Neutral null models for diversity in serial transfer evolution experiments.

PubMed

Harpak, Arbel; Sella, Guy

2014-09-01

Evolution experiments with microorganisms coupled with genome-wide sequencing now allow for the systematic study of population genetic processes under a wide range of conditions. In learning about these processes in natural, sexual populations, neutral models that describe the behavior of diversity and divergence summaries have played a pivotal role. It is therefore natural to ask whether neutral models, suitably modified, could be useful in the context of evolution experiments. Here, we introduce coalescent models for polymorphism and divergence under the most common experimental evolution assay, a serial transfer experiment. This relatively simple setting allows us to address several issues that could affect diversity patterns in evolution experiments, whether selection is operating or not: the transient behavior of neutral polymorphism in an experiment beginning from a single clone, the effects of randomness in the timing of cell division and noisiness in population size in the dilution stage. In our analyses and discussion, we emphasize the implications for experiments aimed at measuring diversity patterns and making inferences about population genetic processes based on these measurements. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods

PubMed Central

Burbrink, Frank T.; McKelvy, Alexander D.; Pyron, R. Alexander; Myers, Edward A.

2015-01-01

Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should have a higher probability of occurring on adjacent islands. In contrast to UNTB, if certain groups have traits that permit them to disperse to islands better than other taxa, then phylogeny may be more predictive of which taxa will occur on islands. Taking surveys of 54 island snake communities in the Eastern Nearctic along with mainland communities that have abundance data for each species, we use phylogenetic assembly methods and UNTB estimates to predict island communities. Species richness is predicted by island area, whereas turnover from the mainland to island communities is random with respect to phylogeny. Community structure appears to be ecologically neutral and abundance on the mainland is the best predictor of presence on islands. With regard to young and proximate islands, where allopatric or cladogenetic speciation is not a factor, we find that simple neutral models following UNTB and ETIB predict the structure of island communities. PMID:26609083

Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods.

PubMed

Burbrink, Frank T; McKelvy, Alexander D; Pyron, R Alexander; Myers, Edward A

2015-11-22

Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should have a higher probability of occurring on adjacent islands. In contrast to UNTB, if certain groups have traits that permit them to disperse to islands better than other taxa, then phylogeny may be more predictive of which taxa will occur on islands. Taking surveys of 54 island snake communities in the Eastern Nearctic along with mainland communities that have abundance data for each species, we use phylogenetic assembly methods and UNTB estimates to predict island communities. Species richness is predicted by island area, whereas turnover from the mainland to island communities is random with respect to phylogeny. Community structure appears to be ecologically neutral and abundance on the mainland is the best predictor of presence on islands. With regard to young and proximate islands, where allopatric or cladogenetic speciation is not a factor, we find that simple neutral models following UNTB and ETIB predict the structure of island communities. © 2015 The Author(s).

Combining DSMC Simulations and ROSINA/COPS Data of Comet 67P/Churyumov-Gerasimenko to Develop a Realistic Empirical Coma Model and to Determine Accurate Production Rates

NASA Astrophysics Data System (ADS)

Hansen, K. C.; Fougere, N.; Bieler, A. M.; Altwegg, K.; Combi, M. R.; Gombosi, T. I.; Huang, Z.; Rubin, M.; Tenishev, V.; Toth, G.; Tzou, C. Y.

2015-12-01

We have previously published results from the AMPS DSMC (Adaptive Mesh Particle Simulator Direct Simulation Monte Carlo) model and its characterization of the neutral coma of comet 67P/Churyumov-Gerasimenko through detailed comparison with data collected by the ROSINA/COPS (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis/COmet Pressure Sensor) instrument aboard the Rosetta spacecraft [Bieler, 2015]. Results from these DSMC models have been used to create an empirical model of the near comet coma (<200 km) of comet 67P. The empirical model characterizes the neutral coma in a comet centered, sun fixed reference frame as a function of heliocentric distance, radial distance from the comet, local time and declination. The model is a significant improvement over more simple empirical models, such as the Haser model. While the DSMC results are a more accurate representation of the coma at any given time, the advantage of a mean state, empirical model is the ease and speed of use. One use of such an empirical model is in the calculation of a total cometary coma production rate from the ROSINA/COPS data. The COPS data are in situ measurements of gas density and velocity along the ROSETTA spacecraft track. Converting the measured neutral density into a production rate requires knowledge of the neutral gas distribution in the coma. Our empirical model provides this information and therefore allows us to correct for the spacecraft location to calculate a production rate as a function of heliocentric distance. We will present the full empirical model as well as the calculated neutral production rate for the period of August 2014 - August 2015 (perihelion).

Selfish genes, pleiotropy and the origin of recombination.

PubMed Central

Hey, J

1998-01-01

If multiple linked polymorphisms are under natural selection, then conflicts arise and the efficiency of natural selection is hindered relative to the case of no linkage. This simple interaction between linkage and natural selection creates an opportunity for mutations that raise the level of recombination to increase in frequency and have an enhanced chance of fixation. This important finding by S. Otto and N. Barton means that mutations that raise the recombination rate, but are otherwise neutral, will be selectively favored under fairly general circumstances of multilocus selection and linkage. The effect described by Otto and Barton, which was limited to neutral modifiers, can also be extended to include all modifiers of recombination, both beneficial and deleterious. Computer simulations show that beneficial mutations that also increase recombination have an increased chance of fixation. Similarly, deleterious mutations that also decrease recombination have an increased chance of fixation. The results suggest that a simple model of recombination modifiers, including both neutral and pleiotropic modifiers, is a necessary explanation for the evolutionary origin of recombination. PMID:9691060

Ultrametric distribution of culture vectors in an extended Axelrod model of cultural dissemination.

PubMed

Stivala, Alex; Robins, Garry; Kashima, Yoshihisa; Kirley, Michael

2014-05-02

The Axelrod model of cultural diffusion is an apparently simple model that is capable of complex behaviour. A recent work used a real-world dataset of opinions as initial conditions, demonstrating the effects of the ultrametric distribution of empirical opinion vectors in promoting cultural diversity in the model. Here we quantify the degree of ultrametricity of the initial culture vectors and investigate the effect of varying degrees of ultrametricity on the absorbing state of both a simple and extended model. Unlike the simple model, ultrametricity alone is not sufficient to sustain long-term diversity in the extended Axelrod model; rather, the initial conditions must also have sufficiently large variance in intervector distances. Further, we find that a scheme for evolving synthetic opinion vectors from cultural "prototypes" shows the same behaviour as real opinion data in maintaining cultural diversity in the extended model; whereas neutral evolution of cultural vectors does not.

Ultrametric distribution of culture vectors in an extended Axelrod model of cultural dissemination

NASA Astrophysics Data System (ADS)

Stivala, Alex; Robins, Garry; Kashima, Yoshihisa; Kirley, Michael

2014-05-01

The Axelrod model of cultural diffusion is an apparently simple model that is capable of complex behaviour. A recent work used a real-world dataset of opinions as initial conditions, demonstrating the effects of the ultrametric distribution of empirical opinion vectors in promoting cultural diversity in the model. Here we quantify the degree of ultrametricity of the initial culture vectors and investigate the effect of varying degrees of ultrametricity on the absorbing state of both a simple and extended model. Unlike the simple model, ultrametricity alone is not sufficient to sustain long-term diversity in the extended Axelrod model; rather, the initial conditions must also have sufficiently large variance in intervector distances. Further, we find that a scheme for evolving synthetic opinion vectors from cultural ``prototypes'' shows the same behaviour as real opinion data in maintaining cultural diversity in the extended model; whereas neutral evolution of cultural vectors does not.

Volume shift and charge instability of simple-metal clusters

NASA Astrophysics Data System (ADS)

Brajczewska, M.; Vieira, A.; Fiolhais, C.; Perdew, J. P.

1996-12-01

Experiment indicates that small clusters show changes (mostly contractions) of the bond lengths with respect to bulk values. We use the stabilized jellium model to study the self-expansion and self-compression of spherical clusters (neutral or ionized) of simple metals. Results from Kohn - Sham density functional theory are presented for small clusters of Al and Na, including negatively-charged ones. We also examine the stability of clusters with respect to charging.

SimpleBox 4.0: Improving the model while keeping it simple….

PubMed

Hollander, Anne; Schoorl, Marian; van de Meent, Dik

2016-04-01

Chemical behavior in the environment is often modeled with multimedia fate models. SimpleBox is one often-used multimedia fate model, firstly developed in 1986. Since then, two updated versions were published. Based on recent scientific developments and experience with SimpleBox 3.0, a new version of SimpleBox was developed and is made public here: SimpleBox 4.0. In this new model, eight major changes were implemented: removal of the local scale and vegetation compartments, addition of lake compartments and deep ocean compartments (including the thermohaline circulation), implementation of intermittent rain instead of drizzle and of depth dependent soil concentrations, adjustment of the partitioning behavior for organic acids and bases as well as of the value for enthalpy of vaporization. In this paper, the effects of the model changes in SimpleBox 4.0 on the predicted steady-state concentrations of chemical substances were explored for different substance groups (neutral organic substances, acids, bases, metals) in a standard emission scenario. In general, the largest differences between the predicted concentrations in the new and the old model are caused by the implementation of layered ocean compartments. Undesirable high model complexity caused by vegetation compartments and a local scale were removed to enlarge the simplicity and user friendliness of the model. Copyright © 2016 Elsevier Ltd. All rights reserved.

A method to estimate the neutral atmospheric density near the ionospheric main peak of Mars

NASA Astrophysics Data System (ADS)

Zou, Hong; Ye, Yu Guang; Wang, Jin Song; Nielsen, Erling; Cui, Jun; Wang, Xiao Dong

2016-04-01

A method to estimate the neutral atmospheric density near the ionospheric main peak of Mars is introduced in this study. The neutral densities at 130 km can be derived from the ionospheric and atmospheric measurements of the Radio Science experiment on board Mars Global Surveyor (MGS). The derived neutral densities cover a large longitude range in northern high latitudes from summer to late autumn during 3 Martian years, which fills the gap of the previous observations for the upper atmosphere of Mars. The simulations of the Laboratoire de Météorologie Dynamique Mars global circulation model can be corrected with a simple linear equation to fit the neutral densities derived from the first MGS/RS (Radio Science) data sets (EDS1). The corrected simulations with the same correction parameters as for EDS1 match the derived neutral densities from two other MGS/RS data sets (EDS2 and EDS3) very well. The derived neutral density from EDS3 shows a dust storm effect, which is in accord with the Mars Express (MEX) Spectroscopy for Investigation of Characteristics of the Atmosphere of Mars measurement. The neutral density derived from the MGS/RS measurements can be used to validate the Martian atmospheric models. The method presented in this study can be applied to other radio occultation measurements, such as the result of the Radio Science experiment on board MEX.

A Web Application For Visualizing Empirical Models of the Space-Atmosphere Interface Region: AtModWeb

NASA Astrophysics Data System (ADS)

Knipp, D.; Kilcommons, L. M.; Damas, M. C.

2015-12-01

We have created a simple and user-friendly web application to visualize output from empirical atmospheric models that describe the lower atmosphere and the Space-Atmosphere Interface Region (SAIR). The Atmospheric Model Web Explorer (AtModWeb) is a lightweight, multi-user, Python-driven application which uses standard web technology (jQuery, HTML5, CSS3) to give an in-browser interface that can produce plots of modeled quantities such as temperature and individual species and total densities of neutral and ionized upper-atmosphere. Output may be displayed as: 1) a contour plot over a map projection, 2) a pseudo-color plot (heatmap) which allows visualization of a variable as a function of two spatial coordinates, or 3) a simple line plot of one spatial coordinate versus any number of desired model output variables. The application is designed around an abstraction of an empirical atmospheric model, essentially treating the model code as a black box, which makes it simple to add additional models without modifying the main body of the application. Currently implemented are the Naval Research Laboratory NRLMSISE00 model for neutral atmosphere and the International Reference Ionosphere (IRI). These models are relevant to the Low Earth Orbit environment and the SAIR. The interface is simple and usable, allowing users (students and experts) to specify time and location, and choose between historical (i.e. the values for the given date) or manual specification of whichever solar or geomagnetic activity drivers are required by the model. We present a number of use-case examples from research and education: 1) How does atmospheric density between the surface and 1000 km vary with time of day, season and solar cycle?; 2) How do ionospheric layers change with the solar cycle?; 3 How does the composition of the SAIR vary between day and night at a fixed altitude?

The coalescent process in models with selection and recombination.

PubMed

Hudson, R R; Kaplan, N L

1988-11-01

The statistical properties of the process describing the genealogical history of a random sample of genes at a selectively neutral locus which is linked to a locus at which natural selection operates are investigated. It is found that the equations describing this process are simple modifications of the equations describing the process assuming that the two loci are completely linked. Thus, the statistical properties of the genealogical process for a random sample at a neutral locus linked to a locus with selection follow from the results obtained for the selected locus. Sequence data from the alcohol dehydrogenase (Adh) region of Drosophila melanogaster are examined and compared to predictions based on the theory. It is found that the spatial distribution of nucleotide differences between Fast and Slow alleles of Adh is very similar to the spatial distribution predicted if balancing selection operates to maintain the allozyme variation at the Adh locus. The spatial distribution of nucleotide differences between different Slow alleles of Adh do not match the predictions of this simple model very well.

Exploratory reconstructability analysis of accident TBI data

NASA Astrophysics Data System (ADS)

Zwick, Martin; Carney, Nancy; Nettleton, Rosemary

2018-02-01

This paper describes the use of reconstructability analysis to perform a secondary study of traumatic brain injury data from automobile accidents. Neutral searches were done and their results displayed with a hypergraph. Directed searches, using both variable-based and state-based models, were applied to predict performance on two cognitive tests and one neurological test. Very simple state-based models gave large uncertainty reductions for all three DVs and sizeable improvements in percent correct for the two cognitive test DVs which were equally sampled. Conditional probability distributions for these models are easily visualized with simple decision trees. Confounding variables and counter-intuitive findings are also reported.

Survival of mutations arising during invasions.

PubMed

Miller, Judith R

2010-03-01

When a neutral mutation arises in an invading population, it quickly either dies out or 'surfs', i.e. it comes to occupy almost all the habitat available at its time of origin. Beneficial mutations can also surf, as can deleterious mutations over finite time spans. We develop descriptive statistical models that quantify the relationship between the probability that a mutation will surf and demographic parameters for a cellular automaton model of surfing. We also provide a simple analytic model that performs well at predicting the probability of surfing for neutral and beneficial mutations in one dimension. The results suggest that factors - possibly including even abiotic factors - that promote invasion success may also increase the probability of surfing and associated adaptive genetic change, conditioned on such success.

On the Overdispersed Molecular Clock

PubMed Central

Takahata, Naoyuki

1987-01-01

Rates of molecular evolution at some loci are more irregular than described by simple Poisson processes. Three situations under which molecular evolution would not follow simple Poisson processes are reevaluated from the viewpoint of the neutrality hypothesis: (i) concomitant or multiple substitutions in a gene, (ii) fluctuating substitution rates in time caused by coupled effects of deleterious mutations and bottlenecks, and (iii) changes in the degree of selective constraints against a gene (neutral space) caused by successive substitutions. The common underlying assumption that these causes are lineage nonspecific excludes the case where mutation rates themselves change systematically among lineages or taxonomic groups, and severely limits the extent of variation in the number of substitutions among lineages. Even under this stringent condition, however, the third hypothesis, the fluctuating neutral space model, can generate fairly large variation. This is described by a time-dependent renewal process, which does not exhibit any episodic nature of molecular evolution. It is argued that the observed elevated variances in the number of nucleotide or amino acid substitutions do not immediately call for positive Darwinian selection in molecular evolution. PMID:3596230

Magnetic field, reconnection, and particle acceleration in extragalactic jets

NASA Technical Reports Server (NTRS)

Romanova, M. M.; Lovelace, R. V. E.

1992-01-01

Extra-galactic radio jets are investigated theoretically taking into account that the jet magnetic field is dragged out from the central rotating source by the jet flow. Thus, magnetohydrodynamic models of jets are considered with zero net poloidal current and flux, and consequently a predominantly toroidal magnetic field. The magnetic field naturally has a cylindrical neutral layer. Collisionless reconnection of the magnetic field in the vicinity of the neutral layer acts to generate a non-axisymmetric radial magnetic field. In turn, axial shear-stretching of reconnected toroidal field gives rise to a significant axial magnetic field if the flow energy-density is larger than the energy-density of the magnetic field. This can lead to jets with an apparent longitudinal magnetic field as observed in the Fanaroff-Riley class II jets. In the opposite limit, where the field energy-density is large, the field remains mainly toroidal as observed in Fanaroff-Riley class I jets. Driven collisionless reconnection at neutral layers may lead to acceleration of electrons to relativistic energies in the weak electrostatic field of the neutral layer. A simple model is discussed for particle acceleration at neutral layers in electron/positron and electron/proton plasmas.

Space-charge compensation measurements in electron cyclotron resonance ion source low energy beam transport lines with a retarding field analyzer

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

Winklehner, D.; Leitner, D., E-mail: leitnerd@nscl.msu.edu; Cole, D.

2014-02-15

In this paper we describe the first systematic measurement of beam neutralization (space charge compensation) in the ECR low energy transport line with a retarding field analyzer, which can be used to measure the potential of the beam. Expected trends for the space charge compensation levels such as increase with residual gas pressure, beam current, and beam density could be observed. However, the overall levels of neutralization are consistently low (<60%). The results and the processes involved for neutralizing ion beams are discussed for conditions typical for ECR injector beam lines. The results are compared to a simple theoretical beammore » plasma model as well as simulations.« less

Preliminary studies for a beam-generated plasma neutralizer test in NIO1

NASA Astrophysics Data System (ADS)

Sartori, E.; Veltri, P.; Balbinot, L.; Cavenago, M.; Veranda, M.; Antoni, V.; Serianni, G.

2017-08-01

The deployment of neutral beam injectors in future fusion plants is beset by the particularly poor efficiency of the neutralization process. Beam-generated plasma neutralizers were proposed as a passive and intrinsically safe scheme of efficient plasma neutralizers. The concept is based on the natural ionization of the gas target by the beam, and on a suitable confinement of the secondary plasma. The technological challenge of such a concept is the magnetic confinement of the secondary plasma: a proof-of-principle for the concept is needed. The possibility to test of such a system in the small negative ion beam system NIO1 is discussed in this paper. The constraints given by the facility are first discussed. A model of beam-gas interaction is developed to provide the charge-state of beam particles along the neutralizer, and to provide the source terms of plasma generation. By using a cylindrical model of plasma diffusion in magnetic fields, the ionization degree of the target is estimated. In the absence of magnetic fields the diffusion model is validated against experimental measurements of the space-charge compensation plasma in the drift region of NIO1. Finally, the feasibility study for a beam-generated plasma neutralizer in NIO is presented. The neutralizer length, required gas target thickness, and a very simple magnetic setup were considered, taking into account the integration in NIO1. For the basic design a low ionization degree (1%) is obtained, however a promising plasma density up to hundred times the beam density was calculated. The proposed test in NIO1 can be the starting point for studying advanced schemes of magnetic confinement aiming at ionization degrees in the order of 10%.

A complex speciation–richness relationship in a simple neutral model

PubMed Central

Desjardins-Proulx, Philippe; Gravel, Dominique

2012-01-01

Speciation is the “elephant in the room” of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities. We focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. We use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations. PMID:22957181

Survival of mutations arising during invasions

PubMed Central

Miller, Judith R

2010-01-01

When a neutral mutation arises in an invading population, it quickly either dies out or ‘surfs’, i.e. it comes to occupy almost all the habitat available at its time of origin. Beneficial mutations can also surf, as can deleterious mutations over finite time spans. We develop descriptive statistical models that quantify the relationship between the probability that a mutation will surf and demographic parameters for a cellular automaton model of surfing. We also provide a simple analytic model that performs well at predicting the probability of surfing for neutral and beneficial mutations in one dimension. The results suggest that factors – possibly including even abiotic factors – that promote invasion success may also increase the probability of surfing and associated adaptive genetic change, conditioned on such success. PMID:25567912

A forecast for extinction debt in the presence of speciation.

PubMed

Sgardeli, Vasiliki; Iwasa, Yoh; Varvoglis, Harry; Halley, John M

2017-02-21

Predicting biodiversity relaxation following a disturbance is of great importance to conservation biology. Recently-developed models of stochastic community assembly allow us to predict the evolution of communities on the basis of mechanistic processes at the level of individuals. The neutral model of biodiversity, in particular, has provided closed-form solutions for the relaxation of biodiversity in isolated communities (no immigration or speciation). Here, we extend these results by deriving a relaxation curve for a neutral community in which new species are introduced through the mechanism of random fission speciation (RFS). The solution provides simple closed-form expressions for the equilibrium species richness, the relaxation time and the species-individual curve, which are good approximation to the more complicated formulas existing for the same model. The derivation of the relaxation curve is based on the assumption of a broken-stick species-abundance distribution (SAD) as an initial community configuration; yet for commonly observed SADs, the maximum deviation from the curve does not exceed 10%. Importantly, the solution confirms theoretical results and observations showing that the relaxation time increases with community size and thus habitat area. Such simple and analytically tractable models can help crystallize our ideas on the leading factors affecting biodiversity loss. Copyright © 2016 Elsevier Ltd. All rights reserved.

Population Genetics of Three Dimensional Range Expansions

NASA Astrophysics Data System (ADS)

Lavrentovich, Maxim; Nelson, David

2014-03-01

We develop a simple model of genetic diversity in growing spherical cell clusters, where the growth is confined to the cluster surface. This kind of growth occurs in cells growing in soft agar, and can also serve as a simple model of avascular tumors. Mutation-selection balance in these radial expansions is strongly influenced by scaling near a neutral, voter model critical point and by the inflating frontier. We develop a scaling theory to describe how the dynamics of mutation-selection balance is cut off by inflation. Genetic drift, i.e., local fluctuations in the genetic diversity, also plays an important role, and can lead to the extinction even of selectively advantageous strains. We calculate this extinction probability, taking into account the effect of rough population frontiers.

Evaluating Models Of The Neutral, Barotropic Planetary Boundary Layer Using Integral Measures: Part Ii. Modelling Observed Conditions

NASA Astrophysics Data System (ADS)

Hess, G. D.; Garratt, J. R.

The steady-state, horizontally homogeneous, neutral, barotropiccase forms the foundation of our theoretical understanding of the planetary boundary layer (PBL).While simple analytical models and first-order closure models simulate atmospheric observationsof this case well, more sophisticated models, in general, do not. In this paperwe examine how well three higher-order closure models, E - - l, E - l, and LRR - l,which have been especially modified for PBL applications, perform in predicting the behaviour of thecross-isobaric angle 0, the geostrophic drag coefficient Cg, and the integral of the dissipationrate over the boundary layer, as a function of the surface Rossby number Ro. For comparison we alsoexamine the performance of three first-order closure mixing-length models, two proposed byA. K. Blackadar and one by H. H. Lettau, and the performance of the standard model forsecond-order closure and a modification of it designed to reduce the overprediction of turbulence inthe upper part of the boundary layer.

Bottleneck Effect on Evolutionary Rate in the Nearly Neutral Mutation Model

PubMed Central

Araki, H.; Tachida, H.

1997-01-01

Variances of evolutionary rates among lineages in some proteins are larger than those expected from simple Poisson processes. This phenomenon is called overdispersion of the molecular clock. If population size N is constant, the overdispersion is observed only in a limited range of 2Nσ under the nearly neutral mutation model, where σ represents the standard deviation of selection coefficients of new mutants. In this paper, we investigated effects of changing population size on the evolutionary rate by computer simulations assuming the nearly neutral mutation model. The size was changed cyclically between two numbers, N(1) and N(2) (N(1) > N(2)), in the simulations. The overdispersion is observed if 2N(2)σ is less than two and the state of reduced size (bottleneck state) continues for more than ~0.1/u generations, where u is the mutation rate. The overdispersion results mainly because the average fitnesses of only a portion of populations go down when the population size is reduced and only in these populations subsequent advantageous substitutions occur after the population size becomes large. Since the fitness reduction after the bottleneck is stochastic, acceleration of the evolutionary rate does not necessarily occur uniformly among loci. From these results, we argue that the nearly neutral mutation model is a candidate mechanism to explain the overdispersed molecular clock. PMID:9335622

Biophysical implications of sphingosine accumulation in membrane properties at neutral and acidic pH.

PubMed

Zupancic, Eva; Carreira, Ana C; de Almeida, Rodrigo F M; Silva, Liana C

2014-05-08

Sphingosine (Sph) is a simple lipid involved in the regulation of several biological processes. When accumulated in the late endosomal/lysosomal compartments, Sph causes changes in ion signaling and membrane trafficking, leading to the development of Niemann-Pick disease type C. Little is known about Sph interaction with other lipids in biological membranes; however, understanding the effect of Sph in the physical state of membranes might provide insights into its mode of action. Using complementary established fluorescence approaches, we show that Sph accumulation leads to the formation of Sph-enriched gel domains in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/sphingomyelin (SM)/cholesterol (Chol) model membranes. These domains are more easily formed in membrane models mimicking the neutral pH plasma membrane environment (PM) as compared to the acidic lysosomal membrane environment (LM), where higher Sph concentrations (or lower temperatures) are required. Electrophoretic light scattering measurements further revealed that in PM-raft models (POPC/SM/Chol), Sph is mainly neutral, whereas in LM models, the positive charge of Sph leads to electrostatic repulsion, reducing the Sph ability to form gel domains. Thus, formation of Sph-enriched domains in cellular membranes might be strongly regulated by Sph charge.

Simple Process-Based Simulators for Generating Spatial Patterns of Habitat Loss and Fragmentation: A Review and Introduction to the G-RaFFe Model

PubMed Central

Pe'er, Guy; Zurita, Gustavo A.; Schober, Lucia; Bellocq, Maria I.; Strer, Maximilian; Müller, Michael; Pütz, Sandro

2013-01-01

Landscape simulators are widely applied in landscape ecology for generating landscape patterns. These models can be divided into two categories: pattern-based models that generate spatial patterns irrespective of the processes that shape them, and process-based models that attempt to generate patterns based on the processes that shape them. The latter often tend toward complexity in an attempt to obtain high predictive precision, but are rarely used for generic or theoretical purposes. Here we show that a simple process-based simulator can generate a variety of spatial patterns including realistic ones, typifying landscapes fragmented by anthropogenic activities. The model “G-RaFFe” generates roads and fields to reproduce the processes in which forests are converted into arable lands. For a selected level of habitat cover, three factors dominate its outcomes: the number of roads (accessibility), maximum field size (accounting for land ownership patterns), and maximum field disconnection (which enables field to be detached from roads). We compared the performance of G-RaFFe to three other models: Simmap (neutral model), Qrule (fractal-based) and Dinamica EGO (with 4 model versions differing in complexity). A PCA-based analysis indicated G-RaFFe and Dinamica version 4 (most complex) to perform best in matching realistic spatial patterns, but an alternative analysis which considers model variability identified G-RaFFe and Qrule as performing best. We also found model performance to be affected by habitat cover and the actual land-uses, the latter reflecting on land ownership patterns. We suggest that simple process-based generators such as G-RaFFe can be used to generate spatial patterns as templates for theoretical analyses, as well as for gaining better understanding of the relation between spatial processes and patterns. We suggest caution in applying neutral or fractal-based approaches, since spatial patterns that typify anthropogenic landscapes are often non-fractal in nature. PMID:23724108

Simple process-based simulators for generating spatial patterns of habitat loss and fragmentation: a review and introduction to the G-RaFFe model.

PubMed

Pe'er, Guy; Zurita, Gustavo A; Schober, Lucia; Bellocq, Maria I; Strer, Maximilian; Müller, Michael; Pütz, Sandro

2013-01-01

Landscape simulators are widely applied in landscape ecology for generating landscape patterns. These models can be divided into two categories: pattern-based models that generate spatial patterns irrespective of the processes that shape them, and process-based models that attempt to generate patterns based on the processes that shape them. The latter often tend toward complexity in an attempt to obtain high predictive precision, but are rarely used for generic or theoretical purposes. Here we show that a simple process-based simulator can generate a variety of spatial patterns including realistic ones, typifying landscapes fragmented by anthropogenic activities. The model "G-RaFFe" generates roads and fields to reproduce the processes in which forests are converted into arable lands. For a selected level of habitat cover, three factors dominate its outcomes: the number of roads (accessibility), maximum field size (accounting for land ownership patterns), and maximum field disconnection (which enables field to be detached from roads). We compared the performance of G-RaFFe to three other models: Simmap (neutral model), Qrule (fractal-based) and Dinamica EGO (with 4 model versions differing in complexity). A PCA-based analysis indicated G-RaFFe and Dinamica version 4 (most complex) to perform best in matching realistic spatial patterns, but an alternative analysis which considers model variability identified G-RaFFe and Qrule as performing best. We also found model performance to be affected by habitat cover and the actual land-uses, the latter reflecting on land ownership patterns. We suggest that simple process-based generators such as G-RaFFe can be used to generate spatial patterns as templates for theoretical analyses, as well as for gaining better understanding of the relation between spatial processes and patterns. We suggest caution in applying neutral or fractal-based approaches, since spatial patterns that typify anthropogenic landscapes are often non-fractal in nature.

Epistasis increases the rate of conditionally neutral substitution in an adapting population.

PubMed

Draghi, Jeremy A; Parsons, Todd L; Plotkin, Joshua B

2011-04-01

Kimura observed that the rate of neutral substitution should equal the neutral mutation rate. This classic result is central to our understanding of molecular evolution, and it continues to influence phylogenetics, genomics, and the interpretation of evolution experiments. By demonstrating that neutral mutations substitute at a rate independent of population size and selection at linked sites, Kimura provided an influential justification for the idea of a molecular clock and emphasized the importance of genetic drift in shaping molecular evolution. But when epistasis among sites is common, as numerous empirical studies suggest, do neutral mutations substitute according to Kimura's expectation? Here we study simulated, asexual populations of RNA molecules, and we observe that conditionally neutral mutations--i.e., mutations that do not alter the fitness of the individual in which they arise, but that may alter the fitness effects of subsequent mutations--substitute much more often than expected while a population is adapting. We quantify these effects using a simple population-genetic model that elucidates how the substitution rate at conditionally neutral sites depends on the population size, mutation rate, strength of selection, and prevalence of epistasis. We discuss the implications of these results for our understanding of the molecular clock, and for the interpretation of molecular variation in laboratory and natural populations.

Epistasis Increases the Rate of Conditionally Neutral Substitution in an Adapting Population

PubMed Central

Draghi, Jeremy A.; Parsons, Todd L.; Plotkin, Joshua B.

2011-01-01

Kimura observed that the rate of neutral substitution should equal the neutral mutation rate. This classic result is central to our understanding of molecular evolution, and it continues to influence phylogenetics, genomics, and the interpretation of evolution experiments. By demonstrating that neutral mutations substitute at a rate independent of population size and selection at linked sites, Kimura provided an influential justification for the idea of a molecular clock and emphasized the importance of genetic drift in shaping molecular evolution. But when epistasis among sites is common, as numerous empirical studies suggest, do neutral mutations substitute according to Kimura's expectation? Here we study simulated, asexual populations of RNA molecules, and we observe that conditionally neutral mutations—i.e., mutations that do not alter the fitness of the individual in which they arise, but that may alter the fitness effects of subsequent mutations—substitute much more often than expected while a population is adapting. We quantify these effects using a simple population-genetic model that elucidates how the substitution rate at conditionally neutral sites depends on the population size, mutation rate, strength of selection, and prevalence of epistasis. We discuss the implications of these results for our understanding of the molecular clock, and for the interpretation of molecular variation in laboratory and natural populations. PMID:21288876

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

NASA Astrophysics Data System (ADS)

Adli, E.; Lindstrøm, C. A.; Allen, J.; Clarke, C. I.; Frederico, J.; Gessner, S. J.; Green, S. Z.; Hogan, M. J.; Litos, M. D.; O'Shea, B.; Yakimenko, V.; An, W.; Clayton, C. E.; Marsh, K. A.; Mori, W. B.; Joshi, C.; Vafaei-Najafabadi, N.; Corde, S.; Lu, W.

2016-10-01

We report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. The attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam-plasma interactions in general and plasma wakefield accelerator technology in particular.

Coincidence degree and periodic solutions of neutral equations

NASA Technical Reports Server (NTRS)

Hale, J. K.; Mawhin, J.

1973-01-01

The problem of existence of periodic solutions for some nonautonomous neutral functional differential equations is examined. It is an application of a basic theorem on the Fredholm alternative for periodic solutions of some linear neutral equations and of a generalized Leray-Schauder theory. Although proofs are simple, the results are nontrivial extensions to the neutral case of existence theorems for periodic solutions of functional differential equations.

A study of the electric field in an open magnetospheric model

NASA Technical Reports Server (NTRS)

Stern, D. P.

1973-01-01

Recently, Svalgaard and Heppner reported two separate features of the polar electromagnetic field that correlate with the dawn-dusk component of the interplanetary magnetic field. This work attempts to explain these findings in terms of properties of the open magnetosphere. The topology and qualitative properties of the open magnetosphere are first studied by means of a simple model, consisting of a dipole in a constant field. Many such properties are found to depend on the separation line, a curve connecting neutral points and separating different field line regimes. In the simple model it turns out that the electric field in the central polar cap tends to point from dawn to dusk for a wide variety of external fields, but, near the boundary of the polar cap, electric equipotentials are deformed into crescents.

Cosmological signals of a mirror twin Higgs

DOE PAGES

Craig, Nathaniel; Koren, Seth; Trott, Timothy

2017-05-08

We investigate the cosmology of the minimal model of neutral naturalness, the mirror Twin Higgs. The softly-broken mirror symmetry relating the Standard Model to its twin counterpart leads to significant dark radiation in tension with BBN and CMB observations. We quantify this tension and illustrate how it can be mitigated in several simple scenarios that alter the relative energy densities of the two sectors while respecting the softly-broken mirror symmetry. In particular, we consider both the out-of-equilibrium decay of a new scalar as well as reheating in a toy model of twinned inflation, Twinflation. In both cases the dilution ofmore » energy density in the twin sector does not merely reconcile the existence of a mirror Twin Higgs with cosmological constraints, but predicts contributions to cosmological observables that may be probed in current and future CMB experiments. This raises the prospect of discovering evidence of neutral naturalness through cosmology rather than colliders.« less

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

Craig, Nathaniel; Koren, Seth; Trott, Timothy

We investigate the cosmology of the minimal model of neutral naturalness, the mirror Twin Higgs. The softly-broken mirror symmetry relating the Standard Model to its twin counterpart leads to significant dark radiation in tension with BBN and CMB observations. We quantify this tension and illustrate how it can be mitigated in several simple scenarios that alter the relative energy densities of the two sectors while respecting the softly-broken mirror symmetry. In particular, we consider both the out-of-equilibrium decay of a new scalar as well as reheating in a toy model of twinned inflation, Twinflation. In both cases the dilution ofmore » energy density in the twin sector does not merely reconcile the existence of a mirror Twin Higgs with cosmological constraints, but predicts contributions to cosmological observables that may be probed in current and future CMB experiments. This raises the prospect of discovering evidence of neutral naturalness through cosmology rather than colliders.« less

Evolutionary advantage via common action of recombination and neutrality

NASA Astrophysics Data System (ADS)

Saakian, David B.; Hu, Chin-Kun

2013-11-01

We investigate evolution models with recombination and neutrality. We consider the Crow-Kimura (parallel) mutation-selection model with the neutral fitness landscape, in which there is a central peak with high fitness A, and some of 1-point mutants have the same high fitness A, while the fitness of other sequences is 0. We find that the effect of recombination and neutrality depends on the concrete version of both neutrality and recombination. We consider three versions of neutrality: (a) all the nearest neighbor sequences of the peak sequence have the same high fitness A; (b) all the l-point mutations in a piece of genome of length l≥1 are neutral; (c) the neutral sequences are randomly distributed among the nearest neighbors of the peak sequences. We also consider three versions of recombination: (I) the simple horizontal gene transfer (HGT) of one nucleotide; (II) the exchange of a piece of genome of length l, HGT-l; (III) two-point crossover recombination (2CR). For the case of (a), the 2CR gives a rather strong contribution to the mean fitness, much stronger than that of HGT for a large genome length L. For the random distribution of neutral sequences there is a critical degree of neutrality νc, and for μ<μc and (μc-μ) is not large, the 2CR suppresses the mean fitness while HGT increases it; for ν much larger than νc, the 2CR and HGT-l increase the mean fitness larger than that of the HGT. We also consider the recombination in the case of smooth fitness landscapes. The recombination gives some advantage in the evolutionary dynamics, where recombination distinguishes clearly the mean-field-like evolutionary factors from the fluctuation-like ones. By contrast, mutations affect the mean-field-like and fluctuation-like factors similarly. Consequently, recombination can accelerate the non-mean-field (fluctuation) type dynamics without considerably affecting the mean-field-like factors.

Webcam camera as a detector for a simple lab-on-chip time based approach.

PubMed

Wongwilai, Wasin; Lapanantnoppakhun, Somchai; Grudpan, Supara; Grudpan, Kate

2010-05-15

A modification of a webcam camera for use as a small and low cost detector was demonstrated with a simple lab-on-chip reactor. Real time continuous monitoring of the reaction zone could be done. Acid-base neutralization with phenolphthalein indicator was used as a model reaction. The fading of pink color of the indicator when the acidic solution diffused into the basic solution zone was recorded as the change of red, blue and green colors (%RBG.) The change was related to acid concentration. A low cost portable semi-automation analysis system was achieved.

A simple formula for estimating Stark widths of neutral lines. [of stellar atmospheres

NASA Technical Reports Server (NTRS)

Freudenstein, S. A.; Cooper, J.

1978-01-01

A simple formula for the prediction of Stark widths of neutral lines similar to the semiempirical method of Griem (1968) for ion lines is presented. This formula is a simplification of the quantum-mechanical classical path impact theory and can be used for complicated atoms for which detailed calculations are not readily available, provided that the effective position of the closest interacting level is known. The expression does not require the use of a computer. The formula has been applied to a limited number of neutral lines of interest, and the width obtained is compared with the much more complete calculations of Bennett and Griem (1971). The agreement generally is well within 50% of the published value for the lines investigated. Comparisons with other formulas are also made. In addition, a simple estimate for the ion-broadening parameter is given.

A Novel Strategy for Development of Recombinant Antitoxin Therapeutics Tested in a Mouse Botulism Model

PubMed Central

Leysath, Clinton E.; Ofori, Kwasi; Baldwin, Karen; Feng, Xiaochuan; Bedenice, Daniela; Webb, Robert P.; Wright, Patrick M.; Smith, Leonard A.; Tzipori, Saul; Shoemaker, Charles B.

2012-01-01

Antitoxins are needed that can be produced economically with improved safety and shelf life compared to conventional antisera-based therapeutics. Here we report a practical strategy for development of simple antitoxin therapeutics with substantial advantages over currently available treatments. The therapeutic strategy employs a single recombinant ‘targeting agent’ that binds a toxin at two unique sites and a ‘clearing Ab’ that binds two epitopes present on each targeting agent. Co-administration of the targeting agent and the clearing Ab results in decoration of the toxin with up to four Abs to promote accelerated clearance. The therapeutic strategy was applied to two Botulinum neurotoxin (BoNT) serotypes and protected mice from lethality in two different intoxication models with an efficacy equivalent to conventional antitoxin serum. Targeting agents were a single recombinant protein consisting of a heterodimer of two camelid anti-BoNT heavy-chain-only Ab VH (VHH) binding domains and two E-tag epitopes. The clearing mAb was an anti-E-tag mAb. By comparing the in vivo efficacy of treatments that employed neutralizing vs. non-neutralizing agents or the presence vs. absence of clearing Ab permitted unprecedented insight into the roles of toxin neutralization and clearance in antitoxin efficacy. Surprisingly, when a post-intoxication treatment model was used, a toxin-neutralizing heterodimer agent fully protected mice from intoxication even in the absence of clearing Ab. Thus a single, easy-to-produce recombinant protein was as efficacious as polyclonal antiserum in a clinically-relevant mouse model of botulism. This strategy should have widespread application in antitoxin development and other therapies in which neutralization and/or accelerated clearance of a serum biomolecule can offer therapeutic benefit. PMID:22238680

A novel strategy for development of recombinant antitoxin therapeutics tested in a mouse botulism model.

PubMed

Mukherjee, Jean; Tremblay, Jacqueline M; Leysath, Clinton E; Ofori, Kwasi; Baldwin, Karen; Feng, Xiaochuan; Bedenice, Daniela; Webb, Robert P; Wright, Patrick M; Smith, Leonard A; Tzipori, Saul; Shoemaker, Charles B

2012-01-01

Antitoxins are needed that can be produced economically with improved safety and shelf life compared to conventional antisera-based therapeutics. Here we report a practical strategy for development of simple antitoxin therapeutics with substantial advantages over currently available treatments. The therapeutic strategy employs a single recombinant 'targeting agent' that binds a toxin at two unique sites and a 'clearing Ab' that binds two epitopes present on each targeting agent. Co-administration of the targeting agent and the clearing Ab results in decoration of the toxin with up to four Abs to promote accelerated clearance. The therapeutic strategy was applied to two Botulinum neurotoxin (BoNT) serotypes and protected mice from lethality in two different intoxication models with an efficacy equivalent to conventional antitoxin serum. Targeting agents were a single recombinant protein consisting of a heterodimer of two camelid anti-BoNT heavy-chain-only Ab V(H) (VHH) binding domains and two E-tag epitopes. The clearing mAb was an anti-E-tag mAb. By comparing the in vivo efficacy of treatments that employed neutralizing vs. non-neutralizing agents or the presence vs. absence of clearing Ab permitted unprecedented insight into the roles of toxin neutralization and clearance in antitoxin efficacy. Surprisingly, when a post-intoxication treatment model was used, a toxin-neutralizing heterodimer agent fully protected mice from intoxication even in the absence of clearing Ab. Thus a single, easy-to-produce recombinant protein was as efficacious as polyclonal antiserum in a clinically-relevant mouse model of botulism. This strategy should have widespread application in antitoxin development and other therapies in which neutralization and/or accelerated clearance of a serum biomolecule can offer therapeutic benefit.

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

PubMed Central

Munteanu, Andreea; Solé, Ricard V.

2008-01-01

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles. PMID:19023404

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

DOE PAGES

Adli, Erik; Lindstrom, C. A.; Allen, J.; ...

2016-10-12

Here, we report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. Themore » attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam–plasma interactions in general and plasma wakefield accelerator technology in particular.« less

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

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

Adli, Erik; Lindstrom, C. A.; Allen, J.

Here, we report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. Themore » attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam–plasma interactions in general and plasma wakefield accelerator technology in particular.« less

In-silico studies of neutral drift for functional protein interaction networks

NASA Astrophysics Data System (ADS)

Ali, Md Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

We have developed a minimal physically-motivated model of protein-protein interaction networks. Our system consists of two classes of enzymes, activators (e.g. kinases) and deactivators (e.g. phosphatases), and the enzyme-mediated activation/deactivation rates are determined by sequence-dependent binding strengths between enzymes and their targets. The network is evolved by introducing random point mutations in the binding sequences where we assume that each new mutation is either fixed or entirely lost. We apply this model to studies of neutral drift in networks that yield oscillatory dynamics, where we start, for example, with a relatively simple network and allow it to evolve by adding nodes and connections while requiring that dynamics be conserved. Our studies demonstrate both the importance of employing a sequence-based evolutionary scheme and the relative rapidity (in evolutionary time) for the redistribution of function over new nodes via neutral drift. Surprisingly, in addition to this redistribution time we discovered another much slower timescale for network evolution, reflecting hidden order in sequence space that we interpret in terms of sparsely connected domains.

Do large rate coefficients for ion-polar neutral reactions have a serious effect on chemical models of dense clouds?

NASA Technical Reports Server (NTRS)

Herbst, E.; Leung, C. M.

1986-01-01

In order to incorporate large ion-polar neutral rate coefficients into existing gas phase reaction networks, it is necessary to utilize simplified theoretical treatments because of the significant number of rate coefficients needed. The authors have used two simple theoretical treatments: the locked dipole approach of Moran and Hamill for linear polar neutrals and the trajectory scaling approach of Su and Chesnavich for nonlinear polar neutrals. The former approach is suitable for linear species because in the interstellar medium these are rotationally relaxed to a large extent and the incoming charged reactants can lock their dipoles into the lowest energy configuration. The latter approach is a better approximation for nonlinear neutral species, in which rotational relaxation is normally less severe and the incoming charged reactants are not as effective at locking the dipoles. The treatments are in reasonable agreement with more detailed long range theories and predict an inverse square root dependence on kinetic temperature for the rate coefficient. Compared with the locked dipole method, the trajectory scaling approach results in rate coefficients smaller by a factor of approximately 2.5.

Modeling of electron cyclotron resonance discharges

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

Meyyappan, M.; Govindan, T.R.

The current trend in plasma processing is the development of high density plasma sources to achieve high deposition and etch rates, uniformity over large ares, and low wafer damage. Here, is a simple model to predict the spatially-averaged plasma characteristics of electron cyclotron resonance (ECR) reactors is presented. The model consists of global conservation equations for species concentration, electron density and energy. A gas energy balance is used to predict the neutral temperature self-consistently. The model is demonstrated for an ECR argon discharge. The predicted behavior of the discharge as a function of system variables agrees well with experimental observations.

Processing of unattended, simple negative pictures resists perceptual load.

PubMed

Sand, Anders; Wiens, Stefan

2011-05-11

As researchers debate whether emotional pictures can be processed irrespective of spatial attention and perceptual load, negative and neutral pictures of simple figure-ground composition were shown at fixation and were surrounded by one, two, or three letters. When participants performed a picture discrimination task, there was evidence for motivated attention; that is, an early posterior negativity (EPN) and late positive potential (LPP) to negative versus neutral pictures. When participants performed a letter discrimination task, the EPN was unaffected whereas the LPP was reduced. Although performance decreased substantially with the number of letters (one to three), the LPP did not decrease further. Therefore, attention to simple, negative pictures at fixation seems to resist manipulations of perceptual load.

Neutral-beam deposition in large, finite-beta noncircular tokamak plasmas

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

Wieland, R.M.; Houlberg, W.A.

1982-02-01

A parametric pencil beam model is introduced for describing the attenuation of an energetic neutral beam moving through a tokamak plasma. The nonnegligible effects of a finite beam cross section and noncircular shifted plasma cross sections are accounted for in a simple way by using a smoothing algorithm dependent linearly on beam radius and by including information on the plasma flux surface geometry explicitly. The model is benchmarked against more complete and more time-consuming two-dimensional Monte Carlo calculations for the case of a large D-shaped tokamak plasma with minor radius a = 120 cm and elongation b/a = 1.6. Depositionmore » profiles are compared for deuterium beam energies of 120 to 150 keV, central plasma densities of 8 x 10/sup 13/ - 2 x 10/sup 14/ cm/sup -3/, and beam orientation ranging from perpendicular to tangential to the inside wall.« less

Low-lying Photoexcited States of a One-Dimensional Ionic Extended Hubbard Model

NASA Astrophysics Data System (ADS)

Yokoi, Kota; Maeshima, Nobuya; Hino, Ken-ichi

2017-10-01

We investigate the properties of low-lying photoexcited states of a one-dimensional (1D) ionic extended Hubbard model at half-filling. Numerical analysis by using the full and Lanczos diagonalization methods shows that, in the ionic phase, there exist low-lying photoexcited states below the charge transfer gap. As a result of comparison with numerical data for the 1D antiferromagnetic (AF) Heisenberg model, it was found that, for a small alternating potential Δ, these low-lying photoexcited states are spin excitations, which is consistent with a previous analytical study [Katsura et al., Phys. Rev. Lett. 103, 177402 (2009)]. As Δ increases, the spectral intensity of the 1D ionic extended Hubbard model rapidly deviates from that of the 1D AF Heisenberg model and it is clarified that this deviation is due to the neutral-ionic domain wall, an elementary excitation near the neutral-ionic transition point.

Anisotropy of diamagnetic susceptibility in Thassos marble: A comparison between measured and modeled data

NASA Astrophysics Data System (ADS)

de Wall, Helga; Bestmann, Michel; Ullemeyer, Klaus

2000-11-01

A study of shear zones within the calcite marble complex of the island of Thassos (Greece) shows that the low field anisotropy of magnetic susceptibility (AMS)-technique can be successfully applied to diamagnetic rocks for characterizing rock fabrics. The strain path involves both an early pure shear stage and a simple shear overprint that is documented by a transition from triaxial (neutral) to uniaxial (prolate) shapes of AMS ellipsoids. The maximum susceptibility is oriented perpendicular to the rock foliation, reflecting the preferred orientation of calcite c-axes in the protolith as well as in the mylonites. For three samples that represent different types of calcite fabrics, the AMS was recalculated from neutron and electron backscatter diffraction textural data. A comparison of the measured and modeled data shows a good coincidence for the orientation of the principal AMS axes and for the recalculated anisotropy data. Both measured and modeled data sets reflect the change from neutral to distinct prolate ellipsoids during progressive deformation.

Fish community reassembly after a coral mass mortality: higher trophic groups are subject to increased rates of extinction.

PubMed

Alonso, David; Pinyol-Gallemí, Aleix; Alcoverro, Teresa; Arthur, Rohan

2015-05-01

Since Gleason and Clements, our understanding of community dynamics has been influenced by theories emphasising either dispersal or niche assembly as central to community structuring. Determining the relative importance of these processes in structuring real-world communities remains a challenge. We tracked reef fish community reassembly after a catastrophic coral mortality in a relatively unfished archipelago. We revisited the stochastic model underlying MacArthur and Wilson's Island Biogeography Theory, with a simple extension to account for trophic identity. Colonisation and extinction rates calculated from decadal presence-absence data based on (1) species neutrality, (2) trophic identity and (3) site-specificity were used to model post-disturbance reassembly, and compared with empirical observations. Results indicate that species neutrality holds within trophic guilds, and trophic identity significantly increases overall model performance. Strikingly, extinction rates increased clearly with trophic position, indicating that fish communities may be inherently susceptible to trophic downgrading even without targeted fishing of top predators. © 2015 John Wiley & Sons Ltd/CNRS.

A Selected Library of Transport Coefficients for Combustion and Plasma Physics Applications

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

Cloutman, L.D.

2000-08-01

COYOTE and similar combustion programs based on the multicomponent Navier-Stokes equations require the mixture viscosity, thermal conductivity, and species transport coefficients as input. This report documents a model of these molecular transport coefficients that is simpler than the general theory, but which provides adequate accuracy for many purposes. This model leads to a computationally convenient, self-contained, and easy-to-use source of such data in a format suitable for use by such programs. We present the data for various neutral species in two forms. The first form is a simple functional fit to the transport coefficients. The second form is the usemore » of tabulated Lennard-Jones parameters in simple theoretical expressions for the gas-phase transport coefficients. The model then is extended to the case of a two-temperature plasma. Lennard-Jones parameters are given for a number of chemical species of interest in combustion research.« less

SiMa Cells for a Serotype Specific and Sensitive Cell-Based Neutralization Test for Botulinum Toxin A and E.

PubMed

Bak, Nicola; Rajagopal, Shalini; Stickings, Paul; Sesardic, Dorothea

2017-07-20

Botulinum toxins (BoNTs), of which there are seven serotypes, are among the most potent neurotoxins, with serotypes A, B and E causing human botulism. Antitoxins form the first line of treatment for botulism, and functional, highly sensitive in vitro methods for toxin neutralization are needed to replace the current in vivo methods used for determination of antitoxin potency. In this preliminary proof of concept study, we report the development of a neutralization test using the neuroblastoma SiMa cell line. The assay is serotype specific for either BoNT/A or BoNT/E, which both cleave unique sequences on SNAP-25 within SiMa cells. The end point is simple immunodetection of cleaved SNAP-25 from cell lysates with antibodies detecting only the newly exposed sequence on SNAP-25. Neutralizing antibodies prevent the toxin-induced cleavage of SNAP-25. The toxin neutralization assay, with an EC50 of ~2 mIU/mL determined with a standardized reference antiserum, is more sensitive than the mouse bioassays. Relevance was demonstrated with commercial and experimental antitoxins targeting different functional domains, and of known in vivo neutralizing activities. This is the first report describing a simple, specific, in vitro cell-based assay for the detection of neutralizing antibodies against BoNT/A and BoNT/E with a sensitivity exceeding that of the mouse bioassay.

SiMa Cells for a Serotype Specific and Sensitive Cell-Based Neutralization Test for Botulinum Toxin A and E

PubMed Central

Bak, Nicola; Rajagopal, Shalini; Stickings, Paul; Sesardic, Dorothea

2017-01-01

Botulinum toxins (BoNTs), of which there are seven serotypes, are among the most potent neurotoxins, with serotypes A, B and E causing human botulism. Antitoxins form the first line of treatment for botulism, and functional, highly sensitive in vitro methods for toxin neutralization are needed to replace the current in vivo methods used for determination of antitoxin potency. In this preliminary proof of concept study, we report the development of a neutralization test using the neuroblastoma SiMa cell line. The assay is serotype specific for either BoNT/A or BoNT/E, which both cleave unique sequences on SNAP-25 within SiMa cells. The end point is simple immunodetection of cleaved SNAP-25 from cell lysates with antibodies detecting only the newly exposed sequence on SNAP-25. Neutralizing antibodies prevent the toxin-induced cleavage of SNAP-25. The toxin neutralization assay, with an EC50 of ~2 mIU/mL determined with a standardized reference antiserum, is more sensitive than the mouse bioassays. Relevance was demonstrated with commercial and experimental antitoxins targeting different functional domains, and of known in vivo neutralizing activities. This is the first report describing a simple, specific, in vitro cell-based assay for the detection of neutralizing antibodies against BoNT/A and BoNT/E with a sensitivity exceeding that of the mouse bioassay. PMID:28726719

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.

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

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

Liu, Qing; Shi, Chaowei; Yu, Lu

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in amore » defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.« less

Minimal Unified Resolution to R_{K^{(*)}} and R(D^{(*)}) Anomalies with Lepton Mixing.

PubMed

Choudhury, Debajyoti; Kundu, Anirban; Mandal, Rusa; Sinha, Rahul

2017-10-13

It is a challenging task to explain, in terms of a simple and compelling new physics scenario, the intriguing discrepancies between the standard model expectations and the data for the neutral-current observables R_{K} and R_{K^{*}}, as well as the charged-current observables R(D) and R(D^{*}). We show that this can be achieved in an effective theory with only two unknown parameters. In addition, this class of models predicts some interesting signatures in the context of both B decays as well as high-energy collisions.

On the improbability of intelligent extraterrestrials

NASA Astrophysics Data System (ADS)

Bond, A.

1982-05-01

Discussions relating to the prevalence of extraterrestrial life generally remain ambiguous due to the lack of a suitable model for the development of biology. In this paper a simple model is proposed based on neutral evolution theory which leads to quantitative values for the genome growth rate within a biosphere. It is hypothesised that the genome size is a measure of organism complexity and hence an indicator of the likelihood of intelligence. The calculations suggest that organisms with the complexity of human beings may be rare and only occur with a probability below once per galaxy.

Improvements to the ICRH antenna time-domain 3D plasma simulation model

NASA Astrophysics Data System (ADS)

Smithe, David N.; Jenkins, Thomas G.; King, J. R.

2015-12-01

We present a summary of ongoing improvements to the 3D time-domain plasma modeling software that has been used to look at ICRH antennas on Alcator C-Mod, NSTX, and ITER [1]. Our past investigations have shown that in low density cases where the slow wave is propagating, strong amplitude lower hybrid resonant fields can occur. Such a scenario could result in significant parasitic power loss in the SOL. The primary resonance broadening in this case is likely collisions with neutral gas, and thus we are upgrading the model to include realistic neutral gas in the SOL, in order to provide a better understanding of energy balance in these situations. Related to this, we are adding a temporal variation capability to the local plasma density in front of the antenna in order to investigate whether the near fields of the antenna could modify the local density sufficiently to initiate a low density situation. We will start with a simple scalar ponderomotive potential density expulsion model [2] for the density evolution, but are also looking to eventually couple to a more complex fluid treatment that would include tensor pressures and convective physics and sources of neutrals and ionization. We also review continued benchmarking efforts, and ongoing and planned improvements to the computational algorithms, resulting from experience gained during our recent supercomputing runs on the Titan supercomputer, including GPU operations.

Influence of pH on Drug Absorption from the Gastrointestinal Tract: A Simple Chemical Model

NASA Astrophysics Data System (ADS)

Hickman, Raymond J. S.; Neill, Jane

1997-07-01

A simple model of the gastrointestinal tract is obtained by placing ethyl acetate in contact with water at pH 2 and pH 8 in separate test tubes. The ethyl acetate corresponds to the lipid material lining the tract while the water corresponds to the aqueous contents of the stomach (pH 2) and intestine (pH 8). The compounds aspirin, paracetamol and 3-aminophenol are used as exemplars of acidic, neutral and basic drugs respectively to illustrate the influence which pH has on the distribution of each class of drug between the aqueous and organic phases of the model. The relative concentration of drug in the ethyl acetate is judged by applying microlitre-sized samples of ethyl acetate to a layer of fluorescent silica which, after evaporation of the ethyl acetate, is viewed under an ultraviolet lamp. Each of the three drugs, if present in the ethyl acetate, becomes visible as a dark spot on the silica layer. The observations made in the model system correspond well to the patterns of drug absorption from the gastrointestinal tract described in pharmacology texts and these observations are convincingly explained in terms of simple acid-base chemistry.

Radial Variations in the Io Plasma Torus during the Cassini Era

NASA Technical Reports Server (NTRS)

Delamere, P. A.; Bagenal, F.; Steffl, A.

2005-01-01

A radial scan through the midnight sector of the Io plasma torus was made by the Cassini Ultraviolet Imaging Spectrograph on 14 January 2001, shortly after closest approach to Jupiter. From these data, Steffl et al. (2004a) derived electron temperature, plasma composition (ion mixing ratios), and electron column density as a function of radius from L = 6 to 0 as well as the total luminosity. We have advanced our homogeneous model of torus physical chemistry (Delamere and Bagenal, 2003) to include latitudinal and radial variations in a manner similar to the two-dimensional model by Schreier et al. (1998). The model variables include: (1) neutral source rate, (2) radial transport coefficient, (3) the hot electron fraction, (4) hot electron temperature, and (5) the neutral O/S ratio. The radial variation of parameters 1-4 are described by simple power laws, making a total of nine parameters. We have explored the sensitivity of the model results to variations in these parameters and compared the best fit with previous Voyager era models (schreier et al., 1998), galileo data (Crary et al., 1998), and Cassini observations (steffl et al., 2004a). We find that radial variations during the Cassini era are consistent with a neutral source rate of 700-1200 kg/s, an integrated transport time from L = 6 to 9 of 100-200 days, and that the core electron temperature is largely determined by a spatially and temporally varying superthermal electron population.

Modelling ultraviolet-line diagnostics of stars, the ionized and the neutral interstellar medium in star-forming galaxies

NASA Astrophysics Data System (ADS)

Vidal-García, A.; Charlot, S.; Bruzual, G.; Hubeny, I.

2017-09-01

We combine state-of-the-art models for the production of stellar radiation and its transfer through the interstellar medium (ISM) to investigate ultraviolet-line diagnostics of stars, the ionized and the neutral ISM in star-forming galaxies. We start by assessing the reliability of our stellar population synthesis modelling by fitting absorption-line indices in the ISM-free ultraviolet spectra of 10 Large Magellanic Cloud clusters. In doing so, we find that neglecting stochastic sampling of the stellar initial mass function in these young (∼10-100 Myr), low-mass clusters affects negligibly ultraviolet-based age and metallicity estimates but can lead to significant overestimates of stellar mass. Then, we proceed and develop a simple approach, based on an idealized description of the main features of the ISM, to compute in a physically consistent way the combined influence of nebular emission and interstellar absorption on ultraviolet spectra of star-forming galaxies. Our model accounts for the transfer of radiation through the ionized interiors and outer neutral envelopes of short-lived stellar birth clouds, as well as for radiative transfer through a diffuse intercloud medium. We use this approach to explore the entangled signatures of stars, the ionized and the neutral ISM in ultraviolet spectra of star-forming galaxies. We find that, aside from a few notable exceptions, most standard ultraviolet indices defined in the spectra of ISM-free stellar populations are prone to significant contamination by the ISM, which increases with metallicity. We also identify several nebular-emission and interstellar-absorption features, which stand out as particularly clean tracers of the different phases of the ISM.

Transition from moving to stationary double layers in a single-ended Q machine

NASA Technical Reports Server (NTRS)

Song, Bin; Merlino, R. L.; D'Angelo, N.

1990-01-01

Large-amplitude (less than about 100 percent) relaxation oscillations in the plasma potential are known to be generated when the cold endplate of a single-ended Q machine is biased positively. These oscillations are associated with double layers that form near the hot plate (plasma source) and travel toward the endplate at about the ion-acoustic velocity. At the endplate they dissolve and then form again near the hot plate, the entire process repeating itself in a regular manner. By admitting a sufficient amount of neutral gas into the system, the moving double layers were slowed down and eventually stopped. The production of stationary double layers requires an ion source on the high-potential side of the double layers. These ions are provided by ionization of the neutral gas by electrons that are accelerated through the double layer. The dependence of the critical neutral gas pressure required for stationary double-layer formation on endplate voltage, magnetic field strength, and neutral atom mass has been examined. These results are discussed in terms of a simple model of ion production and loss, including ion losses across the magnetic field.

What Can Galaxies Tell Us About The Epoch of Reionization?

NASA Astrophysics Data System (ADS)

Mason, Charlotte; GLASS, BoRG

2018-01-01

The reionization of neutral hydrogen in the intergalactic medium (IGM) in the universe's first billion years (z>6) was likely driven by the first stars and galaxies, and its history encodes information about their properties. But the timeline of reionization is not well-measured and it is still unclear whether galaxies alone can produce the required ionizing photons. I will describe two key ways in which galaxies at our current observational frontiers can constrain reionization.One tool is the UV luminosity function (LF), which traces the evolution of star-forming galaxies and their ionizing photons. I will describe a Bayesian technique to account for gravitational lensing magnification bias in galaxy surveys to produce accurate LFs. I will then describe a simple, but powerful, model for LF evolution and its implications for reionization and z>10 galaxy surveys with JWST. Secondly, Lyman alpha (Lya) emission from galaxies is a potential probe of the IGM ionization state as Lya photons are strongly attenuated by neutral hydrogen, but requires disentangling physics on pc to Gpc scales. I will introduce a new forward-modeling Bayesian framework which combines cosmological IGM simulations with models of interstellar medium conditions to infer the IGM neutral fraction from observations of Lya emission. I will present our new measurement of the neutral fraction at z~7 and place it in the context of other constraints of the reionization history. I will describe ongoing efforts to build larger samples of Lya emitting galaxies for more accurate measurements with the HST survey GLASS, and will describe future prospects with JWST.

Limits to CO2-Neutrality of Burning Wood. (Review)

NASA Astrophysics Data System (ADS)

Abolins, J.; Gravitis, J.

2016-08-01

Consumption of wood as a source of energy is discussed with respect to efficiency and restraints to ensure sustainability of the environment on the grounds of a simple analytical model describing dynamics of biomass accumulation in forest stands - a particular case of the well-known empirical Richards' equation. Amounts of wood harvested under conditions of maximum productivity of forest land are presented in units normalised with respect to the maximum of the mean annual increment and used to determine the limits of CO2-neutrality. The ecological "footprint" defined by the area of growing stands necessary to absorb the excess amount of CO2 annually released from burning biomass is shown to be equal to the land area of a plantation providing sustainable supply of fire-wood.

Spectroscopic measurements of hydrogen ion temperature during divertor recombination

NASA Astrophysics Data System (ADS)

Stotler, D. P.; Skinner, C. H.; Karney, C. F. F.

1999-01-01

We explore the possibility of using the neutral Hα spectral line profile to measure the ion temperature, Ti, in a recombining plasma. Since the Hα emissions due to recombination are larger than those due to other mechanisms, interference from nonrecombining regions contributing to the chord integrated data is insignificant. A Doppler and Stark broadened Hα spectrum is simulated by the DEGAS 2 neutral transport code using assumed plasma conditions. The application of a simple fitting procedure to this spectrum yields an electron density, ne, and Ti consistent with the assumed plasma parameters if the spectrum is dominated by recombination from a region of modest ne variation. General measurements of the ion temperature by Hα spectroscopy appear feasible within the context of a model for the entire divertor plasma.

Reconstructing particle masses in events with displaced vertices

NASA Astrophysics Data System (ADS)

Cottin, Giovanna

2018-03-01

We propose a simple way to extract particle masses given a displaced vertex signature in event topologies where two long-lived mother particles decay to visible particles and an invisible daughter. The mother could be either charged or neutral and the neutral daughter could correspond to a dark matter particle in different models. The method allows to extract the parent and daughter masses by using on-shell conditions and energy-momentum conservation, in addition to the displaced decay positions of the parents, which allows to solve the kinematic equations fully on an event-by-event basis. We show the validity of the method by means of simulations including detector effects. If displaced events are seen in discovery searches at the Large Hadron Collider (LHC), this technique can be applied.

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes.

PubMed

Lv, Jie; Havlak, Paul; Putnam, Nicholas H

2011-10-05

Many metazoan genomes conserve chromosome-scale gene linkage relationships ("macro-synteny") from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation. We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context ("DCJ-[C]"), and is available as open source software from http://github.com/putnamlab/dcj-c. A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.

Impurity-induced photoconductivity of narrow-gap Cadmium–Mercury–Telluride structures

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

Kozlov, D. V., E-mail: dvkoz@impras.ru; Rumyantsev, V. V.; Morozov, S. V.

2015-12-15

The photoconductivity (PC) spectra of CdHgTe (MCT) solid solutions with a Cd fraction of 17 and 19% are measured. A simple model for calculating the states of doubly charged acceptors in MCT solid solutions, which makes it possible to describe satisfactorily the observed photoconductivity spectra, is proposed. The found lines in the photoconductivity spectra of narrow-gap MCT structures are associated with transitions between the states of both charged and neutral acceptor centers.

A simple spectral model of the dynamics of the Venus ionosphere

NASA Technical Reports Server (NTRS)

Singhal, R. P.; Whitten, R. C.

1987-01-01

A two-dimensional model of the ionosphere of Venus has been constructed by expanding pertinent quantities in Legendre polynomials. The model is simplified by including only a single ion species, O(+). Horizontal plasma flow velocity and plasma density have been calculated as a coupled system. The calculated plasma flow velocity is found to be in good agreement with observations and the results of earlier studies. Solar zenith angle dependence of plasma density, particularly on the nightside, shows some features which differ from results of earlier studies and observed values. Effects of raising or lowering the ionopause height and changing the nightside neutral atmosphere have been discussed.

Analysis of Plasma Communication Schemes for Hypersonic Vehicles: Final Report

DTIC Science & Technology

2009-02-01

repel the more mobile species. In this way quasi -neutrality can be maintained in the plasma. The potential drops near the conducting surfaces are of... potential VM cannot be determined from a quasi - neutral diffusion theory and depends on the details of sheath physics at electrode surfaces. In the...the mid potential VM, which cannot be determined by simple quasi -neutral fluid theory, is in general a function of L. This L dependence, which

An alternative derivation of the stationary distribution of the multivariate neutral Wright-Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data.

PubMed

Schrempf, Dominik; Hobolth, Asger

2017-04-01

Recently, Burden and Tang (2016) provided an analytical expression for the stationary distribution of the multivariate neutral Wright-Fisher model with low mutation rates. In this paper we present a simple, alternative derivation that illustrates the approximation. Our proof is based on the discrete multivariate boundary mutation model which has three key ingredients. First, the decoupled Moran model is used to describe genetic drift. Second, low mutation rates are assumed by limiting mutations to monomorphic states. Third, the mutation rate matrix is separated into a time-reversible part and a flux part, as suggested by Burden and Tang (2016). An application of our result to data from several great apes reveals that the assumption of stationarity may be inadequate or that other evolutionary forces like selection or biased gene conversion are acting. Furthermore we find that the model with a reversible mutation rate matrix provides a reasonably good fit to the data compared to the one with a non-reversible mutation rate matrix. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

A Monte Carlo simulation of the effect of ion self-collisions on the ion velocity distribution function in the high-latitude F-region

NASA Technical Reports Server (NTRS)

Barghouthi, I. A.; Barakat, A. R.; Schunk, R. W.

1994-01-01

Non-Maxwellian ion velocity distribution functions have been theoretically predicted and confirmed by observations, to occur at high latitudes. These distributions deviate from Maxwellian due to the combined effect of the E x B drift and ion-neutral collisions. At high altitude and/or for solar maximum conditions, the ion-to-neutral density ratio increases and, hence, the role of ion self-collisions becomes appreciable. A Monte Carlo simulation was used to investigate the behavior of O(+) ions that are E x B-drifting through a background of neutral O, with the effect of O(+) (Coulomb) self-collisions included. Wide ranges of the ion-to-neutral density ratio n(sub i)/n(sub n) and the electrostatic field E were considered in order to investigate the change of ion behavior with solar cycle and with altitude. For low altitudes and/or solar minimum (n(sub i)/n(sub n) less than or equal to 10(exp -5)), the effect of self-collisions is negligible. For higher values of n(sub i)/n(sub n), the effect of self-collisions becomes significant and, hence, the non-Maxwellian features of the O(+) distribution are reduced. The Monte Carlo results were compared to those that used simplified collision models in order to assess their validity. In general, the simple collision models tend to be more accurate for low E and for high n(sub i)/n(sub n).

Depletion region surface effects in electron beam induced current measurements.

PubMed

Haney, Paul M; Yoon, Heayoung P; Gaury, Benoit; Zhitenev, Nikolai B

2016-09-07

Electron beam induced current (EBIC) is a powerful characterization technique which offers the high spatial resolution needed to study polycrystalline solar cells. Current models of EBIC assume that excitations in the p - n junction depletion region result in perfect charge collection efficiency. However we find that in CdTe and Si samples prepared by focused ion beam (FIB) milling, there is a reduced and nonuniform EBIC lineshape for excitations in the depletion region. Motivated by this, we present a model of the EBIC response for excitations in the depletion region which includes the effects of surface recombination from both charge-neutral and charged surfaces. For neutral surfaces we present a simple analytical formula which describes the numerical data well, while the charged surface response depends qualitatively on the location of the surface Fermi level relative to the bulk Fermi level. We find the experimental data on FIB-prepared Si solar cells is most consistent with a charged surface, and discuss the implications for EBIC experiments on polycrystalline materials.

A zero-equation turbulence model for two-dimensional hybrid Hall thruster simulations

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

Cappelli, Mark A., E-mail: cap@stanford.edu; Young, Christopher V.; Cha, Eunsun

2015-11-15

We present a model for electron transport across the magnetic field of a Hall thruster and integrate this model into 2-D hybrid particle-in-cell simulations. The model is based on a simple scaling of the turbulent electron energy dissipation rate and the assumption that this dissipation results in Ohmic heating. Implementing the model into 2-D hybrid simulations is straightforward and leverages the existing framework for solving the electron fluid equations. The model recovers the axial variation in the mobility seen in experiments, predicting the generation of a transport barrier which anchors the region of plasma acceleration. The predicted xenon neutral andmore » ion velocities are found to be in good agreement with laser-induced fluorescence measurements.« less

Uncertainty analysis on simple mass balance model to calculate critical loads for soil acidity.

PubMed

Li, Harbin; McNulty, Steven G

2007-10-01

Simple mass balance equations (SMBE) of critical acid loads (CAL) in forest soil were developed to assess potential risks of air pollutants to ecosystems. However, to apply SMBE reliably at large scales, SMBE must be tested for adequacy and uncertainty. Our goal was to provide a detailed analysis of uncertainty in SMBE so that sound strategies for scaling up CAL estimates to the national scale could be developed. Specifically, we wanted to quantify CAL uncertainty under natural variability in 17 model parameters, and determine their relative contributions in predicting CAL. Results indicated that uncertainty in CAL came primarily from components of base cation weathering (BC(w); 49%) and acid neutralizing capacity (46%), whereas the most critical parameters were BC(w) base rate (62%), soil depth (20%), and soil temperature (11%). Thus, improvements in estimates of these factors are crucial to reducing uncertainty and successfully scaling up SMBE for national assessments of CAL.

The plasma-wall transition layers in the presence of collisions with a magnetic field parallel to the wall

NASA Astrophysics Data System (ADS)

Moritz, J.; Faudot, E.; Devaux, S.; Heuraux, S.

2018-01-01

The plasma-wall transition is studied by means of a particle-in-cell (PIC) simulation in the configuration of a parallel to the wall magnetic field (B), with collisions between charged particles vs. neutral atoms taken into account. The investigated system consists of a plasma bounded by two absorbing walls separated by 200 electron Debye lengths (λd). The strength of the magnetic field is chosen such as the ratio λ d / r l , with rl being the electron Larmor radius, is smaller or larger than unity. Collisions are modelled with a simple operator that reorients randomly ion or electron velocity, keeping constant the total kinetic energy of both the neutral atom (target) and the incident charged particle. The PIC simulations show that the plasma-wall transition consists in a quasi-neutral region (pre-sheath), from the center of the plasma towards the walls, where the electric potential or electric field profiles are well described by an ambipolar diffusion model, and in a second region at the vicinity of the walls, called the sheath, where the quasi-neutrality breaks down. In this peculiar geometry of B and for a certain range of the mean-free-path, the sheath is found to be composed of two charged layers: the positive one, close to the walls, and the negative one, towards the plasma and before the neutral pre-sheath. Depending on the amplitude of B, the spatial variation of the electric potential can be non-monotonic and presents a maximum within the sheath region. More generally, the sheath extent as well as the potential drop within the sheath and the pre-sheath is studied with respect to B, the mean-free-path, and the ion and electron temperatures.

Distinguishing Positive Selection From Neutral Evolution: Boosting the Performance of Summary Statistics

PubMed Central

Lin, Kao; Li, Haipeng; Schlötterer, Christian; Futschik, Andreas

2011-01-01

Summary statistics are widely used in population genetics, but they suffer from the drawback that no simple sufficient summary statistic exists, which captures all information required to distinguish different evolutionary hypotheses. Here, we apply boosting, a recent statistical method that combines simple classification rules to maximize their joint predictive performance. We show that our implementation of boosting has a high power to detect selective sweeps. Demographic events, such as bottlenecks, do not result in a large excess of false positives. A comparison to other neutrality tests shows that our boosting implementation performs well compared to other neutrality tests. Furthermore, we evaluated the relative contribution of different summary statistics to the identification of selection and found that for recent sweeps integrated haplotype homozygosity is very informative whereas older sweeps are better detected by Tajima's π. Overall, Watterson's θ was found to contribute the most information for distinguishing between bottlenecks and selection. PMID:21041556

A study of the electric field in an open magnetospheric model

NASA Technical Reports Server (NTRS)

Stern, D. P.

1972-01-01

The qualitative properties of an open magnetosphere and its electric field are examined and compared to a simple model of a dipole in a constant field and to actual observations. Many of these properties are found to depend on the separatrix, a curve connecting neutral points and separating different field-line regimes. In the simple model, the electric field in the central polar cap tends to point from dawn to dusk for a wide choice of external fields. Near the boundary of the polar cap electric equipotentials curve and become crescent-shaped, which may explain the correlation of polar magnetic variations with the azimuthal component of the interplanetary magnetic field, reported by Svalgaard. Modifications expected to occur in the actual magnetosphere are also investigated: in particular, it appears that bending of equipotentials may be reduced by cross-field flow during the merging of field lines and that open field lines connected to the polar caps emerge from a long and narrow slot extending along the tail.

Ion thruster performance model

NASA Technical Reports Server (NTRS)

Brophy, J. R.

1984-01-01

A model of ion thruster performance is developed for high flux density, cusped magnetic field thruster designs. This model is formulated in terms of the average energy required to produce an ion in the discharge chamber plasma and the fraction of these ions that are extracted to form the beam. The direct loss of high energy (primary) electrons from the plasma to the anode is shown to have a major effect on thruster performance. The model provides simple algebraic equations enabling one to calculate the beam ion energy cost, the average discharge chamber plasma ion energy cost, the primary electron density, the primary-to-Maxwellian electron density ratio and the Maxwellian electron temperature. Experiments indicate that the model correctly predicts the variation in plasma ion energy cost for changes in propellant gas (Ar, Kr and Xe), grid transparency to neutral atoms, beam extraction area, discharge voltage, and discharge chamber wall temperature. The model and experiments indicate that thruster performance may be described in terms of only four thruster configuration dependent parameters and two operating parameters. The model also suggests that improved performance should be exhibited by thruster designs which extract a large fraction of the ions produced in the discharge chamber, which have good primary electron and neutral atom containment and which operate at high propellant flow rates.

Stability and Evolution of Supernova Fallback Disks

NASA Astrophysics Data System (ADS)

Menou, Kristen; Perna, Rosalba; Hernquist, Lars

2001-10-01

We show that thin accretion disks made of carbon or oxygen are subject to the same thermal ionization instability as hydrogen and helium disks. We argue that the instability applies to disks of any metal content. The relevance of the instability to supernova fallback disks probably means that their power-law evolution breaks down when they first become neutral. We construct simple analytical models for the viscous evolution of fallback disks to show that it is possible for these disks to become neutral when they are still young (ages of a few 103 to 104 yr), compact in size (a few 109 to 1011 cm) and generally accreting at sub-Eddington rates (M~a few 1014-1018 g s-1). Based on recent results on the nature of viscosity in the disks of close binaries, we argue that this time may also correspond to the end of the disk activity period. Indeed, in the absence of a significant source of viscosity in the neutral phase, the entire disk will likely turn to dust and become passive. We discuss various applications of the evolutionary model, including anomalous X-ray pulsars and young radio pulsars. Our analysis indicates that metal-rich fallback disks around newly born neutron stars and black holes become neutral generally inside the tidal truncation radius (Roche limit) for planets at ~1011 cm. Consequently, the efficiency of the planetary formation process in this context will mostly depend on the ability of the resulting disk of rocks to spread via collisions beyond the Roche limit. It appears easier for the merger product of a doubly degenerate binary, whether it is a massive white dwarf or a neutron star, to harbor planets because its remnant disk has a rather large initial angular momentum, which allows it to spread beyond the Roche limit before becoming neutral. The early super-Eddington phase of accretion is a source of uncertainty for the disk evolution models presented here.

Reverse Current in Solar Flares

NASA Technical Reports Server (NTRS)

Knight, J. W.; Sturrock, P. A.

1976-01-01

The theory that impulsive X ray bursts are produced by high energy electrons streaming from the corona to the chromosphere is investigated. Currents associated with these streams are so high that either the streams do not exist or their current is neutralized by a reverse current. Analysis of a simple model indicates that the primary electron stream leads to the development of an electric field in the ambient corona which decelerates the primary beam and produces a neutralizing reverse current. It appears that, in some circumstances, this electric field could prevent the primary beam from reaching the chromosphere. In any case, the electric field acts as an energy exchange mechanism, extracting kinetic energy from the primary beam and using it to heat the ambient plasma. This heating is typically so rapid that it must be expected to have important dynamical consequences.

Stability of multiply charged fullerene anions and cations

NASA Astrophysics Data System (ADS)

Wang, Yang; Zettergren, Henning; Alcamí, Manuel; Martín, Fernando

2009-09-01

We present a systematic study of the stability of highly charged cationic and anionic fullerenes whose most stable neutral counterparts follow the isolated pentagon rule (IPR). In agreement with recent studies, we have found that, for many highly charged fullerenes, non-IPR isomers are significantly more stable than the IPR ones. To understand this behavior, we compare the results of elaborate density-functional theory (DFT) calculations to those of a simple Hückel molecular-orbital theory in which the DFT energies of the corresponding neutral systems are used as a reference. The model leads to a reasonable estimate of the relative stability of the IPR and non-IPR isomers as a function of charge, which can be used to identify, among the thousands of possible isomers and charge states, the non-IPR species that are likely more stable than the IPR isomers.

Experimental Observation of a Current-Driven Instability in a Neutral Electron-Positron Beam.

PubMed

Warwick, J; Dzelzainis, T; Dieckmann, M E; Schumaker, W; Doria, D; Romagnani, L; Poder, K; Cole, J M; Alejo, A; Yeung, M; Krushelnick, K; Mangles, S P D; Najmudin, Z; Reville, B; Samarin, G M; Symes, D D; Thomas, A G R; Borghesi, M; Sarri, G

2017-11-03

We report on the first experimental observation of a current-driven instability developing in a quasineutral matter-antimatter beam. Strong magnetic fields (≥1  T) are measured, via means of a proton radiography technique, after the propagation of a neutral electron-positron beam through a background electron-ion plasma. The experimentally determined equipartition parameter of ε_{B}≈10^{-3} is typical of values inferred from models of astrophysical gamma-ray bursts, in which the relativistic flows are also expected to be pair dominated. The data, supported by particle-in-cell simulations and simple analytical estimates, indicate that these magnetic fields persist in the background plasma for thousands of inverse plasma frequencies. The existence of such long-lived magnetic fields can be related to analog astrophysical systems, such as those prevalent in lepton-dominated jets.

Experimental Observation of a Current-Driven Instability in a Neutral Electron-Positron Beam

NASA Astrophysics Data System (ADS)

Warwick, J.; Dzelzainis, T.; Dieckmann, M. E.; Schumaker, W.; Doria, D.; Romagnani, L.; Poder, K.; Cole, J. M.; Alejo, A.; Yeung, M.; Krushelnick, K.; Mangles, S. P. D.; Najmudin, Z.; Reville, B.; Samarin, G. M.; Symes, D. D.; Thomas, A. G. R.; Borghesi, M.; Sarri, G.

2017-11-01

We report on the first experimental observation of a current-driven instability developing in a quasineutral matter-antimatter beam. Strong magnetic fields (≥1 T ) are measured, via means of a proton radiography technique, after the propagation of a neutral electron-positron beam through a background electron-ion plasma. The experimentally determined equipartition parameter of ɛB≈10-3 is typical of values inferred from models of astrophysical gamma-ray bursts, in which the relativistic flows are also expected to be pair dominated. The data, supported by particle-in-cell simulations and simple analytical estimates, indicate that these magnetic fields persist in the background plasma for thousands of inverse plasma frequencies. The existence of such long-lived magnetic fields can be related to analog astrophysical systems, such as those prevalent in lepton-dominated jets.

Evolution of the rate of biological aging using a phenotype based computational model.

PubMed

Kittas, Aristotelis

2010-10-07

In this work I introduce a simple model to study how natural selection acts upon aging, which focuses on the viability of each individual. It is able to reproduce the Gompertz law of mortality and can make predictions about the relation between the level of mutation rates (beneficial/deleterious/neutral), age at reproductive maturity and the degree of biological aging. With no mutations, a population with low age at reproductive maturity R stabilizes at higher density values, while with mutations it reaches its maximum density, because even for large pre-reproductive periods each individual evolves to survive to maturity. Species with very short pre-reproductive periods can only tolerate a small number of detrimental mutations. The probabilities of detrimental (P(d)) or beneficial (P(b)) mutations are demonstrated to greatly affect the process. High absolute values produce peaks in the viability of the population over time. Mutations combined with low selection pressure move the system towards weaker phenotypes. For low values in the ratio P(d)/P(b), the speed at which aging occurs is almost independent of R, while higher values favor significantly species with high R. The value of R is critical to whether the population survives or dies out. The aging rate is controlled by P(d) and P(b) and the amount of the viability of each individual is modified, with neutral mutations allowing the system more "room" to evolve. The process of aging in this simple model is revealed to be fairly complex, yielding a rich variety of results. 2010 Elsevier Ltd. All rights reserved.

Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens.

PubMed

Shaffer, J Scott; Moore, Penny L; Kardar, Mehran; Chakraborty, Arup K

2016-10-24

Strategies to elicit Abs that can neutralize diverse strains of a highly mutable pathogen are likely to result in a potent vaccine. Broadly neutralizing Abs (bnAbs) against HIV have been isolated from patients, proving that the human immune system can evolve them. Using computer simulations and theory, we study immunization with diverse mixtures of variant antigens (Ags). Our results show that particular choices for the number of variant Ags and the mutational distances separating them maximize the probability of inducing bnAbs. The variant Ags represent potentially conflicting selection forces that can frustrate the Darwinian evolutionary process of affinity maturation. An intermediate level of frustration maximizes the chance of evolving bnAbs. A simple model makes vivid the origin of this principle of optimal frustration. Our results, combined with past studies, suggest that an appropriately chosen permutation of immunization with an optimally designed mixture (using the principles that we describe) and sequential immunization with variant Ags that are separated by relatively large mutational distances may best promote the evolution of bnAbs.

Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens

PubMed Central

Shaffer, J. Scott; Moore, Penny L.; Kardar, Mehran; Chakraborty, Arup K.

2016-01-01

Strategies to elicit Abs that can neutralize diverse strains of a highly mutable pathogen are likely to result in a potent vaccine. Broadly neutralizing Abs (bnAbs) against HIV have been isolated from patients, proving that the human immune system can evolve them. Using computer simulations and theory, we study immunization with diverse mixtures of variant antigens (Ags). Our results show that particular choices for the number of variant Ags and the mutational distances separating them maximize the probability of inducing bnAbs. The variant Ags represent potentially conflicting selection forces that can frustrate the Darwinian evolutionary process of affinity maturation. An intermediate level of frustration maximizes the chance of evolving bnAbs. A simple model makes vivid the origin of this principle of optimal frustration. Our results, combined with past studies, suggest that an appropriately chosen permutation of immunization with an optimally designed mixture (using the principles that we describe) and sequential immunization with variant Ags that are separated by relatively large mutational distances may best promote the evolution of bnAbs. PMID:27791170

On possible microscopic origins of the swelling of neutral lipid bilayers induced by simple salts.

PubMed

Manciu, Marian; Ruckenstein, Eli

2007-05-01

It was recently suggested that the swelling of neutral multilipid bilayers upon addition of a salt can be simply explained only by the electrolyte screening of the van der Waals attractions, while assuming that the hydration force and the repulsion due to thermal undulations of membranes are unaffected by the salt. While we agree that the screening of the van der Waals interactions plays a role, we suggest that the increase in the hydration force upon addition of a salt has also to be taken into account. In a statistical model, which accounts for the membrane undulations, parameters could be found to explain the multibilayer swelling even when the van der Waals attraction is considered unaffected by the electrolyte screening. These results point out that the decrease by a factor of three of the Hamaker constant upon addition of a salt, suggested recently to be responsible for the swelling of neutral multilipid bilayers, is perhaps too large, and a smaller decrease in Hamaker constant, coupled with the above mentioned effects might explain the swelling.

Effect of artificial length scales in large eddy simulation of a neutral atmospheric boundary layer flow: A simple solution to log-layer mismatch

NASA Astrophysics Data System (ADS)

Chatterjee, Tanmoy; Peet, Yulia T.

2017-07-01

A large eddy simulation (LES) methodology coupled with near-wall modeling has been implemented in the current study for high Re neutral atmospheric boundary layer flows using an exponentially accurate spectral element method in an open-source research code Nek 5000. The effect of artificial length scales due to subgrid scale (SGS) and near wall modeling (NWM) on the scaling laws and structure of the inner and outer layer eddies is studied using varying SGS and NWM parameters in the spectral element framework. The study provides an understanding of the various length scales and dynamics of the eddies affected by the LES model and also the fundamental physics behind the inner and outer layer eddies which are responsible for the correct behavior of the mean statistics in accordance with the definition of equilibrium layers by Townsend. An economical and accurate LES model based on capturing the near wall coherent eddies has been designed, which is successful in eliminating the artificial length scale effects like the log-layer mismatch or the secondary peak generation in the streamwise variance.

Prebiotic Peptide (Amide) Bond Synthesis Accelerated by Glycerol and Bicarbonate Under Neutral to Alkaline Dry-Down Conditions

NASA Technical Reports Server (NTRS)

Forsythe, J. G.; Weber, A. L.

2017-01-01

Past studies of prebiotic peptide bond synthesis have generally been carried out in the acidic to neutral pH range [1, 2]. Here we report a new process for peptide bond (amide) synthesis in the neutral to alkaline pH range that involves simple dry-down heating of amino acids in the presence of glycerol and bicarbonate. Glycerol was included in the reaction mixture as a solvent and to provide hydroxyl groups for possible formation of ester intermediates previously implicated in peptide bond synthesis under acidic to neutral conditions [1]. Bicarbonate was added to raise the reaction pH to 8-9.

ON THE ELECTRON-TO-NEUTRAL NUMBER DENSITY RATIO IN THE COMA OF COMET 67P/CHURYUMOV–GERASIMENKO: GUIDING EXPRESSION AND SOURCES FOR DEVIATIONS

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

Vigren, E.; Eriksson, A. I.; Edberg, N. J. T.

2015-10-10

We compute partial photoionization frequencies of H{sub 2}O, CO{sub 2}, and CO, the major molecules in the coma of comet 67P/Churyumov–Gerasimenko, the target comet of the ongoing ESA Rosetta mission. Values are computed from Thermosphere Ionosphere Mesosphere Energy and Dynamics/Solar EUV Experiment solar EUV spectra for 2014 August 1, 2015 March 1, and for perihelion (2015 August, as based on prediction). From the varying total photoionization frequency of H{sub 2}O, as computed from 2014 August 1 to 2015 May 20, we derive a simple analytical expression for the electron-to-neutral number density ratio as a function of cometocentric and heliocentric distance. Themore » underlying model assumes radial movement of the coma constituents and does not account for chemical loss or the presence of electric fields. We discuss various effects/processes that can cause deviations between values from the analytical expression and actual electron-to-neutral number density ratios. The analytical expression is thus not strictly meant as predicting the actual electron-to-neutral number density ratio, but is useful in comparisons with observations as an indicator of processes at play in the cometary coma.« less

pH-dependent biotransformation of ionizable organic micropollutants in activated sludge.

PubMed

Gulde, Rebekka; Helbling, Damian E; Scheidegger, Andreas; Fenner, Kathrin

2014-12-02

Removal of micropollutants (MPs) during activated sludge treatment can mainly be attributed to biotransformation and sorption to sludge flocs, whereby the latter process is known to be of minor importance for polar organic micropollutants. In this work, we investigated the influence of pH on the biotransformation of MPs with cationic-neutral speciation in an activated sludge microbial community. We performed batch biotransformation, sorption control, and abiotic control experiments for 15 MPs with cationic-neutral speciation, one control MP with neutral-anionic speciation, and two neutral MPs at pHs 6, 7, and 8. Biotransformation rate constants corrected for sorption and abiotic processes were estimated from measured concentration time series with Bayesian inference. We found that biotransformation is pH-dependent and correlates qualitatively with the neutral fraction of the ionizable MPs. However, a simple speciation model based on the assumption that only the neutral species is efficiently taken up and biotransformed by the cells tends to overpredict the effect of speciation. Therefore, additional mechanisms such as uptake of the ionic species and other more complex attenutation mechanisms are discussed. Finally, we observed that the sorption coefficients derived from our control experiments were small and showed no notable pH-dependence. From this we conclude that pH-dependent removal of polar, ionizable organic MPs in activated sludge systems is less likely an effect of pH-dependent sorption but rather of pH-dependent biotransformation. The latter has the potential to cause marked differences in the removal of polar, ionizable MPs at different operational pHs during activated sludge treatment.

Multi-shell model of ion-induced nucleic acid condensation

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

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois

2016-04-21

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes in- duced by tri-valent cobalt hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. The duplex aggregation free energy is de- composed into attraction and repulsion components represented by simple analytic expressions. The source of the short-range attraction between NA duplexes in the aggregated phase is the in- teraction of CoHex ions in the overlapping regions of the “external” shells with the oppositely chargedmore » duplexes. The attraction depends on CoHex binding affinity to the “external” shell of nearly neutralized duplex and the number of ions in the shell overlapping volume. For a given NA duplex sequence and structure, these parameters are estimated from molecular dynamics simula- tion. The attraction is opposed by the residual repulsion of nearly neutralized duplexes as well as duplex configurational entropy loss upon aggregation. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA conden- sation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. The model also predicts that longer NA fragments will condense easier than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation, lends support to proposed NA condensation picture based on the multivalent “ion binding shells”.« less

Multi-shell model of ion-induced nucleic acid condensation

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois; Baker, Nathan A.; Onufriev, Alexey V.

2016-04-01

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into "external" and "internal" ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the "external" shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the "internal" shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent "ion binding shells."

From sparse to dense and from assortative to disassortative in online social networks

PubMed Central

Li, Menghui; Guan, Shuguang; Wu, Chensheng; Gong, Xiaofeng; Li, Kun; Wu, Jinshan; Di, Zengru; Lai, Choy-Heng

2014-01-01

Inspired by the analysis of several empirical online social networks, we propose a simple reaction-diffusion-like coevolving model, in which individuals are activated to create links based on their states, influenced by local dynamics and their own intention. It is shown that the model can reproduce the remarkable properties observed in empirical online social networks; in particular, the assortative coefficients are neutral or negative, and the power law exponents γ are smaller than 2. Moreover, we demonstrate that, under appropriate conditions, the model network naturally makes transition(s) from assortative to disassortative, and from sparse to dense in their characteristics. The model is useful in understanding the formation and evolution of online social networks. PMID:24798703

From sparse to dense and from assortative to disassortative in online social networks.

PubMed

Li, Menghui; Guan, Shuguang; Wu, Chensheng; Gong, Xiaofeng; Li, Kun; Wu, Jinshan; Di, Zengru; Lai, Choy-Heng

2014-05-06

Inspired by the analysis of several empirical online social networks, we propose a simple reaction-diffusion-like coevolving model, in which individuals are activated to create links based on their states, influenced by local dynamics and their own intention. It is shown that the model can reproduce the remarkable properties observed in empirical online social networks; in particular, the assortative coefficients are neutral or negative, and the power law exponents γ are smaller than 2. Moreover, we demonstrate that, under appropriate conditions, the model network naturally makes transition(s) from assortative to disassortative, and from sparse to dense in their characteristics. The model is useful in understanding the formation and evolution of online social networks.

Simple and accurate method for determining dissolved inorganic carbon in environmental water by reaction headspace gas chromatography.

PubMed

Xie, Wei-Qi; Gong, Yi-Xian; Yu, Kong-Xian

2018-03-01

We investigate a simple and accurate method for quantitatively analyzing dissolved inorganic carbon in environmental water by reaction headspace gas chromatography. The neutralization reaction between the inorganic carbon species (i.e. bicarbonate ions and carbonate ions) in environmental water and hydrochloric acid is carried out in a sealed headspace vial, and the carbon dioxide formed from the neutralization reaction, the self-decomposition of carbonic acid, and dissolved carbon dioxide in environmental water is then analyzed by headspace gas chromatography. The data show that the headspace gas chromatography method has good precision (relative standard deviation ≤ 1.63%) and accuracy (relative differences ≤ 5.81% compared with the coulometric titration technique). The headspace gas chromatography method is simple, reliable, and can be well applied in the dissolved inorganic carbon detection in environmental water. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development and Implementation of a Simple, Engaging Acid Rain Neutralization Experiment and Corresponding Animated Instructional Video for Introductory Chemistry Students

ERIC Educational Resources Information Center

Rand, Danielle; Yennie, Craig J.; Lynch, Patrick; Lowry, Gregory; Budarz, James; Zhu, Wenlei; Wang, Li-Qiong

2016-01-01

Here we describe an acid rain neutralization laboratory experiment and its corresponding instructional video. This experiment has been developed and implemented for use in the teaching laboratory of a large introductory chemistry course at Brown University. It provides a contextually relevant example to introduce beginner-level students with…

David Hume's Monetary Theory Revisited: Was He Really a Quantity Theorist and an Inflationist?

ERIC Educational Resources Information Center

Wennerlind, Carl

2005-01-01

David Hume's monetary theory has been controversial since its formulation. Lately, the focus has been on Hume's alleged misapplication of the quantity theory of money. While he appears to subscribe to a simple quantity theory with money neutrality, in a famously contested passage in the essay Of Money, he violates the neutrality condition by…

Mutual neutralization of He{sup +} with the anions Cl{sup −}, Br{sup −}, I{sup −}, and SF{sub 6}{sup −}

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

Wiens, Justin P.; Shuman, Nicholas S.; Miller, Thomas M.

2016-05-28

Mutual neutralization (MN) rate coefficients k{sub MN} for He{sup +} with the anions Cl{sup −}, Br{sup −}, I{sup −}, and SF{sub 6}{sup −} are reported from 300 to 500 K. The measured rate coefficients may contain a contribution from transfer ionization, i.e., double ionization of the anion. The large rate coefficient for He{sup +} + SF{sub 6}{sup −} (2.4 × 10{sup −7} cm{sup 3} s{sup −1} at 300 K) is consistent with earlier polyatomic MN results found to have a reduced mass dependence of μ{sup −1/2}. Neutralization of He{sup +} by the atomic halides follows the trend observed earlier for Ne{sup +},more » Ar{sup +}, Kr{sup +}, and Xe{sup +} neutralized by atomic halides, k{sub MN} (Cl{sup −}) < k{sub MN} (Br{sup −}) < k{sub MN} (I{sup −}). Only an upper limit could be measured for the neutralization of He{sup +} by Cl{sup −}. Predictions of the rate coefficients from a previously proposed simple model of atomic–atomic MN results are consistent with the present He{sup +}–halide rate coefficients. The temperature dependences are modestly negative for Br{sup −} and I{sup −}, while that for SF{sub 6}{sup −} is small or negligible.« less

Absence of Disorder-Driven Metal-Insulator Transitions in Simple Holographic Models

NASA Astrophysics Data System (ADS)

Grozdanov, Sašo; Lucas, Andrew; Sachdev, Subir; Schalm, Koenraad

2015-11-01

We study electrical transport in a strongly coupled strange metal in two spatial dimensions at finite temperature and charge density, holographically dual to the Einstein-Maxwell theory in an asymptotically four-dimensional anti-de Sitter space spacetime, with arbitrary spatial inhomogeneity, up to mild assumptions including emergent isotropy. In condensed matter, these are candidate models for exotic strange metals without long-lived quasiparticles. We prove that the electrical conductivity is bounded from below by a universal minimal conductance: the quantum critical conductivity of a clean, charge-neutral plasma. Beyond nonperturbatively justifying mean-field approximations to disorder, our work demonstrates the practicality of new hydrodynamic insight into holographic transport.

Efficient solar-assisted O2 reduction by a cofacial iron porphyrin dimer integrated to a p-CuBi2O4 photocathode prepared by a simple novel method.

PubMed

Zahran, Zaki N; Mohamed, Eman A; Naruta, Yoshinori; Haleem, Ashraf

2017-10-04

A cofacial iron porphyrin hetero-dimer, Fe2TPFPP-TMP showed high electro-catalytic activity, selectivity, and stability for the O2 reduction to H2O both in homogeneous non-aqueous and heterogeneous neutral aqueous solutions. Moreover, when it is integrated to FTO/p-CuBi2O4 (FTO = fluorine doped tin oxide) photocathode prepared by a simple novel method, a remarkable efficient solar-assisted O2 reduction is achieved in neutral potassium phosphate (KPi) or basic NaOH solutions saturated with O2. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-fluid Modeling of Magnetosonic Wave Propagation in the Solar Chromosphere: Effects of Impact Ionization and Radiative Recombination

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

Maneva, Yana G.; Laguna, Alejandro Alvarez; Poedts, Stefaan

2017-02-20

In order to study chromospheric magnetosonic wave propagation including, for the first time, the effects of ion–neutral interactions in the partially ionized solar chromosphere, we have developed a new multi-fluid computational model accounting for ionization and recombination reactions in gravitationally stratified magnetized collisional media. The two-fluid model used in our 2D numerical simulations treats neutrals as a separate fluid and considers charged species (electrons and ions) within the resistive MHD approach with Coulomb collisions and anisotropic heat flux determined by Braginskiis transport coefficients. The electromagnetic fields are evolved according to the full Maxwell equations and the solenoidality of the magneticmore » field is enforced with a hyperbolic divergence-cleaning scheme. The initial density and temperature profiles are similar to VAL III chromospheric model in which dynamical, thermal, and chemical equilibrium are considered to ensure comparison to existing MHD models and avoid artificial numerical heating. In this initial setup we include simple homogeneous flux tube magnetic field configuration and an external photospheric velocity driver to simulate the propagation of MHD waves in the partially ionized reactive chromosphere. In particular, we investigate the loss of chemical equilibrium and the plasma heating related to the steepening of fast magnetosonic wave fronts in the gravitationally stratified medium.« less

Laboratory Experiments Enabling Electron Beam use in Tenuous Space Plasmas

NASA Astrophysics Data System (ADS)

Miars, G.; Leon, O.; Gilchrist, B. E.; Delzanno, G. L.; Castello, F. L.; Borovsky, J.

2017-12-01

A mission concept is under development which involves firing a spacecraft-mounted electron beam from Earth's magnetosphere to connect distant magnetic field lines in real time. To prevent excessive spacecraft charging and consequent beam return, the spacecraft must be neutralized in the tenuous plasma environment of the magnetosphere. Particle-In-Cell (PIC) simulations suggest neutralization can be accomplished by emitting a neutral plasma with the electron beam. Interpretation of these simulations also led to an ion emission model in which ion current is emitted from a quasi-neutral plasma as defined by the space charge limit [1,2]. Experiments were performed at the University of Michigan's Plasmadynamics and Electric Propulsion Laboratory (PEPL) to help validate the ion emission model. A hollow cathode plasma contactor was used as a representative spacecraft and charged with respect to the chamber walls to examine the effect of spacecraft charging on ion emission. Retarding Potential Analyzer (RPA) measurements were performed to understand ion flow velocity as this parameter relates directly to the expected space charge limit. Planar probe measurements were also made to identify where ion emission primarily occurred and to determine emission current density levels. Evidence of collisions within the plasma (particularly charge exchange collisions) and a simple model predicting emitted ion velocities are presented. While a detailed validation of the ion emission model and of the simulation tools used in [1,2] is ongoing, these measurements add to the physical understanding of ion emission as it may occur in the magnetosphere. 1. G.L. Delzanno, J.E. Borovsky, M.F. Thomsen, J.D. Moulton, and E.A. MacDonald, J. Geophys. Res. Space Physics 120, 3647, 2015. 2. G.L. Delzanno, J.E. Borovsky, M.F. Thomsen, and J.D. Moulton, J. Geophys. Res. Space Physics 120, 3588, 2015. ________________________________ * This work is supported by Los Alamos National Laboratory.

Reverse current in solar flares

NASA Technical Reports Server (NTRS)

Knight, J. W.; Sturrock, P. A.

1977-01-01

We examine the proposal that impulsive X-ray bursts are produced by high-energy electrons streaming from the corona to the chromosphere. It is known that the currents associated with these streams are so high that either the streams do not exist or their current is neutralized by a reverse current. Analysis of a simple model in which the reverse current is stable indicates that the primary electron stream leads to the development of an electric field in the ambient corona which (a) decelerates the primary beam and (b) produces a neutralizing reverse current. It appears that, in some circumstances, this electric field could prevent the primary beam from reaching the chromosphere. In any case, the electric field acts as an energy exchange mechanism, extracting kinetic energy from the primary beam and using it to heat the ambient plasma. This heating is typically so rapid that it must be expected to have important dynamical consequences.

Solar activity beyond the disk and variations of the cosmic ray gradient

NASA Technical Reports Server (NTRS)

Belov, A. V.; Dorman, L. I.; Eroshenko, E. A.; Ishkov, V. N.; Oleneva, V. A.

1985-01-01

Part of galactic cosmic rays (CR) observed near the Earth and on the Earth come from beyond-disk regions of circumsolar space. But CR of those energies which undergo substantial modulation cover too large a path across the lines of force of the interplanetary magnetic field (IMF) in order that they could provide an effective transfer of information about beyond-disk solar activity. And if it is still possible, the most probable channel for transferring such information must be a neutral layer of heliomagnetosphere in which the transverse CR transport is facilitated by their drift in an inhomogeneous magnetic field. A simple diffusion model for an expected CR variation in a neutral layer near the Earth is discussed. It is of importance that variations of the CR gradient are not at all always accompanied by considerable variations of IMF and solar wind velocity at the point of observation.

Experimental Observation of a Current-Driven Instability in a Neutral Electron-Positron Beam

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

Warwick, J.; Dzelzainis, T.; Dieckmann, M. E.

Here, we report on the first experimental observation of a current-driven instability developing in a quasineutral matter-antimatter beam. Strong magnetic fields (≥ 1T) are measured, via means of a proton radiography technique, after the propagation of a neutral electron-positron beam through a background electron-ion plasma. The experimentally determined equipartition parameter of ε B ≈ 10 -3 is typical of values inferred from models of astrophysical gamma-ray bursts, in which the relativistic flows are also expected to be pair dominated. The data, supported by particle-in-cell simulations and simple analytical estimates, indicate that these magnetic fields persist in the background plasma formore » thousands of inverse plasma frequencies. The existence of such long-lived magnetic fields can be related to analog astrophysical systems, such as those prevalent in lepton-dominated jets.« less

Preliminary measurements of kinetic dust temperature using stereoscopic particle image velocimetry

NASA Astrophysics Data System (ADS)

Williams, Jeremiah; Thomas, Edward

2004-11-01

A dusty (or complex) plasma is a four-component system composed of ions, electrons, neutral particles and charged microparticles. The presence of the microparticle (i.e., dust) component alters the plasma environment, giving rise to a wide variety of new plasma phenomena. Recently, the Auburn Plasma Sciences Laboratory (PSL) has acquired and installed a stereoscopic PIV (stereo-PIV) diagnostic tool for dusty plasma investigations [Thomas, et. al., Phys. Plasmas, 11, L37 (2004)]. This presentation discusses the use of the stereo-PIV technique for determining the velocity space distribution function of the microparticle component of a dc glow discharge dusty plasma. These distribution functions are then used to make preliminary estimates of the kinetic temperature of the dust component. The data is compared to a simple energy balance model that relates the dust temperature to the electric field and neutral pressure.

Experimental Observation of a Current-Driven Instability in a Neutral Electron-Positron Beam

DOE PAGES

Warwick, J.; Dzelzainis, T.; Dieckmann, M. E.; ...

2017-11-03

Here, we report on the first experimental observation of a current-driven instability developing in a quasineutral matter-antimatter beam. Strong magnetic fields (≥ 1T) are measured, via means of a proton radiography technique, after the propagation of a neutral electron-positron beam through a background electron-ion plasma. The experimentally determined equipartition parameter of ε B ≈ 10 -3 is typical of values inferred from models of astrophysical gamma-ray bursts, in which the relativistic flows are also expected to be pair dominated. The data, supported by particle-in-cell simulations and simple analytical estimates, indicate that these magnetic fields persist in the background plasma formore » thousands of inverse plasma frequencies. The existence of such long-lived magnetic fields can be related to analog astrophysical systems, such as those prevalent in lepton-dominated jets.« less

New physics with ultra-high-energy neutrinos

DOE PAGES

Marfatia, D.; McKay, D. W.; Weiler, T. J.

2015-07-03

Now that PeV neutrinos have been discovered by IceCube, we optimistically entertain the possibility that neutrinos with energy above 100PeV exist. Here, we evaluate the dependence of event rates of such neutrinos on the neutrino-nucleon cross section at observatories that detect particles, atmospheric fluorescence, or Cherenkov radiation, initiated by neutrino interactions. We consider how (i)a simple scaling of the total standard model neutrino-nucleon cross section, (ii) a new elastic neutral current interaction, and (iii) anew completely inelastic interaction, individually impact event rates.

Andreev bound states. Some quasiclassical reflections

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

Lin, Y., E-mail: yiriolin@illinois.edu; Leggett, A. J.

2014-12-15

We discuss a very simple and essentially exactly solvable model problem which illustrates some nice features of Andreev bound states, namely, the trapping of a single Bogoliubov quasiparticle in a neutral s-wave BCS superfluid by a wide and shallow Zeeman trap. In the quasiclassical limit, the ground state is a doublet with a splitting which is proportional to the exponentially small amplitude for “normal” reflection by the edges of the trap. We comment briefly on a prima facie paradox concerning the continuity equation and conjecture a resolution to it.

Tracking and Control of a Neutral Particle Beam Using Multiple Model Adaptive Meer Filter.

DTIC Science & Technology

1987-12-01

34 method incorporated by Zicker in 1983 [32]. Once the beam estimation problem had been solved, the problem of beam control was examined. Zicker conducted a...filter. Then, the methods applied by Meer, and later Zicker , to reduce the computational load of a simple Meer filter, will be presented. 2.5.1 Basic...number of possible methods to prune the hypothesis tree and chose the "Best Half Method" as the most viable (21). Zicker [323, applied the work of Weiss

Catenaries in viscous fluid

NASA Astrophysics Data System (ADS)

Hanna, James; Chakrabarti, Brato

2015-11-01

Slender structures live in fluid flows across many scales, from towed instruments to plant blades to microfluidic valves. The present work details a simple model of a flexible structure in a uniform flow. We present analytical solutions for the translating, axially flowing equilibria of strings subjected to a uniform body force and linear drag forces. This is an extension of the classical catenaries to a five-parameter family of solutions, represented as trajectories in angle-curvature ``phase space.'' Limiting cases include neutrally buoyant towed cables and freely sedimenting flexible filaments. Now at University of California, San Diego.

Andreev bound states. Some quasiclassical reflections

NASA Astrophysics Data System (ADS)

Lin, Y.; Leggett, A. J.

2014-12-01

We discuss a very simple and essentially exactly solvable model problem which illustrates some nice features of Andreev bound states, namely, the trapping of a single Bogoliubov quasiparticle in a neutral s-wave BCS superfluid by a wide and shallow Zeeman trap. In the quasiclassical limit, the ground state is a doublet with a splitting which is proportional to the exponentially small amplitude for "normal" reflection by the edges of the trap. We comment briefly on a prima facie paradox concerning the continuity equation and conjecture a resolution to it.

Molecular dynamics studies of simple membrane-water interfaces: Structure and functions in the beginnings of cellular life

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.

1995-01-01

Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

Depletion region surface effects in electron beam induced current measurements

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

Haney, Paul M.; Zhitenev, Nikolai B.; Yoon, Heayoung P.

2016-09-07

Electron beam induced current (EBIC) is a powerful characterization technique which offers the high spatial resolution needed to study polycrystalline solar cells. Current models of EBIC assume that excitations in the p-n junction depletion region result in perfect charge collection efficiency. However, we find that in CdTe and Si samples prepared by focused ion beam (FIB) milling, there is a reduced and nonuniform EBIC lineshape for excitations in the depletion region. Motivated by this, we present a model of the EBIC response for excitations in the depletion region which includes the effects of surface recombination from both charge-neutral and chargedmore » surfaces. For neutral surfaces, we present a simple analytical formula which describes the numerical data well, while the charged surface response depends qualitatively on the location of the surface Fermi level relative to the bulk Fermi level. We find that the experimental data on FIB-prepared Si solar cells are most consistent with a charged surface and discuss the implications for EBIC experiments on polycrystalline materials.« less

Can the Discrepancy between Locally and Globally Derived Neutral Hydrogen Mass Functions be Explained by a Varying Value of M ⋆?

NASA Astrophysics Data System (ADS)

Minchin, Robert F.

2017-09-01

I investigate whether it is possible to reconcile the recent Arecibo Legacy Fast Arecibo L-band Feed Array (ALFALFA) observation that the neutral hydrogen mass function (HIMF) across different galactic densities has the same, non-flat, faint-end slope, with observations of isolated galaxies and many galaxy groups that show their HIMFs to have flat faint-end slopes. I find that a fairly simple model in which the position of the knee in the mass function of each individual group is allowed to vary is able to account for both of these observations. If this model reflects reality, the ALFALFA results point to an interesting “conspiracy” whereby the differing group HIMFs always sum up to form global HIMFs with the same faint-end slope in different environments. More generally, this result implies that global environmental HIMFs do not necessarily reflect the HIMFs in individual groups belonging to that environment and cannot be used to directly measure variations in group-specific HIMFs with environment.

The role of electronic mechanisms in surface erosion and glow phenomena

NASA Technical Reports Server (NTRS)

Haglund, Richard F., Jr.

1987-01-01

Experimental studies of desorption induced by electronic transitions (DIET) are described. Such studies are producing an increasingly complete picture of the dynamical pathways through which incident electronic energy is absorbed and rechanneled to produce macroscopic erosion and glow. These mechanistic studies can determine rate constants for erosion and glow processes in model materials and provide valuable guidance in materials selection and development. Extensive experiments with electron, photon, and heavy particle irradiation of alkali halides and other simple model materials have produced evidence showing that: (1) surface erosion, consisting primarily in the ejection or desorption of ground-state neutral atoms, occurs with large efficiencies for all irradiated species; (2) surface glow, resulting from the radiative decay of desorbed atoms, likewise occurs for all irradiating species; (3) the typical mechanism for ground-state neutral desorption is exciton formation, followed by relaxation to a permanent, mobile electronic defect which is the precursor to bond-breaking in the surface or near-surface bulk of the material; and (4) the mechanisms for excited atom formation may include curve crossing in atomic collisions, interactions with surface defect or impurity states, or defect diffusion.

Modeling Neutral Densities Downstream of a Gridded Ion Thruster

NASA Technical Reports Server (NTRS)

Soulas, George C.

2010-01-01

The details of a model for determining the neutral density downstream of a gridded ion thruster are presented. An investigation of the possible sources of neutrals emanating from and surrounding a NEXT ion thruster determined that the most significant contributors to the downstream neutral density include discharge chamber neutrals escaping through the perforated grids, neutrals escaping from the neutralizer, and vacuum facility background neutrals. For the neutral flux through the grids, near- and far-field equations are presented for rigorously determining the neutral density downstream of a cylindrical aperture. These equations are integrated into a spherically-domed convex grid geometry with a hexagonal array of apertures for determining neutral densities downstream of the ion thruster grids. The neutrals escaping from an off-center neutralizer are also modeled assuming diffuse neutral emission from the neutralizer keeper orifice. Finally, the effect of the surrounding vacuum facility neutrals is included and assumed to be constant. The model is used to predict the neutral density downstream of a NEXT ion thruster with and without neutralizer flow and a vacuum facility background pressure. The impacts of past simplifying assumptions for predicting downstream neutral densities are also examined for a NEXT ion thruster.

Stark width regularities within spectral series of the lithium isoelectronic sequence

NASA Astrophysics Data System (ADS)

Tapalaga, Irinel; Trklja, Nora; Dojčinović, Ivan P.; Purić, Jagoš

2018-03-01

Stark width regularities within spectral series of the lithium isoelectronic sequence have been studied in an approach that includes both neutrals and ions. The influence of environmental conditions and certain atomic parameters on the Stark widths of spectral lines has been investigated. This study gives a simple model for the calculation of Stark broadening data for spectral lines within the lithium isoelectronic sequence. The proposed model requires fewer parameters than any other model. The obtained relations were used for predictions of Stark widths for transitions that have not yet been measured or calculated. In the framework of the present research, three algorithms for fast data processing have been made and they enable quality control and provide verification of the theoretically calculated results.

Hydrogeomorphology explains acidification-driven variation in aquatic biological communities in the Neversink Basin, USA

USGS Publications Warehouse

Harpold, Adrian A.; Burns, Douglas A.; Walter, M.T.; Steenhuis, Tammo S.

2013-01-01

Describing the distribution of aquatic habitats and the health of biological communities can be costly and time-consuming; therefore, simple, inexpensive methods to scale observations of aquatic biota to watersheds that lack data would be useful. In this study, we explored the potential of a simple “hydrogeomorphic” model to predict the effects of acid deposition on macroinvertebrate, fish, and diatom communities in 28 sub-watersheds of the 176-km2 Neversink River basin in the Catskill Mountains of New York State. The empirical model was originally developed to predict stream-water acid neutralizing capacity (ANC) using the watershed slope and drainage density. Because ANC is known to be strongly related to aquatic biological communities in the Neversink, we speculated that the model might correlate well with biotic indicators of ANC response. The hydrogeomorphic model was strongly correlated to several measures of macroinvertebrate and fish community richness and density, but less strongly correlated to diatom acid tolerance. The model was also strongly correlated to biological communities in 18 sub-watersheds independent of the model development, with the linear correlation capturing the strongly acidic nature of small upland watersheds (2). Overall, we demonstrated the applicability of geospatial data sets and a simple hydrogeomorphic model for estimating aquatic biological communities in areas with stream-water acidification, allowing estimates where no direct field observations are available. Similar modeling approaches have the potential to complement or refine expensive and time-consuming measurements of aquatic biota populations and to aid in regional assessments of aquatic health.

How does negative emotion cause false memories?

PubMed

Brainerd, C J; Stein, L M; Silveira, R A; Rohenkohl, G; Reyna, V F

2008-09-01

Remembering negative events can stimulate high levels of false memory, relative to remembering neutral events. In experiments in which the emotional valence of encoded materials was manipulated with their arousal levels controlled, valence produced a continuum of memory falsification. Falsification was highest for negative materials, intermediate for neutral materials, and lowest for positive materials. Conjoint-recognition analysis produced a simple process-level explanation: As one progresses from positive to neutral to negative valence, false memory increases because (a) the perceived meaning resemblance between false and true items increases and (b) subjects are less able to use verbatim memories of true items to suppress errors.

Synergistic Effects of the Membrane Actions of Cecropin-Melittin Antimicrobial Hybrid Peptide BP100

PubMed Central

Ferre, Rafael; Melo, Manuel N.; Correia, Ana D.; Feliu, Lidia; Bardají, Eduard; Planas, Marta; Castanho, Miguel

2009-01-01

BP100 (KKLFKKILKYL-NH2) is a short cecropin A-melittin hybrid peptide, obtained through a combinatorial chemistry approach, which is highly effective in inhibiting both the in vitro and in vivo growth of economically important plant pathogenic Gram-negatives. The intrinsic Tyr fluorescence of BP100 was taken advantage of to study the peptide's binding affinity and damaging effect on phospholipid bilayers modeling the bacterial and mammalian cytoplasmic membranes. In vitro cytotoxic effects of this peptide were also studied on mammalian fibroblast cells. Results show a stronger selectivity of BP100 toward anionic bacterial membrane models as indicated by the high obtained partition constants, one order of magnitude greater than for the neutral mammalian membrane models. For the anionic systems, membrane saturation was observed at high peptide/lipid ratios and found to be related with BP100-induced vesicle permeabilization, membrane electroneutrality, and vesicle aggregation. Occurrence of BP100 translocation was unequivocally detected at both high and low peptide/lipid ratios using a novel and extremely simple method. Moreover, cytotoxicity against mammalian models was reached at a concentration considerably higher than the minimum inhibitory concentration. Our findings unravel the relationships among the closely coupled processes of charge neutralization, permeabilization, and translocation in the mechanism of action of antimicrobial peptides. PMID:19254540

Study of chromatic adaptation using memory color matches, Part I: neutral illuminants.

PubMed

Smet, Kevin A G; Zhai, Qiyan; Luo, Ming R; Hanselaer, Peter

2017-04-03

Twelve corresponding color data sets have been obtained using the long-term memory colors of familiar objects as target stimuli. Data were collected for familiar objects with neutral, red, yellow, green and blue hues under 4 approximately neutral illumination conditions on or near the blackbody locus. The advantages of the memory color matching method are discussed in light of other more traditional asymmetric matching techniques. Results were compared to eight corresponding color data sets available in literature. The corresponding color data was used to test several linear (von Kries, RLAB, etc.) and nonlinear (Hunt & Nayatani) chromatic adaptation transforms (CAT). It was found that a simple two-step von Kries, whereby the degree of adaptation D is optimized to minimize the DEu'v' prediction errors, outperformed all other tested models for both memory color and literature corresponding color sets, whereby prediction errors were lower for the memory color sets. The predictive errors were substantially smaller than the standard uncertainty on the average observer and were comparable to what are considered just-noticeable-differences in the CIE u'v' chromaticity diagram, supporting the use of memory color based internal references to study chromatic adaptation mechanisms.

On the stability analysis of sharply stratified shear flows

NASA Astrophysics Data System (ADS)

Churilov, Semyon

2018-05-01

When the stability of a sharply stratified shear flow is studied, the density profile is usually taken stepwise and a weak stratification between pycnoclines is neglected. As a consequence, in the instability domain of the flow two-sided neutral curves appear such that the waves corresponding to them are neutrally stable, whereas the neighboring waves on either side of the curve are unstable, in contrast with the classical result of Miles (J Fluid Mech 16:209-227, 1963) who proved that in stratified flows unstable oscillations can be only on one side of the neutral curve. In the paper, the contradiction is resolved and changes in the flow stability pattern under transition from a model stepwise to a continuous density profile are analyzed. On this basis, a simple self-consistent algorithm is proposed for studying the stability of sharply stratified shear flows with a continuous density variation and an arbitrary monotonic velocity profile without inflection points. Because our calculations and the algorithm are both based on the method of stability analysis (Churilov J Fluid Mech 539:25-55, 2005; ibid, 617, 301-326, 2008), which differs essentially from usually used, the paper starts with a brief review of the method and results obtained with it.

Evaluating Models of The Neutral, Barotropic Planetary Boundary Layer using Integral Measures: Part I. Overview

NASA Astrophysics Data System (ADS)

Hess, G. D.; Garratt, J. R.

Data for the cross-isobaric angle 0, the geostrophic drag coefficient Cg, and the functions A and B of Rossby number similarity theory, obtained from meteorological field experiments, are used to evaluate a range of models of the neutral, barotropic planetary boundary layer. The data give well-defined relationships for 0, Cg, and the integrated dissipation rate over the boundary layer, as a function of the surface Rossby number. Lettau's first-order closure mixing-length model gives an excellent fit to the data; other simple models give reasonable agreement. However more sophisticated models, e.g., higher-order closure, large-eddy simulation, direct numerical simulation and laboratory models, give poor fits to the data. The simplemodels have (at least) one free parameter in their turbulence closure that is matched toatmospheric observations; the more sophisticated models either base their closure onmore general flows or have no free closure parameters. It is suggested that all of theatmospheric experiments that we could locate violate the strict simplifying assumptionsof steady, homogeneous, neutral, barotropic flow required by the sophisticated models.The angle 0 is more sensitive to violations of the assumptions than is Cg.

Rosenzweig instability in a thin layer of a magnetic fluid

NASA Astrophysics Data System (ADS)

Korovin, V. M.

2013-12-01

A simple mathematical model of the initial stage of nonlinear evolution of the Rosenzweig instability in a thin layer of a nonlinearly magnetized viscous ferrofluid coating a horizontal nonmagnetizable plate is constructed on the basis of the system of equations and boundary conditions of ferrofluid dynamics. A dispersion relation is derived and analyzed using the linearized equations of this model. The critical magnetization of the initial layer with a flat free surface, the threshold wavenumber, and the characteristic time of evolution of the most rapidly growing mode are determined. The equation for the neutral stability curve, which is applicable for any physically admissible law of magnetization of a ferrofluid, is derived analytically.

Effects of stream topology on ecological community results from neutral models

EPA Science Inventory

While neutral theory and models have stimulated considerable literature, less well investigated is the effect of topology on neutral metacommunity model simulations. We implemented a neutral metacommunity model using two different stream network topologies, a widely branched netw...

New Parameterizations for Neutral and Ion-Induced Sulfuric Acid-Water Particle Formation in Nucleation and Kinetic Regimes

NASA Astrophysics Data System (ADS)

Määttänen, Anni; Merikanto, Joonas; Henschel, Henning; Duplissy, Jonathan; Makkonen, Risto; Ortega, Ismael K.; Vehkamäki, Hanna

2018-01-01

We have developed new parameterizations of electrically neutral homogeneous and ion-induced sulfuric acid-water particle formation for large ranges of environmental conditions, based on an improved model that has been validated against a particle formation rate data set produced by Cosmics Leaving OUtdoor Droplets (CLOUD) experiments at European Organization for Nuclear Research (CERN). The model uses a thermodynamically consistent version of the Classical Nucleation Theory normalized using quantum chemical data. Unlike the earlier parameterizations for H2SO4-H2O nucleation, the model is applicable to extreme dry conditions where the one-component sulfuric acid limit is approached. Parameterizations are presented for the critical cluster sulfuric acid mole fraction, the critical cluster radius, the total number of molecules in the critical cluster, and the particle formation rate. If the critical cluster contains only one sulfuric acid molecule, a simple formula for kinetic particle formation can be used: this threshold has also been parameterized. The parameterization for electrically neutral particle formation is valid for the following ranges: temperatures 165-400 K, sulfuric acid concentrations 104-1013 cm-3, and relative humidities 0.001-100%. The ion-induced particle formation parameterization is valid for temperatures 195-400 K, sulfuric acid concentrations 104-1016 cm-3, and relative humidities 10-5-100%. The new parameterizations are thus applicable for the full range of conditions in the Earth's atmosphere relevant for binary sulfuric acid-water particle formation, including both tropospheric and stratospheric conditions. They are also suitable for describing particle formation in the atmosphere of Venus.

New analytic results for speciation times in neutral models.

PubMed

Gernhard, Tanja

2008-05-01

In this paper, we investigate the standard Yule model, and a recently studied model of speciation and extinction, the "critical branching process." We develop an analytic way-as opposed to the common simulation approach-for calculating the speciation times in a reconstructed phylogenetic tree. Simple expressions for the density and the moments of the speciation times are obtained. Methods for dating a speciation event become valuable, if for the reconstructed phylogenetic trees, no time scale is available. A missing time scale could be due to supertree methods, morphological data, or molecular data which violates the molecular clock. Our analytic approach is, in particular, useful for the model with extinction, since simulations of birth-death processes which are conditioned on obtaining n extant species today are quite delicate. Further, simulations are very time consuming for big n under both models.

Comparison of fluid neutral models for one-dimensional plasma edge modeling with a finite volume solution of the Boltzmann equation

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

Horsten, N., E-mail: niels.horsten@kuleuven.be; Baelmans, M.; Dekeyser, W.

2016-01-15

We derive fluid neutral approximations for a simplified 1D edge plasma model, suitable to study the neutral behavior close to the target of a nuclear fusion divertor, and compare its solutions to the solution of the corresponding kinetic Boltzmann equation. The plasma is considered as a fixed background extracted from a detached 2D simulation. We show that the Maxwellian equilibrium distribution is already obtained very close to the target, justifying the use of a fluid approximation. We compare three fluid neutral models: (i) a diffusion model; (ii) a pressure-diffusion model (i.e., a combination of a continuity and momentum equation) assumingmore » equal neutral and ion temperatures; and (iii) the pressure-diffusion model coupled to a neutral energy equation taking into account temperature differences between neutrals and ions. Partial reflection of neutrals reaching the boundaries is included in both the kinetic and fluid models. We propose two methods to obtain an incident neutral flux boundary condition for the fluid models: one based on a diffusion approximation and the other assuming a truncated Chapman-Enskog distribution. The pressure-diffusion model predicts the plasma sources very well. The diffusion boundary condition gives slightly better results overall. Although including an energy equation still improves the results, the assumption of equal ion and neutral temperature already gives a very good approximation.« less

Implementation of a plasma-neutral model in NIMROD

NASA Astrophysics Data System (ADS)

Taheri, S.; Shumlak, U.; King, J. R.

2016-10-01

Interaction between plasma fluid and neutral species is of great importance in the edge region of magnetically confined fusion plasmas. The presence of neutrals can have beneficial effects such as fueling burning plasmas and quenching the disruptions in tokamaks, as well as deleterious effects like depositing high energy particles on the vessel wall. The behavior of edge plasmas in magnetically confined systems has been investigated using computational approaches that utilize the fluid description for the plasma and Monte Carlo transport for neutrals. In this research a reacting plasma-neutral model is implemented in NIMROD to study the interaction between plasma and neutral fluids. This model, developed by E. T. Meier and U. Shumlak, combines a single-fluid magnetohydrodynamic (MHD) plasma model with a gas dynamic neutral fluid model which accounts for electron-impact ionization, radiative recombination, and resonant charge exchange. Incorporating this model into NIMROD allows the study of the interaction between neutrals and plasma in a variety of plasma science problems. An accelerated plasma moving through a neutral gas background in a coaxial electrode configuration is modeled, and the results are compared with previous calculations from the HiFi code.

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

Weeks, J.M.; Svendsen, C.

A simple subcellular histochemical staining technique employing the lysosomal probe neutral red has been developed for use with the epiendogeic earthworm Lumbricus rubellus Hoffmeister. Coelomocytes extracted from the coelomic cavity of earthworms into an isotonic earthworm Ringer solution were allowed to adhere to a microscope slide for 30 s before the application of a neutral red dye. This red dye was rapidly accumulated within the lysosomes. Observation of the loss of this dye from these lysosomes into the surrounding cytosol has enabled the quantification of the degree of lysosomal damage caused to earthworms with exposure to an increasing range ofmore » soil copper concentrations, in both laboratory and mesocosm studies. This simple in vitro biomarker has potential for the rapid assessment of the toxic effects to earthworms from soils contaminated with heavy metals and metalloids.« less

The Neutralization of Ion-Rocket Beams

NASA Technical Reports Server (NTRS)

Kaufman, Harold R.

1961-01-01

The experimental ion-beam behavior obtained without neutralizers is compared with both simple collision theory and plasma-wave theory. This comparison indicates that plasma waves play an important part in beam behavior, although the present state of plasma-wave theory does not permit more than a qualitative comparison. The theories of immersed-emitter and electron-trap neutralizer operation are discussed; and, to the extent permitted by experimental data, the theory is compared with experimental results. Experimental data are lacking completely at the present time for operation in space. The results that might be expected in space and the means of simulating such operation in Earth-bound facilities, however, are discussed.

Optimalization of Poly(neutral red) Coated-wire Electrode for Determination of Citrate in Soft Drinks

PubMed Central

Broncová, Gabriela; Shishkanova, Tatiana V.; Krondak, Martin; Volf, Radko; Král, Vladimír

2008-01-01

This report presents an optimization of potentiometric measurements with citrate-selective electropolymerized poly(neutral red) electrodes. The optimal background electrolyte for these measurements is a TRIS buffer with nitrate at pH 8.5. The electrodes described here exhibit stable and reproducible near-Nernstian response to citrates with a low detection limit of 6 × 10-6 M. Electrodes polymerized from sulfuric acid and acetonitrile are compared in detail. Simple and sensitive method for quantification of citrate in real-life samples by potentiometry with poly(neutral red) electrodes are presented. Data from potentiometric measurements of citrate are compared with capillary electrophoresis. PMID:27879724

Computational models of the Posner simple and choice reaction time tasks

PubMed Central

Feher da Silva, Carolina; Baldo, Marcus V. C.

2015-01-01

The landmark experiments by Posner in the late 1970s have shown that reaction time (RT) is faster when the stimulus appears in an expected location, as indicated by a cue; since then, the so-called Posner task has been considered a “gold standard” test of spatial attention. It is thus fundamental to understand the neural mechanisms involved in performing it. To this end, we have developed a Bayesian detection system and small integrate-and-fire neural networks, which modeled sensory and motor circuits, respectively, and optimized them to perform the Posner task under different cue type proportions and noise levels. In doing so, main findings of experimental research on RT were replicated: the relative frequency effect, suboptimal RTs and significant error rates due to noise and invalid cues, slower RT for choice RT tasks than for simple RT tasks, fastest RTs for valid cues and slowest RTs for invalid cues. Analysis of the optimized systems revealed that the employed mechanisms were consistent with related findings in neurophysiology. Our models predict that (1) the results of a Posner task may be affected by the relative frequency of valid and neutral trials, (2) in simple RT tasks, input from multiple locations are added together to compose a stronger signal, and (3) the cue affects motor circuits more strongly in choice RT tasks than in simple RT tasks. In discussing the computational demands of the Posner task, attention has often been described as a filter that protects the nervous system, whose capacity is limited, from information overload. Our models, however, reveal that the main problems that must be overcome to perform the Posner task effectively are distinguishing signal from external noise and selecting the appropriate response in the presence of internal noise. PMID:26190997

Flux transfer events: Reconnection without separators. [magnetopause

NASA Technical Reports Server (NTRS)

Hesse, M.; Birn, J.; Schindler, K.

1989-01-01

A topological analysis of a simple model magnetic field of a perturbation at the magnetopause modeling an apparent flux transfer event is presented. It is shown that a localized perturbation at the magnetopause can in principle open a closed magnetosphere by establishing magnetic connections across the magnetopause. Although the model field exhibits neutral points, these are not involved in the magnetic connection of the flux tubes. The topological substructure of a localized perturbation is analyzed in a simpler configuration. The presence of both signs of the magnetic field component normal to the magnetopause leads to a linkage of topologically different flux tubes, described as a flux knot, and a filamentary substructure of field lines of different topological types which becomes increasingly complicated for decreasing magnetic shear at the magnetopause.

Fourth Generation Parity

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

Lee, Hye-Sung; Soni, Amarjit

2013-01-01

We present a very simple 4th-generation (4G) model with an Abelian gauge interaction under which only the 4G fermions have nonzero charge. The U(1) gauge symmetry can have a Z_2 residual discrete symmetry (4G-parity), which can stabilize the lightest 4G particle (L4P). When the 4G neutrino is the L4P, it would be a neutral and stable particle and the other 4G fermions would decay into the L4P leaving the trace of missing energy plus the standard model fermions. Because of the new symmetry, the 4G particle creation and decay modes are different from those of the sequential 4G model, andmore » the 4G particles can be appreciably lighter than typical experimental bounds.« less

Comparison of model predictions for the composition of the ionosphere of Mars to MAVEN NGIMS data

NASA Astrophysics Data System (ADS)

Withers, Paul; Vogt, Marissa; Mayyasi, Majd; Mahaffy, Paul; Benna, Mehdi; Elrod, Meredith; Bougher, Stephen; Dong, Chuanfei; Chaufray, Jean-Yves; Ma, Yingjuan; Jakosky, Bruce

2015-11-01

Prior to the arrival of the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft at Mars, the only available measurements of the composition of the planet's ionosphere were those acquired by the two Viking Landers during their atmospheric entries. Many numerical models of the composition of the ionosphere of Mars have been developed, but these have only been validated for species, altitudes, and conditions for which Viking data exist. Here we compare the ionospheric composition and structure predicted by 10 ionospheric models at solar zenith angles of 45-60° against ion density measurements acquired by the MAVEN Neutral Gas and Ion Mass Spectrometer (NGIMS). The most successful models included three-dimensional plasma transport driven by interactions with the surrounding space environment but had relatively simple ionospheric chemistry.

Multi-shell model of ion-induced nucleic acid condensation

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

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(III) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derivedmore » from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the “external” shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the “internal” shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent “ion binding shells.”.« less

Scaling theory in a model of corrosion and passivation.

PubMed

Aarão Reis, F D A; Stafiej, Janusz; Badiali, J-P

2006-09-07

We study a model for corrosion and passivation of a metallic surface after small damage of its protective layer using scaling arguments and simulation. We focus on the transition between an initial regime of slow corrosion rate (pit nucleation) to a regime of rapid corrosion (propagation of the pit), which takes place at the so-called incubation time. The model is defined in a lattice in which the states of the sites represent the possible states of the metal (bulk, reactive, and passive) and the solution (neutral, acidic, or basic). Simple probabilistic rules describe passivation of the metal surface, dissolution of the passive layer, which is enhanced in acidic media, and spatially separated electrochemical reactions, which may create pH inhomogeneities in the solution. On the basis of a suitable matching of characteristic times of creation and annihilation of pH inhomogeneities in the solution, our scaling theory estimates the average radius of the dissolved region at the incubation time as a function of the model parameters. Among the main consequences, that radius decreases with the rate of spatially separated reactions and the rate of dissolution in acidic media, and it increases with the diffusion coefficient of H(+) and OH(-) ions in solution. The average incubation time can be written as the sum of a series of characteristic times for the slow dissolution in neutral media, until significant pH inhomogeneities are observed in the dissolved cavity. Despite having a more complex dependence on the model parameters, it is shown that the average incubation time linearly increases with the rate of dissolution in neutral media, under the reasonable assumption that this is the slowest rate of the process. Our theoretical predictions are expected to apply in realistic ranges of values of the model parameters. They are confirmed by numerical simulation in two-dimensional lattices, and the expected extension of the theory to three dimensions is discussed.

Multi-shell model of ion-induced nucleic acid condensation

PubMed Central

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois; Onufriev, Alexey V.

2016-01-01

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the “external” shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the “internal” shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent “ion binding shells.” PMID:27389241

Effect of chemoepitaxial guiding underlayer design on the pattern quality and shape of aligned lamellae for fabrication of line-space patterns

NASA Astrophysics Data System (ADS)

Nation, Benjamin D.; Peters, Andrew J.; Lawson, Richard A.; Ludovice, Peter J.; Henderson, Clifford L.

2017-10-01

Chemoepitaxial guidance of block copolymer directed self-assembly in thin films is explored using a coarse-grained molecular dynamics model. The underlayers studied are 2× density multiplying line-space patterns composed of repeating highly preferential pinning stripes of various widths separated by larger, more neutral, background regions of various compositions. Decreasing the pinning stripe width or making the background region more neutral is found to increase the line edge roughness (LER) of the lines, but these conditions are found to give the straightest sidewalls for the formed lines. Varying these underlayer properties is found to have minimal effect on linewidth roughness. A larger pinning stripe causes the pinned line (PL) to foot (expand near the substrate), and a preferential background region causes the unpinned line (UPL) to undercut (contract near the substrate). A simple model was developed to predict the optimal conditions to eliminate footing. Using this model, conditions are found that decrease footing of the PL, but these conditions increase undercutting in the UPL. Deformations in either the PL or UPL propagate to the other line. There exists a trade-off between LER and the footing/undercutting, that is, decreasing LER increases footing/undercutting and vice versa.

A numerical study of neutral-plasma interaction in magnetically confined plasmas

NASA Astrophysics Data System (ADS)

Taheri, S.; Shumlak, U.; King, J. R.

2017-10-01

Interactions between plasma and neutral species can have a large effect on the dynamic behavior of magnetically confined plasma devices, such as the edge region of tokamaks and the plasma formation of Z-pinches. The presence of neutrals can affect the stability of the pinch and change the dynamics of the pinch collapse, and they can lead to deposition of high energy particles on the first wall. However, plasma-neutral interactions can also have beneficial effects such as quenching the disruptions in tokamaks. In this research a reacting plasma-neutral model, which combines a magnetohydrodynamic (MHD) plasma model with a gas dynamic neutral fluid model, is used to study the interaction between plasma and neutral gas. Incorporating this model into NIMROD allows the study of electron-impact ionization, radiative recombination, and resonant charge-exchange in plasma-neutral systems. An accelerated plasma moving through a neutral gas background is modeled in both a parallel plate and a coaxial electrode configuration to explore the effect of neutral gas in pinch-like devices. This work is supported by a Grant from US DOE.

Simple systematization of vibrational excitation cross-section calculations for resonant electron-molecule scattering in the boomerang and impulse models.

PubMed

Sarma, Manabendra; Adhikari, S; Mishra, Manoj K

2007-01-28

Vibrational excitation (nu(f)<--nu(i)) cross-sections sigma(nu(f)<--nu(i) )(E) in resonant e-N(2) and e-H(2) scattering are calculated from transition matrix elements T(nu(f),nu(i) )(E) obtained using Fourier transform of the cross correlation function , where psi(nu(i))(R,t) approximately =e(-iH(A(2))-(R)t/h phi(nu(i))(R) with time evolution under the influence of the resonance anionic Hamiltonian H(A(2) (-))(A(2) (-)=N(2)(-)/H(2) (-)) implemented using Lanczos and fast Fourier transforms. The target (A(2)) vibrational eigenfunctions phi(nu(i))(R) and phi(nu(f))(R) are calculated using Fourier grid Hamiltonian method applied to potential energy (PE) curves of the neutral target. Application of this simple systematization to calculate vibrational structure in e-N(2) and e-H(2) scattering cross-sections provides mechanistic insights into features underlying presence/absence of structure in e-N(2) and e-H(2) scattering cross-sections. The results obtained with approximate PE curves are in reasonable agreement with experimental/calculated cross-section profiles, and cross correlation functions provide a simple demarcation between the boomerang and impulse models.

Contribution of inorganic and organic components to sorption of neutral and ionizable pharmaceuticals by sediment/soil.

PubMed

Yamamoto, Hiroshi; Takemoto, Kohei; Tamura, Ikumi; Shin-Oka, Norihiro; Nakano, Takahiro; Nishida, Masayo; Honda, Yuta; Moriguchi, Shigemi; Nakamura, Yudai

2018-03-01

Our previous study showed that the sorption coefficient of certain polar pharmaceuticals to river sediment, especially particular amines, was unexpectedly high. Thus, we conducted sorption experiments of selected polar pharmaceuticals and pyrene derivatives, including amines, carboxylic acids, and neutral compounds, to model clay minerals, i.e., montmorillonite and kaolin, in addition to silica sands and humic substances. The contribution of each component was roughly estimated by simple fractionation of the individual sorption coefficients. Relatively high sorption coefficients (K d values) were found, especially for amines on clay minerals, which suggest that electrochemical affinity may play an important role. The estimated contribution percentage suggests a relatively large contribution from inorganic constituents, such as clay minerals, for silt loam soil; in contrast, organic components predominantly contribute for sandy river sediments. These findings could be the key to understanding not only the fate and transport but also bioavailability and environmental risks of pharmaceuticals, which are mostly polar and/or ionizable.

Comparative Evaluation of Biological Performance, Biosecurity, and Availability of Cellulose-Based Absorbable Hemostats.

PubMed

Wu, Yadong; Wang, Fang; Huang, Yudong

2018-05-01

Hemorrhage remains a leading cause of death after trauma, and developing a hemostat with excellent performance and good biosecurity is an extremely active area of research and commercial product development. Although oxidized regenerated cellulose (ORC) has been developed to address these problems, it is not always efficient and its biosecurity is not perfect. We aimed to refine ORC via a simple and mild neutralization method. The prepared neutralized oxidized regenerated cellulose (NORC) showed a superior gel property due to its chemical structure. The biological performance of both ORC and NORC was systematically evaluated; the results showed that ORC would induce erythema and edema in the irritation test, whereas NORC did not cause any adverse inflammation, indicating NORC had desirable biocompatibility. We further demonstrated that NORC confirmed to the toxicity requirements of International Organization for Standardization (ISO) standards; however, ORC showed an unacceptable cytotoxicity. The rabbit hepatic defect model stated that NORC exhibited better ability of hemostasis, which was attributed to its significant gel performance in physiological environment.

Oxidative desulfurization of model diesel via dual activation by a protic ionic liquid.

PubMed

Lü, Hongying; Wang, Shunan; Deng, Changliang; Ren, Wanzhong; Guo, Baocun

2014-08-30

A novel and green carboxylate-anion-based protic ionic liquid (PIL), [Hnmp]HCOO, was prepared through a simple and atom economic neutralization reaction between N-methyl-2-pyrrolidonium (NMP) and formic acids. Both FT-IR spectra and (1)H NMR confirmed its simple salt structure. [Hnmp]HCOO exhibited so high catalytic activity that the dibenzothiophene (DBT) removal reached 99% at 50°C in 3h under conditions of VPIL/Vmodel oil=1:10 and H2O2/DBT (O/S, molar ratio)=5. The catalytic oxidation reactivity of S-compounds was found to be in the order of DBT>4,6-dimethyldibenzothiophene (4,6-DMDBT)>benzothiophene (BT). The investigation on mechanism showed that oxidative desulfurization was realized through dual activation of PIL. Moreover, [Hnmp]HCOO can be recycled for five times with an unnoticeable decrease in desulfurization activity. Copyright © 2014 Elsevier B.V. All rights reserved.

Simulations of induced-charge electro-osmosis in microfluidic devices

NASA Astrophysics Data System (ADS)

Ben, Yuxing

2005-03-01

Theories of nonlinear electrokinetic phenomena generally assume a uniform, neutral bulk electroylte in contact with a polarizable thin double layer near a metal or dielectric surface, which acts as a "capacitor skin". Induced-charge electro-osmosis (ICEO) is the general effect of nonlinear electro-osmotic slip, when an applied electric field acts on its own induced (diffuse) double-layer charge. In most theoretical and experimental work, ICEO has been studied in very simple geometries, such as colloidal spheres and planar, periodic micro-electrode arrays. Here we use finite-element simulations to predict how more complicated geometries of polarizable surfaces and/or electrodes yield flow profiles with subtle dependence on the amplitude and frequency of the applied voltage. We also consider how the simple model equations break down, due to surface conduction, bulk diffusion, and concentration polarization, for large applied voltages (as in most experiments).

The decline and fall of Esperanto: lessons for standards committees.

PubMed

Patterson, R; Huff, S M

1999-01-01

In 1887, Polish physician Ludovic Zamenhof introduced Esperanto, a simple, easy-to-learn planned language. His goal was to erase communication barriers between ethnic groups by providing them with a politically neutral, culturally free standard language. His ideas received both praise and condemnation from the leaders of his time. Interest in Esperanto peaked in the 1970s but has since faded somewhat. Despite the logical concept and intellectual appeal of a standard language, Esperanto has not evolved into a dominant worldwide language. Instead, English, with all its idiosyncrasies, is closest to an international lingua franca. Like Zamenhof, standards committees in medical informatics have recognized communication chaos and have tried to establish working models, with mixed results. In some cases, previously shunned proprietary systems have become the standard. A proposed standard, no matter how simple, logical, and well designed, may have difficulty displacing an imperfect but functional "real life" system.

The Decline and Fall of Esperanto

PubMed Central

Patterson, Robert; Huff, Stanley M.

1999-01-01

In 1887, Polish physician Ludovic Zamenhof introduced Esperanto, a simple, easy-to-learn planned language. His goal was to erase communication barriers between ethnic groups by providing them with a politically neutral, culturally free standard language. His ideas received both praise and condemnation from the leaders of his time. Interest in Esperanto peaked in the 1970s but has since faded somewhat. Despite the logical concept and intellectual appeal of a standard language, Esperanto has not evolved into a dominant worldwide language. Instead, English, with all its idiosyncrasies, is closest to an international lingua franca. Like Zamenhof, standards committees in medical informatics have recognized communication chaos and have tried to establish working models, with mixed results. In some cases, previously shunned proprietary systems have become the standard. A proposed standard, no matter how simple, logical, and well designed, may have difficulty displacing an imperfect but functional “real life” system. PMID:10579602

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

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

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonitemore » edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites (‘spillover’ effect).« less

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

DOE PAGES

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.; ...

2017-10-06

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonitemore » edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites (‘spillover’ effect).« less

Air-Parcel Residence Times Within Forest Canopies

NASA Astrophysics Data System (ADS)

Gerken, Tobias; Chamecki, Marcelo; Fuentes, Jose D.

2017-10-01

We present a theoretical model, based on a simple model of turbulent diffusion and first-order chemical kinetics, to determine air-parcel residence times and the out-of-canopy export of reactive gases emitted within forest canopies under neutral conditions. Theoretical predictions of the air-parcel residence time are compared to values derived from large-eddy simulation for a range of canopy architectures and turbulence levels under neutral stratification. Median air-parcel residence times range from a few sec in the upper canopy to approximately 30 min near the ground and the distribution of residence times is skewed towards longer times in the lower canopy. While the predicted probability density functions from the theoretical model and large-eddy simulation are in good agreement with each other, the theoretical model requires only information on canopy height and eddy diffusivities inside the canopy. The eddy-diffusivity model developed additionally requires the friction velocity at canopy top and a parametrized profile of the standard deviation of vertical velocity. The theoretical model of air-parcel residence times is extended to include first-order chemical reactions over a range of of Damköhler numbers ( Da) characteristic of plant-emitted hydrocarbons. The resulting out-of-canopy export fractions range from near 1 for Da =10^{-3} to less than 0.3 at Da = 10. These results highlight the necessity for dense and tall forests to include the impacts of air-parcel residence times when calculating the out-of-canopy export fraction for reactive trace gases.

Benchmark of 3D halo neutral simulation in TRANSP and FIDASIM and application to projected neutral-beam-heated NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Liu, D.; Medley, S. S.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

2014-10-01

A cloud of halo neutrals is created in the vicinity of beam footprint during the neutral beam injection and the halo neutral density can be comparable with beam neutral density. Proper modeling of halo neutrals is critical to correctly interpret neutral particle analyzers (NPA) and fast ion D-alpha (FIDA) signals since these signals strongly depend on local beam and halo neutral density. A 3D halo neutral model has been recently developed and implemented inside TRANSP code. The 3D halo neutral code uses a ``beam-in-a-box'' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce thermal halo neutrals that are tracked through successive halo neutral generations until an ionization event occurs or a descendant halo exits the box. A benchmark between 3D halo neural model in TRANSP and in FIDA/NPA synthetic diagnostic code FIDASIM is carried out. Detailed comparison of halo neutral density profiles from two codes will be shown. The NPA and FIDA simulations with and without 3D halos are applied to projections of plasma performance for the National Spherical Tours eXperiment-Upgrade (NSTX-U) and the effects of halo neutral density on NPA and FIDA signal amplitude and profile will be presented. Work supported by US DOE.

Neutrino masses from neutral top partners

NASA Astrophysics Data System (ADS)

Batell, Brian; McCullough, Matthew

2015-10-01

We present theories of "natural neutrinos" in which neutral fermionic top partner fields are simultaneously the right-handed neutrinos (RHN), linking seemingly disparate aspects of the Standard Model structure: (a) The RHN top partners are responsible for the observed small neutrino masses, (b) they help ameliorate the tuning in the weak scale and address the little hierarchy problem, and (c) the factor of 3 arising from Nc in the top-loop Higgs mass corrections is countered by a factor of 3 from the number of vectorlike generations of RHN. The RHN top partners may arise in pseudo-Nambu-Goldstone-Boson Higgs models such as the twin Higgs, as well as more general composite, little, and orbifold Higgs scenarios, and three simple example models are presented. This framework firmly predicts a TeV-scale seesaw, as the RHN masses are bounded to be below the TeV scale by naturalness. The generation of light neutrino masses relies on a collective breaking of the lepton number, allowing for comparatively large neutrino Yukawa couplings and a rich associated phenomenology. The structure of the neutrino mass mechanism realizes in certain limits the inverse or linear classes of seesaw. Natural neutrino models are testable at a variety of current and future experiments, particularly in tests of lepton universality, searches for lepton flavor violation, and precision electroweak and Higgs coupling measurements possible at high energy e+e- and hadron colliders.

Experiment-Model Comparisons of Turbulence, Transport, and Flows in a Magnetized Linear Plasma Using a Global Two-Fluid Braginskii Solver

NASA Astrophysics Data System (ADS)

Gilmore, M.; Fisher, D. M.; Kelly, R. F.; Hatch, M. W.; Rogers, B. N.

2017-10-01

Ongoing experiments and numerical modeling of the dynamics of electrostatic turbulence and transport in the presence of flow shear are being conducted in helicon plasmas in the linear HelCat (Helicon-Cathode) device. Modeling is being done using GBS, a 3D, global two-fluid Braginskii code that solves self-consistently for plasma equilibrium as well as fluctuations. Past experimental measurements of flows have been difficult to reconcile with simple expectations, such as azimuthal flows being dominated by Er x Bz rotation. Therefore, recent measurements have focused on understanding plasma flows, and the role of neutral dynamics. In the model, a set of two-fluid drift-reduced Braginskii equations are evolved using the Global Braginskii Solver Code (GBS). For low-field helicon-sourced Ar plasmas a non-negligible cross-field thermal collisional term must be added to shift the electric potential in the ion momentum and vorticity equations as the ions are unmagnetized. Significant radially and axially dependent neutral profiles are also included in the simulations to try and match those observed in HelCat. Ongoing simulations show a mode dependence on the axial magnetic field along with strong axial variations that suggest drift waves may be important in the low-field case. Supported by U.S. National Science Foundation Award 1500423.

Lossed in translation: an off-the-shelf method to recover probabilistic beliefs from loss-averse agents.

PubMed

Offerman, Theo; Palley, Asa B

2016-01-01

Strictly proper scoring rules are designed to truthfully elicit subjective probabilistic beliefs from risk neutral agents. Previous experimental studies have identified two problems with this method: (i) risk aversion causes agents to bias their reports toward the probability of [Formula: see text], and (ii) for moderate beliefs agents simply report [Formula: see text]. Applying a prospect theory model of risk preferences, we show that loss aversion can explain both of these behavioral phenomena. Using the insights of this model, we develop a simple off-the-shelf probability assessment mechanism that encourages loss-averse agents to report true beliefs. In an experiment, we demonstrate the effectiveness of this modification in both eliminating uninformative reports and eliciting true probabilistic beliefs.

Pre-sheath density drop induced by ion-neutral friction along plasma blobs and implications for blob velocities

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

Furno, I.; Chabloz, V.; Fasoli, A.

2014-01-15

The pre-sheath density drop along the magnetic field in field-aligned, radially propagating plasma blobs is investigated in the TORPEX toroidal experiment [Fasoli et al., Plasma Phys. Controlled Fusion 52, 124020 (2010)]. Using Langmuir probes precisely aligned along the magnetic field, we measure the density n{sub se} at a poloidal limiter, where blobs are connected, and the upstream density n{sub 0} at a location half way to the other end of the blobs. The pre-sheath density drop n{sub se}/n{sub 0} is then computed and its dependence upon the neutral background gas pressure is studied. At low neutral gas pressures, the pre-sheathmore » density drop is ≈0.4, close to the value of 0.5 expected in the collisionless case. In qualitative agreement with a simple model, this value decreases with increasing gas pressure. No significant dependence of the density drop upon the radial distance into the limiter shadow is observed. The effect of reduced blob density near the limiter on the blob radial velocity is measured and compared with predictions from a blob speed-versus-size scaling law [Theiler et al., Phys. Rev. Lett. 103, 065001 (2009)].« less

Blowing in the Milky Way Wind: Neutral Hydrogen Clouds Tracing the Galactic Nuclear Outflow

NASA Astrophysics Data System (ADS)

Di Teodoro, Enrico M.; McClure-Griffiths, N. M.; Lockman, Felix J.; Denbo, Sara R.; Endsley, Ryan; Ford, H. Alyson; Harrington, Kevin

2018-03-01

We present the results of a new sensitive survey of neutral hydrogen above and below the Galactic Center with the Green Bank Telescope. The observations extend up to Galactic latitude | b| < 10^\\circ with an effective angular resolution of 9.‧5 and an average rms brightness temperature noise of 40 mK in a 1 {km} {{{s}}}-1 channel. The survey reveals the existence of a population of anomalous high-velocity clouds extending up to heights of about 1.5 kpc from the Galactic plane and showing no signature of Galactic rotation. These clouds have local standard of rest velocities | {V}LSR}| ≲ 360 {km} {{{s}}}-1, and assuming a Galactic Center origin, they have sizes of a few tens of parsec and neutral hydrogen masses spanning 10{--}{10}5 {M}ȯ . Accounting for selection effects, the cloud population is symmetric in longitude, latitude, and V LSR. We model the cloud kinematics in terms of an outflow expanding from the Galactic Center and find the population consistent with being material moving with radial velocity {V}{{w}}≃ 330 {km} {{{s}}}-1 distributed throughout a bicone with opening angle α > 140^\\circ . This simple model implies an outflow luminosity {L}{{w}}> 3× {10}40 erg s‑1 over the past 10 Myr, consistent with star formation feedback in the inner region of the Milky Way, with a cold gas mass-loss rate ≲ 0.1 {{M}ȯ {yr}}-1. These clouds may represent the cold gas component accelerated in the nuclear wind driven by our Galaxy, although some of the derived properties challenge current theoretical models of the entrainment process.

Deep-down ionization of protoplanetary discs

NASA Astrophysics Data System (ADS)

Glassgold, A. E.; Lizano, S.; Galli, D.

2017-12-01

The possible occurrence of dead zones in protoplanetary discs subject to the magneto-rotational instability highlights the importance of disc ionization. We present a closed-form theory for the deep-down ionization by X-rays at depths below the disc surface dominated by far-ultraviolet radiation. Simple analytic solutions are given for the major ion classes, electrons, atomic ions, molecular ions and negatively charged grains. In addition to the formation of molecular ions by X-ray ionization of H2 and their destruction by dissociative recombination, several key processes that operate in this region are included, e.g. charge exchange of molecular ions and neutral atoms and destruction of ions by grains. Over much of the inner disc, the vertical decrease in ionization with depth into the disc is described by simple power laws, which can easily be included in more detailed modelling of magnetized discs. The new ionization theory is used to illustrate the non-ideal magnetohydrodynamic effects of Ohmic, Hall and Ambipolar diffusion for a magnetic model of a T Tauri star disc using the appropriate Elsasser numbers.

Krein signature for instability of PT-symmetric states

NASA Astrophysics Data System (ADS)

Chernyavsky, Alexander; Pelinovsky, Dmitry E.

2018-05-01

Krein quantity is introduced for isolated neutrally stable eigenvalues associated with the stationary states in the PT-symmetric nonlinear Schrödinger equation. Krein quantity is real and nonzero for simple eigenvalues but it vanishes if two simple eigenvalues coalesce into a defective eigenvalue. A necessary condition for bifurcation of unstable eigenvalues from the defective eigenvalue is proved. This condition requires the two simple eigenvalues before the coalescence point to have opposite Krein signatures. The theory is illustrated with several numerical examples motivated by recent publications in physics literature.

Evolutionary dynamics on networks of selectively neutral genotypes: effects of topology and sequence stability.

PubMed

Aguirre, Jacobo; Buldú, Javier M; Manrubia, Susanna C

2009-12-01

Networks of selectively neutral genotypes underlie the evolution of populations of replicators in constant environments. Previous theoretical analysis predicted that such populations will evolve toward highly connected regions of the genome space. We first study the evolution of populations of replicators on simple networks and quantify how the transient time to equilibrium depends on the initial distribution of sequences on the neutral network, on the topological properties of the latter, and on the mutation rate. Second, network neutrality is broken through the introduction of an energy for each sequence. This allows to study the competition between two features (neutrality and energetic stability) relevant for survival and subjected to different selective pressures. In cases where the two features are negatively correlated, the population experiences sudden migrations in the genome space for values of the relevant parameters that we calculate. The numerical study of larger networks indicates that the qualitative behavior to be expected in more realistic cases is already seen in representative examples of small networks.

Evolutionary dynamics on networks of selectively neutral genotypes: Effects of topology and sequence stability

NASA Astrophysics Data System (ADS)

Aguirre, Jacobo; Buldú, Javier M.; Manrubia, Susanna C.

2009-12-01

Networks of selectively neutral genotypes underlie the evolution of populations of replicators in constant environments. Previous theoretical analysis predicted that such populations will evolve toward highly connected regions of the genome space. We first study the evolution of populations of replicators on simple networks and quantify how the transient time to equilibrium depends on the initial distribution of sequences on the neutral network, on the topological properties of the latter, and on the mutation rate. Second, network neutrality is broken through the introduction of an energy for each sequence. This allows to study the competition between two features (neutrality and energetic stability) relevant for survival and subjected to different selective pressures. In cases where the two features are negatively correlated, the population experiences sudden migrations in the genome space for values of the relevant parameters that we calculate. The numerical study of larger networks indicates that the qualitative behavior to be expected in more realistic cases is already seen in representative examples of small networks.

Efficient simulation and likelihood methods for non-neutral multi-allele models.

PubMed

Joyce, Paul; Genz, Alan; Buzbas, Erkan Ozge

2012-06-01

Throughout the 1980s, Simon Tavaré made numerous significant contributions to population genetics theory. As genetic data, in particular DNA sequence, became more readily available, a need to connect population-genetic models to data became the central issue. The seminal work of Griffiths and Tavaré (1994a , 1994b , 1994c) was among the first to develop a likelihood method to estimate the population-genetic parameters using full DNA sequences. Now, we are in the genomics era where methods need to scale-up to handle massive data sets, and Tavaré has led the way to new approaches. However, performing statistical inference under non-neutral models has proved elusive. In tribute to Simon Tavaré, we present an article in spirit of his work that provides a computationally tractable method for simulating and analyzing data under a class of non-neutral population-genetic models. Computational methods for approximating likelihood functions and generating samples under a class of allele-frequency based non-neutral parent-independent mutation models were proposed by Donnelly, Nordborg, and Joyce (DNJ) (Donnelly et al., 2001). DNJ (2001) simulated samples of allele frequencies from non-neutral models using neutral models as auxiliary distribution in a rejection algorithm. However, patterns of allele frequencies produced by neutral models are dissimilar to patterns of allele frequencies produced by non-neutral models, making the rejection method inefficient. For example, in some cases the methods in DNJ (2001) require 10(9) rejections before a sample from the non-neutral model is accepted. Our method simulates samples directly from the distribution of non-neutral models, making simulation methods a practical tool to study the behavior of the likelihood and to perform inference on the strength of selection.

A Heterodimer of a VHH (Variable Domains of Camelid Heavy Chain-only) Antibody That Inhibits Anthrax Toxin Cell Binding Linked to a VHH Antibody That Blocks Oligomer Formation Is Highly Protective in an Anthrax Spore Challenge Model*

PubMed Central

Moayeri, Mahtab; Leysath, Clinton E.; Tremblay, Jacqueline M.; Vrentas, Catherine; Crown, Devorah; Leppla, Stephen H.; Shoemaker, Charles B.

2015-01-01

Anthrax disease is caused by a toxin consisting of protective antigen (PA), lethal factor, and edema factor. Antibodies against PA have been shown to be protective against the disease. Variable domains of camelid heavy chain-only antibodies (VHHs) with affinity for PA were obtained from immunized alpacas and screened for anthrax neutralizing activity in macrophage toxicity assays. Two classes of neutralizing VHHs were identified recognizing distinct, non-overlapping epitopes. One class recognizes domain 4 of PA at a well characterized neutralizing site through which PA binds to its cellular receptor. A second neutralizing VHH (JKH-C7) recognizes a novel epitope. This antibody inhibits conversion of the PA oligomer from “pre-pore” to its SDS and heat-resistant “pore” conformation while not preventing cleavage of full-length 83-kDa PA (PA83) by cell surface proteases to its oligomer-competent 63-kDa form (PA63). The antibody prevents endocytosis of the cell surface-generated PA63 subunit but not preformed PA63 oligomers formed in solution. JKH-C7 and the receptor-blocking VHH class (JIK-B8) were expressed as a heterodimeric VHH-based neutralizing agent (VNA2-PA). This VNA displayed improved neutralizing potency in cell assays and protected mice from anthrax toxin challenge with much better efficacy than the separate component VHHs. The VNA protected virtually all mice when separately administered at a 1:1 ratio to toxin and protected mice against Bacillus anthracis spore infection. Thus, our studies show the potential of VNAs as anthrax therapeutics. Due to their simple and stable nature, VNAs should be amenable to genetic delivery or administration via respiratory routes. PMID:25564615

A heterodimer of a VHH (variable domains of camelid heavy chain-only) antibody that inhibits anthrax toxin cell binding linked to a VHH antibody that blocks oligomer formation is highly protective in an anthrax spore challenge model.

PubMed

Moayeri, Mahtab; Leysath, Clinton E; Tremblay, Jacqueline M; Vrentas, Catherine; Crown, Devorah; Leppla, Stephen H; Shoemaker, Charles B

2015-03-06

Anthrax disease is caused by a toxin consisting of protective antigen (PA), lethal factor, and edema factor. Antibodies against PA have been shown to be protective against the disease. Variable domains of camelid heavy chain-only antibodies (VHHs) with affinity for PA were obtained from immunized alpacas and screened for anthrax neutralizing activity in macrophage toxicity assays. Two classes of neutralizing VHHs were identified recognizing distinct, non-overlapping epitopes. One class recognizes domain 4 of PA at a well characterized neutralizing site through which PA binds to its cellular receptor. A second neutralizing VHH (JKH-C7) recognizes a novel epitope. This antibody inhibits conversion of the PA oligomer from "pre-pore" to its SDS and heat-resistant "pore" conformation while not preventing cleavage of full-length 83-kDa PA (PA83) by cell surface proteases to its oligomer-competent 63-kDa form (PA63). The antibody prevents endocytosis of the cell surface-generated PA63 subunit but not preformed PA63 oligomers formed in solution. JKH-C7 and the receptor-blocking VHH class (JIK-B8) were expressed as a heterodimeric VHH-based neutralizing agent (VNA2-PA). This VNA displayed improved neutralizing potency in cell assays and protected mice from anthrax toxin challenge with much better efficacy than the separate component VHHs. The VNA protected virtually all mice when separately administered at a 1:1 ratio to toxin and protected mice against Bacillus anthracis spore infection. Thus, our studies show the potential of VNAs as anthrax therapeutics. Due to their simple and stable nature, VNAs should be amenable to genetic delivery or administration via respiratory routes. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives

PubMed Central

Matthews, Thomas J; Whittaker, Robert J

2014-01-01

Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research. PMID:25360266

Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives.

PubMed

Matthews, Thomas J; Whittaker, Robert J

2014-06-01

Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.

Two-fluid (plasma-neutral) Extended-MHD simulations of spheromak configurations in the HIT-SI experiment with PSI-Tet

NASA Astrophysics Data System (ADS)

Sutherland, D. A.; Hansen, C. J.; Jarboe, T. R.

2017-10-01

A self-consistent, two-fluid (plasma-neutral) dynamic neutral model has been implemented into the 3-D, Extended-MHD code PSI-Tet. A monatomic, hydrogenic neutral fluid reacts with a plasma fluid through elastic scattering collisions and three inelastic collision reactions: electron-impact ionization, radiative recombination, and resonant charge-exchange. Density, momentum, and energy are evolved for both the plasma and neutral species. The implemented plasma-neutral model in PSI-Tet is being used to simulate decaying spheromak configurations in the HIT-SI experimental geometry, which is being compare to two-photon absorption laser induced fluorescence measurements (TALIF) made on the HIT-SI3 experiment. TALIF is used to measure the absolute density and temperature of monatomic deuterium atoms. Neutral densities on the order of 1015 m-3 and neutral temperatures between 0.6-1.7 eV were measured towards the end of decay of spheromak configurations with initial toroidal currents between 10-12 kA. Validation results between TALIF measurements and PSI-Tet simulations with the implemented dynamic neutral model will be presented. Additionally, preliminary dynamic neutral simulations of the HIT-SI/HIT-SI3 spheromak plasmas sustained with inductive helicity injection will be presented. Lastly, potential benefits of an expansion of the two-fluid model into a multi-fluid model that includes multiple neutral species and tracking of charge states will be discussed.

Applying ecological models to communities of genetic elements: the case of neutral theory.

PubMed

Linquist, Stefan; Cottenie, Karl; Elliott, Tyler A; Saylor, Brent; Kremer, Stefan C; Gregory, T Ryan

2015-07-01

A promising recent development in molecular biology involves viewing the genome as a mini-ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational-hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub 'fitness neutrality' and 'competitive neutrality'. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size. © 2015 John Wiley & Sons Ltd.

Dissipative instability in a partially ionised prominence plasma slab

NASA Astrophysics Data System (ADS)

Ballai, I.; Pintér, B.; Oliver, R.; Alexandrou, M.

2017-07-01

Aims: We aim to investigate the nature of dissipative instability appearing in a prominence planar thread filled with partially ionised plasma in the incompressible limit. The importance of partial ionisation is investigated in terms of the ionisation factor and the wavelength of sausage and kink waves propagating in the slab. Methods: In order to highlight the role of partial ionisation, we have constructed models describing various situations we can meet in solar prominence fine structure. Matching the solutions for the transversal component of the velocity and total pressure at the interfaces between the prominence slab and surrounding plasmas, we derived a dispersion relation whose imaginary part describes the evolution of the instability. Results were obtained in the limit of weak dissipation. We have investigated the appearance of instabilities in prominence dark plumes using single and two-fluid approximations. Results: Using simple analytical methods, we show that dissipative instabilities appear for flow speeds that are less than the Kelvin-Helmholtz instability threshold. The onset of instability is determined by the equilibrium flow strength, the ionisation factor of the plasma, the wavelength of waves and the ion-neutral collisional rate. For a given wavelength and for ionisation degrees closer to a neutral gas, the propagating waves become unstable for a narrow band of flow speeds, meaning that neutrals have a stabilising effect. Our results show that the partially ionised plasma describing prominence dark plumes becomes unstable only in a two-fluid (charged particles-neutrals) model, that is for periods that are smaller than the ion-neutral collision time. Conclusions: The present study improves our understanding of the complexity of dynamical processes and stability of solar prominences and the role partial ionisation in destabilising the plasma. We showed the necessity of two-fluid approximation when discussing the nature of instabilities: waves in a single fluid approximation show a great deal of stability. Our results clearly show that the problem of partial ionisation introduces new aspects of plasma stability with consequences on the evolution of partially ionised plasmas and solar prominences, in particular.

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models.

PubMed

Leontyev, Igor V; Stuchebrukhov, Alexei A

2014-07-07

Earlier, using phenomenological approach, we showed that in some cases polarizable models of condensed phase systems can be reduced to nonpolarizable equivalent models with scaled charges. Examples of such systems include ionic liquids, TIPnP-type models of water, protein force fields, and others, where interactions and dynamics of inherently polarizable species can be accurately described by nonpolarizable models. To describe electrostatic interactions, the effective charges of simple ionic liquids are obtained by scaling the actual charges of ions by a factor of 1/√(ε(el)), which is due to electronic polarization screening effect; the scaling factor of neutral species is more complicated. Here, using several theoretical models, we examine how exactly the scaling factors appear in theory, and how, and under what conditions, polarizable Hamiltonians are reduced to nonpolarizable ones. These models allow one to trace the origin of the scaling factors, determine their values, and obtain important insights on the nature of polarizable interactions in condensed matter systems.

Reionization Simulations Powered by Graphics Processing Units. I. On the Structure of the Ultraviolet Radiation Field

NASA Astrophysics Data System (ADS)

Aubert, Dominique; Teyssier, Romain

2010-11-01

We present a set of cosmological simulations with radiative transfer in order to model the reionization history of the universe from z = 18 down to z = 6. Galaxy formation and the associated star formation are followed self-consistently with gas and dark matter dynamics using the RAMSES code, while radiative transfer is performed as a post-processing step using a moment-based method with the M1 closure relation in the ATON code. The latter has been ported to a multiple Graphics Processing Unit (GPU) architecture using the CUDA language together with the MPI library, resulting in an overall acceleration that allows us to tackle radiative transfer problems at a significantly higher resolution than previously reported: 10243 + 2 levels of refinement for the hydrodynamic adaptive grid and 10243 for the radiative transfer Cartesian grid. We reach a typical acceleration factor close to 100× when compared to the CPU version, allowing us to perform 1/4 million time steps in less than 3000 GPU hr. We observe good convergence properties between our different resolution runs for various volume- and mass-averaged quantities such as neutral fraction, UV background, and Thomson optical depth, as long as the effects of finite resolution on the star formation history are properly taken into account. We also show that the neutral fraction depends on the total mass density, in a way close to the predictions of photoionization equilibrium, as long as the effect of self-shielding are included in the background radiation model. Although our simulation suite has reached unprecedented mass and spatial resolution, we still fail in reproducing the z ~ 6 constraints on the neutral fraction of hydrogen and the intensity of the UV background. In order to account for unresolved density fluctuations, we have modified our chemistry solver with a simple clumping factor model. Using our most spatially resolved simulation (12.5 Mpc h -1 with 10243 particles) to calibrate our subgrid model, we have resimulated our largest box (100 Mpc h -1 with 10243 particles) with the modified chemistry, successfully reproducing the observed level of neutral hydrogen in the spectra of high-redshift quasars. We however did not reproduce the average photoionization rate inferred from the same observations. We argue that this discrepancy could be partly explained by the fact that the average radiation intensity and the average neutral fraction depend on different regions of the gas density distribution, so that one quantity cannot be simply deduced from the other.

Fiscal Neutrality and Local Choice in Public Education.

ERIC Educational Resources Information Center

Weber, William L.

1991-01-01

Extends Feldstein's notion of wealth neutrality to embrace fiscal neutrality, using a representative consumer context. Employs an "ideal" demand system to model school district expenditures in a general equilibrium framework. Rejects constant price and income elasticity demand models. Supports the fiscally neutral elasticity model…

Thermal Conductivity of the Multicomponent Neutral Atmosphere

NASA Astrophysics Data System (ADS)

Pavlov, A. V.

2017-12-01

Approximate expressions for the thermal conductivity coefficient of the multicomponent neutral atmosphere consisting of N2, O2, O, He, and H are analyzed and evaluated for the atmospheric conditions by comparing them with that given by the rigorous hydrodynamic theory. The new approximations of the thermal conductivity coefficients of simple gases N2, O2, O, He, and H are derived and used. It is proved that the modified Mason and Saxena approximation of the atmospheric thermal conductivity coefficient is more accurate in reproducing the atmospheric values of the rigorous hydrodynamic thermal conductivity coefficient in comparison with those that are generally accepted in atmospheric studies. This approximation of the thermal conductivity coefficient is recommended to use in calculations of the neutral temperature of the atmosphere.

[Studies on the interaction between RNA with neutral red and determination of RNA by spectrophotometry].

PubMed

Si, Wen-Hui

2007-06-01

An analytical method for the determination of ribonucleic acid by spectrophotometry was established. At the maximum absorption wavelength for neutral red in B-R buffer solution, and under the best conditions, the decrease in the absorbance was linear with the amount of ribonucleic acid. The linearity range was 0.0-9.0 microg x mL(-1), the detection limit was 0.52 microg x mL(-1), and the correlation coeffient was 0.999 8. This method was simple, rapid, and selective. So its application to the determination of ribonucleic acid was satisfactory. The reaction mechanism was that the electrostatic interaction leads to molecular association of RNA with neutral red, resulting in anti-ion permutation and bonding reaction.

Motion of Molecular Probes and Viscosity Scaling in Polyelectrolyte Solutions at Physiological Ionic Strength

PubMed Central

Sozanski, Krzysztof; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Sznajder, Anna; Holyst, Robert

2016-01-01

We investigate transport properties of model polyelectrolyte systems at physiological ionic strength (0.154 M). Covering a broad range of flow length scales—from diffusion of molecular probes to macroscopic viscous flow—we establish a single, continuous function describing the scale dependent viscosity of high-salt polyelectrolyte solutions. The data are consistent with the model developed previously for electrically neutral polymers in a good solvent. The presented approach merges the power-law scaling concepts of de Gennes with the idea of exponential length scale dependence of effective viscosity in complex liquids. The result is a simple and applicable description of transport properties of high-salt polyelectrolyte solutions at all length scales, valid for motion of single molecules as well as macroscopic flow of the complex liquid. PMID:27536866

Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction.

PubMed

Palmer, David S; Frolov, Andrey I; Ratkova, Ekaterina L; Fedorov, Maxim V

2010-12-15

We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).

Three-dimensional modeling of the neutral gas depletion effect in a helicon discharge plasma

NASA Astrophysics Data System (ADS)

Kollasch, Jeffrey; Schmitz, Oliver; Norval, Ryan; Reiter, Detlev; Sovinec, Carl

2016-10-01

Helicon discharges provide an attractive radio-frequency driven regime for plasma, but neutral-particle dynamics present a challenge to extending performance. A neutral gas depletion effect occurs when neutrals in the plasma core are not replenished at a sufficient rate to sustain a higher plasma density. The Monte Carlo neutral particle tracking code EIRENE was setup for the MARIA helicon experiment at UW Madison to study its neutral particle dynamics. Prescribed plasma temperature and density profiles similar to those in the MARIA device are used in EIRENE to investigate the main causes of the neutral gas depletion effect. The most dominant plasma-neutral interactions are included so far, namely electron impact ionization of neutrals, charge exchange interactions of neutrals with plasma ions, and recycling at the wall. Parameter scans show how the neutral depletion effect depends on parameters such as Knudsen number, plasma density and temperature, and gas-surface interaction accommodation coefficients. Results are compared to similar analytic studies in the low Knudsen number limit. Plans to incorporate a similar Monte Carlo neutral model into a larger helicon modeling framework are discussed. This work is funded by the NSF CAREER Award PHY-1455210.

Light neutral C P -even Higgs boson within the next-to-minimal supersymmetric standard model at the Large Hadron Electron Collider

NASA Astrophysics Data System (ADS)

Das, Siba Prasad; Nowakowski, Marek

2017-09-01

We analyze the prospects of observing the light charge parity (C P )-even neutral Higgs bosons (h1) in their decays into b b ¯ quarks, in the neutral and charged current production processes e h1q and ν h1q at the upcoming Large Hadron Electron Collider (LHeC), with √{s }≈1.296 TeV . Assuming that the intermediate Higgs boson (h2 ) is Standard Model (SM)-like, we study the Higgs production within the framework of next-to-minimal supersymmetric Standard Model (NMSSM). We consider the constraints from dark-matter, sparticle masses, and the Higgs boson data. The signal in our analysis can be classified as three jets, with electron (missing energy) coming from the neutral (charged) current interaction. We demand that the number of b -tagged jets in the central rapidity region be greater or equal to two. The remaining jet is tagged in the forward regions. With this forward jet and two b -tagged jets in the central region, we reconstructed three jets invariant masses. Applying some lower limits on these invariant masses turns out to be an essential criterion to enhance the signal-to-background rates, with slightly different sets of kinematical selections in the two different channels. We consider almost all reducible and irreducible SM background processes. We find that the non-SM like Higgs boson, h1, would be accessible in some of the NMSSM benchmark points, at approximately the 0.4 σ (2.5 σ ) level in the e +3 j channel up to Higgs boson masses of 75 GeV, and in the ET +3 j channel could be discovered with the 1.7 σ (2.4 σ ) level up to Higgs boson masses of 88 GeV with 100 fb-1 of data in a simple cut-based (with optimization) selection. With ten times more data accumulation at the end of the LHeC run, and using optimization, one can have 5 σ discovery in the electron (missing energy) channel up to 85 (more than 90) GeV.

A Statistical Model of the Magnetotail Neutral Sheet

NASA Astrophysics Data System (ADS)

Xiao, Sudong; Zhang, Tielong; Baumjohann, Wolfgang; Nakamura, Rumi; Ge, Yasong; Du, Aimin; Wang, Guoqiang; Lu, Quanming

2015-04-01

The neutral sheet of the magnetotail is characterized by weak magnetic field, strong cross tail current, and a reversal of the magnetic field direction across it. The dynamics of the earth's magnetosphere is greatly influenced by physical processes that occur near the neutral sheet. However, the exact position of the neutral sheet is variable in time. It is therefore essential to have a reliable estimate of the average position of the neutral sheet. Magnetic field data from ten years of Cluster, nineteen years of Geotail, four years of TC 1, and seven years of THEMIS observations have been incorporated to obtain a model of the magnetotail neutral sheet. All data in aberrated GSM (Geocentric Solar Magnetospheric) coordinate system are normalized to the same solar wind pressure condition. The shape and position of the neutral sheet, illustrated directly by the separator of positive and negative Bx on the YZ cross sections, are fitted with a displaced ellipse model. It is consistent with previous studies that the neutral sheet becomes curvier in the YZ cross section when the dipole tilt increases, yet our model shows the curviest neutral sheet compared with previous models. The new model reveals a hinging distance very close to 10 RE at a reference solar wind dynamic pressure of 2 nPa. We find that the earth dipole tilt angle not only affects the neutral sheet configuration in the YZ cross section but also in the XZ cross section. The neutral sheet becomes more tilting in the XZ cross section when the dipole tilt increases. The effect of an interplanetary magnetic field (IMF) penetration is studied, and an IMF By-related twisting of about 3° is found. Anticlockwise twisting of the neutral sheet is observed, looking along the downtail direction, for a positive IMF By, and clockwise twisting of the neutral sheet for a negative IMF By.

Development of SSUBPIC code for modeling the neutral gas depletion effect in helicon discharges

NASA Astrophysics Data System (ADS)

Kollasch, Jeffrey; Sovenic, Carl; Schmitz, Oliver

2017-10-01

The SSUBPIC (steady-state unstructured-boundary particle-in-cell) code is being developed to model helicon plasma devices. The envisioned modeling framework incorporates (1) a kinetic neutral particle model, (2) a kinetic ion model, (3) a fluid electron model, and (4) an RF power deposition model. The models are loosely coupled and iterated until convergence to steady-state. Of the four required solvers, the kinetic ion and neutral particle simulation can now be done within the SSUBPIC code. Recent SSUBPIC modifications include implementation and testing of a Coulomb collision model (Lemons et al., JCP, 228(5), pp. 1391-1403) allowing efficient coupling of kineticly-treated ions to fluid electrons, and implementation of a neutral particle tracking mode with charge-exchange and electron impact ionization physics. These new simulation capabilities are demonstrated working independently and coupled to ``dummy'' profiles for RF power deposition to converge on steady-state plasma and neutral profiles. The geometry and conditions considered are similar to those of the MARIA experiment at UW-Madison. Initial results qualitatively show the expected neutral gas depletion effect in which neutrals in the plasma core are not replenished at a sufficient rate to sustain a higher plasma density. This work is funded by the NSF CAREER award PHY-1455210 and NSF Grant PHY-1206421.

Vecksler-Macmillan phase stability for neutral atoms accelerated by a laser beam

NASA Astrophysics Data System (ADS)

Mel'nikov, I. V.; Haus, J. W.; Kazansky, P. G.

2003-05-01

We use a Fokker-Planck equation to study the phenomenon of accelerating a neutral atom bunch by a chirped optical beam. This method enables us to obtain a semi-analytical solution to the problem in which a wide range of parameters can be studied. In addition it provides a simple physical interpretation where the problem is reduced to an analogous problem of charged particles accelerators, that is, the Vecksler-Macmillan principle of phase stability. A possible experimental scenario is suggested, which uses a photonic crystal fiber as the guiding medium.

Kelvin-Voigt model of wave propagation in fragmented geomaterials with impact damping

NASA Astrophysics Data System (ADS)

Khudyakov, Maxim; Pasternak, Elena; Dyskin, Arcady

2017-04-01

When a wave propagates through real materials, energy dissipation occurs. The effect of loss of energy in homogeneous materials can be accounted for by using simple viscous models. However, a reliable model representing the effect in fragmented geomaterials has not been established yet. The main reason for that is a mechanism how vibrations are transmitted between the elements (fragments) in these materials. It is hypothesised that the fragments strike against each other, in the process of oscillation, and the impacts lead to the energy loss. We assume that the energy loss is well represented by the restitution coefficient. The principal element of this concept is the interaction of two adjacent blocks. We model it by a simple linear oscillator (a mass on an elastic spring) with an additional condition: each time the system travels through the neutral point, where the displacement is equal to zero, the velocity reduces by multiplying itself by the restitution coefficient, which characterises an impact of the fragments. This additional condition renders the system non-linear. We show that the behaviour of such a model averaged over times much larger than the system period can approximately be represented by a conventional linear oscillator with linear damping characterised by a damping coefficient expressible through the restitution coefficient. Based on this the wave propagation at times considerably greater than the resonance period of oscillations of the neighbouring blocks can be modelled using the Kelvin-Voigt model. The wave velocities and the dispersion relations are obtained.

Efficient in situ separation and production of L-lactic acid by Bacillus coagulans using weak basic anion-exchange resin.

PubMed

Zhang, Yitong; Qian, Zijun; Liu, Peng; Liu, Lei; Zheng, Zhaojuan; Ouyang, Jia

2018-02-01

To get rid of the dependence on lactic acid neutralizer, a simple and economical approach for efficient in situ separation and production of L-lactic acid was established by Bacillus coagulans using weak basic anion-exchange resin. During ten tested resins, the 335 weak basic anion-exchange resins demonstrated the highest adsorption capacity and selectivity for lactic acid recovery. The adsorption study of the 335 resins for lactic acid confirmed that it is an efficient adsorbent under fermentation condition. Langmuir models gave a good fit to the equilibrium data at 50 °C and the maximum adsorption capacity for lactic acid by 335 resins was about 402 mg/g. Adsorption kinetic experiments showed that pseudo-second-order kinetics model gave a good fit to the adsorption rate. When it was used for in situ fermentation, the yield of L-lactic acid by B. coagulans CC17 was close to traditional fermentation and still maintained at about 82% even after reuse by ten times. These results indicated that in situ separation and production of L-lactic acid using the 335 resins were efficient and feasible. This process could greatly reduce the dosage of neutralizing agent and potentially be used in industry.

Continuing Development of a Hybrid Model (VSH) of the Neutral Thermosphere

NASA Technical Reports Server (NTRS)

Burns, Alan

1996-01-01

We propose to continue the development of a new operational model of neutral thermospheric density, composition, temperatures and winds to improve current engineering environment definitions of the neutral thermosphere. This model will be based on simulations made with the National Center for Atmospheric Research (NCAR) Thermosphere-Ionosphere- Electrodynamic General Circulation Model (TIEGCM) and on empirical data. It will be capable of using real-time geophysical indices or data from ground-based and satellite inputs and provides neutral variables at specified locations and times. This "hybrid" model will be based on a Vector Spherical Harmonic (VSH) analysis technique developed (over the last 8 years) at the University of Michigan that permits the incorporation of the TIGCM outputs and data into the model. The VSH model will be a more accurate version of existing models of the neutral thermospheric, and will thus improve density specification for satellites flying in low Earth orbit (LEO).

A simple and rapid Hepatitis A Virus (HAV) titration assay based on antibiotic resistance of infected cells: evaluation of the HAV neutralization potency of human immune globulin preparations

PubMed Central

Konduru, Krishnamurthy; Virata-Theimer, Maria Luisa; Yu, Mei-ying W; Kaplan, Gerardo G

2008-01-01

Background Hepatitis A virus (HAV), the causative agent of acute hepatitis in humans, is an atypical Picornaviridae that grows poorly in cell culture. HAV titrations are laborious and time-consuming because the virus in general does not cause cytopathic effect and is detected by immunochemical or molecular probes. Simple HAV titration assays could be developed using currently available viral construct containing selectable markers. Results We developed an antibiotic resistance titration assay (ARTA) based on the infection of human hepatoma cells with a wild type HAV construct containing a blasticidin (Bsd) resistance gene. Human hepatoma cells infected with the HAV-Bsd construct survived selection with 2 μg/ml of blasticidin whereas uninfected cells died within a few days. At 8 days postinfection, the color of the pH indicator phenol red in cell culture media correlated with the presence of HAV-Bsd-infected blasticidin-resistant cells: an orange-to-yellow color indicated the presence of growing cells whereas a pink-to-purple color indicated that the cells were dead. HAV-Bsd titers were determined by an endpoint dilution assay based on the color of the cell culture medium scoring orange-to-yellow wells as positive and pink-to-purple wells as negative for HAV. As a proof-of-concept, we used the ARTA to evaluate the HAV neutralization potency of two commercially available human immune globulin (IG) preparations and a WHO International Standard for anti-HAV. The three IG preparations contained comparable levels of anti-HAV antibodies that neutralized approximately 1.5 log of HAV-Bsd. Similar neutralization results were obtained in the absence of blasticidin by an endpoint dilution ELISA at 2 weeks postinfection. Conclusion The ARTA is a simple and rapid method to determine HAV titers without using HAV-specific probes. We determined the HAV neutralization potency of human IG preparations in 8 days by ARTA compared to the 14 days required by the endpoint dilution ELISA. The ARTA reduced the labour, time, and cost of HAV titrations making it suitable for high throughput screening of sera and antivirals, determination of anti-HAV antibodies in human immune globulin preparations, and research applications that involve the routine evaluation of HAV titers. PMID:19094229

Interstellar Matters: Neutral Hydrogen and the Galactic Magnetic Field

NASA Astrophysics Data System (ADS)

Verschuur, Gerrit; Schmelz, Joan T.; Asgari-Targhi asgari-Targhi, M.

2018-01-01

The physics of the interstellar medium was revolutionized by the observations of the Galactic Arecibo L-Band Feed Array (GALFA) HI survey done at the Arecibo Observatory. The high-resolution, high-sensitivity, high-dynamic- range images show complex, tangled, extended filaments, and reveal that the fabric of the neutral interstellar medium is deeply tied to the structure of the ambient magnetic field. This discovery prompts an obvious question – how exactly is the interstellar {\\it neutral} hydrogen being affected by the galactic magnetic field? We look into this question by examining a set of GALFA-HI data in great detail. We have chosen a long, straight filament in the southern galactic sky. This structure is both close by and isolated in velocity space. Gaussian analysis of profiles both along and across the filament reveal internal structure – braided strands that can be traced through the simplest part, but become tangled in more complex segments. These braids do not resemble in any way the old spherical HI clouds and rudimentary pressure balance models that were used to explain the pre-GALFA- HI interstellar medium. It is clear that these structures are created, constrained, and dominated by magnetic fields. Like many subfields of astronomy before it, e.g., physics of the solar coronal, extragalactic radio jets, and pulsar environment, scientists are confronted with observations that simply cannot be explained by simple hydrodynamics and are forced to consider magneto-hydrodynamics.

In-group modulation of perceptual matching.

PubMed

Moradi, Zargol; Sui, Jie; Hewstone, Miles; Humphreys, Glyn W

2015-10-01

We report a novel effect of in-group bias on a task requiring simple perceptual matching of stimuli. Football fans were instructed to associate the badges of their favorite football team (in-group), a rival team (out-group), and neutral teams with simple geometric shapes. Responses to matching in-group stimuli were more efficient, and discriminability was enhanced, as compared to out-group stimuli (rival and neutral)-a result that occurred even when participants responded only to the (equally familiar) geometric shapes. Across individuals, the in-group bias on shape matching was correlated with measures of group satisfaction, and similar results were found when football fans performed the task, in the context of both the football ground and a laboratory setting. We also observed effects of in-group bias on the response criteria in some but not all of the experiments. In control studies, the advantage for in-group stimuli was not found in an independent sample of participants who were not football fans. This indicates that there was not an intrinsic advantage for the stimuli that were "in-group" for football fans. Also, performance did not differ for familiar versus unfamiliar stimuli without in-group associations. These findings indicate that group identification can affect simple shape matching.

An atomic and molecular fluid model for efficient edge-plasma transport simulations at high densities

NASA Astrophysics Data System (ADS)

Rognlien, Thomas; Rensink, Marvin

2016-10-01

Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.

Oxygen, Neon, and Iron X-Ray Absorption in the Local Interstellar Medium

NASA Technical Reports Server (NTRS)

Gatuzz, Efrain; Garcia, Javier; Kallman, Timothy R.; Mendoza, Claudio

2016-01-01

We present a detailed study of X-ray absorption in the local interstellar medium by analyzing the X-ray spectra of 24 galactic sources obtained with the Chandra High Energy Transmission Grating Spectrometer and the XMM-Newton Reflection Grating Spectrometer. Methods. By modeling the continuum with a simple broken power-law and by implementing the new ISMabs X-ray absorption model, we have estimated the total H, O, Ne, and Fe column densities towards the observed sources. Results. We have determined the absorbing material distribution as a function of source distance and galactic latitude longitude. Conclusions. Direct estimates of the fractions of neutrally, singly, and doubly ionized species of O, Ne, and Fe reveal the dominance of the cold component, thus indicating an overall low degree of ionization. Our results are expected to be sensitive to the model used to describe the continuum in all sources.

Spatial vs. individual variability with inheritance in a stochastic Lotka-Volterra system

NASA Astrophysics Data System (ADS)

Dobramysl, Ulrich; Tauber, Uwe C.

2012-02-01

We investigate a stochastic spatial Lotka-Volterra predator-prey model with randomized interaction rates that are either affixed to the lattice sites and quenched, and / or specific to individuals in either population. In the latter situation, we include rate inheritance with mutations from the particles' progenitors. Thus we arrive at a simple model for competitive evolution with environmental variability and selection pressure. We employ Monte Carlo simulations in zero and two dimensions to study the time evolution of both species' densities and their interaction rate distributions. The predator and prey concentrations in the ensuing steady states depend crucially on the environmental variability, whereas the temporal evolution of the individualized rate distributions leads to largely neutral optimization. Contrary to, e.g., linear gene expression models, this system does not experience fixation at extreme values. An approximate description of the resulting data is achieved by means of an effective master equation approach for the interaction rate distribution.

Phase space effects on fast ion transport modeling in tokamaks

NASA Astrophysics Data System (ADS)

Podesta, Mario

2015-11-01

Simulations of burning plasmas require a consistent treatment of energetic particles (EP), possibly including the effects of instabilities. Reduced EP transport models are emerging as an effective tool to account for those effects in long time-scale simulations. Available models essentially differ for the main transport drive, which is associated to gradients in real or phase space. It is crucial to assess to what extent those different assumptions affect computed quantities such as EP profile, Neutral Beam (NB) driven current and energy/momentum transfer to the thermal populations. These issues are investigated through a kick model, which includes modifications of the EP distribution by instabilities in real and velocity space. TRANSP simulations including the kick model are applied to NB-heated NSTX discharges featuring unstable toroidal Alfvén eigenmodes (TAEs). Results show that TAEs mainly affect fast ions with large parallel velocity, i.e. the most effective for NB current drive. Other portions of the EP distribution are nearly unperturbed. Core NB driven current decreases by 10-30%, with even larger relative changes toward the plasma edge. When TAEs evolve in so-called avalanches, the model reproduces measured drops of ~ 10% in the neutron rate. Consistently with previous results, the drop is caused by both EP energy loss and EP redistribution. These results are compared to those from a simple diffusive model and a ``critical gradient'' model, which postulates radial EP gradient as the only transport drive. The importance of EP velocity space modifications is discussed in terms of accuracy of the predictions, with emphasis on Neutral Beam driven current. Work supported by U.S. DOE Contract DE-AC02-09CH11466.

Spectroscopic Measurements of Hydrogen Ion Temperature During Divertor Recombination

NASA Astrophysics Data System (ADS)

Stotler, D. P.; Skinner, C. H.; Karney, C. F. F.

1998-11-01

We explore the possibility of using the neutral H_α spectral line profile to measure the ion temperature Ti in a recombining plasma. Since the H_α emissions due to recombination are larger than those due to other mechanisms, interference from non-recombining regions contributing to the chord integrated data is insignificant. A chord integrated, Doppler and Stark broadened H_α spectrum is simulated by the DEGAS 2 Monte Carlo neutral transport code(D. Stotler and C. Karney, Contrib. Plasma Phys.) 34, 392 (1994). using assumed plasma conditions. The application of a simple fitting procedure to this spectrum yields an average electron density ne and Ti consistent with the assumed plasma parameters if the spectrum is dominated by recombination from a region of modest ne variation. The interpretation of experimental data is complicated by Zeeman splitting and light reflection off surfaces. Ion temperature measurements by H_α spectroscopy appear feasible within the context of a model for the entire divertor plasma that takes these effects into account.

Spectral Simulations and Abundance Determinations in the Interstellar Medium of Active Galaxies

NASA Astrophysics Data System (ADS)

Ferguson, Jason W.

The narrow emission line spectra of gas illuminated by the nuclear region of active galaxies cannot be described by models involving simple photoionization calculations. In this project we develop the numerical tools necessary to accurately simulate observed spectra from such regions. We begin by developing a compact model hydrogen atom, and show that a moderate number of atomic levels can reproduce the emission of much larger, definitive calculations. We discuss the excitation mechanism of the gas, that is, whether the emission we see is a result of either local shock excitation or direct photoionization by the central source. We show that photoionization plus continuum fluorescence can mimic excitation by shocks, and we suggest an observational test to distinguish between photoionization due to shocks and the central source. We extend to the narrow line region of active galaxies the 'locally optimally-emitting cloud' (LOC) model, wherein the observed spectra are predominantly determined by a simple, yet powerful selection effect. Namely, nature provides the emitting line region with clouds of a vast ensemble of properties, and we observe emission lines from those clouds that are most efficient at emitting them. We have calculated large grids of photoionization models of narrow line clouds for a wide range of gas density and distances from the ionizing source. We show that when coupled to a simple Keplerian velocity field, the LOC naturally reproduces the line width - critical density correlation observed in many narrow line objects. In addition, we calculate classical diagnostic line ratios and use simple LOC integrations over gas density to simulate the radial emission of the narrow lines and compare with observations. The effects of including dust in the simulations is discussed and we show that the more neutral gas is likely to be dusty, while the more highly ionized gas is dust-free. This implies a variety of cloud origins.

Decoding negative affect personality trait from patterns of brain activation to threat stimuli.

PubMed

Fernandes, Orlando; Portugal, Liana C L; Alves, Rita de Cássia S; Arruda-Sanchez, Tiago; Rao, Anil; Volchan, Eliane; Pereira, Mirtes; Oliveira, Letícia; Mourao-Miranda, Janaina

2017-01-15

Pattern recognition analysis (PRA) applied to functional magnetic resonance imaging (fMRI) has been used to decode cognitive processes and identify possible biomarkers for mental illness. In the present study, we investigated whether the positive affect (PA) or negative affect (NA) personality traits could be decoded from patterns of brain activation in response to a human threat using a healthy sample. fMRI data from 34 volunteers (15 women) were acquired during a simple motor task while the volunteers viewed a set of threat stimuli that were directed either toward them or away from them and matched neutral pictures. For each participant, contrast images from a General Linear Model (GLM) between the threat versus neutral stimuli defined the spatial patterns used as input to the regression model. We applied a multiple kernel learning (MKL) regression combining information from different brain regions hierarchically in a whole brain model to decode the NA and PA from patterns of brain activation in response to threat stimuli. The MKL model was able to decode NA but not PA from the contrast images between threat stimuli directed away versus neutral with a significance above chance. The correlation and the mean squared error (MSE) between predicted and actual NA were 0.52 (p-value=0.01) and 24.43 (p-value=0.01), respectively. The MKL pattern regression model identified a network with 37 regions that contributed to the predictions. Some of the regions were related to perception (e.g., occipital and temporal regions) while others were related to emotional evaluation (e.g., caudate and prefrontal regions). These results suggest that there was an interaction between the individuals' NA and the brain response to the threat stimuli directed away, which enabled the MKL model to decode NA from the brain patterns. To our knowledge, this is the first evidence that PRA can be used to decode a personality trait from patterns of brain activation during emotional contexts. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Investigation of Relationship between QBO and Ionospheric Neutral Temperature

NASA Astrophysics Data System (ADS)

Saǧır, Selçuk; Atıcı, Ramazan; Özcan, Osman

2016-07-01

The relationship between Quasi Biennial Oscillation (QBO) measured at 10 hPa altitude and neutral temperature obtained from NRLMSIS-00 model for 90 km altitude of ionosphere is statistically investigated. For this study, multiple-regression model is used. To see effect on neutral temperature of QBO directions, Dummy variables are added to model established. In the results of performed analysis, it is observed that QBO is effected on neutral temperature of ionosphere. It is determined that 57% of variations at neutral temperature can be explainable by QBO. According to the established model, statistical explainable ratio was determined as 1% that it is the highest rate. Also, it is seen that an increase/a decrease of 1 meter per second at QBO give rise to an increase/a decrease of 0,07 K at neutral temperature.

Lunar Neutral Exposphere Properties from Pickup Ion Analysis

NASA Technical Reports Server (NTRS)

Hartle, R. E.; Sarantos, M.; Killen, R.; Sittler, E. C. Jr.; Halekas, J.; Yokota, S.; Saito, Y.

2009-01-01

Composition and structure of neutral constituents in the lunar exosphere can be determined through measurements of phase space distributions of pickup ions borne from the exosphere [1]. An essential point made in an early study [ 1 ] and inferred by recent pickup ion measurements [2, 3] is that much lower neutral exosphere densities can be derived from ion mass spectrometer measurements of pickup ions than can be determined by conventional neutral mass spectrometers or remote sensing instruments. One approach for deriving properties of neutral exospheric source gasses is to first compare observed ion spectra with pickup ion model phase space distributions. Neutral exosphere properties are then inferred by adjusting exosphere model parameters to obtain the best fit between the resulting model pickup ion distributions and the observed ion spectra. Adopting this path, we obtain ion distributions from a new general pickup ion model, an extension of a simpler analytic description obtained from the Vlasov equation with an ion source [4]. In turn, the ion source is formed from a three-dimensional exospheric density distribution, which can range from the classical Chamberlain type distribution to one with variable exobase temperatures and nonthermal constituents as well as those empirically derived. The initial stage of this approach uses the Moon's known neutral He and Na exospheres to deriv e He+ and Na+ pickup ion exospheres, including their phase space distributions, densities and fluxes. The neutral exospheres used are those based on existing models and remote sensing studies. As mentioned, future ion measurements can be used to constrain the pickup ion model and subsequently improve the neutral exosphere descriptions. The pickup ion model is also used to estimate the exosphere sources of recently observed pickup ions on KAGUYA [3]. Future missions carrying ion spectrometers (e.g., ARTEMIS) will be able to study the lunar neutral exosphere with great sensitivity, yielding the necessary ion velocity spectra needed to further analysis of parent neutral exosphere properties.

Influence of hot and cold neutrals on scrape-off layer tokamak plasma turbulence

NASA Astrophysics Data System (ADS)

Bisai, N.; Kaw, P. K.

2018-01-01

The modification of interchange plasma turbulence in the scrape-off layer (SOL) region by the presence of hot and cold neutral gas molecules has been studied. The nonlinear equations have been solved numerically using two different simulations ("uniform-Te" and "varying-Te"), and the results obtained from both of the models have been compared. The hot neutrals, responsible for the increase in the electron density in the SOL, also account for more ionization of the cold molecules. The effect of hot and cold neutrals on the interchange turbulence is almost similar in the "uniform-Te" model, but in the "varying-Te" model, the influence of the hot neutrals is very small, specifically in the far SOL region. The neutral gas in the "varying Te" model decreases the heat load on the material walls by about 7%. A reduction in the radial velocity by about 25% and effective diffusion coefficient of the plasma particles has been found by the influence of the neutral gas.

The atmospheric emission method of calculating the neutral atmosphere and charged particle densities in the upper atmosphere

NASA Astrophysics Data System (ADS)

McElroy, Kenneth L., Jr.

1992-12-01

A method is presented for the determination of neutral gas densities in the ionosphere from rocket-borne measurements of UV atmospheric emissions. Computer models were used to calculate an initial guess for the neutral atmosphere. Using this neutral atmosphere, intensity profiles for the N2 (0,5) Vegard-Kaplan band, the N2 Lyman-Birge-Hopfield band system, and the OI2972 A line were calculated and compared with the March 1990 NPS MUSTANG data. The neutral atmospheric model was modified and the intensity profiles recalculated until a fit with the data was obtained. The neutral atmosphere corresponding to the intensity profile that fit the data was assumed to be the atmospheric composition prevailing at the time of the observation. The ion densities were then calculated from the neutral atmosphere using a photochemical model. The electron density profile calculated by this model was compared with the electron density profile measured by the U.S. Air Force Geophysics Laboratory at a nearby site.

Cultural selection drives the evolution of human communication systems

PubMed Central

Tamariz, Monica; Ellison, T. Mark; Barr, Dale J.; Fay, Nicolas

2014-01-01

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems. PMID:24966310

Cultural selection drives the evolution of human communication systems.

PubMed

Tamariz, Monica; Ellison, T Mark; Barr, Dale J; Fay, Nicolas

2014-08-07

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems.

Scan patterns when viewing natural scenes: Emotion, complexity, and repetition

PubMed Central

Bradley, Margaret M.; Houbova, Petra; Miccoli, Laura; Costa, Vincent D.; Lang, Peter J.

2011-01-01

Eye movements were monitored during picture viewing and effects of hedonic content, perceptual composition, and repetition on scanning assessed. In Experiment 1, emotional and neutral pictures that were figure-ground compositions or more complex scenes were presented for a 6 s free viewing period. Viewing emotional pictures or complex scenes prompted more fixations and broader scanning of the visual array, compared to neutral pictures or simple figure-ground compositions. Effects of emotion and composition were independent, supporting the hypothesis that these oculomotor indices reflect enhanced information seeking. Experiment 2 tested an orienting hypothesis by repeatedly presenting the same pictures. Although repetition altered specific scan patterns, emotional, compared to neutral, picture viewing continued to prompt oculomotor differences, suggesting that motivationally relevant cues enhance information seeking in appetitive and defensive contexts. PMID:21649664

Modeling of neutral entrainment in an FRC thruster

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

Brackbill, Jeremiah; Gimelshein, Natalia; Gimelshein, Sergey

2012-11-27

Neutral entrainment in a field reversed configuration thruster is modeled numerically with an implicit PIC code extended to include thermal and chemical interactions between plasma and neutral particles. The contribution of charge exchange and electron impact ionization reactions is analyzed, and the sensitivity of the entrainment efficiency to the plasmoid translation velocity and neutral density is evaluated.

The role of weak selection and high mutation rates in nearly neutral evolution.

PubMed

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2009-04-21

Neutral dynamics occur in evolution if all types are 'effectively equal' in their reproductive success, where the definition of 'effectively equal' depends on the population size and the details of mutations. Empirically observed neutral genetic evolution in extremely large clonal populations can only be explained under current models if selection is completely absent. Such models typically consider the case where population dynamics occurs on a different timescale to evolution. However, this assumption is invalid when mutations are not rare in a whole population. We show that this has important consequences for the occurrence of neutral evolution in clonal populations. In highly connected type spaces, neutral dynamics can occur for all population sizes despite significant selective differences, via the forming of effectively neutral networks connecting rare neutral types. Biological implications include an explanation for the high diversity of rare types that survive in large clonal populations, and a theoretical justification for the use of neutral null models.

Consistent three-equation model for thin films

NASA Astrophysics Data System (ADS)

Richard, Gael; Gisclon, Marguerite; Ruyer-Quil, Christian; Vila, Jean-Paul

2017-11-01

Numerical simulations of thin films of newtonian fluids down an inclined plane use reduced models for computational cost reasons. These models are usually derived by averaging over the fluid depth the physical equations of fluid mechanics with an asymptotic method in the long-wave limit. Two-equation models are based on the mass conservation equation and either on the momentum balance equation or on the work-energy theorem. We show that there is no two-equation model that is both consistent and theoretically coherent and that a third variable and a three-equation model are required to solve all theoretical contradictions. The linear and nonlinear properties of two and three-equation models are tested on various practical problems. We present a new consistent three-equation model with a simple mathematical structure which allows an easy and reliable numerical resolution. The numerical calculations agree fairly well with experimental measurements or with direct numerical resolutions for neutral stability curves, speed of kinematic waves and of solitary waves and depth profiles of wavy films. The model can also predict the flow reversal at the first capillary trough ahead of the main wave hump.

Household Schooling Behaviors and Decentralization.

ERIC Educational Resources Information Center

Behrman, Jere R.; King, Elizabeth M.

2001-01-01

Presents a simple framework for (1) demonstrating how households determine schooling investments through choice and voice; and (2) considering effects of decentralization on household behaviors, given information problems. Some aspects of decentralization may increase efficiency; others may be neutral or decrease efficiency. Further research is…

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Science.gov Websites

charged tracks or associated with photons or neutral hadrons. Hardware effort: A Digital Hadron fine segmentation, the energy resolution for single hadrons is preserved with a simple digital readout Physics Division Digital Hadron Calorimeter with RPCs (US effort) CALICE Collaboration American Linear

Quantifying evolutionary dynamics from variant-frequency time series

NASA Astrophysics Data System (ADS)

Khatri, Bhavin S.

2016-09-01

From Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

Quantifying evolutionary dynamics from variant-frequency time series.

PubMed

Khatri, Bhavin S

2016-09-12

From Kimura's neutral theory of protein evolution to Hubbell's neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher's angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

Relaxation and self-organization in two-dimensional plasma and neutral fluid flow systems

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

Das, Amita

Extensive numerical studies in the framework of a simplified two-dimensional model for neutral and plasma fluid for a variety of initial configurations and for both decaying and driven cases are carried out to illustrate relaxation toward a self-organized state. The dynamical model equation constitutes a simple choice for this purpose, e.g., the vorticity equation of the Navier-Stokes dynamics for the incompressible neutral fluids and the Hasegawa-Mima equation for plasma fluid flow system. Scatter plots are employed to observe a development of functional relationship, if any, amidst the generalized vorticity and its Laplacian. It is seen that they do not satisfymore » a linear relationship as the well known variational approach of enstrophy minimization subject to constancy of the energy integral for the two-dimensional (2D) system suggests. The observed nonlinear functional relationship is understood by separating the contribution to the scatter plot from spatial regions with intense vorticity patches and those of the background flow region where the background vorticity is weak or absent altogether. It is shown that such a separation has close connection with the known exact analytical solutions of the system. The analytical solutions are typically obtained by assuming a finite source of vorticity for the inner core of the localized structure, which is then matched with the solution in the outer region where vorticity is chosen to be zero. The work also demonstrates that the seemingly ad hoc choice of the linear vorticity source function for the inner region is in fact consistent with the self-organization paradigm of the 2D 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.

Principles and implementations of electrolysis systems for water splitting

DOE PAGES

Xiang, Chengxiang; Papadantonakis, Kimberly M.; Lewis, Nathan S.

2016-02-12

Efforts to develop renewable sources of carbon-neutral fuels have brought a renewed focus to research and development of sunlight-driven water-splitting systems. Electrolysis of water to produce H 2 and O 2 gases is the foundation of such systems, is conceptually and practically simple, and has been practiced both in the laboratory and industrially for many decades. In this Focus article, the fundamentals of water splitting and practices which distinguish commercial water-electrolysis systems from simple laboratory-scale demonstrations are described.

Selective Strolls: Fixation and Extinction in Diploids Are Slower for Weakly Selected Mutations Than for Neutral Ones.

PubMed

Mafessoni, Fabrizio; Lachmann, Michael

2015-12-01

In finite populations, an allele disappears or reaches fixation due to two main forces, selection and drift. Selection is generally thought to accelerate the process: a selected mutation will reach fixation faster than a neutral one, and a disadvantageous one will quickly disappear from the population. We show that even in simple diploid populations, this is often not true. Dominance and recessivity unexpectedly slow down the evolutionary process for weakly selected alleles. In particular, slightly advantageous dominant and mildly deleterious recessive mutations reach fixation slightly more slowly than neutral ones (at most 5%). This phenomenon determines genetic signatures opposite to those expected under strong selection, such as increased instead of decreased genetic diversity around the selected site. Furthermore, we characterize a new phenomenon: mildly deleterious recessive alleles, thought to represent a wide fraction of newly arising mutations, on average survive in a population slightly longer than neutral ones, before getting lost. Consequently, these mutations are on average slightly older than neutral ones, in contrast with previous expectations. Furthermore, they slightly increase the amount of weakly deleterious polymorphisms, as a consequence of the longer unconditional sojourn times compared to neutral mutations. Copyright © 2015 by the Genetics Society of America.

Physics of giant electromagnetic pulse generation in short-pulse laser experiments.

PubMed

Poyé, A; Hulin, S; Bailly-Grandvaux, M; Dubois, J-L; Ribolzi, J; Raffestin, D; Bardon, M; Lubrano-Lavaderci, F; D'Humières, E; Santos, J J; Nicolaï, Ph; Tikhonchuk, V

2015-04-01

In this paper we describe the physical processes that lead to the generation of giant electromagnetic pulses (GEMPs) at powerful laser facilities. Our study is based on experimental measurements of both the charging of a solid target irradiated by an ultra-short, ultra-intense laser and the detection of the electromagnetic emission in the GHz domain. An unambiguous correlation between the neutralization current in the target holder and the electromagnetic emission shows that the source of the GEMP is the remaining positive charge inside the target after the escape of fast electrons accelerated by the ultra-intense laser. A simple model for calculating this charge in the thick target case is presented. From this model and knowing the geometry of the target holder, it becomes possible to estimate the intensity and the dominant frequencies of the GEMP at any facility.

Zonostrophic instability driven by discrete particle noise

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

St-Onge, D. A.; Krommes, J. A.

The consequences of discrete particle noise for a system possessing a possibly unstable collective mode are discussed. It is argued that a zonostrophic instability (of homogeneous turbulence to the formation of zonal flows) occurs just below the threshold for linear instability. The scenario provides a new interpretation of the random forcing that is ubiquitously invoked in stochastic models such as the second-order cumulant expansion or stochastic structural instability theory; neither intrinsic turbulence nor coupling to extrinsic turbulence is required. A representative calculation of the zonostrophic neutral curve is made for a simple two-field model of toroidal ion-temperature-gradient-driven modes. To themore » extent that the damping of zonal flows is controlled by the ion-ion collision rate, the point of zonostrophic instability is independent of that rate. Published by AIP Publishing.« less

Zonostrophic instability driven by discrete particle noise

DOE PAGES

St-Onge, D. A.; Krommes, J. A.

2017-04-01

The consequences of discrete particle noise for a system possessing a possibly unstable collective mode are discussed. It is argued that a zonostrophic instability (of homogeneous turbulence to the formation of zonal flows) occurs just below the threshold for linear instability. The scenario provides a new interpretation of the random forcing that is ubiquitously invoked in stochastic models such as the second-order cumulant expansion or stochastic structural instability theory; neither intrinsic turbulence nor coupling to extrinsic turbulence is required. A representative calculation of the zonostrophic neutral curve is made for a simple two-field model of toroidal ion-temperature-gradient-driven modes. To themore » extent that the damping of zonal flows is controlled by the ion-ion collision rate, the point of zonostrophic instability is independent of that rate. Published by AIP Publishing.« less

Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Medley, S. S.; Liu, D.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

2016-02-01

A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a ‘beam-in-a-box’ model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.

Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

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

Medley, S. S.; Liu, D.; Gorelenkova, M. V.

2016-01-12

A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a 'beam-in-a-box' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components producemore » first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.« less

Collisional spreading of Enceladus’ neutral cloud

NASA Astrophysics Data System (ADS)

Cassidy, T. A.; Johnson, R. E.

2010-10-01

We describe a direct simulation Monte Carlo (DSMC) model of Enceladus' neutral cloud and compare its results to observations of OH and O orbiting Saturn. The OH and O are observed far from Enceladus (at 3.95 R S), as far out as 25 R S for O. Previous DSMC models attributed this breadth primarily to ion/neutral scattering (including charge exchange) and molecular dissociation. However, the newly reported O observations and a reinterpretation of the OH observations (Melin, H., Shemansky, D.E., Liu, X. [2009] Planet. Space Sci., 57, 1743-1753, PS&S) showed that the cloud is broader than previously thought. We conclude that the addition of neutral/neutral scattering (Farmer, A.J. [2009] Icarus, 202, 280-286), which was underestimated by previous models, brings the model results in line with the new observations. Neutral/neutral collisions primarily happen in the densest part of the cloud, near Enceladus' orbit, but contribute to the spreading by pumping up orbital eccentricity. Based on the cloud model presented here Enceladus maybe the ultimate source of oxygen for the upper atmospheres of Titan and Saturn. We also predict that large quantities of OH, O and H 2O bombard Saturn's icy satellites.

Neutral surfaces and potential vorticity in the world's oceans

NASA Astrophysics Data System (ADS)

You, Yuzhu; McDougall, Trevor J.

1990-08-01

Several neutral surfaces are mapped in this paper and their properties are contrasted with those of potential density surfaces. It is shown that the Pacific is relatively forgiving to the use of potential density, while more care must be taken in the Atlantic and Indian oceans because of the larger compensating lateral gradients of potential temperature and salinity along neutral surfaces in these oceans. The dynamically important tracer, neutral-surface potential vorticity (NSPV), defined to be proportional to f/h (where f is the Coriolis frequency and h is the height between two neutral surfaces), is mapped on several neutral surfaces in each of the world's oceans. At a depth of 1000m in the Atlantic and Indian oceans, the epineutral gradient of NSPV is different to the isopycnal variations of fN2 by as much as a factor of two (here N is the buoyancy frequency). Maps of isopycnal potential vorticity (IPV) resemble those of fN2, but the values of IPV are less by the simple factor μ, defined by μ = c[Rρ-1]/[Rρ-c], where Rρ is the stability ratio of the water column and c is the ratio of the values of α/β at the in situ pressure to that at the reference pressure (α and β being the thermal expansion and saline contraction coefficients, respectively). Layered models of the ocean circulation often take the vertical shear between layers (the thermal wind) to be given by the product of the interface slope and the contrast of potential density across the interface. The true thermal wind equation involves the interfaeial difference of in situ density, which is larger than the corresponding difference of potential density by the factor μ that is mapped in this paper, taking values up to 1.25 at a depth of 1000 m. This implies that the thermal wind is currently underestimated by up to 25% in layered ocean models. The differences between the slopes of neutral surfaces and potential density surfaces can be quantified Using the factory μ. The magnitudes of these slopes are illustrated here with contour maps and with vertical profiles, One would think that by choosing the reference pressure of potential density to be at the central pressure of a data set, the conservation equation of potential vorticity could be expressed with respect to these potential density surfaces with sufficient accuracy. Here it is shown that even the best potential density variable is significantly in error at thermoclinic frontal regions. This is linked to the fact that diapycnal velocities are not simply due to vertical mixing processes, but are also partly caused by epineutral mixing.

Toroidal rotation in neutral beam heated discharges in DIII-D

NASA Astrophysics Data System (ADS)

de Grassie, J. S.; Baker, D. R.; Burrell, K. H.; Gohil, P.; Greenfield, C. M.; Groebner, R. J.; Thomas, D. M.

2003-02-01

It is known that the toroidal angular momentum and the ion thermal energy are correlated in tokamak discharges heated by neutral beam injection. Here, data from ten years of measurements on DIII-D are considered, for representative discharges from all types and all conditions. The ratio of simple replacement times for momentum and energy is found to order this correlation indicating that these times are approximately equal, across the minor radius. Representative discharges of several types are discussed in more detail, as well as transport analysis results for the momentum and thermal ion diffusivities.

The distribution of Enceladus water-group neutrals in Saturn’s Magnetosphere

NASA Astrophysics Data System (ADS)

Smith, Howard T.; Richardson, John D.

2017-10-01

Saturn’s magnetosphere is unique in that the plumes from the small icy moon, Enceladus, serve at the primary source for heavy particles in Saturn’s magnetosphere. The resulting co-orbiting neutral particles interact with ions, electrons, photons and other neutral particles to generate separate H2O, OH and O tori. Characterization of these toroidal distributions is essential for understanding Saturn magnetospheric sources, composition and dynamics. Unfortunately, limited direct observations of these features are available so modeling is required. A significant modeling challenge involves ensuring that either the plasma and neutral particle populations are not simply input conditions but can provide feedback to each population (i.e. are self-consistent). Jurac and Richardson (2005) executed such a self-consistent model however this research was performed prior to the return of Cassini data. In a similar fashion, we have coupled a 3-D neutral particle model (Smith et al. 2004, 2005, 2006, 2007, 2009, 2010) with a plasma transport model (Richardson 1998; Richardson & Jurac 2004) to develop a self-consistent model which is constrained by all available Cassini observations and current findings on Saturn’s magnetosphere and the Enceladus plume source resulting in much more accurate neutral particle distributions. Here a new self-consistent model of the distribution of the Enceladus-generated neutral tori that is validated by all available observations. We also discuss the implications for source rate and variability.

Io: IUE observations of its atmosphere and the plasma torus

NASA Technical Reports Server (NTRS)

Ballester, G. E.; Moos, H. W.; Feldman, P. D.; Strobel, D. F.; Skinner, T. E.; Bertaux, J.-L.; Festou, M. C.

1988-01-01

Two of the main components of the atmosphere of Io, neutral oxygen and sulfur, were detected with the IUE. Four observations yield brightnesses that are similar, regardless of whether the upstream or the downstream sides of the torus plasma flow around Io is observed. A simple model requires the emissions to be produced by the interaction of O and S columns in the exospheric range with 2 eV electrons. Cooling of the 5 eV torus electrons is required prior to their interaction with the atmosphere of Io. Inconsistencies in the characteristics of the spectra that cannot be accounted for in this model require further analysis with improved atomic data. The Io plasma torus was monitored with the IUE. The long-term stability of the warm torus is established. The observed brightnesses were analyzed using a model of the torus, and variations of less than 30 percent in the composition are observed, the quantitative results being model dependent.

Fault model of the M7.1 intraslab earthquake on April 7 following the 2011 Great Tohoku earthquake (M9.0) estimated by the dense GPS network data

NASA Astrophysics Data System (ADS)

Miura, S.; Ohta, Y.; Ohzono, M.; Kita, S.; Iinuma, T.; Demachi, T.; Tachibana, K.; Nakayama, T.; Hirahara, S.; Suzuki, S.; Sato, T.; Uchida, N.; Hasegawa, A.; Umino, N.

2011-12-01

We propose a source fault model of the large intraslab earthquake with M7.1 deduced from a dense GPS network. The coseismic displacements obtained by GPS data analysis clearly show the spatial pattern specific to intraslab earthquakes not only in the horizontal components but also the vertical ones. A rectangular fault with uniform slip was estimated by a non-linear inversion approach. The results indicate that the simple rectangular fault model can explain the overall features of the observations. The amount of moment released is equivalent to Mw 7.17. The hypocenter depth of the main shock estimated by the Japan Meteorological Agency is slightly deeper than the neutral plane between down-dip compression (DC) and down-dip extension (DE) stress zones of the double-planed seismic zone. This suggests that the depth of the neutral plane was deepened by the huge slip of the 2011 M9.0 Tohoku earthquake, and the rupture of the thrust M7.1 earthquake was initiated at that depth, although more investigations are required to confirm this idea. The estimated fault plane has an angle of ~60 degrees from the surface of subducting Pacific plate. It is consistent with the hypothesis that intraslab earthquakes are thought to be reactivation of the preexisting hydrated weak zones made in bending process of oceanic plates around outer-rise regions.

Scan patterns when viewing natural scenes: emotion, complexity, and repetition.

PubMed

Bradley, Margaret M; Houbova, Petra; Miccoli, Laura; Costa, Vincent D; Lang, Peter J

2011-11-01

Eye movements were monitored during picture viewing, and effects of hedonic content, perceptual composition, and repetition on scanning assessed. In Experiment 1, emotional and neutral pictures that were figure-ground compositions or more complex scenes were presented for a 6-s free viewing period. Viewing emotional pictures or complex scenes prompted more fixations and broader scanning of the visual array, compared to neutral pictures or simple figure-ground compositions. Effects of emotion and composition were independent, supporting the hypothesis that these oculomotor indices reflect enhanced information seeking. Experiment 2 tested an orienting hypothesis by repeatedly presenting the same pictures. Although repetition altered specific scan patterns, emotional, compared to neutral, picture viewing continued to prompt oculomotor differences, suggesting that motivationally relevant cues enhance information seeking in appetitive and defensive contexts. Copyright © 2011 Society for Psychophysiological Research.

Sadness and susceptibility to judgmental bias: the case of anchoring.

PubMed

Bodenhausen, G V; Gabriel, S; Lineberger, M

2000-07-01

In a wide range of empirical paradigms, sadness has been associated with more extensive and detail-oriented thinking than happiness, resulting in reductions in judgmental bias that arise from reliance on stereotypes and other simple decision heuristics. It was hypothesized that anchoring would constitute a significant exception to this general pattern. Recent research on anchoring indicates that an active thought process underlies the emergence of this bias. If sad people are likely to think more actively about the judgmental anchor than their neutral-mood counterparts, their subsequent judgments should be more likely to be assimilated toward this reference point. This prediction was confirmed in two experiments demonstrating that sad people are indeed more susceptible to anchoring bias than are people in a neutral mood. Moreover, this effect generalized over judgments in positive, neutral, and negative content domains.

Optimizing congestion and emissions via tradable credit charge and reward scheme without initial credit allocations

NASA Astrophysics Data System (ADS)

Zhu, Wenlong; Ma, Shoufeng; Tian, Junfang

2017-01-01

This paper investigates the revenue-neutral tradable credit charge and reward scheme without initial credit allocations that can reassign network traffic flow patterns to optimize congestion and emissions. First, we prove the existence of the proposed schemes and further decentralize the minimum emission flow pattern to user equilibrium. Moreover, we design the solving method of the proposed credit scheme for minimum emission problem. Second, we investigate the revenue-neutral tradable credit charge and reward scheme without initial credit allocations for bi-objectives to obtain the Pareto system optimum flow patterns of congestion and emissions; and present the corresponding solutions are located in the polyhedron constituted by some inequalities and equalities system. Last, numerical example based on a simple traffic network is adopted to obtain the proposed credit schemes and verify they are revenue-neutral.

Modelling the solar wind interaction with Mercury by a quasi-neutral hybrid model

NASA Astrophysics Data System (ADS)

Kallio, E.; Janhunen, P.

2003-11-01

Quasi-neutral hybrid model is a self-consistent modelling approach that includes positively charged particles and an electron fluid. The approach has received an increasing interest in space plasma physics research because it makes it possible to study several plasma physical processes that are difficult or impossible to model by self-consistent fluid models, such as the effects associated with the ions’ finite gyroradius, the velocity difference between different ion species, or the non-Maxwellian velocity distribution function. By now quasi-neutral hybrid models have been used to study the solar wind interaction with the non-magnetised Solar System bodies of Mars, Venus, Titan and comets. Localized, two-dimensional hybrid model runs have also been made to study terrestrial dayside magnetosheath. However, the Hermean plasma environment has not yet been analysed by a global quasi-neutral hybrid model.

Fast imaging measurements and modeling of neutral and impurity density on C-2U

NASA Astrophysics Data System (ADS)

Granstedt, Erik; Deng, B.; Dettrick, S.; Gupta, D. K.; Osin, D.; Roche, T.; Zhai, K.; TAE Team

2016-10-01

The C-2U device employed neutral beam injection and end-biasing to sustain an advanced beam-driven Field-Reversed Configuration plasma for 5+ ms, beyond characteristic transport time-scales. Three high-speed, filtered cameras observed visible light emission from neutral hydrogen and impurities, as well as deuterium pellet ablation and compact-toroid injection which were used for auxiliary particle fueling. Careful vacuum practices and titanium gettering successfully reduced neutral recycling from the confinement vessel wall. As a result, a large fraction of the remaining neutrals originate from charge-exchange between the neutral beams and plasma ions. Measured H/D- α emission is used with DEGAS2 neutral particle modeling to reconstruct the strongly non-axissymmetric neutral distribution. This is then used in fast-ion modeling to more accurately estimate their charge-exchange loss rate. Oxygen emission due to electron-impact excitation and charge-exchange recombination has also been measured using fast imaging. Reconstructed emissivity of O4+ is localized on the outboard side of the core plasma near the estimated location of the separatrix inferred by external magnetic measurements. Tri Alpha Energy.

Noradrenergic Mechanisms of Arousal’s Bidirectional Effects on Episodic Memory

PubMed Central

Clewett, David; Sakaki, Michiko; Nielsen, Shawn; Petzinger, Giselle; Mather, Mara

2016-01-01

Arousal’s selective effects on cognition go beyond the simple enhancement of emotional stimuli, sometimes enhancing and other times impairing processing of proximal neutral information. Past work shows that arousal impairs encoding of subsequent neutral stimuli regardless of their top-down priority via the engagement of β-adrenoreceptors. In contrast, retrograde amnesia induced by emotional arousal can flip to enhancement when preceding neutral items are prioritized in top-down attention. Whether β-adrenoreceptors also contribute to this retrograde memory enhancement of goal-relevant neutral stimuli is unclear. In this pharmacological study, we administered 40mg of propranolol or 40mg of placebo to healthy young adults to examine whether emotional arousal’s bidirectional effects on declarative memory relies on β-adrenoreceptor activation. Following pill intake, participants completed an emotional oddball task in which they were asked to prioritize a neutral object appearing just before an emotional or neutral oddball image within a sequence of 7 neutral objects. Under placebo, emotional oddballs impaired memory for lower priority oddball+1 objects but had no effect on memory for high priority oddball−1 objects. Propranolol blocked this anterograde amnesic effect of arousal. Emotional oddballs also enhanced selective memory trade-offs significantly more in the placebo than drug condition, such that high priority oddball−1 objects were more likely to be remembered at the cost of their corresponding lower priority oddball+1 objects under arousal. Lastly, those who recalled more high priority oddball−1 objects preceding an emotional versus neutral oddball image showed greater increases in salivary alpha-amylase, a biomarker of noradrenergic system activation, across the task. Together these findings suggest that different noradrenergic mechanisms contribute to the anterograde and retrograde mnemonic effects of arousal on proximal neutral memoranda. PMID:27815214

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site.

PubMed

Cheng, Hao D; Grimm, Sebastian K; Gilman, Morgan Sa; Gwom, Luc Christian; Sok, Devin; Sundling, Christopher; Donofrio, Gina; Hedestam, Gunilla B Karlsson; Bonsignori, Mattia; Haynes, Barton F; Lahey, Timothy P; Maro, Isaac; von Reyn, C Fordham; Gorny, Miroslaw K; Zolla-Pazner, Susan; Walker, Bruce D; Alter, Galit; Burton, Dennis R; Robb, Merlin L; Krebs, Shelly J; Seaman, Michael S; Bailey-Kellogg, Chris; Ackerman, Margaret E

2018-03-08

Major advances in donor identification, antigen probe design, and experimental methods to clone pathogen-specific antibodies have led to an exponential growth in the number of newly characterized broadly neutralizing antibodies (bnAbs) that recognize the HIV-1 envelope glycoprotein. Characterization of these bnAbs has defined new epitopes and novel modes of recognition that can result in potent neutralization of HIV-1. However, the translation of envelope recognition profiles in biophysical assays into an understanding of in vivo activity has lagged behind, and identification of subjects and mAbs with potent antiviral activity has remained reliant on empirical evaluation of neutralization potency and breadth. To begin to address this discrepancy between recombinant protein recognition and virus neutralization, we studied the fine epitope specificity of a panel of CD4-binding site (CD4bs) antibodies to define the molecular recognition features of functionally potent humoral responses targeting the HIV-1 envelope site bound by CD4. Whereas previous studies have used neutralization data and machine-learning methods to provide epitope maps, here, this approach was reversed, demonstrating that simple binding assays of fine epitope specificity can prospectively identify broadly neutralizing CD4bs-specific mAbs. Building on this result, we show that epitope mapping and prediction of neutralization breadth can also be accomplished in the assessment of polyclonal serum responses. Thus, this study identifies a set of CD4bs bnAb signature amino acid residues and demonstrates that sensitivity to mutations at signature positions is sufficient to predict neutralization breadth of polyclonal sera with a high degree of accuracy across cohorts and across clades.

Noradrenergic mechanisms of arousal's bidirectional effects on episodic memory.

PubMed

Clewett, David; Sakaki, Michiko; Nielsen, Shawn; Petzinger, Giselle; Mather, Mara

2017-01-01

Arousal's selective effects on cognition go beyond the simple enhancement of emotional stimuli, sometimes enhancing and other times impairing processing of proximal neutral information. Past work shows that arousal impairs encoding of subsequent neutral stimuli regardless of their top-down priority via the engagement of β-adrenoreceptors. In contrast, retrograde amnesia induced by emotional arousal can flip to enhancement when preceding neutral items are prioritized in top-down attention. Whether β-adrenoreceptors also contribute to this retrograde memory enhancement of goal-relevant neutral stimuli is unclear. In this pharmacological study, we administered 40mg of propranolol or 40mg of placebo to healthy young adults to examine whether emotional arousal's bidirectional effects on declarative memory relies on β-adrenoreceptor activation. Following pill intake, participants completed an emotional oddball task in which they were asked to prioritize a neutral object appearing just before an emotional or neutral oddball image within a sequence of 7 neutral objects. Under placebo, emotional oddballs impaired memory for lower priority oddball+1 objects but had no effect on memory for high priority oddball-1 objects. Propranolol blocked this anterograde amnesic effect of arousal. Emotional oddballs also enhanced selective memory trade-offs significantly more in the placebo than drug condition, such that high priority oddball-1 objects were more likely to be remembered at the cost of their corresponding lower priority oddball+1 objects under arousal. Lastly, those who recalled more high priority oddball-1 objects preceding an emotional versus neutral oddball image showed greater increases in salivary alpha-amylase, a biomarker of noradrenergic system activation, across the task. Together these findings suggest that different noradrenergic mechanisms contribute to the anterograde and retrograde mnemonic effects of arousal on proximal neutral memoranda. Copyright © 2016 Elsevier Inc. All rights reserved.

Hot electrons and radial transport in Saturn's inner magetosphere: Modeling the effects on ion chemistry

NASA Astrophysics Data System (ADS)

Fleshman, Bobby L.

The E-ring of Saturn, located just beyond the main rings at four Saturn radii, was known to be made mostly of water and its by-products before the Cassini spacecraft arrived at Saturn in 2005. Since then, Cassini has observed water geysers on the tiny moon of Enceladus ejecting ≈ 100 kg of water per second into orbit around Saturn, which most agree is the chief contributor to neutrals in the E-ring. Following several key reactions, many of these neutrals go on to populate large, tenuous structures, known as neutral clouds, extending 10s of Saturn radii. The other side of the story are the ions, which are largely created by the ionization of same neutrals sourced from Enceladus. A key distinction between the neutrals and ions is that ions are carried along by Saturn's magnetic field, and revolve around Saturn at the rotation rate of the planet, while neutrals generally have much slower Keplerian speeds. It is the study of the chemical interaction of these separate, but related populations that is the subject of this thesis. We have developed a series of models to study how the coupling of these systems affect details of the other, such as composition. The first step (Chapter 2) was the development of a water-group physical chemistry model, which includes suprathermal electrons and the effect of radial ion transport. With this "one-box" model, we are able to reproduce observed water and hydrogen ion densities in Enceladus's orbit, but only when the hot electron density is ≈ 0.5% of the total plasma density. Radial transport is found to be slow, requiring 26 days to remove ions from the orbit of Enceladus. Moving toward the development of a radial model of ion chemistry, in Chapter 4 we present a model of Saturn's neutral clouds, which are made of material outgassing from Enceladus. The effects of dissociation and charge exchange are considered, where the details of the latter prove to be of great consequence on neutral cloud morphology. The oxygen cloud is found to the most extended, followed by H2O, and finally OH. The above efforts are combined in Chapter 5, where a neutral cloud model is used to construct a radial model of ion chemistry. It is shown that neutral H2O requires more spreading than yet modeled in order to recover observed water and hydrogen ion abundances near Enceladus. The relative abundance of water-group ion species presented will be useful for analyses of CAPS-IMS data, while loss rates derived from the model can be used to improve neutral cloud models. The case is made that ion chemistry models and neutral cloud models must be developed alongside one another in order to improve understanding of these interrelated populations at Saturn.

When Can Species Abundance Data Reveal Non-neutrality?

PubMed Central

Al Hammal, Omar; Alonso, David; Etienne, Rampal S.; Cornell, Stephen J.

2015-01-01

Species abundance distributions (SAD) are probably ecology’s most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable. PMID:25793889

Preferential amygdala reactivity to the negative assessment of neutral faces.

PubMed

Blasi, Giuseppe; Hariri, Ahmad R; Alce, Guilna; Taurisano, Paolo; Sambataro, Fabio; Das, Saumitra; Bertolino, Alessandro; Weinberger, Daniel R; Mattay, Venkata S

2009-11-01

Prior studies suggest that the amygdala shapes complex behavioral responses to socially ambiguous cues. We explored human amygdala function during explicit behavioral decision making about discrete emotional facial expressions that can represent socially unambiguous and ambiguous cues. During functional magnetic resonance imaging, 43 healthy adults were required to make complex social decisions (i.e., approach or avoid) about either relatively unambiguous (i.e., angry, fearful, happy) or ambiguous (i.e., neutral) facial expressions. Amygdala activation during this task was compared with that elicited by simple, perceptual decisions (sex discrimination) about the identical facial stimuli. Angry and fearful expressions were more frequently judged as avoidable and happy expressions most often as approachable. Neutral expressions were equally judged as avoidable and approachable. Reaction times to neutral expressions were longer than those to angry, fearful, and happy expressions during social judgment only. Imaging data on stimuli judged to be avoided revealed a significant task by emotion interaction in the amygdala. Here, only neutral facial expressions elicited greater activity during social judgment than during sex discrimination. Furthermore, during social judgment only, neutral faces judged to be avoided were associated with greater amygdala activity relative to neutral faces that were judged as approachable. Moreover, functional coupling between the amygdala and both dorsolateral prefrontal (social judgment > sex discrimination) and cingulate (sex discrimination > social judgment) cortices was differentially modulated by task during processing of neutral faces. Our results suggest that increased amygdala reactivity and differential functional coupling with prefrontal circuitries may shape complex decisions and behavioral responses to socially ambiguous cues.

Preferential Amygdala Reactivity to the Negative Assessment of Neutral Faces

PubMed Central

Blasi, Giuseppe; Hariri, Ahmad R.; Alce, Guilna; Taurisano, Paolo; Sambataro, Fabio; Das, Saumitra; Bertolino, Alessandro; Weinberger, Daniel R.; Mattay, Venkata S.

2010-01-01

Background Prior studies suggest that the amygdala shapes complex behavioral responses to socially ambiguous cues. We explored human amygdala function during explicit behavioral decision making about discrete emotional facial expressions that can represent socially unambiguous and ambiguous cues. Methods During functional magnetic resonance imaging, 43 healthy adults were required to make complex social decisions (i.e., approach or avoid) about either relatively unambiguous (i.e., angry, fearful, happy) or ambiguous (i.e., neutral) facial expressions. Amygdala activation during this task was compared with that elicited by simple, perceptual decisions (sex discrimination) about the identical facial stimuli. Results Angry and fearful expressions were more frequently judged as avoidable and happy expressions most often as approachable. Neutral expressions were equally judged as avoidable and approachable. Reaction times to neutral expressions were longer than those to angry, fearful, and happy expressions during social judgment only. Imaging data on stimuli judged to be avoided revealed a significant task by emotion interaction in the amygdala. Here, only neutral facial expressions elicited greater activity during social judgment than during sex discrimination. Furthermore, during social judgment only, neutral faces judged to be avoided were associated with greater amygdala activity relative to neutral faces that were judged as approachable. Moreover, functional coupling between the amygdala and both dorsolateral prefrontal (social judgment > sex discrimination) and cingulate (sex discrimination > social judgment) cortices was differentially modulated by task during processing of neutral faces. Conclusions Our results suggest that increased amygdala reactivity and differential functional coupling with prefrontal circuitries may shape complex decisions and behavioral responses to socially ambiguous cues. PMID:19709644

Two Multipurpose Thermochemical Experiments for General Chemistry.

ERIC Educational Resources Information Center

Wentworth, R. A. D.

1988-01-01

Describes two experiments designed to provide concepts on the difference between heat and temperature and also bond energy. Investigates both a neutralization experiment and a ligation experiment. Notes inexpensive chemicals are used along with simple equipment. Discusses the sharing of lab results for a single class value. (MVL)

Spreadsheet-Based Program for Simulating Atomic Emission Spectra

ERIC Educational Resources Information Center

Flannigan, David J.

2014-01-01

A simple Excel spreadsheet-based program for simulating atomic emission spectra from the properties of neutral atoms (e.g., energies and statistical weights of the electronic states, electronic partition functions, transition probabilities, etc.) is described. The contents of the spreadsheet (i.e., input parameters, formulas for calculating…

Fully Bayesian tests of neutrality using genealogical summary statistics.

PubMed

Drummond, Alexei J; Suchard, Marc A

2008-10-31

Many data summary statistics have been developed to detect departures from neutral expectations of evolutionary models. However questions about the neutrality of the evolution of genetic loci within natural populations remain difficult to assess. One critical cause of this difficulty is that most methods for testing neutrality make simplifying assumptions simultaneously about the mutational model and the population size model. Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome. Here we harness posterior predictive simulation to exploit summary statistics of both the data and model parameters to test the goodness-of-fit of standard models of evolution. We apply the method to test the selective neutrality of molecular evolution in non-recombining gene genealogies and we demonstrate the utility of our method on four real data sets, identifying significant departures of neutrality in human influenza A virus, even after controlling for variation in population size. Importantly, by employing a full model-based Bayesian analysis, our method separates the effects of demography from the effects of selection. The method also allows multiple summary statistics to be used in concert, thus potentially increasing sensitivity. Furthermore, our method remains useful in situations where analytical expectations and variances of summary statistics are not available. This aspect has great potential for the analysis of temporally spaced data, an expanding area previously ignored for limited availability of theory and methods.

Estimating the Stoichiometry of HIV Neutralization

PubMed Central

Magnus, Carsten; Regoes, Roland R.

2010-01-01

HIV-1 virions infect target cells by first establishing contact between envelope glycoprotein trimers on the virion's surface and CD4 receptors on a target cell, recruiting co-receptors, fusing with the cell membrane and finally releasing the genetic material into the target cell. Specific experimental setups allow the study of the number of trimer-receptor-interactions needed for infection, i.e., the stoichiometry of entry and also the number of antibodies needed to prevent one trimer from engaging successfully in the entry process, i.e., the stoichiometry of (trimer) neutralization. Mathematical models are required to infer the stoichiometric parameters from these experimental data. Recently, we developed mathematical models for the estimations of the stoichiometry of entry [1]. In this article, we show how our models can be extended to investigate the stoichiometry of trimer neutralization. We study how various biological parameters affect the estimate of the stoichiometry of neutralization. We find that the distribution of trimer numbers—which is also an important determinant of the stoichiometry of entry—influences the estimated value of the stoichiometry of neutralization. In contrast, other parameters, which characterize the experimental system, diminish the information we can extract from the data about the stoichiometry of neutralization, and thus reduce our confidence in the estimate. We illustrate the use of our models by re-analyzing previously published data on the neutralization sensitivity [2], which contains measurements of neutralization sensitivity of viruses with different envelope proteins to antibodies with various specificities. Our mathematical framework represents the formal basis for the estimation of the stoichiometry of neutralization. Together with the stoichiometry of entry, the stoichiometry of trimer neutralization will allow one to calculate how many antibodies are required to neutralize a virion or even an entire population of virions. PMID:20333245

VUV absorption spectroscopy measurements of the role of fast neutral atoms in a high-power gap breakdown

NASA Astrophysics Data System (ADS)

Filuk, A. B.; Bailey, J. E.; Cuneo, M. E.; Lake, P. W.; Nash, T. J.; Noack, D. D.; Maron, Y.

2000-12-01

The maximum power achieved in a wide variety of high-power devices, including electron and ion diodes, z pinches, and microwave generators, is presently limited by anode-cathode gap breakdown. A frequently discussed hypothesis for this effect is ionization of fast neutral atoms injected throughout the anode-cathode gap during the power pulse. We describe a newly developed diagnostic tool that provides a direct test of this hypothesis. Time-resolved vacuum-ultraviolet absorption spectroscopy is used to directly probe fast neutral atoms with 1-mm spatial resolution in the 10-mm anode-cathode gap of the SABRE 5 MV, 1 TW applied-B ion diode. Absorption spectra collected during Ar RF glow discharges and with CO2 gas fills confirm the reliability of the diagnostic technique. Throughout the 50-100 ns ion diode pulses no measurable neutral absorption was seen, setting upper limits of (0.12-1.5)×1014 cm-3 for ground-state fast neutral atom densities of H, C, N, O, and F. The absence of molecular absorption bands also sets upper limits of (0.16-1.2)×1015 cm-3 for common simple molecules. These limits are low enough to rule out ionization of fast neutral atoms as a breakdown mechanism. Breakdown due to ionization of molecules is also found to be unlikely. This technique can now be applied to quantify the role of neutral atoms in other high-power devices.

Time-dependent MHD modeling of the global structure of the heliosphere

NASA Technical Reports Server (NTRS)

Liewer, P. C.; Brackbill, J. U.; Karmesin, S. Roy

1995-01-01

We present results from time-dependent modeling of the global structure of the heliosphere with neutral and magnetic field effects included. The magnetic field is assumed parallel to the interstellar flow in this two-dimensional axisymmetric model; the neutrals are treated as a fluid. The effects of interstellar neutrals and the interplanetary magnetic field on the location of the termination shock are studied using the most recent estimate of the interstellar medium parameters, results will be compared to those of Baranov and Zaitsev. The effect of the solar wind - VLISM interaction on the density and velocity of interstellar neutrals within the heliosphere will also be presented and related to observations. The response of the termination shock to the solar cycle variation in the solar wind will be compared to the response found previously using an axisymmetric hydrodynamic model without neutrals.

Time-course, negative-stain electron microscopy–based analysis for investigating protein–protein interactions at the single-molecule level

PubMed Central

Nogal, Bartek; Bowman, Charles A.; Ward, Andrew B.

2017-01-01

Several biophysical approaches are available to study protein–protein interactions. Most approaches are conducted in bulk solution, and are therefore limited to an average measurement of the ensemble of molecular interactions. Here, we show how single-particle EM can enrich our understanding of protein–protein interactions at the single-molecule level and potentially capture states that are unobservable with ensemble methods because they are below the limit of detection or not conducted on an appropriate time scale. Using the HIV-1 envelope glycoprotein (Env) and its interaction with receptor CD4-binding site neutralizing antibodies as a model system, we both corroborate ensemble kinetics-derived parameters and demonstrate how time-course EM can further dissect stoichiometric states of complexes that are not readily observable with other methods. Visualization of the kinetics and stoichiometry of Env–antibody complexes demonstrated the applicability of our approach to qualitatively and semi-quantitatively differentiate two highly similar neutralizing antibodies. Furthermore, implementation of machine-learning techniques for sorting class averages of these complexes into discrete subclasses of particles helped reduce human bias. Our data provide proof of concept that single-particle EM can be used to generate a “visual” kinetic profile that should be amenable to studying many other protein–protein interactions, is relatively simple and complementary to well-established biophysical approaches. Moreover, our method provides critical insights into broadly neutralizing antibody recognition of Env, which may inform vaccine immunogen design and immunotherapeutic development. PMID:28972148

Time-resolved ion energy and charge state distributions in pulsed cathodic arc plasmas of Nb‑Al cathodes in high vacuum

NASA Astrophysics Data System (ADS)

Zöhrer, Siegfried; Anders, André; Franz, Robert

2018-05-01

Cathodic arcs have been utilized in various applications including the deposition of thin films and coatings, ion implantation, and high current switching. Despite substantial progress in recent decades, the physical mechanisms responsible for the observed plasma properties are still a matter of dispute, particularly for multi-element cathodes, which can play an essential role in applications. The analysis of plasma properties is complicated by the generally occurring neutral background of metal atoms, which perturbs initial ion properties. By using a time-resolved method in combination with pulsed arcs and a comprehensive Nb‑Al cathode model system, we investigate the influence of cathode composition on the plasma, while making the influence of neutrals visible for the observed time frame. The results visualize ion detections of 600 μs plasma pulses, extracted 0.27 m from the cathode, resolved in mass-per-charge, energy-per-charge and time. Ion properties are found to be strongly dependent on the cathode material in a way that cannot be deduced by simple linear extrapolation. Subsequently, current hypotheses in cathodic arc physics applying to multi-element cathodes, like the so-called ‘velocity rule’ or the ‘cohesive energy rule’, are tested for early and late stages of the pulse. Apart from their fundamental character, the findings could be useful in optimizing or designing plasma properties for applications, by actively utilizing effects on ion distributions caused by composite cathode materials and charge exchange with neutrals.

Pulling it all together: the self-consistent distribution of neutral tori in Saturn's Magnetosphere based on all Cassini observations

NASA Astrophysics Data System (ADS)

Smith, H. T.; Richardson, J. D.

2017-12-01

Saturn's magnetosphere is unique in that the plumes from the small icy moon, Enceladus, serve at the primary source for heavy particles in Saturn's magnetosphere. The resulting co-orbiting neutral particles interact with ions, electrons, photons and other neutral particles to generate separate H2O, OH and O tori. Characterization of these toroidal distributions is essential for understanding Saturn magnetospheric sources, composition and dynamics. Unfortunately, limited direct observations of these features are available so modeling is required. A significant modeling challenge involves ensuring that either the plasma and neutral particle populations are not simply input conditions but can provide feedback to each population (i.e. are self-consistent). Jurac and Richardson (2005) executed such a self-consistent model however this research was performed prior to the return of Cassini data. In a similar fashion, we have coupled a 3-D neutral particle model (Smith et al. 2004, 2005, 2006, 2007, 2009, 2010) with a plasma transport model (Richardson 1998; Richardson & Jurac 2004) to develop a self-consistent model which is constrained by all available Cassini observations and current findings on Saturn's magnetosphere and the Enceladus plume source resulting in much more accurate neutral particle distributions. We present a new self-consistent model of the distribution of the Enceladus-generated neutral tori that is validated by all available observations. We also discuss the implications for source rate and variability.

Effect of different levels of rapidly degradable carbohydrates calculated by a simple rumen model on performance of lactating dairy cows.

PubMed

Doorenbos, J; Martín-Tereso, J; Dijkstra, J; van Laar, H

2017-07-01

Aggregating rumen degradation characteristics of different carbohydrate components into the term modeled rapidly degradable carbohydrates (mRDC) can simplify diet formulation by accounting for differences in rate and extent of carbohydrate degradation within and between feedstuffs. This study sought to evaluate responses of lactating dairy cows to diets formulated with increasing levels of mRDC, keeping the supply of other nutrients as constant as possible. The mRDC content of feedstuffs was calculated based on a simple rumen model including soluble, washable, and nonwashable but potentially degradable fractions, as well as the fractional degradation and passage rates, of sugar, starch, neutral detergent fiber, and other carbohydrates. The mRDC term effectively represents the total amount of carbohydrates degraded in the rumen within 2 h after ingestion. Fifty-two lactating Holstein cows (of which 4 were rumen fistulated) were assigned to 4 treatments in a 4 × 4 Latin square design. Treatments were fed as a total mixed ration consisting of 25.4% corn silage, 23.1% grass silage, 11.6% grass hay, and 39.9% concentrate on a dry matter basis. Differences in mRDC were created by exchanging nonforage neutral detergent fiber-rich ingredients (mainly sugar beet pulp) with starch-rich ingredients (mainly wheat) and by exchanging corn (slowly degradable starch) with wheat (rapidly degradable starch) in the concentrate, resulting in 4 treatments that varied in dietary mRDC level of 167, 181, 194, or 208 g/kg of dry matter. Level of mRDC did not affect dry matter intake. Fat- and protein-corrected milk production and milk fat and lactose yield were greatest at 181 mRDC and decreased with further increases in mRDC. Milk protein yield and concentration increased with increasing mRDC level. Mean rumen pH and diurnal variation in ruminal pH did not differ between treatments. Total daily meal time and number of visits per meal were smaller at 181 and 194 mRDC. Despite milk production responses, increasing dietary mRDC levels, while maintaining net energy and intestinal digestible protein as well as other nutrients at similar levels, did not influence rumen pH parameter estimates and had minor effects on feeding behavior. These results indicate that aggregating rapidly degradable carbohydrate content into one term may be a simple way to further improve predictability of production responses in practical diet formulation for lactating dairy cows. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Modelling injection rates of PUIs from photoionization using kinetic simulations of interstellar neutrals traversing the heliosphere

NASA Astrophysics Data System (ADS)

Keilbach, D.; Drews, C.; Taut, A.; Wimmer-Schweingruber, R. F.

2016-12-01

Recent studies of the inflow direction of the local insterstellar medium from PUI density distributions have shown that the extrema of the longitudinal distribution of PUI velocities (with respect to the solar wind speed) can be attributed to the radial velocity of the interstellar neutral seed population and is symmetric around the inflow direction of the local interstellar medium. This work is aimed to model pickup ion injection rates from photoionization (which is the main process of interstellar PUI production) throughout the heliosphere. To that end a seed population of interstellar neutrals is injected into a model heliosphere at 60 AU distance from the sun, whereas each particle's initial speed is given by a maxwellian distribution at a temperature of 1 eV and an inflow speed of 22 km/s. Then the density of the interstellar neutrals is integrated over the model heliosphere, while the movement of the neutrals is simulated using timestep methods. To model the focusing of the interstellar neutral trajectories from the sun's gravitational potential the model heliosphere contains a central gravitational potential.Each neutral test particle can be ionized via photoionization with a per-timestep probability antiproportional to the neutral's distance to the sun squared. By tracking the ionization rate location-dependently, PUI injection rates have been determined. Therefore using these simulations the density distributions of different species of interstellar neutrals have been calculated. In addition location-dependent injection rates of different species of PUIs have been calculated, which show an increased rate of PUI production in the focusing cone region (e.g. for He+ PUIs), but also in the crescent region (e.g. for O+ PUIs).Furthermore the longitudinal distribution of the neutrals' velocity at 1 AU is calculated from the simulation's results in order to estimate the PUI cut-off as a function of ecliptic longitude. Figure: Simulated He neutral density (left) and simulated He PUI production rates from photoionization (right). The sun is located at 0 AU at both x-and y-axes.

Neutral winds and electric fields from model studies using reduced ionograms

NASA Technical Reports Server (NTRS)

Baran, D. E.

1974-01-01

A relationship between the vertical component of the ion velocity and electron density profiles derived from reduced ionograms is developed. Methods for determining the horizontal components of the neutral winds and electric fields by using this relationship and making use of the variations of the inclinations and declinations of the earth's magnetic field are presented. The effects that electric fields have on the neutral wind calculations are estimated to be small but not second order. Seasonal and latitudinal variations of the calculated neutral winds are presented. From the calculated neutral winds a new set of neutral pressure gradients is determined. The new pressure gradients are compared with those generated from several static neutral atmospheric models. Sensitivity factors relating the pressure gradients and neutral winds are calculated and these indicate that mode coupling and harmonic generation are important to studies which assume linearized theories.

Results from the OH-PT model: a Kinetic-MHD Model of the Outer Heliosphere within SWMF

NASA Astrophysics Data System (ADS)

Michael, A.; Opher, M.; Tenishev, V.; Borovikov, D.; Toth, G.

2017-12-01

We present an update of the OH-PT model, a kinetic-MHD model of the outer heliosphere. The OH-PT model couples the Outer Heliosphere (OH) and Particle Tracker (PT) components within the Space Weather Modeling Framework (SWMF). The OH component utilizes the Block-Adaptive Tree Solarwind Roe-type Upwind Scheme (BATS-R-US) MHD code, a highly parallel, 3D, and block-adaptive solver. As a stand-alone model, the OH component solves the ideal MHD equations for the plasma and a separate set of Euler's equations for the different populations of neutral atoms. The neutrals and plasma in the outer heliosphere are coupled through charge-exchange. While this provides an accurate solution for the plasma, it is an inaccurate description of the neutrals. The charge-exchange mean free path is on the order of the size of the heliosphere; therefore the neutrals cannot be described as a fluid. The PT component is based on the Adaptive Mesh Particle Simulator (AMPS) model, a 3D, direct simulation Monte Carlo model that solves the Boltzmann equation for the motion and interaction of multi-species plasma and is used to model the neutral distribution functions throughout the domain. The charge-exchange process occurs within AMPS, which handles each event on a particle-by-particle basis and calculates the resulting source terms to the MHD equations. The OH-PT model combines the MHD solution for the plasma with the kinetic solution for the neutrals to form a self-consistent model of the heliosphere. In this work, we present verification and validation of the model as well as demonstrate the codes capabilities. Furthermore we provide a comparison of the OH-PT model to our multi-fluid approximation and detail the differences between the models in both the plasma solution and neutral distribution functions.

Four-fluid MHD simulations of the plasma and neutral gas environment of comet 67P/Churyumov-Gerasimenko near perihelion

NASA Astrophysics Data System (ADS)

Huang, Zhenguang; Tóth, Gábor; Gombosi, Tamas I.; Jia, Xianzhe; Rubin, Martin; Fougere, Nicolas; Tenishev, Valeriy; Combi, Michael R.; Bieler, Andre; Hansen, Kenneth C.; Shou, Yinsi; Altwegg, Kathrin

2016-05-01

The neutral and plasma environment is critical in understanding the interaction of the solar wind and comet 67P/Churyumov-Gerasimenko (CG), the target of the European Space Agency's Rosetta mission. To serve this need and support the Rosetta mission, we have developed a 3-D four-fluid model, which is based on BATS-R-US (Block-Adaptive Tree Solarwind Roe-type Upwind Scheme) within SWMF (Space Weather Modeling Framework) that solves the governing multifluid MHD equations and the Euler equations for the neutral gas fluid. These equations describe the behavior and interactions of the cometary heavy ions, the solar wind protons, the electrons, and the neutrals. This model incorporates different mass loading processes, including photoionization and electron impact ionization, charge exchange, dissociative ion-electron recombination, and collisional interactions between different fluids. We simulated the plasma and neutral gas environment near perihelion in three different cases: an idealized comet with a spherical body and uniform neutral gas outflow, an idealized comet with a spherical body and illumination-driven neutral gas outflow, and comet CG with a realistic shape model and illumination-driven neutral gas outflow. We compared the results of the three cases and showed that the simulations with illumination-driven neutral gas outflow have magnetic reconnection, a magnetic pileup region and nucleus directed plasma flow inside the nightside reconnection region, which have not been reported in the literature.

Virtual Characters: Visual Realism Affects Response Time and Decision-Making

ERIC Educational Resources Information Center

Sibuma, Bernadette

2012-01-01

This study integrates agent research with a neurocognitive technique to study how character faces affect cognitive processing. The N170 event-related potential (ERP) was used to study face processing during simple decision-making tasks. Twenty-five adults responded to facial expressions (fear/neutral) presented in three designs…

Instruction, Rationality and Learning to be Moral.

ERIC Educational Resources Information Center

Hyland, J. T.

1986-01-01

Defines rationality and morality and contends that learning to be moral must be based on more than value-neutral approaches which stress process over content. Argues that instruction in moral principles need not be simple bald exposition, but must include proofs, evidences, and arguments, making it nondogmatic and fully compatible with the…

War Coverage: The Case of the Falklands.

ERIC Educational Resources Information Center

Bellando, Edourado

The Falkland-Malvinas conflict is a classic example of how a government can manage news in wartime. The rules of the game as evinced by the British government and Ministry of Defense were simple and effective. They controlled access to the fighting, controlled all communications facilities, excluded all neutral correspondents and carefully…

75 FR 56477 - Technical Amendments for Marine Spark-Ignition Engines and Vessels

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-16

... spillage, incorporating safe recommended practices will result in a net benefit to the environment and lead... portable fuel tanks to these new requirements, manufacturers working together on systems integration.... We have engaged the industry to identify a simple, safe, and emissions neutral solution to this...

The formation of stable pH gradients with weak monovalent buffers for isoelectric focusing in free solution

NASA Technical Reports Server (NTRS)

Mosher, Richard A.; Thormann, Wolfgang; Graham, Aly; Bier, Milan

1985-01-01

Two methods which utilize simple buffers for the generation of stable pH gradients (useful for preparative isoelectric focusing) are compared and contrasted. The first employs preformed gradients comprised of two simple buffers in density-stabilized free solution. The second method utilizes neutral membranes to isolate electrolyte reservoirs of constant composition from the separation column. It is shown by computer simulation that steady-state gradients can be formed at any pH range with any number of components in such a system.

Merging domino and redox chemistry: stereoselective access to di- and trisubstituted β,γ-unsaturated acids and esters.

PubMed

Tejedor, David; Méndez-Abt, Gabriela; Cotos, Leandro; García-Tellado, Fernando

2012-03-19

Merging is the game! The coupling of a domino reaction and an internal neutral redox reaction constitutes an excellent manifold for the stereoselective synthesis of di- and trisubstituted olefins featuring a malonate unit, an ester, or a free carboxylic acid as substituents at the allylic position (see scheme; MW=microwave). The reaction utilizes simple starting materials (propargyl vinyl ethers), methanol or water as solvents, and a very simple and bench-friendly protocol. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spacecraft-charging mitigation of a high-power electron beam emitted by a magnetospheric spacecraft: Simple theoretical model for the transient of the spacecraft potential

DOE PAGES

Castello, Federico Lucco; Delzanno, Gian Luca; Borovsky, Joseph E.; ...

2018-05-29

A spacecraft-charging mitigation scheme necessary for the operation of a high-power electron beam in the low-density magnetosphere is analyzed. The scheme is based on a plasma contactor, i.e. a high-density charge-neutral plasma emitted prior to and during beam emission, and its ability to emit high ion currents without strong space-charge limitations. A simple theoretical model for the transient of the spacecraft potential and contactor expansion during beam emission is presented. The model focuses on the contactor ion dynamics and is valid in the limit when the ion contactor current is equal to the beam current. The model is found inmore » very good agreement with Particle-In-Cell simulations over a large parametric study that varies the initial expansion time of the contactor, the contactor current and the ion mass. The model highlights the physics of the spacecraft-charging mitigation scheme, indicating that the most important part of the dynamics is the evolution of the outermost ion front which is pushed away by the charge accumulated in the system by the beam. The model can be also used to estimate the long-time evolution of the spacecraft potential. For a short contactor expansion (0.3 or 0.6 ms Helium plasma or 0.8 ms Argon plasma, both with 1 mA current) it yields a peak spacecraft potential of the order of 1-3 kV. This implies that a 1-mA relativistic electron beam would be easily emitted by the spacecraft.« less

Probabilistic Design Storm Method for Improved Flood Estimation in Ungauged Catchments

NASA Astrophysics Data System (ADS)

Berk, Mario; Å pačková, Olga; Straub, Daniel

2017-12-01

The design storm approach with event-based rainfall-runoff models is a standard method for design flood estimation in ungauged catchments. The approach is conceptually simple and computationally inexpensive, but the underlying assumptions can lead to flawed design flood estimations. In particular, the implied average recurrence interval (ARI) neutrality between rainfall and runoff neglects uncertainty in other important parameters, leading to an underestimation of design floods. The selection of a single representative critical rainfall duration in the analysis leads to an additional underestimation of design floods. One way to overcome these nonconservative approximations is the use of a continuous rainfall-runoff model, which is associated with significant computational cost and requires rainfall input data that are often not readily available. As an alternative, we propose a novel Probabilistic Design Storm method that combines event-based flood modeling with basic probabilistic models and concepts from reliability analysis, in particular the First-Order Reliability Method (FORM). The proposed methodology overcomes the limitations of the standard design storm approach, while utilizing the same input information and models without excessive computational effort. Additionally, the Probabilistic Design Storm method allows deriving so-called design charts, which summarize representative design storm events (combinations of rainfall intensity and other relevant parameters) for floods with different return periods. These can be used to study the relationship between rainfall and runoff return periods. We demonstrate, investigate, and validate the method by means of an example catchment located in the Bavarian Pre-Alps, in combination with a simple hydrological model commonly used in practice.

Spacecraft-charging mitigation of a high-power electron beam emitted by a magnetospheric spacecraft: Simple theoretical model for the transient of the spacecraft potential

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

Castello, Federico Lucco; Delzanno, Gian Luca; Borovsky, Joseph E.

A spacecraft-charging mitigation scheme necessary for the operation of a high-power electron beam in the low-density magnetosphere is analyzed. The scheme is based on a plasma contactor, i.e. a high-density charge-neutral plasma emitted prior to and during beam emission, and its ability to emit high ion currents without strong space-charge limitations. A simple theoretical model for the transient of the spacecraft potential and contactor expansion during beam emission is presented. The model focuses on the contactor ion dynamics and is valid in the limit when the ion contactor current is equal to the beam current. The model is found inmore » very good agreement with Particle-In-Cell simulations over a large parametric study that varies the initial expansion time of the contactor, the contactor current and the ion mass. The model highlights the physics of the spacecraft-charging mitigation scheme, indicating that the most important part of the dynamics is the evolution of the outermost ion front which is pushed away by the charge accumulated in the system by the beam. The model can be also used to estimate the long-time evolution of the spacecraft potential. For a short contactor expansion (0.3 or 0.6 ms Helium plasma or 0.8 ms Argon plasma, both with 1 mA current) it yields a peak spacecraft potential of the order of 1-3 kV. This implies that a 1-mA relativistic electron beam would be easily emitted by the spacecraft.« less

Particles with nonlinear electric response: Suppressing van der Waals forces by an external field.

PubMed

Soo, Heino; Dean, David S; Krüger, Matthias

2017-01-01

We study the classical thermal component of Casimir, or van der Waals, forces between point particles with highly anharmonic dipole Hamiltonians when they are subjected to an external electric field. Using a model for which the individual dipole moments saturate in a strong field (a model that mimics the charges in a neutral, perfectly conducting sphere), we find that the resulting Casimir force depends strongly on the strength of the field, as demonstrated by analytical results. For a certain angle between the external field and center-to-center axis, the fluctuation force can be tuned and suppressed to arbitrarily small values. We compare the forces between these particles with those between particles with harmonic Hamiltonians and also provide a simple formula for asymptotically large external fields, which we expect to be generally valid for the case of saturating dipole moments.

Underscreening in ionic liquids: a first principles analysis.

PubMed

Rotenberg, Benjamin; Bernard, Olivier; Hansen, Jean-Pierre

2018-02-07

An attempt is made to understand the underscreening effect, observed in concentrated electrolyte solutions or melts, on the basis of simple, admittedly crude models involving charged (for the ions) and neutral (for the solvent molecules) hard spheres. The thermodynamic and structural properties of these 'primitive' and 'semi-primitive' models are calculated within mean spherical approximation, which provides the basic input required to determine the partial density response functions. The screening length [Formula: see text], which is unambiguously defined in terms of the wave-number-dependent response functions, exhibits a cross-over from a low density, Debye-like regime, to a regime where [Formula: see text] increases with density beyond a critical density at which the Debye length [Formula: see text] becomes comparable to the ion diameter. In this high density regime the ratio [Formula: see text] increases according to a power law, in qualitative agreement with experimental measurements, albeit at a much slower rate.

Underscreening in ionic liquids: a first principles analysis

NASA Astrophysics Data System (ADS)

Rotenberg, Benjamin; Bernard, Olivier; Hansen, Jean-Pierre

2018-02-01

An attempt is made to understand the underscreening effect, observed in concentrated electrolyte solutions or melts, on the basis of simple, admittedly crude models involving charged (for the ions) and neutral (for the solvent molecules) hard spheres. The thermodynamic and structural properties of these ‘primitive’ and ‘semi-primitive’ models are calculated within mean spherical approximation, which provides the basic input required to determine the partial density response functions. The screening length λS , which is unambiguously defined in terms of the wave-number-dependent response functions, exhibits a cross-over from a low density, Debye-like regime, to a regime where λS increases with density beyond a critical density at which the Debye length λD becomes comparable to the ion diameter. In this high density regime the ratio λ_S/λD increases according to a power law, in qualitative agreement with experimental measurements, albeit at a much slower rate.

The origin of risk aversion

PubMed Central

Zhang, Ruixun; Brennan, Thomas J.; Lo, Andrew W.

2014-01-01

Risk aversion is one of the most basic assumptions of economic behavior, but few studies have addressed the question of where risk preferences come from and why they differ from one individual to the next. Here, we propose an evolutionary explanation for the origin of risk aversion. In the context of a simple binary-choice model, we show that risk aversion emerges by natural selection if reproductive risk is systematic (i.e., correlated across individuals in a given generation). In contrast, risk neutrality emerges if reproductive risk is idiosyncratic (i.e., uncorrelated across each given generation). More generally, our framework implies that the degree of risk aversion is determined by the stochastic nature of reproductive rates, and we show that different statistical properties lead to different utility functions. The simplicity and generality of our model suggest that these implications are primitive and cut across species, physiology, and genetic origins. PMID:25453072

Is the ;Earth-ionosphere capacitor; a valid component in the atmospheric global electric circuit?

NASA Astrophysics Data System (ADS)

Haldoupis, Christos; Rycroft, Michael; Williams, Earle; Price, Colin

2017-11-01

This paper examines whether the Earth-ionosphere capacitor (EIC) model is correct, by comparing observed atmospheric electrical properties with those expected for a spherical capacitor, as defined in electrostatics. The comparisons suggest that the EIC concept cannot be reconciled with, and hence cannot account for, the observations, particularly the rapid reduction of the atmospheric electric field with height that is measured. This means that the spherical EIC concept is incorrect by being too simplistic; it is thus misleading. The reason for this flawed concept is simple: the model disregards the non-uniform conductivity of the atmosphere which requires the presence of a net positive charge in the lower atmosphere that equals in magnitude the Earth's negative charge. This positive charge shields the action of the Earth's negative charge from polarizing the ionosphere positively. Thus, the lower D region ionosphere remains electrically neutral, which makes the EIC concept inappropriate.

Charge exchange in solar wind-cometary interactions

NASA Technical Reports Server (NTRS)

Gombosi, T. I.; Horanyi, M.; Kecskemety, K.; Cravens, T. E.; Nagy, A. F.

1983-01-01

A simple model of a cometary spherically symmetrical atmosphere and ionosphere is considered. An analytic solution of the governing equations describing the radial distribution of the neutral and ion densities is found. The new solution is compared to the well-known solution of the equations containing only ionization terms. Neglecting recombination causes a significant overestimate of the ion density in the vicinity of the comet. An axisymmetric model of the solar wind-cometary interaction is considered, taking into account the loss of solar wind ions due to charge exchange. The calculations predict that for active comets, solar wind absorption due to charge exchange becomes important at a few thousand kilometers from the nucleus, and a surface separating the shocked solar wind from the cometary ionosphere develops in this region. These calculations are in reasonable agreement with the few observations available for the ionopause location at comets.

The origin of risk aversion.

PubMed

Zhang, Ruixun; Brennan, Thomas J; Lo, Andrew W

2014-12-16

Risk aversion is one of the most basic assumptions of economic behavior, but few studies have addressed the question of where risk preferences come from and why they differ from one individual to the next. Here, we propose an evolutionary explanation for the origin of risk aversion. In the context of a simple binary-choice model, we show that risk aversion emerges by natural selection if reproductive risk is systematic (i.e., correlated across individuals in a given generation). In contrast, risk neutrality emerges if reproductive risk is idiosyncratic (i.e., uncorrelated across each given generation). More generally, our framework implies that the degree of risk aversion is determined by the stochastic nature of reproductive rates, and we show that different statistical properties lead to different utility functions. The simplicity and generality of our model suggest that these implications are primitive and cut across species, physiology, and genetic origins.

B-physics anomalies: a guide to combined explanations

NASA Astrophysics Data System (ADS)

Buttazzo, Dario; Greljo, Admir; Isidori, Gino; Marzocca, David

2017-11-01

Motivated by additional experimental hints of Lepton Flavour Universality violation in B decays, both in charged- and in neutral-current processes, we analyse the ingredients necessary to provide a combined description of these phenomena. By means of an Effective Field Theory (EFT) approach, based on the hypothesis of New Physics coupled predominantly to the third generation of left-handed quarks and leptons, we show how this is possible. We demonstrate, in particular, how to solve the problems posed by electroweak precision tests and direct searches with a rather natural choice of model parameters, within the context of a U(2) q ×U(2)ℓ flavour symmetry. We further exemplify the general EFT findings by means of simplified models with explicit mediators in the TeV range: coloured scalar or vector leptoquarks and colour-less vectors. Among these, the case of an SU(2) L -singlet vector leptoquark emerges as a particularly simple and successful framework.

Bond Dissociation Energies of the Tungsten Fluorides and Their Singly-Charged Ions: A Density Functional Survey

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Arnold, James (Technical Monitor)

1999-01-01

The dissociation of WF6 and the related singly-charged cations and anions into the lower fluorides and fluorine atoms has been investigated theoretically using density functional theory (B3LYP) and relativistic effective core potentials, with estimates of spin-orbit effects included using a simple model. The inclusion of spin-orbit is essential for a correct description of the thermochemistry. The total atomization energy of the neutral and anionic WF6 is reproduced to within 25 kcal/mol, but comparison of individual bond dissociation energies with available experimental data shows discrepancies of up to 10 kcal/mol. The results are nevertheless useful to help resolve discrepancies in experimental data and provide estimates of missing data.

Investigating the Chemical Pathways to PAH- and PANH-Based Aerosols in Titan's Atmospheric chemistry

NASA Technical Reports Server (NTRS)

Sciamma-O'Brien, Ella Marion; Contreras, Cesar; Ricketts, Claire Louise; Salama, Farid

2011-01-01

A complex organic chemistry between Titan's two main constituents, N2 and CH4, leads to the production of more complex molecules and subsequently to solid organic aerosols. These aerosols are at the origin of the haze layers giving Titan its characteristic orange color. In situ measurements by the Ion Neutral Mass Spectrometer (INMS) and Cassini Plasma Spectrometer (CAPS) instruments onboard Cassini have revealed the presence of large amounts of neutral, positively and negatively charged heavy molecules in the ionosphere of Titan. In particular, benzene (C6H6) and toluene (C6H5CH3), which are critical precursors of polycyclic aromatic hydrocarbon (PAH) compounds, have been detected, suggesting that PAHs might play a role in the production of Titan s aerosols. Moreover, results from numerical models as well as laboratory simulations of Titan s atmospheric chemistry are also suggesting chemical pathways that link the simple precursor molecules resulting from the first steps of the N2-CH4 chemistry (C2H2, C2H4, HCN ...) to benzene, and to PAHs and nitrogen-containing PAHs (or PANHs) as precursors to the production of solid aerosols.

Numerical investigation of stability of breather-type solutions of the nonlinear Schrödinger equation

NASA Astrophysics Data System (ADS)

Calini, A.; Schober, C. M.

2013-09-01

In this article we present the results of a broad numerical investigation on the stability of breather-type solutions of the nonlinear Schrödinger (NLS) equation, specifically the one- and two-mode breathers for an unstable plane wave, which are frequently used to model rogue waves. The numerical experiments involve large ensembles of perturbed initial data for six typical random perturbations. Ensemble estimates of the "closeness", A(t), of the perturbed solution to an element of the respective unperturbed family indicate that the only neutrally stable breathers are the ones of maximal dimension, that is: given an unstable background with N unstable modes, the only neutrally stable breathers are the N-dimensional ones (obtained as a superimposition of N simple breathers via iterated Backlund transformations). Conversely, breathers which are not fully saturated are sensitive to noisy environments and are unstable. Interestingly, A(t) is smallest for the coalesced two-mode breather indicating the coalesced case may be the most robust two-mode breather in a laboratory setting. The numerical simulations confirm and provide a realistic realization of the stability behavior established analytically by the authors.