quantify the linear electron flux responsible for the production of reductive energy is to directly measure the O2 evolution by (18)O2 labelling and mass spectrometry. The hypothesis that the respective rates of reductive and oxidative cycles of carbon are only determined by the kinetic parameters of Rubisco, the respective concentrations of CO2 and O2 at the Rubisco site and the available electron transport rate, ultimately leads to propose new expressions of biochemical model equations. The modelling of (18)O2 and (16)O2 unidirectional fluxes in plants shows that a simple model can fit the photosynthetic and photorespiration exchanges for a wide range of environmental conditions. Its originality is to express the carboxylation and the oxygenation as a function of external gas concentrations, by the definition of a plant specificity factor Sp that mimics the internal reactions of Rubisco in plants. The difference between the specificity factors of plant (Sp) and of Rubisco (Sr) is directly related to the conductance values to CO2 transfer between the atmosphere and the Rubisco site. This clearly illustrates that the values and the variation of conductance are much more important, in higher C3 plants, than the small variations of the Rubisco specificity factor. The simple model systematically expresses the reciprocal variations of carboxylation and oxygenation exchanges illustrated by a "mirror effect". It explains the protective sink effect of photorespiration, e.g. during water stress. The importance of the CO2 compensation point, in classical models, is reduced at the benefit of the crossing points Cx and Ox, concentration values where carboxylation and oxygenation are equal or where the gross O2 uptake is half of the gross O2 evolution. This concept is useful to illustrate the feedback effects of photorespiration in the atmosphere regulation. The constancy of Sp and of Cx for a great variation of P under several irradiance levels shows that the regulation of the conductance maintains constant the internal CO2 and the ratio of photorespiration to photosynthesis (PR/P). The maintenance of the ratio PR/P, in conditions of which PR could be reduced and the carboxylation increased, reinforces the hypothesis of a positive role of photorespiration and its involvement in the plant-atmosphere co-evolution. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Astrovirology: Viruses at Large in the Universe.

PubMed

Berliner, Aaron J; Mochizuki, Tomohiro; Stedman, Kenneth M

2018-02-01

Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.

Radiocarbon constraints on the extent and evolution of the South Pacific glacial carbon pool

PubMed Central

Ronge, T. A.; Tiedemann, R.; Lamy, F.; Köhler, P.; Alloway, B. V.; De Pol-Holz, R.; Pahnke, K.; Southon, J.; Wacker, L.

2016-01-01

During the last deglaciation, the opposing patterns of atmospheric CO2 and radiocarbon activities (Δ14C) suggest the release of 14C-depleted CO2 from old carbon reservoirs. Although evidences point to the deep Pacific as a major reservoir of this 14C-depleted carbon, its extent and evolution still need to be constrained. Here we use sediment cores retrieved along a South Pacific transect to reconstruct the spatio-temporal evolution of Δ14C over the last 30,000 years. In ∼2,500–3,600 m water depth, we find 14C-depleted deep waters with a maximum glacial offset to atmospheric 14C (ΔΔ14C=−1,000‰). Using a box model, we test the hypothesis that these low values might have been caused by an interaction of aging and hydrothermal CO2 influx. We observe a rejuvenation of circumpolar deep waters synchronous and potentially contributing to the initial deglacial rise in atmospheric CO2. These findings constrain parts of the glacial carbon pool to the deep South Pacific. PMID:27157845

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.

PubMed

Wang, Yong; Waters, Jill; Leung, Marco L; Unruh, Anna; Roh, Whijae; Shi, Xiuqing; Chen, Ken; Scheet, Paul; Vattathil, Selina; Liang, Han; Multani, Asha; Zhang, Hong; Zhao, Rui; Michor, Franziska; Meric-Bernstam, Funda; Navin, Nicholas E

2014-08-14

Sequencing studies of breast tumour cohorts have identified many prevalent mutations, but provide limited insight into the genomic diversity within tumours. Here we developed a whole-genome and exome single cell sequencing approach called nuc-seq that uses G2/M nuclei to achieve 91% mean coverage breadth. We applied this method to sequence single normal and tumour nuclei from an oestrogen-receptor-positive (ER(+)) breast cancer and a triple-negative ductal carcinoma. In parallel, we performed single nuclei copy number profiling. Our data show that aneuploid rearrangements occurred early in tumour evolution and remained highly stable as the tumour masses clonally expanded. In contrast, point mutations evolved gradually, generating extensive clonal diversity. Using targeted single-molecule sequencing, many of the diverse mutations were shown to occur at low frequencies (<10%) in the tumour mass. Using mathematical modelling we found that the triple-negative tumour cells had an increased mutation rate (13.3×), whereas the ER(+) tumour cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.

Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

PubMed

Kijima, T E; Innan, Hideki

2013-11-01

A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

Evolution simulation of lightning discharge based on a magnetohydrodynamics method

NASA Astrophysics Data System (ADS)

Fusheng, WANG; Xiangteng, MA; Han, CHEN; Yao, ZHANG

2018-07-01

In order to solve the load problem for aircraft lightning strikes, lightning channel evolution is simulated under the key physical parameters for aircraft lightning current component C. A numerical model of the discharge channel is established, based on magnetohydrodynamics (MHD) and performed by FLUENT software. With the aid of user-defined functions and a user-defined scalar, the Lorentz force, Joule heating and material parameters of an air thermal plasma are added. A three-dimensional lightning arc channel is simulated and the arc evolution in space is obtained. The results show that the temperature distribution of the lightning channel is symmetrical and that the hottest region occurs at the center of the lightning channel. The distributions of potential and current density are obtained, showing that the difference in electric potential or energy between two points tends to make the arc channel develop downwards. The arc channel comes into expansion on the anode surface due to stagnation of the thermal plasma and there exists impingement on the copper plate when the arc channel comes into contact with the anode plate.

Coastal single-beam bathymetry data collected in 2015 from Raccoon Point to Point Au Fer Island, Louisiana

USGS Publications Warehouse

Stalk, Chelsea A.; DeWitt, Nancy T.; Kindinger, Jack L.; Flocks, James G.; Reynolds, Billy J.; Kelso, Kyle W.; Fredericks, Joseph J.; Tuten, Thomas M.

2017-03-10

As part of the Barrier Island Comprehensive Monitoring Program (BICM), scientists from the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center conducted a nearshore single-beam bathymetry survey along the south-central coast of Louisiana, from Raccoon Point to Point Au Fer Island, in July 2015. The goal of the BICM program is to provide long-term data on Louisiana’s coastline and use this data to plan, design, evaluate, and maintain current and future barrier island restoration projects. The data described in this report will provide baseline bathymetric information for future research investigating island evolution, sediment transport, and recent and long-term geomorphic change, and will support modeling of future changes in response to restoration and storm impacts. The survey area encompasses more than 300 square kilometers of nearshore environment from Raccoon Point to Point Au Fer Island. This data series serves as an archive of processed single-beam bathymetry data, collected from July 22–29, 2015, under USGS Field Activity Number 2015-320-FA. Geographic information system data products include a 200-meter-cell-size interpolated bathymetry grid, trackline maps, and point data files. Additional files include error analysis maps, Field Activity Collection System logs, and formal Federal Geographic Data Committee metadata.

Demand modelling of passenger air travel: An analysis and extension. Volume 1: Background and summary

NASA Technical Reports Server (NTRS)

Jacobson, I. D.

1978-01-01

The framework for a model of travel demand which will be useful in predicting the total market for air travel between two cities is discussed. Variables to be used in determining the need for air transportation where none currently exists and the effect of changes in system characteristics on attracting latent demand are identified. Existing models are examined in order to provide insight into their strong points and shortcomings. Much of the existing behavioral research in travel demand is incorporated to allow the inclusion of non-economic factors, such as convenience. The model developed is characterized as a market segmentation model. This is a consequence of the strengths of disaggregation and its natural evolution to a usable aggregate formulation. The need for this approach both pedagogically and mathematically is discussed.

A Global Optimization Method to Calculate Water Retention Curves

NASA Astrophysics Data System (ADS)

Maggi, S.; Caputo, M. C.; Turturro, A. C.

2013-12-01

Water retention curves (WRC) have a key role for the hydraulic characterization of soils and rocks. The behaviour of the medium is defined by relating the unsaturated water content to the matric potential. The experimental determination of WRCs requires an accurate and detailed measurement of the dependence of matric potential on water content, a time-consuming and error-prone process, in particular for rocky media. A complete experimental WRC needs at least a few tens of data points, distributed more or less uniformly from full saturation to oven dryness. Since each measurement requires to wait to reach steady state conditions (i.e., between a few tens of minutes for soils and up to several hours or days for rocks or clays), the whole process can even take a few months. The experimental data are fitted to the most appropriate parametric model, such as the widely used models of Van Genuchten, Brooks and Corey and Rossi-Nimmo, to obtain the analytic WRC. We present here a new method for the determination of the parameters that best fit the models to the available experimental data. The method is based on differential evolution, an evolutionary computation algorithm particularly useful for multidimensional real-valued global optimization problems. With this method it is possible to strongly reduce the number of measurements necessary to optimize the model parameters that accurately describe the WRC of the samples, allowing to decrease the time needed to adequately characterize the medium. In the present work, we have applied our method to calculate the WRCs of sedimentary carbonatic rocks of marine origin, belonging to 'Calcarenite di Gravina' Formation (Middle Pliocene - Early Pleistocene) and coming from two different quarry districts in Southern Italy. WRC curves calculated using the Van Genuchten model by simulated annealing (dashed curve) and differential evolution (solid curve). The curves are calculated using 10 experimental data points randomly extracted from the full experimental dataset. Simulated annealing is not able to find the optimal solution with this reduced data set.

MSFC Skylab attitude and pointing control system mission evaluation

NASA Technical Reports Server (NTRS)

Chubb, W. B.

1974-01-01

The results of detailed performance analyses of the attitude and pointing control system in-orbit hardware and software on Skylab are reported. Performance is compared with requirements, test results, and prelaunch predictions. A brief history of the altitude and pointing control system evolution leading to the launch configuration is presented. The report states that the attitude and pointing system satisfied all requirements.

Computational Implementation of a Thermodynamically Based Work Potential Model For Progressive Microdamage and Transverse Cracking in Fiber-Reinforced Laminates

NASA Technical Reports Server (NTRS)

Pineda, Evan J.; Waas, Anthony M.; Bednarcyk, Brett A.; Collier, Craig S.

2012-01-01

A continuum-level, dual internal state variable, thermodynamically based, work potential model, Schapery Theory, is used capture the effects of two matrix damage mechanisms in a fiber-reinforced laminated composite: microdamage and transverse cracking. Matrix microdamage accrues primarily in the form of shear microcracks between the fibers of the composite. Whereas, larger transverse matrix cracks typically span the thickness of a lamina and run parallel to the fibers. Schapery Theory uses the energy potential required to advance structural changes, associated with the damage mechanisms, to govern damage growth through a set of internal state variables. These state variables are used to quantify the stiffness degradation resulting from damage growth. The transverse and shear stiffness of the lamina are related to the internal state variables through a set of measurable damage functions. Additionally, the damage variables for a given strain state can be calculated from a set of evolution equations. These evolution equations and damage functions are implemented into the finite element method and used to govern the constitutive response of the material points in the model. Additionally, an axial failure criterion is included in the model. The response of a center-notched, buffer strip-stiffened panel subjected to uniaxial tension is investigated and results are compared to experiment.

Modeling the genealogy of a cultural trait.

PubMed

Aguilar, Elliot; Ghirlanda, Stefano

2015-05-01

The mathematical study of genealogies has yielded important insights in population biology, such as the ability to estimate the time to the most recent common ancestor (MRCA) of a sample of genetic sequences or of a group of individuals. Here we introduce a model of cultural genealogies that is a step toward answering similar questions for cultural traits. In our model individuals can inherit from a variable, potentially large number of ancestors, rather than from a fixed, small number of ancestors (one or two) as is typical of genetic evolution. We first show that, given a sample of individuals, a cultural common ancestor does not necessarily exist. We then introduce a related concept: the most recent unique ancestor (MRUA), i.e., the most recent single individual who is the earliest cultural ancestor of the sample. We show that, under neutral evolution, the time to the MRUA can be staggeringly larger than the time to MRCA in a single ancestor model, except when the average number of learning opportunities per individuals is small. Our results point out that the properties of cultural genealogies may be very different from those of genetic genealogies, with potential implications for reconstructing the histories of cultural traits. Copyright © 2014 Elsevier Inc. All rights reserved.

Large Eddy Simulation including population dynamics model for polydisperse droplet evolution

NASA Astrophysics Data System (ADS)

Aiyer, Aditya; Yang, Di; Chamecki, Marcelo; Meneveau, Charles

2017-11-01

Previous studies have shown that dispersion patterns of oil droplets in the ocean following a deep sea oil spill depend critically on droplet diameter. Hence predicting the evolution of the droplet size distribution is of critical importance for predicting macroscopic features of dispersion in the ocean. We adopt a population dynamics model of polydisperse droplet distributions for use in LES. We generalize a breakup model from Reynolds averaging approaches to LES in which the breakup is modeled as due to bombardment of droplets by turbulent eddies of various sizes. The breakage rate is expressed as an integral of a collision frequency times a breakage efficiency over all eddy sizes. An empirical fit to the integral is proposed in order to avoid having to recalculate the integral at every LES grid point and time step. The fit is tested by comparison with various stirred tank experiments. As a flow application for LES we consider a jet of bubbles and large droplets injected at the bottom of the tank. The advected velocity and concentration fields of the drops are described using an Eulerian approach. We study the change of the oil droplet distribution due to breakup caused by interaction of turbulence with the oil droplets. This research was made possible by a Grant from the Gulf of Mexico Research Initiative.

The Approach to Equilibrium in a Reflex Triode

DTIC Science & Technology

1990-09-24

once to yield dT ±---27yT"= ’, where y = d/A and the prime also denotes d/ de . The damping length scale is now just a parameter that can be obtained from...pressures near K2 which will figure in the gap shorting time, and the boundary condition evolution at the anode. Aside from the steady conduction...phase evolution of 77 to values near the sin- gular point, one finds that (from an operational point of view in fixing 3) all such auxillary physics

EVOLUTIONARY TRAJECTORIES OF ULTRACOMPACT 'BLACK WIDOW' PULSARS WITH VERY LOW MASS COMPANIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benvenuto, O. G.; De Vito, M. A.; Horvath, J. E., E-mail: obenvenu@fcaglp.unlp.edu.ar, E-mail: adevito@fcaglp.unlp.edu.ar, E-mail: foton@astro.iag.usp.br

The existence of millisecond pulsars with planet-mass companions in close orbits is challenging from the stellar evolution point of view. We calculate in detail the evolution of binary systems self-consistently, including mass transfer, evaporation, and irradiation of the donor by X-ray feedback, demonstrating the existence of a new evolutionary path leading to short periods and compact donors as required by the observations of PSR J1719-1438. We also point out the alternative of an exotic nature of the companion planet-mass star.

A sharp interface model for void growth in irradiated materials

NASA Astrophysics Data System (ADS)

Hochrainer, Thomas; El-Azab, Anter

2015-03-01

A thermodynamic formalism for the interaction of point defects with free surfaces in single-component solids has been developed and applied to the problem of void growth by absorption of point defects in irradiated metals. This formalism consists of two parts, a detailed description of the dynamics of defects within the non-equilibrium thermodynamic frame, and the application of the second law of thermodynamics to provide closure relations for all kinetic equations. Enforcing the principle of non-negative entropy production showed that the description of the problem of void evolution under irradiation must include a relationship between the normal fluxes of defects into the void surface and the driving thermodynamic forces for the void surface motion; these thermodynamic forces are identified for both vacancies and interstitials and the relationships between these forces and the normal point defect fluxes are established using the concepts of transition state theory. The latter theory implies that the defect accommodation into the surface is a thermally activated process. Numerical examples are given to illustrate void growth dynamics in this new formalism and to investigate the effect of the surface energy barriers on void growth. Consequences for phase field models of void growth are discussed.

Helium Star Models with Optically Thick Winds: Implications for the Internal Structures and Mass-loss Rates of Wolf–Rayet Stars

NASA Astrophysics Data System (ADS)

Nakauchi, Daisuke; Saio, Hideyuki

2018-01-01

We construct helium (He) star models with optically thick winds and compare them with the properties of Galactic Wolf–Rayet (WR) stars. Hydrostatic He-core solutions are connected smoothly to trans-sonic wind solutions that satisfy the regularity conditions at the sonic point. Velocity structures in the supersonic parts are assumed by a simple β-type law. By constructing a center-to-surface structure, a mass-loss rate {\\dot{M}}{{w}} can be obtained as an eigenvalue of the equations. Sonic points appear at temperatures ≈ (1.8{--}2.8)× {10}5 {{K}} below the Fe-group opacity peak, where the radiation force becomes comparable to the local gravity. Photospheres are located at radii 3–10 times larger than sonic points. The obtained mass-loss rates are comparable to those of WR stars. Our {\\dot{M}}{{w}}–luminosity relation agrees well with the relation recently obtained by Gräfener et al. Photospheric temperatures of WR stars tend to be cooler than our predictions. We discuss the effects of stellar evolution, detailed radiation transfer, and wind clumping, which are ignored in this paper.

Accurate segmentation framework for the left ventricle wall from cardiac cine MRI

NASA Astrophysics Data System (ADS)

Sliman, H.; Khalifa, F.; Elnakib, A.; Soliman, A.; Beache, G. M.; Gimel'farb, G.; Emam, A.; Elmaghraby, A.; El-Baz, A.

2013-10-01

We propose a novel, fast, robust, bi-directional coupled parametric deformable model to segment the left ventricle (LV) wall borders using first- and second-order visual appearance features. These features are embedded in a new stochastic external force that preserves the topology of LV wall to track the evolution of the parametric deformable models control points. To accurately estimate the marginal density of each deformable model control point, the empirical marginal grey level distributions (first-order appearance) inside and outside the boundary of the deformable model are modeled with adaptive linear combinations of discrete Gaussians (LCDG). The second order visual appearance of the LV wall is accurately modeled with a new rotationally invariant second-order Markov-Gibbs random field (MGRF). We tested the proposed segmentation approach on 15 data sets in 6 infarction patients using the Dice similarity coefficient (DSC) and the average distance (AD) between the ground truth and automated segmentation contours. Our approach achieves a mean DSC value of 0.926±0.022 and AD value of 2.16±0.60 compared to two other level set methods that achieve 0.904±0.033 and 0.885±0.02 for DSC; and 2.86±1.35 and 5.72±4.70 for AD, respectively.

Local Mechanical Response of Superelastic NiTi Shape-Memory Alloy Under Uniaxial Loading

NASA Astrophysics Data System (ADS)

Xiao, Yao; Zeng, Pan; Lei, Liping; Du, Hongfei

2015-11-01

In this paper, we focus on the local mechanical response of superelastic NiTi SMA at different temperatures under uniaxial loading. In situ DIC is applied to measure the local strain of the specimen. Based on the experimental results, two types of mechanical response, which are characterized with localized phase transformation and homogenous phase transformation, are identified, respectively. Motivated by residual strain accumulation phenomenon of the superelastic mechanical response, we conduct controlled experiments, and infer that for a given material point, all (or most) of the irreversibility is accumulated when the transformation front is traversing the material point. A robust constitutive model is established to explain the experimental phenomena and we successfully simulate the evolution of local strain that agrees closely with the experimental results.

Modelling of bio-morphodynamics in braided rivers: applications to the Waitaki river (New Zealand)

NASA Astrophysics Data System (ADS)

Stecca, G.; Zolezzi, G.; Hicks, M.; Measures, R.; Bertoldi, W.

2016-12-01

The planform shape of rivers results from the complex interaction between flow, sediment transport and vegetation processes, and can evolve in time following a change in these controls. The braided planform of the lower Waitaki (New Zealand), for instance, is endangered by the action of artificially-introduced alien vegetation, which spread after the reduction in magnitude of floods following hydropower dam construction. These processes, by favouring the flow concentration into the main channel, would likely promote a shift towards single thread morphology if vegetation was not artificially removed within a central fairway. The purpose of this work is to address the future evolution of these river systems under different management scenarios through two-dimensional numerical modelling. The construction of a suitable model represents a task in itself, since a modelling framework coupling all the relevant processes is not straightforwardly available at present. Our starting point is the GIAMT2D numerical model, solving two-dimensional flow and bedload transport in wet/dry domains, and recently modified by the inclusion of a rule-based bank erosion model. We further develop this model by adding a vegetation module, which accounts in a simplified manner for time-evolving biomass density, and tweaks the local flow roughness, critical shear stress for sediment transport and bank erodibility accordingly. We plan to apply the model to address the decadal-scale evolution of one reach in the Waitaki river, comparing different management scenarios for vegetation control.

Pre-relaxation in weakly interacting models

NASA Astrophysics Data System (ADS)

Bertini, Bruno; Fagotti, Maurizio

2015-07-01

We consider time evolution in models close to integrable points with hidden symmetries that generate infinitely many local conservation laws that do not commute with one another. The system is expected to (locally) relax to a thermal ensemble if integrability is broken, or to a so-called generalised Gibbs ensemble if unbroken. In some circumstances expectation values exhibit quasi-stationary behaviour long before their typical relaxation time. For integrability-breaking perturbations, these are also called pre-thermalisation plateaux, and emerge e.g. in the strong coupling limit of the Bose-Hubbard model. As a result of the hidden symmetries, quasi-stationarity appears also in integrable models, for example in the Ising limit of the XXZ model. We investigate a weak coupling limit, identify a time window in which the effects of the perturbations become significant and solve the time evolution through a mean-field mapping. As an explicit example we study the XYZ spin-\\frac{1}{2} chain with additional perturbations that break integrability. One of the most intriguing results of the analysis is the appearance of persistent oscillatory behaviour. To unravel its origin, we study in detail a toy model: the transverse-field Ising chain with an additional nonlocal interaction proportional to the square of the transverse spin per unit length (2013 Phys. Rev. Lett. 111 197203). Despite being nonlocal, this belongs to a class of models that emerge as intermediate steps of the mean-field mapping and shares many dynamical properties with the weakly interacting models under consideration.

Episodic sediment-discharge events in Cascade Springs, southern Black Hills, South Dakota

USGS Publications Warehouse

Hayes, Timothy Scott

1999-01-01

Cascade Springs is a group of artesian springs in the southern Black Hills, South Dakota, with collective flow of about 19.6 cubic feet per second. Beginning on February 28, 1992, a large discharge of red suspended sediment was observed from two of the six known discharge points. Similar events during 1906-07 and 1969 were documented by local residents and newspaper accounts. Mineralogic and grain-size analyses were performed to identify probable subsurface sources of the sediment. Geochemical modeling was performed to evaluate the geochemical evolution of water discharged from Cascade Springs. Interpretations of results provide a perspective on the role of artesian springs in the regional geohydrologic framework. X-ray diffraction mineralogic analyses of the clay fraction of the suspended sediment were compared to analyses of clay-fraction samples taken from nine geologic units at and stratigraphically below the spring-discharge points. Ongoing development of a subsurface breccia pipe(s) in the upper Minnelusa Formation and/or Opeche Shale was identified as a likely source of the suspended sediment; thus, exposed breccia pipes in lower Hell Canyon were examined. Upper Minnelusa Formation breccia pipes in lower Hell Canyon occur in clusters similar to the discrete discharge points of Cascade Springs. Grain-size analyses showed that breccia masses lack clay fractions and have coarser distributions than the wall rocks, which indicates that the red, fine-grained fractions have been carried out as suspended sediment. These findings support the hypothesis that many breccia pipes were formed as throats of abandoned artesian springs. Geochemical modeling was used to test whether geochemical evolution of ground water is consistent with this hypothesis. The evolution of water at Cascade Springs could not be suitably simulated using only upgradient water from the Minnelusa aquifer. A suitable model involved dissolution of anhydrite accompanied by dedolomitization in the upper Minnelusa Formation, which is caused by upward leakage of relatively fresh water from the Madison aquifer. The anhydrite dissolution and dedolomitization account for the net removal of minerals that would lead to breccia pipe formation by gravitational collapse. Breccia pipes in the lower Minnelusa Formation are uncommon; however, networks of interconnected breccia layers and breccia dikes are common. These networks, along with vertical fractures and faults, are likely pathways for transmitting upward leakage from the Madison aquifer. It is concluded that suspended sediment discharged at Cascade Springs probably results from episodic collapse brecciation that is caused by subsurface dissolution of anhydrite beds and cements of the upper Minnelusa Formation, accompanied by replacement of dolomite by calcite. It is further concluded that many breccia pipes probably are the throats of artesian springs that have been abandoned and exposed by erosion. The locations of artesian spring-discharge points probably have been shifting outwards from the center of the Black Hills uplift, essentially keeping pace with regional erosion over geologic time. Thus, artesian springflow probably is a factor in controlling water levels in the Madison and Minnelusa aquifers, with hydraulic head declining over geologic time, in response to development of new discharge points. Development of breccia pipes as throats of artesian springs would greatly enhance vertical hydraulic conductivity in the immediate vicinity of spring-discharge points. Horizontal hydraulic conductivity in the Minnelusa Formation also may be enhanced by dissolution processes related to upward leakage from the Madison aquifer. Potential processes could include dissolution resulting from leakage in the vicinity of breccia pipes that are abandoned spring throats, active spring discharge, development of subsurface breccias with no visible surface expression or spring discharge, as well as general areal leakage

Computer simulation of a cellular automata model for the immune response in a retrovirus system

NASA Astrophysics Data System (ADS)

Pandey, R. B.

1989-02-01

Immune response in a retrovirus system is modeled by a network of three binary cell elements to take into account some of the main functional features of T4 cells, T8 cells, and viruses. Two different intercell interactions are introduced, one of which leads to three fixed points while the other yields bistable fixed points oscillating between a healthy state and a sick state in a mean field treatment. Evolution of these cells is studied for quenched and annealed random interactions on a simple cubic lattice with a nearest neighbor interaction using inhomogenous cellular automata. Populations of T4 cells and viral cells oscillate together with damping (with constant amplitude) for annealed (quenched) interaction on increasing the value of mixing probability B from zero to a characteristic value B ca ( B cq). For higher B, the average number of T4 cells increases while that of the viral infected cells decreases monotonically on increasing B, suggesting a phase transition at B ca ( B cq).

Effects of axions on Population III stars

NASA Astrophysics Data System (ADS)

Choplin, Arthur; Coc, Alain; Meynet, Georges; Olive, Keith A.; Uzan, Jean-Philippe; Vangioni, Elisabeth

2017-09-01

Aims: Following the renewed interest in axions as a dark matter component, we revisit the effects of energy loss by axion emission on the evolution of the first generation of stars. These stars with zero metallicity are assumed to be massive, more compact, and hotter than subsequent generations. It is hence important to extend previous studies, which were restricted to solar metallicity stars. Methods: Our analysis first compares the evolution of solar metallicity 8, 10, and 12 M⊙ stars to previous work. We then calculate the evolution of 8 zero-metallicity stars with and without axion losses and with masses ranging from 20 to 150 M⊙. Results: For the solar metallicity models, we confirm the disappearance of the blue-loop phase for a value of the axion-photon coupling of gaγ = 10-10 GeV-1. We show that for gaγ = 10-10 GeV-1, the evolution of Population III stars is not much affected by axion losses, except within the range of masses 80-130 M⊙. Such stars show significant differences in both their tracks within the Tc-ρc diagram and their central composition (in particular 20Ne and 24Mg). We discuss the origin of these modifications from the stellar physics point of view, and also their potential observational signatures.

Predictive accuracy of particle filtering in dynamic models supporting outbreak projections.

PubMed

Safarishahrbijari, Anahita; Teyhouee, Aydin; Waldner, Cheryl; Liu, Juxin; Osgood, Nathaniel D

2017-09-26

While a new generation of computational statistics algorithms and availability of data streams raises the potential for recurrently regrounding dynamic models with incoming observations, the effectiveness of such arrangements can be highly subject to specifics of the configuration (e.g., frequency of sampling and representation of behaviour change), and there has been little attempt to identify effective configurations. Combining dynamic models with particle filtering, we explored a solution focusing on creating quickly formulated models regrounded automatically and recurrently as new data becomes available. Given a latent underlying case count, we assumed that observed incident case counts followed a negative binomial distribution. In accordance with the condensation algorithm, each such observation led to updating of particle weights. We evaluated the effectiveness of various particle filtering configurations against each other and against an approach without particle filtering according to the accuracy of the model in predicting future prevalence, given data to a certain point and a norm-based discrepancy metric. We examined the effectiveness of particle filtering under varying times between observations, negative binomial dispersion parameters, and rates with which the contact rate could evolve. We observed that more frequent observations of empirical data yielded super-linearly improved accuracy in model predictions. We further found that for the data studied here, the most favourable assumptions to make regarding the parameters associated with the negative binomial distribution and changes in contact rate were robust across observation frequency and the observation point in the outbreak. Combining dynamic models with particle filtering can perform well in projecting future evolution of an outbreak. Most importantly, the remarkable improvements in predictive accuracy resulting from more frequent sampling suggest that investments to achieve efficient reporting mechanisms may be more than paid back by improved planning capacity. The robustness of the results on particle filter configuration in this case study suggests that it may be possible to formulate effective standard guidelines and regularized approaches for such techniques in particular epidemiological contexts. Most importantly, the work tentatively suggests potential for health decision makers to secure strong guidance when anticipating outbreak evolution for emerging infectious diseases by combining even very rough models with particle filtering method.

Why does shear banding behave like first-order phase transitions? Derivation of a potential from a mechanical constitutive model.

PubMed

Sato, K; Yuan, X-F; Kawakatsu, T

2010-02-01

Numerous numerical and experimental evidence suggest that shear banding behavior looks like first-order phase transitions. In this paper, we demonstrate that this correspondence is actually established in the so-called non-local diffusive Johnson-Segalman model (the DJS model), a typical mechanical constitutive model that has been widely used for describing shear banding phenomena. In the neighborhood of the critical point, we apply the reduction procedure based on the center manifold theory to the governing equations of the DJS model. As a result, we obtain a time evolution equation of the flow field that is equivalent to the time-dependent Ginzburg-Landau (TDGL) equations for modeling thermodynamic first-order phase transitions. This result, for the first time, provides a mathematical proof that there is an analogy between the mechanical instability and thermodynamic phase transition at least in the vicinity of the critical point of the shear banding of DJS model. Within this framework, we can clearly distinguish the metastable branch in the stress-strain rate curve around the shear banding region from the globally stable branch. A simple extension of this analysis to a class of more general constitutive models is also discussed. Numerical simulations for the original DJS model and the reduced TDGL equation is performed to confirm the range of validity of our reduction theory.

Big-bounce cosmology from quantum gravity: The case of a cyclical Bianchi I universe

NASA Astrophysics Data System (ADS)

Moriconi, Riccardo; Montani, Giovanni; Capozziello, Salvatore

2016-07-01

We analyze the classical and quantum dynamics of a Bianchi I model in the presence of a small negative cosmological constant characterizing its evolution in term of the dust-time dualism. We demonstrate that in a canonical metric approach, the cosmological singularity is removed in correspondence to a positive defined value of the dust energy density. Furthermore, the quantum big bounce is connected to the Universe's turning point via a well-defined semiclassical limit. Then we can reliably infer that the proposed scenario is compatible with a cyclical universe picture. We also show how, when the contribution of the dust energy density is sufficiently high, the proposed scenario can be extended to the Bianchi IX cosmology and therefore how it can be regarded as a paradigm for the generic cosmological model. Finally, we investigate the origin of the observed cutoff on the cosmological dynamics, demonstrating how the big-bounce evolution can be mimicked by the same semiclassical scenario, where the negative cosmological constant is replaced via a polymer discretization of the Universe's volume. A direct proportionality law between these two parameters is then established.

Electrical Stressing Induced Monolayer Vacancy Island Growth on TiSe2

NASA Astrophysics Data System (ADS)

Zheng, Husong; Valtierra, Salvador; Ofori-Opoku, Nana; Chen, Chuanhui; Sun, Lifei; Yuan, Shuaishuai; Jiao, Liying; Bevan, Kirk H.; Tao, Chenggang

2018-03-01

To ensure the practical application of atomically thin transition metal dichalcogenides, it is essential to characterize their structural stability under external stimuli such as electric fields and currents. Using vacancy monolayer islands on TiSe2 surfaces as a model system, for the first time we have observed a shape evolution and growth from triangular to hexagonal driven by scanning tunneling microscopy (STM) electrical stressing. The size of islands shows linear growth with a rate of (3.00 +- 0.05) x 10-3 nm/s, when the STM scanning parameters are held fixed at Vs = 1.0 V and I = 1.8 nA. We further quantified how the growth rate is related to the tunneling current magnitude. Our simulations of monolayer island evolution using phase-field modeling are in good agreement with our experimental observations, and point towards preferential edge atom dissociation under STM scanning driving the observed growth. The results could be potentially important for device applications of ultrathin transition metal dichalcogenides and related 2D materials subject to electrical stressing under device operating conditions.

Irradiation-driven Mass Transfer Cycles in Compact Binaries

NASA Astrophysics Data System (ADS)

Büning, A.; Ritter, H.

2005-08-01

We elaborate on the analytical model of Ritter, Zhang, & Kolb (2000) which describes the basic physics of irradiation-driven mass transfer cycles in semi-detached compact binary systems. In particular, we take into account a contribution to the thermal relaxation of the donor star which is unrelated to irradiation and which was neglected in previous studies. We present results of simulations of the evolution of compact binaries undergoing mass transfer cycles, in particular also of systems with a nuclear evolved donor star. These computations have been carried out with a stellar evolution code which computes mass transfer implicitly and models irradiation of the donor star in a point source approximation, thereby allowing for much more realistic simulations than were hitherto possible. We find that low-mass X-ray binaries (LMXBs) and cataclysmic variables (CVs) with orbital periods ⪉ 6hr can undergo mass transfer cycles only for low angular momentum loss rates. CVs containing a giant donor or one near the terminal age main sequence are more stable than previously thought, but can possibly also undergo mass transfer cycles.

Feasibility and effectiveness of a brief, intensive phylogenetics workshop in a middle-income country.

PubMed

Pollett, S; Leguia, M; Nelson, M I; Maljkovic Berry, I; Rutherford, G; Bausch, D G; Kasper, M; Jarman, R; Melendrez, M

2016-01-01

There is an increasing role for bioinformatic and phylogenetic analysis in tropical medicine research. However, scientists working in low- and middle-income regions may lack access to training opportunities in these methods. To help address this gap, a 5-day intensive bioinformatics workshop was offered in Lima, Peru. The syllabus is presented here for others who want to develop similar programs. To assess knowledge gained, a 20-point knowledge questionnaire was administered to participants (21 participants) before and after the workshop, covering topics on sequence quality control, alignment/formatting, database retrieval, models of evolution, sequence statistics, tree building, and results interpretation. Evolution/tree-building methods represented the lowest scoring domain at baseline and after the workshop. There was a considerable median gain in total knowledge scores (increase of 30%, p<0.001) with gains as high as 55%. A 5-day workshop model was effective in improving the pathogen-applied bioinformatics knowledge of scientists working in a middle-income country setting. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Modeling Radiation Fog

NASA Astrophysics Data System (ADS)

K R, Sreenivas; Mohammad, Rafiuddin

2016-11-01

Predicting the fog-onset, its growth and dissipation helps in managing airports and other modes of transport. After sunset, occurrence of fog requires moist air, low wind and clear-sky conditions. Under these circumstances radiative heat transfer plays a vital role in the NBL. Locally, initiation of fog happens when the air temperature falls below the dew-point. Thus, to predict the onset of fog at a given location, one has to compute evolution of vertical temperature profile. Earlier,our group has shown that the presence of aerosols and vertical variation in their number density determines the radiative-cooling and hence development of vertical temperature profile. Aerosols, through radiation in the window-band, provides an efficient path for air layers to lose heat to the cold, upper atmosphere. This process creates cooler air layer between warmer ground and upper air layers and resulting temperature profile facilitate the initiation of fog. Our results clearly indicates that accounting for the presence of aerosols and their radiative-transfer is important in modeling micro-meteorological process of fog formation and its evolution. DST, Govt. INDIA.

Study of fatigue crack propagation in Ti-1Al-1Mn based on the calculation of cold work evolution

NASA Astrophysics Data System (ADS)

Plekhov, O. A.; Kostina, A. A.

2017-05-01

The work proposes a numerical method for lifetime assessment for metallic materials based on consideration of energy balance at crack tip. This method is based on the evaluation of the stored energy value per loading cycle. To calculate the stored and dissipated parts of deformation energy an elasto-plastic phenomenological model of energy balance in metals under the deformation and failure processes was proposed. The key point of the model is strain-type internal variable describing the stored energy process. This parameter is introduced based of the statistical description of defect evolution in metals as a second-order tensor and has a meaning of an additional strain due to the initiation and growth of the defects. The fatigue crack rate was calculated in a framework of a stationary crack approach (several loading cycles for every crack length was considered to estimate the energy balance at crack tip). The application of the proposed algorithm is illustrated by the calculation of the lifetime of the Ti-1Al-1Mn compact tension specimen under cyclic loading.

NIMROD resistive magnetohydrodynamic simulations of spheromak physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hooper, E. B.; Cohen, B. I.; McLean, H. S.

The physics of spheromak plasmas is addressed by time-dependent, three-dimensional, resistive magnetohydrodynamic simulations with the NIMROD code [C. R. Sovinec et al., J. Comput. Phys. 195, 355 (2004)]. Included in some detail are the formation of a spheromak driven electrostatically by a coaxial plasma gun with a flux-conserver geometry and power systems that accurately model the sustained spheromak physics experiment [R. D. Wood et al., Nucl. Fusion 45, 1582 (2005)]. The controlled decay of the spheromak plasma over several milliseconds is also modeled as the programmable current and voltage relax, resulting in simulations of entire experimental pulses. Reconnection phenomena andmore » the effects of current profile evolution on the growth of symmetry-breaking toroidal modes are diagnosed; these in turn affect the quality of magnetic surfaces and the energy confinement. The sensitivity of the simulation results addresses variations in both physical and numerical parameters, including spatial resolution. There are significant points of agreement between the simulations and the observed experimental behavior, e.g., in the evolution of the magnetics and the sensitivity of the energy confinement to the presence of symmetry-breaking magnetic fluctuations.« less

NIMROD Resistive Magnetohydrodynamic Simulations of Spheromak Physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hooper, E B; Cohen, B I; McLean, H S

The physics of spheromak plasmas is addressed by time-dependent, three-dimensional, resistive magneto-hydrodynamic simulations with the NIMROD code. Included in some detail are the formation of a spheromak driven electrostatically by a coaxial plasma gun with a flux-conserver geometry and power systems that accurately model the Sustained Spheromak Physics Experiment (SSPX) (R. D. Wood, et al., Nucl. Fusion 45, 1582 (2005)). The controlled decay of the spheromak plasma over several milliseconds is also modeled as the programmable current and voltage relax, resulting in simulations of entire experimental pulses. Reconnection phenomena and the effects of current profile evolution on the growth ofmore » symmetry-breaking toroidal modes are diagnosed; these in turn affect the quality of magnetic surfaces and the energy confinement. The sensitivity of the simulation results address variations in both physical and numerical parameters, including spatial resolution. There are significant points of agreement between the simulations and the observed experimental behavior, e.g., in the evolution of the magnetics and the sensitivity of the energy confinement to the presence of symmetry-breaking magnetic fluctuations.« less

Punishment in the form of shared cost promotes altruism in the cooperative dilemma games.

PubMed

Zhang, Chunyan; Zhu, Yuying; Chen, Zengqiang; Zhang, Jianlei

2017-05-07

One phenomenon or social institution often observed in multi-agent interactions is the altruistic punishment, i.e. the punishment of unfair behavior by others at a personal cost. Inspired by the works focusing on punishment and the intricate mechanism behind it, we theoretically study the strategy evolution in the framework of two-strategy game models with the punishment on defectors, moreover, the cost of punishing will be evenly shared among the cooperators. Theoretical computations suggest that larger punishment on defectors or smaller punishment cost incurred by cooperators will enhance the fixation of altruistic cooperation in the population. Through the replicate dynamics, the group size of the randomly selected individuals from the sufficiently large population will notably affect the strategy evolution in populations nested within a dilemma. By theoretical modeling the concept of shared cost for punishment from one point of view, our findings underscore the importance of punishment with shared cost as a factor in real-life decisions in an evolutionary game context. Copyright © 2017 Elsevier Ltd. All rights reserved.

Resolving the evolution of sterile worker castes: a window on the advantages and disadvantages of monogamy

PubMed Central

Nonacs, Peter

2014-01-01

Many social Hymenoptera species have morphologically sterile worker castes. It is proposed that the evolutionary routes to this obligate sterility must pass through a ‘monogamy window’, because inclusive fitness favours individuals retaining their reproductive totipotency unless they can rear full siblings. Simulated evolution of sterility, however, finds that ‘point of view’ is critically important. Monogamy is facilitating if sterility is expressed altruistically (i.e. workers defer reproduction to queens), but if sterility results from manipulation by mothers or siblings, monogamy may have no effect or lessen the likelihood of sterility. Overall, the model and data from facultatively eusocial bees suggest that eusociality and sterility are more likely to originate through manipulation than by altruism, casting doubt on a mandatory role for monogamy. Simple kin selection paradigms, such as Hamilton's rule, can also fail to account for significant evolutionary dynamics created by factors, such as population structure, group-level effects or non-random mating patterns. The easy remedy is to always validate apparently insightful predictions from Hamiltonian equations with life-history appropriate genetic models. PMID:24647729

Resolving the evolution of sterile worker castes: a window on the advantages and disadvantages of monogamy.

PubMed

Nonacs, Peter

2014-03-01

Many social Hymenoptera species have morphologically sterile worker castes. It is proposed that the evolutionary routes to this obligate sterility must pass through a 'monogamy window', because inclusive fitness favours individuals retaining their reproductive totipotency unless they can rear full siblings. Simulated evolution of sterility, however, finds that 'point of view' is critically important. Monogamy is facilitating if sterility is expressed altruistically (i.e. workers defer reproduction to queens), but if sterility results from manipulation by mothers or siblings, monogamy may have no effect or lessen the likelihood of sterility. Overall, the model and data from facultatively eusocial bees suggest that eusociality and sterility are more likely to originate through manipulation than by altruism, casting doubt on a mandatory role for monogamy. Simple kin selection paradigms, such as Hamilton's rule, can also fail to account for significant evolutionary dynamics created by factors, such as population structure, group-level effects or non-random mating patterns. The easy remedy is to always validate apparently insightful predictions from Hamiltonian equations with life-history appropriate genetic models.

Holokinetic centromeres and efficient telomere healing enable rapid karyotype evolution.

PubMed

Jankowska, Maja; Fuchs, Jörg; Klocke, Evelyn; Fojtová, Miloslava; Polanská, Pavla; Fajkus, Jiří; Schubert, Veit; Houben, Andreas

2015-12-01

Species with holocentric chromosomes are often characterized by a rapid karyotype evolution. In contrast to species with monocentric chromosomes where acentric fragments are lost during cell division, breakage of holocentric chromosomes creates fragments with normal centromere activity. To decipher the mechanism that allows holocentric species an accelerated karyotype evolution via chromosome breakage, we analyzed the chromosome complements of irradiated Luzula elegans plants. The resulting chromosomal fragments and rearranged chromosomes revealed holocentromere-typical CENH3 and histone H2AThr120ph signals as well as the same mitotic mobility like unfragmented chromosomes. Newly synthesized telomeres at break points become detectable 3 weeks after irradiation. The presence of active telomerase suggests a telomerase-based mechanism of chromosome healing. A successful transmission of holocentric chromosome fragments across different generations was found for most offspring of irradiated plants. Hence, a combination of holokinetic centromere activity and the fast formation of new telomeres at break points enables holocentric species a rapid karyotype evolution involving chromosome fissions and rearrangements.

Complex Interaction Mechanisms between Dislocations and Point Defects Studied in Pure Aluminium by a Two-Wave Acoustic Coupling Technique

NASA Astrophysics Data System (ADS)

Bremnes, O.; Progin, O.; Gremaud, G.; Benoit, W.

1997-04-01

Ultrasonic experiments using a two-wave coupling technique were performed on 99.999% pure Al in order to study the interaction mechanisms occurring between dislocations and point defects. The coupling technique consists in measuring the attenuation of ultrasonic waves during low-frequency stress cycles (t). One obtains closed curves () called signatures whose shape and evolution are characteristic of the interaction mechanism controlling the low-frequency dislocation motion. The signatures observed were attributed to the interaction of the dislocations with extrinsic point defects. A new interpretation of the evolution of the signatures measured below 200 K with respect to temperature and stress frequency had to be established: they are linked to depinning of immobile point defects, whereas a thermally activated depinning mechanism does not fit the observations. The signatures measured between 200 and 370 K were interpreted as dragging and depinning of extrinsic point defects which are increasingly mobile with temperature.

Evolution of branch points for a laser beam propagating through an uplink turbulent atmosphere.

PubMed

Ge, Xiao-Lu; Liu, Xuan; Guo, Cheng-Shan

2014-03-24

Evolution of branch points in the distorted optical field is studied when a laser beam propagates through turbulent atmosphere along an uplink path. Two categories of propagation events are mainly explored for the same propagation height: fixed wavelength with change of the turbulence strength and fixed turbulence strength with change of the wavelength. It is shown that, when the beam propagates to a certain height, the density of the branch-points reaches its maximum and such a height changes with the turbulence strength but nearly remains constant with different wavelengths. The relationship between the density of branch-points and the Rytov number is also given. A fitted formula describing the relationship between the density of branch-points and propagation height with different turbulence strength and wavelength is found out. Interestingly, this formula is very similar to the formula used for describing the Blackbody radiation in physics. The results obtained may be helpful for atmospheric optics, astronomy and optical communication.

Adiabatic Mass Loss Model in Binary Stars

NASA Astrophysics Data System (ADS)

Ge, H. W.

2012-07-01

Rapid mass transfer process in the interacting binary systems is very complicated. It relates to two basic problems in the binary star evolution, i.e., the dynamically unstable Roche-lobe overflow and the common envelope evolution. Both of the problems are very important and difficult to be modeled. In this PhD thesis, we focus on the rapid mass loss process of the donor in interacting binary systems. The application to the criterion of dynamically unstable mass transfer and the common envelope evolution are also included. Our results based on the adiabatic mass loss model could be used to improve the binary evolution theory, the binary population synthetic method, and other related aspects. We build up the adiabatic mass loss model. In this model, two approximations are included. The first one is that the energy generation and heat flow through the stellar interior can be neglected, hence the restructuring is adiabatic. The second one is that he stellar interior remains in hydrostatic equilibrium. We model this response by constructing model sequences, beginning with a donor star filling its Roche lobe at an arbitrary point in its evolution, holding its specific entropy and composition profiles fixed. These approximations are validated by the comparison with the time-dependent binary mass transfer calculations and the polytropic model for low mass zero-age main-sequence stars. In the dynamical time scale mass transfer, the adiabatic response of the donor star drives it to expand beyond its Roche lobe, leading to runaway mass transfer and the formation of a common envelope with its companion star. For donor stars with surface convection zones of any significant depth, this runaway condition is encountered early in mass transfer, if at all; but for main sequence stars with radiative envelopes, it may be encountered after a prolonged phase of thermal time scale mass transfer, so-called delayed dynamical instability. We identify the critical binary mass ratio for the onset of dynamical time scale mass transfer; if the ratio of donor to accretor masses exceeds this critical value, the dynamical time scale mass transfer ensues. The grid of criterion for all stars can be used to be the basic input as the binary population synthetic method, which will be improved absolutely. In common envelope evolution, the dissipation of orbital energy of the binary provides the energy to eject the common envelope; the energy budget for this process essentially consists of the initial orbital energy of the binary and the initial binding energies of the binary components. We emphasize that, because stellar core and envelope contribute mutually to each other's gravitational potential energy, proper evaluation of the total energy of a star requires integration over the entire stellar interior, not the ejected envelope alone as commonly assumed. We show that the change in total energy of the donor star, as a function of its remaining mass along an adiabatic mass-loss sequence, can be calculated. This change in total energy of the donor star, combined with the requirement that both remnant donor and its companion star fit within their respective Roche lobes, then circumscribes energetically possible survivors of common envelope evolution. It is the first time that we can calculate the accurate total energy of the donor star in common envelope evolution, while the results with the old method are inconsistent with observations.

Geomorphometric reconstruction of post-eruptive surfaces of the Virunga Volcanic Province (East African Rift), constraint of erosion ratio and relative chronology

NASA Astrophysics Data System (ADS)

Lahitte, Pierre; Poppe, Sam; Kervyn, Matthieu

2016-04-01

Quaternary volcanic landforms result from a complex evolution, involving volcanic constructional events and destructive ones by collapses and long-term erosion. Quantification, by morphometric approaches, of the evolution through time of the volcano shape allows the estimation of relative ages between volcanoes sharing the same climate and eruptive conditions. We apply such method to six volcanoes of the Virunga Volcanic Province in the western branch of the East African Rift Valley that still has rare geochronological constraints. As they have comparable sizes, volcanic history and erupted products, these edifices may have undergone comparable conditions of erosion which justify the deduction of relative chronology from their erosion pattern. Our GIS-based geomorphometric approach, the SHAPEVOLC algorithm, quantifies erupted or dismantled volumes by numerically modeling topographies resulting from the eruptive construction of each volcano. Constraining points are selected by analyses of morphometric properties of each cell of the current DEM, as the loci where the altitude is still representative of the un-eroded volcanic surfaces. A primary elevation surface is firstly adjusted to these constraining points by modeling a first-order pseudo-radial surface defined by: 1. the curve best fitting the concave-upwards volcano profile; 2. the location and elevation of the volcano summit; and 3. the possible eccentricity and azimuth parameters that allow to stretch and contract contours to adjust the shape of the model to the elliptically-shaped surface of the volcano. A second-order surface is next computed by local adjustment of the first-order surface to the constraining points to obtain the definitive primary elevation surface of the considered volcanic construct. Amount of erosion is obtained by summing the difference in elevation between reconstructed surfaces and current ones that allows to establish relative ages of volcanoes. For the 6 studied Virunga volcanoes, the ratio of the dismantled volume vs. initial volume ranges between 5 to 30 % and up to almost 40 % if volumes removed by landslides are considered. The most preserved volcano is the New Mikeno erupted inside the landslide having affected the older stage of this volcano, whereas the most dismantled one is the Sabinyo volcano. The three-pointed star-like erosion pattern with main valleys having more or less the same orientation, which was observed on four volcanoes, may point to a strong constraint of the erosion processes by the regional tectonic pattern.

Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution

DTIC Science & Technology

2012-05-01

Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution Hyung-June Woo, Ravi Vijaya Satya, Jaques Reifman* DoD Biotechnology High...polymerases are above, near, and below a critical point, respectively. The prebiotic evolution therefore must have crossed this critical region. Over...among many potential oligomers capable of templated replication, RNAs may have evolved to form prebiotic genomes due to the value of their nonenzymatic

Modeling Progressive Damage Using Local Displacement Discontinuities Within the FEAMAC Multiscale Modeling Framework

NASA Technical Reports Server (NTRS)

Ranatunga, Vipul; Bednarcyk, Brett A.; Arnold, Steven M.

2010-01-01

A method for performing progressive damage modeling in composite materials and structures based on continuum level interfacial displacement discontinuities is presented. The proposed method enables the exponential evolution of the interfacial compliance, resulting in unloading of the tractions at the interface after delamination or failure occurs. In this paper, the proposed continuum displacement discontinuity model has been used to simulate failure within both isotropic and orthotropic materials efficiently and to explore the possibility of predicting the crack path, therein. Simulation results obtained from Mode-I and Mode-II fracture compare the proposed approach with the cohesive element approach and Virtual Crack Closure Techniques (VCCT) available within the ABAQUS (ABAQUS, Inc.) finite element software. Furthermore, an eccentrically loaded 3-point bend test has been simulated with the displacement discontinuity model, and the resulting crack path prediction has been compared with a prediction based on the extended finite element model (XFEM) approach.

Forest structure analysis combining laser scanning with digital airborne photogrammetry

NASA Astrophysics Data System (ADS)

Lissak, Candide; Onda, Yuichi; Kato, Hiroaki

2017-04-01

The interest of Light Detection and Ranging (LiDAR) for vegetation structure analysis has been demonstrated in several research context. Indeed, airborne or ground Lidar surveys can provide detailed three-dimensional data of the forest structure from understorey forest to the canopy. To characterize at different timescale the vegetation components in dense cedar forests we can combine several sources point clouds from Lidar survey and photogrammetry data. For our study, Terrestrial Laser Scanning (TLS-Leica ScanStation C10 processed with Cyclone software) have been lead in three forest areas (≈ 200m2 each zone) mainly composed of japanese cedar (Japonica cryptomeria), in the region of Fukushima (Japan). The study areas are characterized by various vegetation densities. For the 3 areas, Terrestrial laser scanning has been performed from several location points and several heights. Various floors shootings (ground, 4m, 6m and 18m high) were able with the use of a several meters high tower implanted to study the canopy evolution following the Fukushima Daiishi nuclear power plant accident. The combination of all scanners provides a very dense 3D point cloud of ground and canopy structure (average 300 000 000 points). For the Tochigi forest area, a first test of a low-cost Unmanned Aerial Vehicle (UAV) photogrammetry has been lead and calibrated by ground GPS measurements to determine the coordinates of points. TLS combined to UAV photogrammetry make it possible to obtain information on vertical and horizontal structure of the Tochigi forest. This combination of technologies will allow the forest structure mapping, morphometry analysis and the assessment of biomass volume evolution from multi-temporal point clouds. In our research, we used a low-cost UAV 3 Advanced (200 m2 cover, 1300 pictures...). Data processing were performed using PotoScan Pro software to obtain a very dense point clouds to combine to TLS data set. This low-cost UAV photogrammetry data has been successfully used to derive information on the canopy cover. The purpose of this poster is to present the usability of combined remote sensing methods for forest structure analysis and 3D model reconstitution for a trend analysis of the forest changes.

Modelling the temperature evolution of bone under high intensity focused ultrasound

NASA Astrophysics Data System (ADS)

ten Eikelder, H. M. M.; Bošnački, D.; Elevelt, A.; Donato, K.; Di Tullio, A.; Breuer, B. J. T.; van Wijk, J. H.; van Dijk, E. V. M.; Modena, D.; Yeo, S. Y.; Grüll, H.

2016-02-01

Magnetic resonance-guided high intensity focused ultrasound (MR-HIFU) has been clinically shown to be effective for palliative pain management in patients suffering from skeletal metastasis. The underlying mechanism is supposed to be periosteal denervation caused by ablative temperatures reached through ultrasound heating of the cortex. The challenge is exact temperature control during sonication as MR-based thermometry approaches for bone tissue are currently not available. Thus, in contrast to the MR-HIFU ablation of soft tissue, a thermometry feedback to the HIFU is lacking, and the treatment of bone metastasis is entirely based on temperature information acquired in the soft tissue adjacent to the bone surface. However, heating of the adjacent tissue depends on the exact sonication protocol and requires extensive modelling to estimate the actual temperature of the cortex. Here we develop a computational model to calculate the spatial temperature evolution in bone and the adjacent tissue during sonication. First, a ray-tracing technique is used to compute the heat production in each spatial point serving as a source term for the second part, where the actual temperature is calculated as a function of space and time by solving the Pennes bio-heat equation. Importantly, our model includes shear waves that arise at the bone interface as well as all geometrical considerations of transducer and bone geometry. The model was compared with a theoretical approach based on the far field approximation and an MR-HIFU experiment using a bone phantom. Furthermore, we investigated the contribution of shear waves to the heat production and resulting temperatures in bone. The temperature evolution predicted by our model was in accordance with the far field approximation and agreed well with the experimental data obtained in phantoms. Our model allows the simulation of the HIFU treatments of bone metastasis in patients and can be extended to a planning tool prior to MR-HIFU treatments.

Spatiotemporal Evolution of Ebola Virus Disease at Sub-National Level during the 2014 West Africa Epidemic: Model Scrutiny and Data Meagreness.

PubMed

Santermans, Eva; Robesyn, Emmanuel; Ganyani, Tapiwa; Sudre, Bertrand; Faes, Christel; Quinten, Chantal; Van Bortel, Wim; Haber, Tom; Kovac, Thomas; Van Reeth, Frank; Testa, Marco; Hens, Niel; Plachouras, Diamantis

2016-01-01

The Ebola outbreak in West Africa has infected at least 27,443 individuals and killed 11,207, based on data until 24 June, 2015, released by the World Health Organization (WHO). This outbreak has been characterised by extensive geographic spread across the affected countries Guinea, Liberia and Sierra Leone, and by localized hotspots within these countries. The rapid recognition and quantitative assessment of localised areas of higher transmission can inform the optimal deployment of public health resources. A variety of mathematical models have been used to estimate the evolution of this epidemic, and some have pointed out the importance of the spatial heterogeneity apparent from incidence maps. However, little is known about the district-level transmission. Given that many response decisions are taken at sub-national level, the current study aimed to investigate the spatial heterogeneity by using a different modelling framework, built on publicly available data at district level. Furthermore, we assessed whether this model could quantify the effect of intervention measures and provide predictions at a local level to guide public health action. We used a two-stage modelling approach: a) a flexible spatiotemporal growth model across all affected districts and b) a deterministic SEIR compartmental model per district whenever deemed appropriate. Our estimates show substantial differences in the evolution of the outbreak in the various regions of Guinea, Liberia and Sierra Leone, illustrating the importance of monitoring the outbreak at district level. We also provide an estimate of the time-dependent district-specific effective reproduction number, as a quantitative measure to compare transmission between different districts and give input for informed decisions on control measures and resource allocation. Prediction and assessing the impact of control measures proved to be difficult without more accurate data. In conclusion, this study provides us a useful tool at district level for public health, and illustrates the importance of collecting and sharing data.

Phase diagram and quench dynamics of the cluster-XY spin chain

NASA Astrophysics Data System (ADS)

Montes, Sebastián; Hamma, Alioscia

2012-08-01

We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

Autonomous multispecies reaction-diffusion systems with more-than-two-site interactions

NASA Astrophysics Data System (ADS)

Shariati, Ahmad; Aghamohammadi, Amir; Khorrami, Mohammad

2001-12-01

Autonomous multispecies systems with more-than-two-neighbor interactions are studied. Conditions necessary and sufficient for the closedness of the evolution equations of the n-point functions are obtained. The average numbers of the particles at each site for one species and three-site interactions, and its generalization to the more-than-three-site interactions, are explicitly obtained. Generalizations of the Glauber model in different directions, using generalized rates, generalized numbers of states at each site, and generalized numbers of interacting sites, are also investigated.

A nonlinear wave equation in nonadiabatic flame propagation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Booty, M.R.; Matalon, M.; Matkowsky, B.J.

1988-06-01

The authors derive a nonlinear wave equation from the diffusional thermal model of gaseous combustion to describe the evolution of a flame front. The equation arises as a long wave theory, for values of the volumeric heat loss in a neighborhood of the extinction point (beyond which planar uniformly propagating flames cease to exist), and for Lewis numbers near the critical value beyond which uniformly propagating planar flames lose stability via a degenerate Hopf bifurcation. Analysis of the equation suggests the possibility of a singularity developing in finite time.

Phase diagram and quench dynamics of the cluster-XY spin chain.

PubMed

Montes, Sebastián; Hamma, Alioscia

2012-08-01

We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

Sensory exploitation and sexual conflict

PubMed Central

Arnqvist, Göran

2006-01-01

Much of the literature on male–female coevolution concerns the processes by which male traits and female preferences for these can coevolve and be maintained by selection. There has been less explicit focus on the origin of male traits and female preferences. Here, I argue that it is important to distinguish origin from subsequent coevolution and that insights into the origin can help us appreciate the relative roles of various coevolutionary processes for the evolution of diversity in sexual dimorphism. I delineate four distinct scenarios for the origin of male traits and female preferences that build on past contributions, two of which are based on pre-existing variation in quality indicators among males and two on exploitation of pre-existing sensory biases among females. Recent empirical research, and theoretical models, suggest that origin by sensory exploitation has been widespread. I argue that this points to a key, but perhaps transient, role for sexually antagonistic coevolution (SAC) in the subsequent evolutionary elaboration of sexual traits, because (i) sensory exploitation is often likely to be initially costly for individuals of the exploited sex and (ii) the subsequent evolution of resistance to sensory exploitation should often be associated with costs due to selective constraints. A review of a few case studies is used to illustrate these points. Empirical data directly relevant to the costs of being sensory exploited and the costs of evolving resistance is largely lacking, and I stress that such data would help determining the general importance of sexual conflict and SAC for the evolution of sexual dimorphism. PMID:16612895

Pulse phase-coherent timing and spectroscopy of CXOU J164710.2-45521 outbursts

NASA Astrophysics Data System (ADS)

Rodríguez Castillo, Guillermo A.; Israel, Gian Luca; Esposito, Paolo; Pons, José A.; Rea, Nanda; Turolla, Roberto; Viganò, Daniele; Zane, Silvia

2014-06-01

We present a long-term phase-coherent timing analysis and pulse-phase resolved spectroscopy for the two outbursts observed from the transient anomalous X-ray pulsar CXOU J164710.2-455216. For the first outburst we used 11 Chandra and XMM-Newton observations between 2006 September and 2009 August, the longest baseline yet for this source. We obtain a coherent timing solution with P = 10.61065583(4) s, Ṗ = 9.72(1) × 10-13 s s-1 and P̈ = -1.05(5) × 10-20 s s-2. Under the standard assumptions this implies a surface dipolar magnetic field of ˜1014 G, confirming this source as a standard B magnetar. We also study the evolution of the pulse profile (shape, intensity and pulsed fraction) as a function of time and energy. Using the phase-coherent timing solution we perform a phase-resolved spectroscopy analysis, following the spectral evolution of pulse-phase features, which hints at the physical processes taking place on the star. The results are discussed from the perspective of magnetothermal evolution models and the untwisting magnetosphere model. Finally, we present similar analysis for the second, less intense, 2011 outburst. For the timing analysis we used Swift data together with 2 XMM-Newton and Chandra pointings. The results inferred for both outbursts are compared and briefly discussed in a more general framework.

Differential Adhesion between Moving Particles as a Mechanism for the Evolution of Social Groups

PubMed Central

Garcia, Thomas; Brunnet, Leonardo Gregory; De Monte, Silvia

2014-01-01

The evolutionary stability of cooperative traits, that are beneficial to other individuals but costly to their carrier, is considered possible only through the establishment of a sufficient degree of assortment between cooperators. Chimeric microbial populations, characterized by simple interactions between unrelated individuals, restrain the applicability of standard mechanisms generating such assortment, in particular when cells disperse between successive reproductive events such as happens in Dicyostelids and Myxobacteria. In this paper, we address the evolutionary dynamics of a costly trait that enhances attachment to others as well as group cohesion. By modeling cells as self-propelled particles moving on a plane according to local interaction forces and undergoing cycles of aggregation, reproduction and dispersal, we show that blind differential adhesion provides a basis for assortment in the process of group formation. When reproductive performance depends on the social context of players, evolution by natural selection can lead to the success of the social trait, and to the concomitant emergence of sizeable groups. We point out the conditions on the microscopic properties of motion and interaction that make such evolutionary outcome possible, stressing that the advent of sociality by differential adhesion is restricted to specific ecological contexts. Moreover, we show that the aggregation process naturally implies the existence of non-aggregated particles, and highlight their crucial evolutionary role despite being largely neglected in theoretical models for the evolution of sociality. PMID:24586133

Professionals' views on the development process of a structural collaboration between child and adolescent psychiatry and child welfare: an exploration through the lens of the life cycle model.

PubMed

Van den Steene, Helena; van West, Dirk; Peeraer, Griet; Glazemakers, Inge

2018-03-23

This study, as a part of a participatory action research project, reports the development process of an innovative collaboration between child and adolescent psychiatry and child welfare, for adolescent girls with multiple and complex needs. The findings emerge from a qualitative descriptive analysis of four focus groups with 30 professionals closely involved in this project, and describe the evolution of the collaborative efforts and outcomes through time. Participants describe large investments and negative consequences of rapid organizational change in the beginning of the collaboration project, while benefits of the intensive collaboration only appeared later. A shared person-centred vision and enhanced professionals' confidence were pointed out as important contributors in the evolution of the collaboration. Findings were compared to the literature and showed significant analogy with the life cycle model for shared service centres that describe the maturation of collaborations from a management perspective. These findings enrich the knowledge about the development process of collaboration in health and social care. In increasingly collaborative services, child and adolescent psychiatrists and policy makers should be aware that gains from a collaboration will possibly only be achieved in the longer term, and benefit from knowing which factors have an influence on the evolution of a collaboration project.

Generalized Brans-Dicke theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Felice, Antonio; Tsujikawa, Shinji, E-mail: defelice@rs.kagu.tus.ac.jp, E-mail: shinji@rs.kagu.tus.ac.jp

2010-07-01

In Brans-Dicke theory a non-linear self interaction of a scalar field φ allows a possibility of realizing the late-time cosmic acceleration, while recovering the General Relativistic behavior at early cosmological epochs. We extend this to more general modified gravitational theories in which a de Sitter solution for dark energy exists without using a field potential. We derive a condition for the stability of the de Sitter point and study the background cosmological dynamics of such theories. We also restrict the allowed region of model parameters from the demand for the avoidance of ghosts and instabilities. A peculiar evolution of themore » field propagation speed allows us to distinguish those theories from the ΛCDM model.« less

Network evolution model for supply chain with manufactures as the core.

PubMed

Fang, Haiyang; Jiang, Dali; Yang, Tinghong; Fang, Ling; Yang, Jian; Li, Wu; Zhao, Jing

2018-01-01

Building evolution model of supply chain networks could be helpful to understand its development law. However, specific characteristics and attributes of real supply chains are often neglected in existing evolution models. This work proposes a new evolution model of supply chain with manufactures as the core, based on external market demand and internal competition-cooperation. The evolution model assumes the external market environment is relatively stable, considers several factors, including specific topology of supply chain, external market demand, ecological growth and flow conservation. The simulation results suggest that the networks evolved by our model have similar structures as real supply chains. Meanwhile, the influences of external market demand and internal competition-cooperation to network evolution are analyzed. Additionally, 38 benchmark data sets are applied to validate the rationality of our evolution model, in which, nine manufacturing supply chains match the features of the networks constructed by our model.

Network evolution model for supply chain with manufactures as the core

PubMed Central

Jiang, Dali; Fang, Ling; Yang, Jian; Li, Wu; Zhao, Jing

2018-01-01

Building evolution model of supply chain networks could be helpful to understand its development law. However, specific characteristics and attributes of real supply chains are often neglected in existing evolution models. This work proposes a new evolution model of supply chain with manufactures as the core, based on external market demand and internal competition-cooperation. The evolution model assumes the external market environment is relatively stable, considers several factors, including specific topology of supply chain, external market demand, ecological growth and flow conservation. The simulation results suggest that the networks evolved by our model have similar structures as real supply chains. Meanwhile, the influences of external market demand and internal competition-cooperation to network evolution are analyzed. Additionally, 38 benchmark data sets are applied to validate the rationality of our evolution model, in which, nine manufacturing supply chains match the features of the networks constructed by our model. PMID:29370201

On the radial evolution of reflection-driven turbulence in the inner solar wind in preparation for Parker Solar Probe

NASA Astrophysics Data System (ADS)

Perez, J. C.; Chandran, B. D. G.

2017-12-01

In this work we present recent results from high-resolution direct numerical simulations and a phenomenological model that describes the radial evolution of reflection-driven Alfven Wave turbulence in the solar atmosphere and the inner solar wind. The simulations are performed inside a narrow magnetic flux tube that models a coronal hole extending from the solar surface through the chromosphere and into the solar corona to approximately 21 solar radii. The simulations include prescribed empirical profiles that account for the inhomogeneities in density, background flow, and the background magnetic field present in coronal holes. Alfven waves are injected into the solar corona by imposing random, time-dependent velocity and magnetic field fluctuations at the photosphere. The phenomenological model incorporates three important features observed in the simulations: dynamic alignment, weak/strong nonlinear AW-AW interactions, and that the outward-propagating AWs launched by the Sun split into two populations with different characteristic frequencies. Model and simulations are in good agreement and show that when the key physical parameters are chosen within observational constraints, reflection-driven Alfven turbulence is a plausible mechanism for the heating and acceleration of the fast solar wind. By flying a virtual Parker Solar Probe (PSP) through the simulations, we will also establish comparisons between the model and simulations with the kind of single-point measurements that PSP will provide.

A Markovian model market—Akerlof's lemons and the asymmetry of information

NASA Astrophysics Data System (ADS)

Tilles, Paulo F. C.; Ferreira, Fernando F.; Francisco, Gerson; Pereira, Carlos de B.; Sarti, Flavia M.

2011-07-01

In this work we study an agent based model to investigate the role of asymmetric information degrees for market evolution. This model is quite simple and may be treated analytically since the consumers evaluate the quality of a certain good taking into account only the quality of the last good purchased plus her perceptive capacity β. As a consequence, the system evolves according to a stationary Markov chain. The value of a good offered by the firms increases along with quality according to an exponent α, which is a measure of the technology. It incorporates all the technological capacity of the production systems such as education, scientific development and techniques that change the productivity rates. The technological level plays an important role to explain how the asymmetry of information may affect the market evolution in this model. We observe that, for high technological levels, the market can detect adverse selection. The model allows us to compute the maximum asymmetric information degree before the market collapses. Below this critical point the market evolves during a limited period of time and then dies out completely. When β is closer to 1 (symmetric information), the market becomes more profitable for high quality goods, although high and low quality markets coexist. The maximum asymmetric information level is a consequence of an ergodicity breakdown in the process of quality evaluation.

Investigating ice cliff evolution and contribution to glacier mass-balance using a physically-based dynamic model

NASA Astrophysics Data System (ADS)

Buri, Pascal; Miles, Evan; Ragettli, Silvan; Brun, Fanny; Steiner, Jakob; Pellicciotti, Francesca

2016-04-01

Supraglacial cliffs are a surface feature typical of debris-covered glaciers, affecting surface evolution, glacier downwasting and mass balance by providing a direct ice-atmosphere interface. As a result, melt rates can be very high and ice cliffs may account for a significant portion of the total glacier mass loss. However, their contribution to glacier mass balance has rarely been quantified through physically-based models. Most cliff energy balance models are point scale models which calculate energy fluxes at individual cliff locations. Results from the only grid based model to date accurately reflect energy fluxes and cliff melt, but modelled backwasting patterns are in some cases unrealistic, as the distribution of melt rates would lead to progressive shallowing and disappearance of cliffs. Based on a unique multitemporal dataset of cliff topography and backwasting obtained from high-resolution terrestrial and aerial Structure-from-Motion analysis on Lirung Glacier in Nepal, it is apparent that cliffs exhibit a range of behaviours but most do not rapidly disappear. The patterns of evolution cannot be explained satisfactorily by atmospheric melt alone, and are moderated by the presence of supraglacial ponds at the base of cliffs and by cliff reburial with debris. Here, we document the distinct patterns of evolution including disappearance, growth and stability. We then use these observations to improve the grid-based energy balance model, implementing periodic updates of the cliff geometry resulting from modelled melt perpendicular to the ice surface. Based on a slope threshold, pixels can be reburied by debris or become debris-free. The effect of ponds are taken into account through enhanced melt rates in horizontal direction on pixels selected based on an algorithm considering distance to the water surface, slope and lake level. We use the dynamic model to first study the evolution of selected cliffs for which accurate, high resolution DEMs are available, and then apply the model to the entirety of Lirung and Langtang glaciers to quantify the total contributions of cliffs to glacier mass balance. Observations and model results suggest a strong dependency of the cliffs' life cycle on supraglacial ponds, as the water body keeps the cliff geometry constant through a combination of backwasting and calving at the bottom and maintenance of steep slopes in the lowest sections. The absence of ponds causes the progressive flattening of the cliff, which finally leads to complete disappearance. Modelled volume losses from May to October 2013 range from 2650 to 9415 m3 w.e., in agreement with the estimates with the SfM-approach. Mean error of modelled elevation within the cliff outline ranges from -1.3 to 0.6m. This work sheds light on mechanisms of cliffs' changes by quantifying them for the first time with a physically-based, dynamic model, and presents the first complete estimate of the relevance of supraglacial ice-cliffs to total glacier mass-balance for two distinct glaciers.

Quantifying the Effect of Stress on Sn Whisker Nucleation Kinetics

NASA Astrophysics Data System (ADS)

Chason, Eric; Vasquez, Justin; Pei, Fei; Jain, Nupur; Hitt, Andrew

2018-01-01

Although Sn whiskers have been studied extensively, there is still a need to understand the driving forces behind whisker nucleation and growth. Many studies point to the role of stress, but confirming this requires a quantitative comparison between controlled stress and the resulting whisker evolution. Recent experimental studies applied stress to a Sn layer via thermal cycling and simultaneously monitored the evolution of the temperature, stress and number of nuclei. In this work, we analyze these nucleation kinetics in terms of classical nucleation theory to relate the observed behavior to underlying mechanisms including a stress dependent activation energy and a temperature and stress-dependent whisker growth rate. Non-linear least squares fitting of the data taken at different temperatures and strain rates to the model shows that the results can be understood in terms of stress decreasing the barrier for whisker nucleation.

Can males contribute to the genetic improvement of a species?

NASA Astrophysics Data System (ADS)

Bernardes, Américo T.

1997-01-01

In the time evolution of finite populations, the accumulation of harmful mutations in further generations might have lead to a temporal decay in the mean fitness of the whole population. This, in turn, would reduce the population size and so lead to its extinction. The production of genetically diverse offspring, through recombination, is a powerful mechanism in order to avoid this catastrophic route. From a selfish point of view, meiotic parthenogenesis can ensure the maintenance of better genomes, while sexual reproduction presents the risk of genome dilution. In this paper, by using Monte Carlo simulations of age-structured populations, through the Penna model, I compare the evolution of populations with different repoductive regimes. It is shown that sexual reproduction with male competition can produce better results than meiotic parthenogenesis. This contradicts results recently published, but agrees with the strong evidence that nature chose sexual reproduction instead of partenogenesis for most of the higher species.

Development, Regeneration, and Evolution of Feathers

PubMed Central

Chen, Chih-Feng; Foley, John; Tang, Pin-Chi; Li, Ang; Jiang, Ting Xin; Wu, Ping; Widelitz, Randall B.; Chuong, Cheng Ming

2017-01-01

The feather is a complex ectodermal organ with hierarchical branching patterns. It provides functions in endothermy, communication, and flight. Studies of feather growth, cycling, and health are of fundamental importance to avian biology and poultry science. In addition, feathers are an excellent model for morphogenesis studies because of their accessibility, and their distinct patterns can be used to assay the roles of specific molecular pathways. Here we review the progress in aspects of development, regeneration, and evolution during the past three decades. We cover the development of feather buds in chicken embryos, regenerative cycling of feather follicle stem cells, formation of barb branching patterns, emergence of intrafeather pigmentation patterns, interplay of hormones and feather growth, and the genetic identification of several feather variants. The discovery of feathered dinosaurs redefines the relationship between feathers and birds. Inspiration from biomaterials and flight research further fuels biomimetic potential of feathers as a multidisciplinary research focal point. PMID:25387232

Coral snakes predict the evolution of mimicry across New World snakes.

PubMed

Davis Rabosky, Alison R; Cox, Christian L; Rabosky, Daniel L; Title, Pascal O; Holmes, Iris A; Feldman, Anat; McGuire, Jimmy A

2016-05-05

Batesian mimicry, in which harmless species (mimics) deter predators by deceitfully imitating the warning signals of noxious species (models), generates striking cases of phenotypic convergence that are classic examples of evolution by natural selection. However, mimicry of venomous coral snakes has remained controversial because of unresolved conflict between the predictions of mimicry theory and empirical patterns in the distribution and abundance of snakes. Here we integrate distributional, phenotypic and phylogenetic data across all New World snake species to demonstrate that shifts to mimetic coloration in nonvenomous snakes are highly correlated with coral snakes in both space and time, providing overwhelming support for Batesian mimicry. We also find that bidirectional transitions between mimetic and cryptic coloration are unexpectedly frequent over both long- and short-time scales, challenging traditional views of mimicry as a stable evolutionary 'end point' and suggesting that insect and snake mimicry may have different evolutionary dynamics.

Coral snakes predict the evolution of mimicry across New World snakes

PubMed Central

Davis Rabosky, Alison R.; Cox, Christian L.; Rabosky, Daniel L.; Title, Pascal O.; Holmes, Iris A.; Feldman, Anat; McGuire, Jimmy A.

2016-01-01

Batesian mimicry, in which harmless species (mimics) deter predators by deceitfully imitating the warning signals of noxious species (models), generates striking cases of phenotypic convergence that are classic examples of evolution by natural selection. However, mimicry of venomous coral snakes has remained controversial because of unresolved conflict between the predictions of mimicry theory and empirical patterns in the distribution and abundance of snakes. Here we integrate distributional, phenotypic and phylogenetic data across all New World snake species to demonstrate that shifts to mimetic coloration in nonvenomous snakes are highly correlated with coral snakes in both space and time, providing overwhelming support for Batesian mimicry. We also find that bidirectional transitions between mimetic and cryptic coloration are unexpectedly frequent over both long- and short-time scales, challenging traditional views of mimicry as a stable evolutionary ‘end point' and suggesting that insect and snake mimicry may have different evolutionary dynamics. PMID:27146100

Quantum space and quantum completeness

NASA Astrophysics Data System (ADS)

Jurić, Tajron

2018-05-01

Motivated by the question whether quantum gravity can "smear out" the classical singularity we analyze a certain quantum space and its quantum-mechanical completeness. Classical singularity is understood as a geodesic incompleteness, while quantum completeness requires a unique unitary time evolution for test fields propagating on an underlying background. Here the crucial point is that quantum completeness renders the Hamiltonian (or spatial part of the wave operator) to be essentially self-adjoint in order to generate a unique time evolution. We examine a model of quantum space which consists of a noncommutative BTZ black hole probed by a test scalar field. We show that the quantum gravity (noncommutative) effect is to enlarge the domain of BTZ parameters for which the relevant wave operator is essentially self-adjoint. This means that the corresponding quantum space is quantum complete for a larger range of BTZ parameters rendering the conclusion that in the quantum space one observes the effect of "smearing out" the singularity.

Modeling Co-evolution of Speech and Biology.

PubMed

de Boer, Bart

2016-04-01

Two computer simulations are investigated that model interaction of cultural evolution of language and biological evolution of adaptations to language. Both are agent-based models in which a population of agents imitates each other using realistic vowels. The agents evolve under selective pressure for good imitation. In one model, the evolution of the vocal tract is modeled; in the other, a cognitive mechanism for perceiving speech accurately is modeled. In both cases, biological adaptations to using and learning speech evolve, even though the system of speech sounds itself changes at a more rapid time scale than biological evolution. However, the fact that the available acoustic space is used maximally (a self-organized result of cultural evolution) is constant, and therefore biological evolution does have a stable target. This work shows that when cultural and biological traits are continuous, their co-evolution may lead to cognitive adaptations that are strong enough to detect empirically. Copyright © 2016 Cognitive Science Society, Inc.

Microbial Evolution: Xenology (Apparently) Trumps Paralogy.

PubMed

Eme, Laura; Doolittle, W Ford

2016-11-21

Within-genome gene duplication is generally considered the source of extra copies when higher dosage is required and a starting point for evolution of new function. A new study suggests that horizontal gene transfer can appear to play both roles. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantifying and Validating Rapid Floodplain Geomorphic Evolution, a Monitoring and Modelling Case Study

NASA Astrophysics Data System (ADS)

Scott, R.; Entwistle, N. S.

2017-12-01

Gravel bed rivers and their associated wider systems present an ideal subject for development and improvement of rapid monitoring tools, with features dynamic enough to evolve within relatively short-term timescales. For detecting and quantifying topographical evolution, UAV based remote sensing has manifested as a reliable, low cost, and accurate means of topographic data collection. Here we present some validated methodologies for detection of geomorphic change at resolutions down to 0.05 m, building on the work of Wheaton et al. (2009) and Milan et al. (2007), to generate mesh based and pointcloud comparison data to produce a reliable picture of topographic evolution. Results are presented for the River Glen, Northumberland, UK. Recent channel avulsion and floodplain interaction, resulting in damage to flood defence structures make this site a particularly suitable case for application of geomorphic change detection methods, with the UAV platform at its centre. We compare multi-temporal, high-resolution point clouds derived from SfM processing, cross referenced with aerial LiDAR data, over a 1.5 km reach of the watercourse. Changes detected included bank erosion, bar and splay deposition, vegetation stripping and incipient channel avulsion. Utilisation of the topographic data for numerical modelling, carried out using CAESAR-Lisflood predicted the avulsion of the main channel, resulting in erosion of and potentially complete circumvention of original channel and flood levees. A subsequent UAV survey highlighted topographic change and reconfiguration of the local sedimentary conveyor as we predicted with preliminary modelling. The combined monitoring and modelling approach has allowed probable future geomorphic configurations to be predicted permitting more informed implementation of channel and floodplain management strategies.

Human intronless genes: Functional groups, associated diseases, evolution, and mRNA processing in absence of splicing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grzybowska, Ewa A., E-mail: ewag@coi.waw.pl

2012-07-20

Highlights: Black-Right-Pointing-Pointer Functional characteristics of intronless genes (IGs). Black-Right-Pointing-Pointer Diseases associated with IGs. Black-Right-Pointing-Pointer Origin and evolution of IGs. Black-Right-Pointing-Pointer mRNA processing without splicing. -- Abstract: Intronless genes (IGs) constitute approximately 3% of the human genome. Human IGs are essentially different in evolution and functionality from the IGs of unicellular eukaryotes, which represent the majority in their genomes. Functional analysis of IGs has revealed a massive over-representation of signal transduction genes and genes encoding regulatory proteins important for growth, proliferation, and development. IGs also often display tissue-specific expression, usually in the nervous system and testis. These characteristics translate into IG-associatedmore » diseases, mainly neuropathies, developmental disorders, and cancer. IGs represent recent additions to the genome, created mostly by retroposition of processed mRNAs with retained functionality. Processing, nuclear export, and translation of these mRNAs should be hampered dramatically by the lack of splice factors, which normally tightly cover mature transcripts and govern their fate. However, natural IGs manage to maintain satisfactory expression levels. Different mechanisms by which IGs solve the problem of mRNA processing and nuclear export are discussed here, along with their possible impact on reporter studies.« less

Compact Objects In Binary Systems: Formation and Evolution of X-ray Binaries and Tides in Double White Dwarfs

NASA Astrophysics Data System (ADS)

Valsecchi, Francesca

Binary star systems hosting black holes, neutron stars, and white dwarfs are unique laboratories for investigating both extreme physical conditions, and stellar and binary evolution. Black holes and neutron stars are observed in X-ray binaries, where mass accretion from a stellar companion renders them X-ray bright. Although instruments like Chandra have revolutionized the field of X-ray binaries, our theoretical understanding of their origin and formation lags behind. Progress can be made by unravelling the evolutionary history of observed systems. As part of my thesis work, I have developed an analysis method that uses detailed stellar models and all the observational constraints of a system to reconstruct its evolutionary path. This analysis models the orbital evolution from compact-object formation to the present time, the binary orbital dynamics due to explosive mass loss and a possible kick at core collapse, and the evolution from the progenitor's Zero Age Main Sequence to compact-object formation. This method led to a theoretical model for M33 X-7, one of the most massive X-ray binaries known and originally marked as an evolutionary challenge. Compact objects are also expected gravitational wave (GW) sources. In particular, double white dwarfs are both guaranteed GW sources and observed electromagnetically. Although known systems show evidence of tidal deformation and a successful GW astronomy requires realistic models of the sources, detached double white dwarfs are generally approximated to point masses. For the first time, I used realistic models to study tidally-driven periastron precession in eccentric binaries. I demonstrated that its imprint on the GW signal yields constrains on the components' masses and that the source would be misclassified if tides are neglected. Beyond this adiabatic precession, tidal dissipation creates a sink of orbital angular momentum. Its efficiency is strongest when tides are dynamic and excite the components' free oscillation modes. Accounting for this effect will determine whether our interpretation of current and future observations will constrain the sources' true physical properties. To investigate dynamic tides I have developed CAFein, a novel code that calculates forced non-adiabatic stellar oscillations using a highly stable and efficient numerical method.

Adaptive 4d Psi-Based Change Detection

NASA Astrophysics Data System (ADS)

Yang, Chia-Hsiang; Soergel, Uwe

2018-04-01

In a previous work, we proposed a PSI-based 4D change detection to detect disappearing and emerging PS points (3D) along with their occurrence dates (1D). Such change points are usually caused by anthropic events, e.g., building constructions in cities. This method first divides an entire SAR image stack into several subsets by a set of break dates. The PS points, which are selected based on their temporal coherences before or after a break date, are regarded as change candidates. Change points are then extracted from these candidates according to their change indices, which are modelled from their temporal coherences of divided image subsets. Finally, we check the evolution of the change indices for each change point to detect the break date that this change occurred. The experiment validated both feasibility and applicability of our method. However, two questions still remain. First, selection of temporal coherence threshold associates with a trade-off between quality and quantity of PS points. This selection is also crucial for the amount of change points in a more complex way. Second, heuristic selection of change index thresholds brings vulnerability and causes loss of change points. In this study, we adapt our approach to identify change points based on statistical characteristics of change indices rather than thresholding. The experiment validates this adaptive approach and shows increase of change points compared with the old version. In addition, we also explore and discuss optimal selection of temporal coherence threshold.

Maximally Entangled States of a Two-Qubit System

NASA Astrophysics Data System (ADS)

Singh, Manu P.; Rajput, B. S.

2013-12-01

Entanglement has been explored as one of the key resources required for quantum computation, the functional dependence of the entanglement measures on spin correlation functions has been established, correspondence between evolution of maximally entangled states (MES) of two-qubit system and representation of SU(2) group has been worked out and the evolution of MES under a rotating magnetic field has been investigated. Necessary and sufficient conditions for the general two-qubit state to be maximally entangled state (MES) have been obtained and a new set of MES constituting a very powerful and reliable eigen basis (different from magic bases) of two-qubit systems has been constructed. In terms of the MES constituting this basis, Bell’s States have been generated and all the qubits of two-qubit system have been obtained. It has shown that a MES corresponds to a point in the SO(3) sphere and an evolution of MES corresponds to a trajectory connecting two points on this sphere. Analysing the evolution of MES under a rotating magnetic field, it has been demonstrated that a rotating magnetic field is equivalent to a three dimensional rotation in real space leading to the evolution of a MES.

Fourier plane modeling of the jet in the galaxy M81

NASA Astrophysics Data System (ADS)

Ramessur, Arvind; Bietenholz, Michael F.; Leeuw, Lerothodi L.; Bartel, Norbert

2015-03-01

The nearby spiral galaxy M81 has a low-luminosity Active Galactic Nucleus in its center with a core and a one-sided curved jet, dubbed M81*, that is barely resolved with VLBI. To derive basic parameters such as the length of the jet, its orientation and curvature, the usual method of model-fitting with point sources and elliptical Gaussians may not always be the most appropriate one. We are developing Fourier-plane models for such sources, in particular an asymmetric triangle model to fit the extensive set of VLBI data of M81* in the u-v plane. This method may have an advantage over conventional ones in extracting information close to the resolution limit to provide us with a more comprehensive picture of the structure and evolution of the jet. We report on preliminary results.

Analysis of dynamically stable patterns in a maze-like corridor using the Wasserstein metric.

PubMed

Ishiwata, Ryosuke; Kinukawa, Ryota; Sugiyama, Yuki

2018-04-23

The two-dimensional optimal velocity (2d-OV) model represents a dissipative system with asymmetric interactions, thus being suitable to reproduce behaviours such as pedestrian dynamics and the collective motion of living organisms. In this study, we found that particles in the 2d-OV model form optimal patterns in a maze-like corridor. Then, we estimated the stability of such patterns using the Wasserstein metric. Furthermore, we mapped these patterns into the Wasserstein metric space and represented them as points in a plane. As a result, we discovered that the stability of the dynamical patterns is strongly affected by the model sensitivity, which controls the motion of each particle. In addition, we verified the existence of two stable macroscopic patterns which were cohesive, stable, and appeared regularly over the time evolution of the model.

A physics-based crystallographic modeling framework for describing the thermal creep behavior of Fe-Cr alloys

DOE PAGES

Wen, Wei; Capolungo, Laurent; Patra, Anirban; ...

2017-02-23

In this work, a physics-based thermal creep model is developed based on the understanding of the microstructure in Fe-Cr alloys. This model is associated with a transition state theory based framework that considers the distribution of internal stresses at sub-material point level. The thermally activated dislocation glide and climb mechanisms are coupled in the obstacle-bypass processes for both dislocation and precipitate-type barriers. A kinetic law is proposed to track the dislocation densities evolution in the subgrain interior and in the cell wall. The predicted results show that this model, embedded in the visco-plastic self-consistent (VPSC) framework, captures well the creepmore » behaviors for primary and steady-state stages under various loading conditions. We also discuss the roles of the mechanisms involved.« less

Dynamical Formation of Kerr Black Holes with Synchronized Hair: An Analytic Model.

PubMed

Herdeiro, Carlos A R; Radu, Eugen

2017-12-29

East and Pretorius have successfully evolved, using fully nonlinear numerical simulations, the superradiant instability of the Kerr black hole (BH) triggered by a massive, complex vector field. Evolutions terminate in stationary states of a vector field condensate synchronized with a rotating BH horizon. We show that these end points are fundamental states of Kerr BHs with synchronized Proca hair. Motivated by the "experimental data" from these simulations, we suggest a universal (i.e., field-spin independent), analytic model for the subset of BHs with synchronized hair that possess a quasi-Kerr horizon, applicable in the weak hair regime. Comparing this model with fully nonlinear numerical solutions of BHs with a synchronized scalar or Proca hair, we show that the model is accurate for hairy BHs that may emerge dynamically from superradiance, whose domain we identify.

Dynamical Formation of Kerr Black Holes with Synchronized Hair: An Analytic Model

NASA Astrophysics Data System (ADS)

Herdeiro, Carlos A. R.; Radu, Eugen

2017-12-01

East and Pretorius have successfully evolved, using fully nonlinear numerical simulations, the superradiant instability of the Kerr black hole (BH) triggered by a massive, complex vector field. Evolutions terminate in stationary states of a vector field condensate synchronized with a rotating BH horizon. We show that these end points are fundamental states of Kerr BHs with synchronized Proca hair. Motivated by the "experimental data" from these simulations, we suggest a universal (i.e., field-spin independent), analytic model for the subset of BHs with synchronized hair that possess a quasi-Kerr horizon, applicable in the weak hair regime. Comparing this model with fully nonlinear numerical solutions of BHs with a synchronized scalar or Proca hair, we show that the model is accurate for hairy BHs that may emerge dynamically from superradiance, whose domain we identify.

Effects of Vegetation and of Heat and Vapor Fluxes from Soil on Snowpack Evolution and Radiobrightness

NASA Technical Reports Server (NTRS)

Chung, Y. C.; England, A. W.; DeRoo, R. D.; Weininger, Etai

2006-01-01

The radiobrightness of a snowpack is strongly linked to the snow moisture content profile, to the point that the only operational inversion algorithms require dry snow. Forward dynamic models do not include the effects of freezing and thawing of the soil beneath the snowpack and the effect of vegetation within the snow or above the snow. To get a more realistic description of the evolution of the snowpack, we reported an addition to the Snow-Soil-Vegetation-Atmosphere- Transfer (SSVAT) model, wherein we coupled soil processes of the Land Surface Process (LSP) model with the snow model SNTHERM. In the near future we will be adding a radiobrightness prediction based on the modeled moisture, temperature and snow grain size profiles. The initial investigations with this SSVAT for a late winter and early spring snow pack indicate that soil processes warm the snowpack and the soil. Vapor diffusion needs to be considered whenever the ground is thawed. In the early spring, heat flow from the ground into a snow and a strong temperature gradient across the snow lead to thermal convection. The buried vegetation can be ignored for a late winter snow pack. The warmer surface snow temperature will affect radiobrightness since it is most sensitive to snow surface characteristics. Comparison to data shows that SSVAT provides a more realistic representation of the temperature and moisture profiles in the snowpack and its underlying soil than SNTHERM. The radiobrightness module will be optimized for the prediction of brightness when the snow is moist. The liquid water content of snow causes considerable absorption compared to dry snow, and so longer wavelengths are likely to be most revealing as to the state of a moist snowpack. For volumetric moisture contents below about 7% (the pendular regime), the water forms rings around the contact points between snow grains. Electrostatic modeling of these pendular rings shows that the absorption of these rings is significantly higher than a sphere of the same volume. The first implementation of the radiobrightness module will therefore be a simple radiative transfer model without scattering.

Analysis of thermal processing of table olives using computational fluid dynamics.

PubMed

Dimou, A; Panagou, E; Stoforos, N G; Yanniotis, S

2013-11-01

In the present work, the thermal processing of table olives in brine in a stationary metal can was studied through computational fluid dynamics (CFD). The flow patterns of the brine and the temperature evolution in the olives and brine during the heating and the cooling cycles of the process were calculated using the CFD code. Experimental temperature measurements at 3 points (2 inside model olive particles and 1 at a point in the brine) in a can (with dimensions of 75 mm × 105 mm) filled with 48 olives in 4% (w/v) brine, initially held at 20 °C, heated in water at 100 °C for 10 min, and thereafter cooled in water at about 20 °C for 10 min, validated model predictions. The distribution of temperature and F-values and the location of the slowest heating zone and the critical point within the product, as far as microbial destruction is concerned, were assessed for several cases. For the cases studied, the critical point was located at the interior of the olives at the 2nd, or between the 1st and the 2nd olive row from the bottom of the container, the exact location being affected by olive size, olive arrangement, and geometry of the container. © 2013 Institute of Food Technologists®

Orbital evolution and escape of Martian Trojans due to the Yarkovsky effect

NASA Astrophysics Data System (ADS)

Christou, Apostolos

2017-06-01

Recently it was shown that the Yarkovsky effect can lead to significant orbit change for Trojans of Mars [1,2] and that the orbital distribution of observed Trojans is consistent with a negative along-track acceleration of the same functional form as seasonal yarkovsky; this feature was used to constrain the age of the Eureka family of Mars Trojan asteroids [2]. In contrast, the Yarkovsky effect appears to have a negligible role in shaping observed families of Jupiter Trojans [3].To explore the evolution and end states of Trojans evolved by the Yarkosky effect, I have numerically integrated test particles under a model of the diurnal variant and for different values of the acceleration strength up to 10-2 AU/Myr for da/dt outside the resonance. I use as a starting point the orbits of the three largest Martian Trojans: 5261 Eureka, (101429) 1998 VF31 and (121514) 1999 UJ7.I find, as in [2], that the evolution of the inclination I and the libration amplitude L depends on the sign of the acceleration and is essentially deterministic. Considering the rate of change of the Tisserand constant [5,6] leads to a simple analytical expression that reproduces well the inclination evolution of the Trojans. The evolution of e is somewhat more stochastic, probably due to chaotic diffusion [4] and/or the influence of Mars’ eccentricity [2].Trojans escape upon reaching the boundaries of stability domains mapped out in [4], demarcated by resonances with principal secular modes and the Kozai resonance. The mechanism of escape is by increasing e and/or the libration amplitude to the point of allowing close encounters with Mars.During the presentation I will describe the ensemble evolution of Trojans under Yarkovsky, how it is related to the lifetime in the 1:1 resonance and discuss the implications for Trojan stability at Earth and Jupiter.[1] Christou, A.A., 2013, Icarus, 224, 144.[2] Ćuk, M., Christou, A.A., Hamilton, D.P., 2015, Icarus, 252, 339.[3] Milani, A., Knezević, Z., Spoto, F., Cellino, A., Novaković, B., Tsirvoulis, G., 2017, Icarus, 288, 240.[4] Scholl, H., Marzari, F., Tricarico, P., 2005, Icarus, 175, 397.[5] Hamilton, D.P., 1994, Icarus, 109, 221[6] Liou, J. C., Zook, H. A., 1997, Icarus, 128, 354.

Energy, time, and channel evolution in catastrophically disturbed fluvial systems

USGS Publications Warehouse

Simon, A.

1992-01-01

Specific energy is shown to decrease nonlinearly with time during channel evolution and provides a measure of reductions in available energy at the channel bed. Data from two sites show convergence towards a minimum specific energy with time. Time-dependent reductions in specific energy at a point act in concert with minimization of the rate of energy dissipation over a reach during channel evolution as the fluvial systems adjust to a new equilibrium.

Slow light in saturable absorbers: Progress in the resolution of a controversy

NASA Astrophysics Data System (ADS)

Macke, Bruno; Razdobreev, Igor; Ségard, Bernard

2017-06-01

There are two opposing models in the analysis of the slow transmission of light pulses through saturable absorbers. The canonical incoherent bleaching model simply explains the slow transmission by combined effects of saturation and of noninstantaneous response of the medium resulting in absorption of the front part of the incident pulse larger than that of its rear. The second model, referred to as the coherent-population-oscillations (CPO) model, considers light beams whose intensity is slightly pulse modulated and attributes the time delay of the transmitted pulse to a reduction of the group velocity. We point out some inconsistencies in the CPO model and show that the two models lie in reality on the same hypotheses, the equations derived in the duly rectified CPO model being local expressions of the integral equations obtained in the incoherent bleaching model. When intense pulses without background are used, the CPO model, based on linearized equations, breaks down. The incoherent bleaching model then predicts that the transmitted light should vanish when the intensity of the incident light is strictly zero. This point is confirmed by the experiments that we have performed on ruby with square-wave incident pulses and we show that the whole shape of the observed pulses agrees with that derived analytically by means of the incoherent bleaching model. We also determine in this model the corresponding evolution of the fluorescence light, which seems to have been evidenced in other experiments.