Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

PubMed Central

Shirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.

2017-01-01

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to a better than 0.1% relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb’s constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison. PMID:27787702

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

NASA Astrophysics Data System (ADS)

Shirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.

2017-01-01

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to better than 0.1 % relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb's constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.

Interactive Web-based Visualization of Atomic Position-time Series Data

NASA Astrophysics Data System (ADS)

Thapa, S.; Karki, B. B.

2017-12-01

Extracting and interpreting the information contained in large sets of time-varying three dimensional positional data for the constituent atoms of simulated material is a challenging task. We have recently implemented a web-based visualization system to analyze the position-time series data extracted from the local or remote hosts. It involves a pre-processing step for data reduction, which involves skipping uninteresting parts of the data uniformly (at full atomic configuration level) or non-uniformly (at atomic species level or individual atom level). Atomic configuration snapshot is rendered using the ball-stick representation and can be animated by rendering successive configurations. The entire atomic dynamics can be captured as the trajectories by rendering the atomic positions at all time steps together as points. The trajectories can be manipulated at both species and atomic levels so that we can focus on one or more trajectories of interest, and can be also superimposed with the instantaneous atomic structure. The implementation was done using WebGL and Three.js for graphical rendering, HTML5 and Javascript for GUI, and Elasticsearch and JSON for data storage and retrieval within the Grails Framework. We have applied our visualization system to the simulation datatsets for proton-bearing forsterite (Mg2SiO4) - an abundant mineral of Earths upper mantle. Visualization reveals that protons (hydrogen ions) incorporated as interstitials are much more mobile than protons substituting the host Mg and Si cation sites. The proton diffusion appears to be anisotropic with high mobility along the x-direction, showing limited discrete jumps in other two directions.

XpressWare Installation User guide

NASA Astrophysics Data System (ADS)

Duffey, K. P.

XpressWare is a set of X terminal software, released by Tektronix Inc, that accommodates the X Window system on a range of host computers. The software comprises boot files (the X server image), configuration files, fonts, and font tools to support the X terminal. The files can be installed on one host or distributed across multiple hosts The purpose of this guide is to present the system or network administrator with a step-by-step account of how to install XpressWare, and how subsequently to configure the X terminals appropriately for the environment in which they operate.

The dynamics of the multi-planet system orbiting Kepler-56

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

Li, Gongjie; Naoz, Smadar; Johnson, John Asher

2014-10-20

Kepler-56 is a multi-planet system containing two coplanar inner planets that are in orbits misaligned with respect to the spin axis of the host star, and an outer planet. Various mechanisms have been proposed to explain the broad distribution of spin-orbit angles among exoplanets, and these theories fall under two broad categories. The first is based on dynamical interactions in a multi-body system, while the other assumes that disk migration is the driving mechanism in planetary configuration and that the star (or disk) is titled with respect to the planetary plane. Here we show that the large observed obliquity ofmore » Kepler 56 system is consistent with a dynamical origin. In addition, we use observations by Huber et al. to derive the obliquity's probability distribution function, thus improving the constrained lower limit. The outer planet may be the cause of the inner planets' large obliquities, and we give the probability distribution function of its inclination, which depends on the initial orbital configuration of the planetary system. We show that even in the presence of precise measurement of the true obliquity, one cannot distinguish the initial configurations. Finally we consider the fate of the system as the star continues to evolve beyond the main sequence, and we find that the obliquity of the system will not undergo major variations as the star climbs the red giant branch. We follow the evolution of the system and find that the innermost planet will be engulfed in ∼129 Myr. Furthermore we put an upper limit of ∼155 Myr for the engulfment of the second planet. This corresponds to ∼3% of the current age of the star.« less

Dynamic localization of MreB in Vibrio parahaemolyticus and in the ectopic host bacterium Escherichia coli.

PubMed

Chiu, Shen-Wen; Chen, Shau-Yan; Wong, Hin-chung

2008-11-01

MreB, a homolog of eukaryotic actin, participates in morphogenesis, cell division, cell polarity, and chromosome segregation in prokaryotes. In this study, a yellow fluorescent protein conjugate (YFP-MreB(Vp)) was generated to investigate the behavior of MreB in merodiploid strain SC9 of the enteropathogen Vibrio parahaemolyticus. Under normal growth conditions, YFP-MreB(Vp) formed helical filaments with a pitch of 0.64 +/- 0.09 microm in about 85% of exponential-phase cells, and different clusters, relaxed coils, and ring configurations were observed in a small proportion of the cells. Overexpression of YFP-MreB(Vp) substantially altered the structure of the MreB cytoskeleton and resulted in swollen and pleomorphic cells. Disturbing the activities of penicillin-binding proteins or adding magnesium suppressed the morphological distortions. These results indicate that mislocalization of cell wall-synthesizing machinery was responsible for morphological abnormality. By expressing YFP-MreB(Vp) in the ectopic host bacterium Escherichia coli, shrinkage, fragmentation, and annealing of MreB(Vp) filaments were directly observed. This work revealed the dynamic pattern of the localization of YFP-MreB(Vp) in V. parahaemolyticus and its relationship to cell morphogenesis, and the YFP-MreB(Vp)-E. coli system may be used to investigate the dynamic spatial structures of the MreB cytoskeleton in vivo.

Distributed Dynamic Host Configuration Protocol (D2HCP)

PubMed Central

Villalba, Luis Javier García; Matesanz, Julián García; Orozco, Ana Lucila Sandoval; Díaz, José Duván Márquez

2011-01-01

Mobile Ad Hoc Networks (MANETs) are multihop wireless networks of mobile nodes without any fixed or preexisting infrastructure. The topology of these networks can change randomly due to the unpredictable mobility of nodes and their propagation characteristics. In most networks, including MANETs, each node needs a unique identifier to communicate. This work presents a distributed protocol for dynamic node IP address assignment in MANETs. Nodes of a MANET synchronize from time to time to maintain a record of IP address assignments in the entire network and detect any IP address leaks. The proposed stateful autoconfiguration scheme uses the OLSR proactive routing protocol for synchronization and guarantees unique IP addresses under a variety of network conditions, including message losses and network partitioning. Simulation results show that the protocol incurs low latency and communication overhead for IP address assignment. PMID:22163856

Distributed Dynamic Host Configuration Protocol (D2HCP).

PubMed

Villalba, Luis Javier García; Matesanz, Julián García; Orozco, Ana Lucila Sandoval; Díaz, José Duván Márquez

2011-01-01

Mobile Ad Hoc Networks (MANETs) are multihop wireless networks of mobile nodes without any fixed or preexisting infrastructure. The topology of these networks can change randomly due to the unpredictable mobility of nodes and their propagation characteristics. In most networks, including MANETs, each node needs a unique identifier to communicate. This work presents a distributed protocol for dynamic node IP address assignment in MANETs. Nodes of a MANET synchronize from time to time to maintain a record of IP address assignments in the entire network and detect any IP address leaks. The proposed stateful autoconfiguration scheme uses the OLSR proactive routing protocol for synchronization and guarantees unique IP addresses under a variety of network conditions, including message losses and network partitioning. Simulation results show that the protocol incurs low latency and communication overhead for IP address assignment.

Co-scheduling of network resource provisioning and host-to-host bandwidth reservation on high-performance network and storage systems

DOEpatents

Yu, Dantong; Katramatos, Dimitrios; Sim, Alexander; Shoshani, Arie

2014-04-22

A cross-domain network resource reservation scheduler configured to schedule a path from at least one end-site includes a management plane device configured to monitor and provide information representing at least one of functionality, performance, faults, and fault recovery associated with a network resource; a control plane device configured to at least one of schedule the network resource, provision local area network quality of service, provision local area network bandwidth, and provision wide area network bandwidth; and a service plane device configured to interface with the control plane device to reserve the network resource based on a reservation request and the information from the management plane device. Corresponding methods and computer-readable medium are also disclosed.

A Plethora of Virulence Strategies Hidden Behind Nuclear Targeting of Microbial Effectors

PubMed Central

Rivas, Susana; Genin, Stéphane

2011-01-01

Plant immune responses depend on the ability to couple rapid recognition of the invading microbe to an efficient response. During evolution, plant pathogens have acquired the ability to deliver effector molecules inside host cells in order to manipulate cellular and molecular processes and establish pathogenicity. Following translocation into plant cells, microbial effectors may be addressed to different subcellular compartments. Intriguingly, a significant number of effector proteins from different pathogenic microorganisms, including viruses, oomycetes, fungi, nematodes, and bacteria, is targeted to the nucleus of host cells. In agreement with this observation, increasing evidence highlights the crucial role played by nuclear dynamics, and nucleocytoplasmic protein trafficking during a great variety of analyzed plant–pathogen interactions. Once in the nucleus, effector proteins are able to manipulate host transcription or directly subvert essential host components to promote virulence. Along these lines, it has been suggested that some effectors may affect histone packing and, thereby, chromatin configuration. In addition, microbial effectors may either directly activate transcription or target host transcription factors to alter their regular molecular functions. Alternatively, nuclear translocation of effectors may affect subcellular localization of their cognate resistance proteins in a process that is essential for resistance protein-mediated plant immunity. Here, we review recent progress in our field on the identification of microbial effectors that are targeted to the nucleus of host plant cells. In addition, we discuss different virulence strategies deployed by microbes, which have been uncovered through examination of the mechanisms that guide nuclear localization of effector proteins. PMID:22639625

Microcomputer software development facilities

NASA Technical Reports Server (NTRS)

Gorman, J. S.; Mathiasen, C.

1980-01-01

A more efficient and cost effective method for developing microcomputer software is to utilize a host computer with high-speed peripheral support. Application programs such as cross assemblers, loaders, and simulators are implemented in the host computer for each of the microcomputers for which software development is a requirement. The host computer is configured to operate in a time share mode for multiusers. The remote terminals, printers, and down loading capabilities provided are based on user requirements. With this configuration a user, either local or remote, can use the host computer for microcomputer software development. Once the software is developed (through the code and modular debug stage) it can be downloaded to the development system or emulator in a test area where hardware/software integration functions can proceed. The microcomputer software program sources reside in the host computer and can be edited, assembled, loaded, and then downloaded as required until the software development project has been completed.

Integrated cluster management at Manchester

NASA Astrophysics Data System (ADS)

McNab, Andrew; Forti, Alessandra

2012-12-01

We describe an integrated management system using third-party, open source components used in operating a large Tier-2 site for particle physics. This system tracks individual assets and records their attributes such as MAC and IP addresses; derives DNS and DHCP configurations from this database; creates each host's installation and re-configuration scripts; monitors the services on each host according to the records of what should be running; and cross references tickets with asset records and per-asset monitoring pages. In addition, scripts which detect problems and automatically remove hosts record these new states in the database which are available to operators immediately through the same interface as tickets and monitoring.

Dynamics of exoplanetary systems, links to their habitability

NASA Astrophysics Data System (ADS)

Bolmont, E.; Raymond, S. N.; Selsis, F.

2014-12-01

Our knowledge of planets' orbital dynamics, which was based on Solar System studies, has been challenged by the diversity of exoplanetary systems. Around cool and ultra cool dwarfs, the influence of tides on the orbital and spin evolution of planets can strongly affect their climate and their capacity to host surface liquid water. We illustrate the role of tides and dynamics with the extreme case of planets orbiting around brown dwarfs. In multiple planet systems, the eccentricity is excited by planet-planet interactions. Planets are therefore heated up from the inside by the tidally-induced friction. This process can heat a habitable zone planet to such a level that surface liquid water cannot exist. We also talk about the newly discovered potentially habitable Earth-sized planet Kepler-186f. Given the poorly estimated age of the system, the planet could still be evolving towards synchronization and have a high obliquity or be pseudo-synchronized with a zero obliquity. These two configurations would have a different effect on the climate of this planet.

Low-Speed Dynamic Wind Tunnel Test Analysis of a Generic 53 Degree Swept UCAV Configuration With Controls

NASA Technical Reports Server (NTRS)

Vicroy, Dan D.; Huber, Kerstin C.; Rohlf, Detlef; Loser, Thomas

2014-01-01

Several static and dynamic forced-motion wind tunnel tests have been conducted on a generic unmanned combat air vehicle (UCAV) configuration with a 53deg swept leading edge. These tests are part of an international research effort to assess and advance the state-of-art of computational fluid dynamics (CFD) methods to predict the static and dynamic stability and control characteristics for this type of configuration. This paper describes the dynamic forced motion data collected from two different models of this UCAV configuration as well as analysis of the control surface deflections on the dynamic forces and moments.

Configuring Airspace Sectors with Approximate Dynamic Programming

NASA Technical Reports Server (NTRS)

Bloem, Michael; Gupta, Pramod

2010-01-01

In response to changing traffic and staffing conditions, supervisors dynamically configure airspace sectors by assigning them to control positions. A finite horizon airspace sector configuration problem models this supervisor decision. The problem is to select an airspace configuration at each time step while considering a workload cost, a reconfiguration cost, and a constraint on the number of control positions at each time step. Three algorithms for this problem are proposed and evaluated: a myopic heuristic, an exact dynamic programming algorithm, and a rollouts approximate dynamic programming algorithm. On problem instances from current operations with only dozens of possible configurations, an exact dynamic programming solution gives the optimal cost value. The rollouts algorithm achieves costs within 2% of optimal for these instances, on average. For larger problem instances that are representative of future operations and have thousands of possible configurations, excessive computation time prohibits the use of exact dynamic programming. On such problem instances, the rollouts algorithm reduces the cost achieved by the heuristic by more than 15% on average with an acceptable computation time.

Plasmon Geometric Phase and Plasmon Hall Shift

NASA Astrophysics Data System (ADS)

Shi, Li-kun; Song, Justin C. W.

2018-04-01

The collective plasmonic modes of a metal comprise a simple pattern of oscillating charge density that yields enhanced light-matter interaction. Here we unveil that beneath this familiar facade plasmons possess a hidden internal structure that fundamentally alters its dynamics. In particular, we find that metals with nonzero Hall conductivity host plasmons with an intricate current density configuration that sharply departs from that of ordinary zero Hall conductivity metals. This nontrivial internal structure dramatically enriches the dynamics of plasmon propagation, enabling plasmon wave packets to acquire geometric phases as they scatter. At boundaries, these phases accumulate allowing plasmon waves that reflect off to experience a nonreciprocal parallel shift. This plasmon Hall shift, tunable by Hall conductivity as well as plasmon wavelength, displaces the incident and reflected plasmon trajectories and can be readily probed by near-field photonics techniques. Anomalous plasmon geometric phases dramatically enrich the nanophotonics toolbox, and yield radical new means for directing plasmonic beams.

A comparative Study of Circulation Patterns at Active Lava Lakes

NASA Astrophysics Data System (ADS)

Lev, Einat; Oppenheimer, Clive; Spampinato, Letizia; Hernandez, Pedro; Unglert, Kathi

2016-04-01

Lava lakes present a rare opportunity to study magma dynamics in a large scaled-up "crucible" and provide a unique natural laboratory to ground-truth dynamic models of magma circulation. The persistence of lava lakes allows for long-term observations of flow dynamics and of lava properties, especially compared to surface lava flows. There are currently five persistent lava lakes in the world: Halemaumau in Kilauea (Hawaii, USA), Erta Ale (Ethiopia), Nyiragongo (Congo), Erebus (Antarctica), and Villarica (Chile). Marum and Benbow craters of Ambrym volcano (Vanuatu) and Masaya (Nicaragua) have often hosted lava lakes as well. We use visible-light and thermal infrared time-lapse and video footage collected at all above lakes (except Villarica, where the lake is difficult to observe), and compare the circulation patterns recorded. We calculate lake surface motion from the footage using the optical flow method (Lev et al., 2012) to produce 2D velocity fields. We mined both the surface temperature field and the surface velocity field for patterns using machine learning techniques such as "self-organizing maps (SOMs)" and "principle component analysis (PCA)". We use automatic detection technique to study the configuration of crustal plates at the lakes' surface. We find striking differences among the lakes, in flow direction, flow speed, frequency of changes in flow direction and speed, location and consistency of upwelling and downwelling, and crustal plate configuration. We relate the differences to lake size, shallow conduit geometry, lava viscosity, crystal and gas content, and crust integrity.

GSM module for wireless radiation monitoring system via SMS

NASA Astrophysics Data System (ADS)

Rahman, Nur Aira Abd; Hisyam Ibrahim, Noor; Lombigit, Lojius; Azman, Azraf; Jaafar, Zainudin; Arymaswati Abdullah, Nor; Hadzir Patai Mohamad, Glam

2018-01-01

A customised Global System for Mobile communication (GSM) module is designed for wireless radiation monitoring through Short Messaging Service (SMS). This module is able to receive serial data from radiation monitoring devices such as survey meter or area monitor and transmit the data as text SMS to a host server. It provides two-way communication for data transmission, status query, and configuration setup. The module hardware consists of GSM module, voltage level shifter, SIM circuit and Atmega328P microcontroller. Microcontroller provides control for sending, receiving and AT command processing to GSM module. The firmware is responsible to handle task related to communication between device and host server. It process all incoming SMS, extract, and store new configuration from Host, transmits alert/notification SMS when the radiation data reach/exceed threshold value, and transmits SMS data at every fixed interval according to configuration. Integration of this module with radiation survey/monitoring device will create mobile and wireless radiation monitoring system with prompt emergency alert at high-level radiation.

The effective propagation constants of SH wave in composites reinforced by dispersive parallel nanofibers

NASA Astrophysics Data System (ADS)

Qiang, FangWei; Wei, PeiJun; Li, Li

2012-07-01

In the present paper, the effective propagation constants of elastic SH waves in composites with randomly distributed parallel cylindrical nanofibers are studied. The surface stress effects are considered based on the surface elasticity theory and non-classical interfacial conditions between the nanofiber and the host are derived. The scattering waves from individual nanofibers embedded in an infinite elastic host are obtained by the plane wave expansion method. The scattering waves from all fibers are summed up to obtain the multiple scattering waves. The interactions among random dispersive nanofibers are taken into account by the effective field approximation. The effective propagation constants are obtained by the configurational average of the multiple scattering waves. The effective speed and attenuation of the averaged wave and the associated dynamical effective shear modulus of composites are numerically calculated. Based on the numerical results, the size effects of the nanofibers on the effective propagation constants and the effective modulus are discussed.

Indicator Expansion with Analysis Pipeline

DTIC Science & Technology

2015-01-13

INTERNAL FILTER trackInfectedHosts FILTER badTraffic SIP infectedHosts 1 DAY END INTERNAL FILTER 11 Step 3 watch where infected hosts go FILTER...nonWhiteListPostInfected SIP IN LIST infectedHosts DIP NOT IN LIST safePopularIPs.set END FILTER 12 Step 4 & 5: Count Hosts Per IP and Alert EVALUATION...CHECK THRESHOLD DISTINCT SIP > 50 TIME WINDOW 36 HOURS END CHECK END EVALUATION 13 Step 6: Report Expanded Indicators LIST CONFIGURATION secondLevelIPs

Eco-evolutionary dynamics in a coevolving host-virus system.

PubMed

Frickel, Jens; Sieber, Michael; Becks, Lutz

2016-04-01

Eco-evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco-evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco-evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host-virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade-off between host resistance and growth then maintained host diversity over time (trade-off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations. © 2016 John Wiley & Sons Ltd/CNRS.

gemcWeb: A Cloud Based Nuclear Physics Simulation Software

NASA Astrophysics Data System (ADS)

Markelon, Sam

2017-09-01

gemcWeb allows users to run nuclear physics simulations from the web. Being completely device agnostic, scientists can run simulations from anywhere with an Internet connection. Having a full user system, gemcWeb allows users to revisit and revise their projects, and share configurations and results with collaborators. gemcWeb is based on simulation software gemc, which is based on standard GEant4. gemcWeb requires no C++, gemc, or GEant4 knowledge. Using a simple but powerful GUI allows users to configure their project from geometries and configurations stored on the deployment server. Simulations are then run on the server, with results being posted to the user, and then securely stored. Python based and open-source, the main version of gemcWeb is hosted internally at Jefferson National Labratory and used by the CLAS12 and Electron-Ion Collider Project groups. However, as the software is open-source, and hosted as a GitHub repository, an instance can be deployed on the open web, or any institution's intra-net. An instance can be configured to host experiments specific to an institution, and the code base can be modified by any individual or group. Special thanks to: Maurizio Ungaro, PhD., creator of gemc; Markus Diefenthaler, PhD., advisor; and Kyungseon Joo, PhD., advisor.

Piezoelectric energy harvesting from an L-shaped beam-mass structure

NASA Astrophysics Data System (ADS)

Erturk, Alper; Renno, Jamil M.; Inman, Daniel J.

2008-03-01

Cantilevered piezoelectric harvesters have been extensively considered in the energy harvesting literature. Mostly, a traditional cantilevered beam with one or more piezoceramic layers is located on a vibrating host structure. Motion of the host structure results in vibrations of the harvester beam and that yields an alternating voltage output. As an alternative to classical cantilevered beams, this paper presents a novel harvesting device; a flexible L-shaped beam-mass structure that can be tuned to have a two-to-one internal resonance to a primary resonance ω II ≅ 2ω I which is not possible for classical cantilevers). The L-shaped structure has been well investigated in the literature of nonlinear dynamics since the two-to-one internal resonance, along with the consideration of quadratic nonlinearities, may yield modal energy exchange (for excitation frequency ω≅ ω Ior the so-called saturation phenomenon (for ω≅ω II). As a part of our ongoing research on piezoelectric energy harvesting, we are investigating the possibility of improving the electrical outputs in energy harvesting by employing these features of the L-shaped structure. This paper aims to introduce the idea, describes the important features of the L-shaped harvester configuration and develops a linear distributed parameter model for predicting the electromechanically coupled response. In addition, this work proposes a direct application of the L-shaped piezoelectric energy harvester configuration for use as landing gears in unmanned air vehicle applications.

Macroparasite dynamics of migratory host populations.

PubMed

Peacock, Stephanie J; Bouhours, Juliette; Lewis, Mark A; Molnár, Péter K

2018-03-01

Spatial variability in host density is a key factor affecting disease dynamics of wildlife, and yet there are few spatially explicit models of host-macroparasite dynamics. This limits our understanding of parasitism in migratory hosts, whose densities change considerably in both space and time. In this paper, we develop a model for host-macroparasite dynamics that considers the directional movement of host populations and their associated parasites. We include spatiotemporal changes in the mean and variance in parasite burden per host, as well as parasite-mediated host mortality and parasite-mediated migratory ability. Reduced migratory ability with increasing parasitism results in heavily infested hosts halting their migration, and higher parasite burdens in stationary hosts than in moving hosts. Simulations reveal the potential for positive feedbacks between parasite-reduced migratory ability and increasing parasite burdens at infection hotspots, such as stopover sites, that may lead to parasite-induced migratory stalling. This framework could help understand how global change might influence wildlife disease via changes to migratory patterns and parasite demographic rates. Copyright © 2018 Elsevier Inc. All rights reserved.

Infections on the move: how transient phases of host movement influence disease spread

PubMed Central

Fenton, A.; Dell, A. I.

2017-01-01

Animal movement impacts the spread of human and wildlife diseases, and there is significant interest in understanding the role of migrations, biological invasions and other wildlife movements in spatial infection dynamics. However, the influence of processes acting on infections during transient phases of host movement is poorly understood. We propose a conceptual framework that explicitly considers infection dynamics during transient phases of host movement to better predict infection spread through spatial host networks. Accounting for host transient movement captures key processes that occur while hosts move between locations, which together determine the rate at which hosts spread infections through networks. We review theoretical and empirical studies of host movement and infection spread, highlighting the multiple factors that impact the infection status of hosts. We then outline characteristics of hosts, parasites and the environment that influence these dynamics. Recent technological advances provide disease ecologists unprecedented ability to track the fine-scale movement of organisms. These, in conjunction with experimental testing of the factors driving infection dynamics during host movement, can inform models of infection spread based on constituent biological processes. PMID:29263283

Empirical evidence that metabolic theory describes the temperature dependency of within-host parasite dynamics.

PubMed

Kirk, Devin; Jones, Natalie; Peacock, Stephanie; Phillips, Jessica; Molnár, Péter K; Krkošek, Martin; Luijckx, Pepijn

2018-02-01

The complexity of host-parasite interactions makes it difficult to predict how host-parasite systems will respond to climate change. In particular, host and parasite traits such as survival and virulence may have distinct temperature dependencies that must be integrated into models of disease dynamics. Using experimental data from Daphnia magna and a microsporidian parasite, we fitted a mechanistic model of the within-host parasite population dynamics. Model parameters comprising host aging and mortality, as well as parasite growth, virulence, and equilibrium abundance, were specified by relationships arising from the metabolic theory of ecology. The model effectively predicts host survival, parasite growth, and the cost of infection across temperature while using less than half the parameters compared to modeling temperatures discretely. Our results serve as a proof of concept that linking simple metabolic models with a mechanistic host-parasite framework can be used to predict temperature responses of parasite population dynamics at the within-host level.

Does homologous reinfection drive multiple-wave influenza outbreaks? Accounting for immunodynamics in epidemiological models.

PubMed

Camacho, A; Cazelles, B

2013-12-01

Epidemiological models of influenza transmission usually assume that recovered individuals instantly develop a fully protective immunity against the infecting strain. However, recent studies have highlighted host heterogeneity in the development of this immune response, characterized by delay and even absence of protection, that could lead to homologous reinfection (HR). Here, we investigate how these immunological mechanisms at the individual level shape the epidemiological dynamics at the population level. In particular, because HR was observed during the successive waves of past pandemics, we assess its role in driving multiple-wave influenza outbreaks. We develop a novel mechanistic model accounting for host heterogeneity in the immune response. Immunological parameters are inferred by fitting our dynamical model to a two-wave influenza epidemic that occurred on the remote island of Tristan da Cunha (TdC) in 1971, and during which HR occurred in 92 of 284 islanders. We then explore the dynamics predicted by our model for various population settings. We find that our model can explain HR over both short (e.g. week) and long (e.g. month) time-scales, as reported during past pandemics. In particular, our results reveal that the HR wave on TdC was a natural consequence of the exceptional contact configuration and high susceptibility of this small and isolated community. By contrast, in larger, less mixed and partially protected populations, HR alone cannot generate multiple-wave outbreaks. However, in the latter case, we find that a significant proportion of infected hosts would remain unprotected at the end of the pandemic season and should therefore benefit from vaccination. Crucially, we show that failing to account for these unprotected individuals can lead to large underestimation of the magnitude of the first post-pandemic season. These results are relevant in the context of the 2009 A/H1N1 influenza post-pandemic era. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Climate, niche, ticks, and models: what they are and how we should interpret them.

PubMed

Estrada-Peña, Agustín

2008-12-01

Ticks spend most of their life cycle in the environment, and all tick life cycle stages are dependent on a complex combination of climate variables. Furthermore, host availability and vegetation significantly modulate the dynamics of tick populations. Tick recruitment is dependent on successful reproduction, which in turn requires sufficient adult tick densities, available blood meal sources, and egg survival. Though many animals can serve as hosts, there are several determinants of host suitability. For example, host availability in time and space is an important determinant of tick bionomics. Shelter and protection from environmental extremes are critical to tick survival. Questing and diapausing ticks are vulnerable to extremes of temperature and humidity. There are concerns about how predicted climate change may alter several critical features of host-parasite relationships of ticks, the potential for invasion of new areas or alteration of patterns of pathogen transmission in particular. However, modeling approaches that relate known occurrences of tick species to climate (and/or landscape) features and predict geographic occurrences are not completely fulfilling our needs to understand how the "tick panorama" can change as a consequence of these climate trends. This is a short review about the concept of ecological niche as applied to ticks, as well as some raised concerns about its evaluation and strict definition, and its usefulness to map geographical suitability for ticks. Comments about how climate, hosts, and landscape configuration are briefly discussed regarding its applicability to tick mapping and with reference about their impact on tick abundance. I will further comment on already published observations about observed changes in the geographical range of ticks in parts of Europe.

Research and realization of key technology in HILS interactive system

NASA Astrophysics Data System (ADS)

Liu, Che; Lu, Huiming; Wang, Fankai

2018-03-01

This paper designed HILS (Hardware In the Loop Simulation) interactive system based on xPC platform . Through the interface between C++ and MATLAB engine, establish the seamless data connection between Simulink and interactive system, complete data interaction between system and Simulink, realize the function development of model configuration, parameter modification and off line simulation. We establish the data communication between host and target machine through TCP/IP protocol to realize the model download and real-time simulation. Use database to store simulation data, implement real-time simulation monitoring and simulation data management. Realize system function integration by Qt graphic interface library and dynamic link library. At last, take the typical control system as an example to verify the feasibility of HILS interactive system.

Experimental verification of dynamic simulation

NASA Technical Reports Server (NTRS)

Yae, K. Harold; Hwang, Howyoung; Chern, Su-Tai

1989-01-01

The dynamics model here is a backhoe, which is a four degree of freedom manipulator from the dynamics standpoint. Two types of experiment are chosen that can also be simulated by a multibody dynamics simulation program. In the experiment, recorded were the configuration and force histories; that is, velocity and position, and force output and differential pressure change from the hydraulic cylinder, in the time domain. When the experimental force history is used as driving force in the simulation model, the forward dynamics simulation produces a corresponding configuration history. Then, the experimental configuration history is used in the inverse dynamics analysis to generate a corresponding force history. Therefore, two sets of configuration and force histories--one set from experiment, and the other from the simulation that is driven forward and backward with the experimental data--are compared in the time domain. More comparisons are made in regard to the effects of initial conditions, friction, and viscous damping.

Spacecraft boost and abort guidance and control systems requirement study, boost dynamics and control analysis study. Exhibit A: Boost dynamics and control anlaysis

NASA Technical Reports Server (NTRS)

Williams, F. E.; Price, J. B.; Lemon, R. S.

1972-01-01

The simulation developments for use in dynamics and control analysis during boost from liftoff to orbit insertion are reported. Also included are wind response studies of the NR-GD 161B/B9T delta wing booster/delta wing orbiter configuration, the MSC 036B/280 inch solid rocket motor configuration, the MSC 040A/L0X-propane liquid injection TVC configuration, the MSC 040C/dual solid rocket motor configuration, and the MSC 049/solid rocket motor configuration. All of the latest math models (rigid and flexible body) developed for the MSC/GD Space Shuttle Functional Simulator, are included.

The Stability of Orbital Configurations and the Ultimate Configurations of Planetary and Satellite Systems

NASA Technical Reports Server (NTRS)

Lissauer, Jack J.; Duncan, Martin J.

2004-01-01

The contents include the following: 1) Dynamical Evolution of the Earth-Moon Progenitors. 2) Dynamical Connections between Giant and Terrestrial Planets. 3) Dynamics of the Upsilon Andromedae Planetary System. 4) Dynamics of the Planets Orbiting GJ 876. and 5) Integrators for Planetary Accretion in Binaries.

The Anglo-Australian Planet Search. XXV. A Candidate Massive Saturn Analog Orbiting HD 30177

NASA Astrophysics Data System (ADS)

Wittenmyer, Robert A.; Horner, Jonathan; Mengel, M. W.; Butler, R. P.; Wright, D. J.; Tinney, C. G.; Carter, B. D.; Jones, H. R. A.; Anglada-Escudé, G.; Bailey, J.; O'Toole, Simon J.

2017-04-01

We report the discovery of a second long-period giant planet orbiting HD 30177, a star previously known to host a massive Jupiter analog (HD 30177b: a = 3.8 ± 0.1 au, m sin I = 9.7 ± 0.5 M Jup). HD 30177c can be regarded as a massive Saturn analog in this system, with a = 9.9 ± 1.0 au and m sin I = 7.6 ± 3.1 M Jup. The formal best-fit solution slightly favors a closer-in planet at a ˜ 7 au, but detailed n-body dynamical simulations show that configuration to be unstable. A shallow local minimum of longer period, lower eccentricity solutions was found to be dynamically stable, and hence we adopt the longer period in this work. The proposed ˜32 year orbit remains incomplete; further monitoring of this and other stars is necessary to reveal the population of distant gas giant planets with orbital separations a ˜ 10 au, analogous to that of Saturn.

Statistical mechanical model of gas adsorption in porous crystals with dynamic moieties

PubMed Central

Braun, Efrem; Carraro, Carlo; Smit, Berend

2017-01-01

Some nanoporous, crystalline materials possess dynamic constituents, for example, rotatable moieties. These moieties can undergo a conformation change in response to the adsorption of guest molecules, which qualitatively impacts adsorption behavior. We pose and solve a statistical mechanical model of gas adsorption in a porous crystal whose cages share a common ligand that can adopt two distinct rotational conformations. Guest molecules incentivize the ligands to adopt a different rotational configuration than maintained in the empty host. Our model captures inflections, steps, and hysteresis that can arise in the adsorption isotherm as a signature of the rotating ligands. The insights disclosed by our simple model contribute a more intimate understanding of the response and consequence of rotating ligands integrated into porous materials to harness them for gas storage and separations, chemical sensing, drug delivery, catalysis, and nanoscale devices. Particularly, our model reveals design strategies to exploit these moving constituents and engineer improved adsorbents with intrinsic thermal management for pressure-swing adsorption processes. PMID:28049851

Statistical mechanical model of gas adsorption in porous crystals with dynamic moieties.

PubMed

Simon, Cory M; Braun, Efrem; Carraro, Carlo; Smit, Berend

2017-01-17

Some nanoporous, crystalline materials possess dynamic constituents, for example, rotatable moieties. These moieties can undergo a conformation change in response to the adsorption of guest molecules, which qualitatively impacts adsorption behavior. We pose and solve a statistical mechanical model of gas adsorption in a porous crystal whose cages share a common ligand that can adopt two distinct rotational conformations. Guest molecules incentivize the ligands to adopt a different rotational configuration than maintained in the empty host. Our model captures inflections, steps, and hysteresis that can arise in the adsorption isotherm as a signature of the rotating ligands. The insights disclosed by our simple model contribute a more intimate understanding of the response and consequence of rotating ligands integrated into porous materials to harness them for gas storage and separations, chemical sensing, drug delivery, catalysis, and nanoscale devices. Particularly, our model reveals design strategies to exploit these moving constituents and engineer improved adsorbents with intrinsic thermal management for pressure-swing adsorption processes.

Towards an eco-phylogenetic framework for infectious disease ecology.

PubMed

Fountain-Jones, Nicholas M; Pearse, William D; Escobar, Luis E; Alba-Casals, Ana; Carver, Scott; Davies, T Jonathan; Kraberger, Simona; Papeş, Monica; Vandegrift, Kurt; Worsley-Tonks, Katherine; Craft, Meggan E

2018-05-01

Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi-host and/or multi-parasite interactions to understand and predict current and future disease threats better, and new tools are needed to help address this task. Eco-phylogenetics (phylogenetic community ecology) provides one avenue for exploring multi-host multi-parasite systems, yet the incorporation of eco-phylogenetic concepts and methods into studies of host pathogen dynamics has lagged behind. Eco-phylogenetics is a transformative approach that uses evolutionary history to infer present-day dynamics. Here, we present an eco-phylogenetic framework to reveal insights into parasite communities and infectious disease dynamics across spatial and temporal scales. We illustrate how eco-phylogenetic methods can help untangle the mechanisms of host-parasite dynamics from individual (e.g. co-infection) to landscape scales (e.g. parasite/host community structure). An improved ecological understanding of multi-host and multi-pathogen dynamics across scales will increase our ability to predict disease threats. © 2017 Cambridge Philosophical Society.

Actively controlling coolant-cooled cold plate configuration

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

Chainer, Timothy J.; Parida, Pritish R.

Cooling apparatuses are provided to facilitate active control of thermal and fluid dynamic performance of a coolant-cooled cold plate. The cooling apparatus includes the cold plate and a controller. The cold plate couples to one or more electronic components to be cooled, and includes an adjustable physical configuration. The controller dynamically varies the adjustable physical configuration of the cold plate based on a monitored variable associated with the cold plate or the electronic component(s) being cooled by the cold plate. By dynamically varying the physical configuration, the thermal and fluid dynamic performance of the cold plate are adjusted to, formore » example, optimally cool the electronic component(s), and at the same time, reduce cooling power consumption used in cooling the electronic component(s). The physical configuration can be adjusted by providing one or more adjustable plates within the cold plate, the positioning of which may be adjusted based on the monitored variable.« less

Resource-driven changes to host population stability alter the evolution of virulence and transmission.

PubMed

Hite, Jessica L; Cressler, Clayton E

2018-05-05

What drives the evolution of parasite life-history traits? Recent studies suggest that linking within- and between-host processes can provide key insight into both disease dynamics and parasite evolution. Still, it remains difficult to understand how to pinpoint the critical factors connecting these cross-scale feedbacks, particularly under non-equilibrium conditions; many natural host populations inherently fluctuate and parasites themselves can strongly alter the stability of host populations. Here, we develop a general model framework that mechanistically links resources to parasite evolution across a gradient of stable and unstable conditions. First, we dynamically link resources and between-host processes (host density, stability, transmission) to virulence evolution, using a 'non-nested' model. Then, we consider a 'nested' model where population-level processes (transmission and virulence) depend on resource-driven changes to individual-level (within-host) processes (energetics, immune function, parasite production). Contrary to 'non-nested' model predictions, the 'nested' model reveals complex effects of host population dynamics on parasite evolution, including regions of evolutionary bistability; evolution can push parasites towards strongly or weakly stabilizing strategies. This bistability results from dynamic feedbacks between resource-driven changes to host density, host immune function and parasite production. Together, these results highlight how cross-scale feedbacks can provide key insights into the structuring role of parasites and parasite evolution.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'. © 2018 The Author(s).

AGARD standard aeroelastic configurations for dynamic response. Candidate configuration I.-wing 445.6

NASA Technical Reports Server (NTRS)

Yates, E. Carson, Jr.

1987-01-01

To promote the evaluation of existing and emerging unsteady aerodynamic codes and methods for applying them to aeroelastic problems, especially for the transonic range, a limited number of aerodynamic configurations and experimental dynamic response data sets are to be designated by the AGARD Structures and Materials Panel as standards for comparison. This set is a sequel to that established several years ago for comparisons of calculated and measured aerodynamic pressures and forces. This report presents the information needed to perform flutter calculations for the first candidate standard configuration for dynamic response along with the related experimental flutter data.

The impact of parasitoid emergence time on host-parasitoid population dynamics.

PubMed

Cobbold, Christina A; Roland, Jens; Lewis, Mark A

2009-01-01

We investigate the effect of parasitoid phenology on host-parasitoid population cycles. Recent experimental research has shown that parasitized hosts can continue to interact with their unparasitized counterparts through competition. Parasitoid phenology, in particular the timing of emergence from the host, determines the duration of this competition. We construct a discrete-time host-parasitoid model in which within-generation dynamics associated with parasitoid timing is explicitly incorporated. We found that late-emerging parasitoids induce less severe, but more frequent, host outbreaks, independent of the choice of competition model. The competition experienced by the parasitized host reduces the parasitoids' numerical response to changes in host numbers, preventing the 'boom-bust' dynamics associated with more efficient parasitoids. We tested our findings against experimental data for the forest tent caterpillar (Malacosoma disstria Hübner) system, where a large number of consecutive years at a high host density is synonymous with severe forest damage.

Host social organization and mating system shape parasite transmission opportunities in three European bat species.

PubMed

van Schaik, J; Kerth, G

2017-02-01

For non-mobile parasites living on social hosts, infection dynamics are strongly influenced by host life history and social system. We explore the impact of host social systems on parasite population dynamics by comparing the infection intensity and transmission opportunities of three mite species of the genus Spinturnix across their three European bat hosts (Myotis daubentonii, Myotis myotis, Myotis nattereri) during the bats' autumn mating season. Mites mainly reproduce in host maternity colonies in summer, but as these colonies are closed, opportunities for inter-colony transmission are limited to host interactions during the autumn mating season. The three investigated hosts differ considerably in their social system, most notably in maternity colony size, mating system, and degree of male summer aggregation. We observed marked differences in parasite infection during the autumn mating period between the species, closely mirroring the predictions made based on the social systems of the hosts. Increased host aggregation sizes in summer yielded higher overall parasite prevalence and intensity, both in male and female hosts. Moreover, parasite levels in male hosts differentially increased throughout the autumn mating season in concordance with the degree of contact with female hosts afforded by the different mating systems of the hosts. Critically, the observed host-specific differences have important consequences for parasite population structure and will thus affect the coevolutionary dynamics between the interacting species. Therefore, in order to accurately characterize host-parasite dynamics in hosts with complex social systems, a holistic approach that investigates parasite infection and transmission across all periods is warranted.

Subsonic static and dynamic stability characteristics of the test technique demonstrator NASP configuration

NASA Technical Reports Server (NTRS)

Boyden, Richmond P.; Dress, David A.; Fox, Charles H., Jr.; Huffman, Jarrett K.; Cruz, Christopher I.

1993-01-01

The paper describes the procedure used for and the results obtained of wind-tunnel tests of the National Aerospace Plane (NASP) configuration, which were conducted in the NASA Langley Research Center High Speed Tunnel using a blended body NASP configuration designed by the research center. Static and dynamic stability characteristics were measured at Mach numbers 0.3, 0.6, and 0.8. In addition to tests of the baseline configuration, component buildup tests with a canard surface and with a body flap were carried out. Results demonstrated a positive static stability of the baseline configuration, except at the higher angles of attack at Mach 0.8. A good agreement was found between the inphase dynamic parameters and the corresponding static data.

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).

PubMed

Godwin, Ryan C; Melvin, Ryan L; Gmeiner, William H; Salsbury, Freddie R

2017-01-31

Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.

Low Power, Low Mass, Modular, Multi-band Software-defined Radios

NASA Technical Reports Server (NTRS)

Haskins, Christopher B. (Inventor); Millard, Wesley P. (Inventor)

2013-01-01

Methods and systems to implement and operate software-defined radios (SDRs). An SDR may be configured to perform a combination of fractional and integer frequency synthesis and direct digital synthesis under control of a digital signal processor, which may provide a set of relatively agile, flexible, low-noise, and low spurious, timing and frequency conversion signals, and which may be used to maintain a transmit path coherent with a receive path. Frequency synthesis may include dithering to provide additional precision. The SDR may include task-specific software-configurable systems to perform tasks in accordance with software-defined parameters or personalities. The SDR may include a hardware interface system to control hardware components, and a host interface system to provide an interface to the SDR with respect to a host system. The SDR may be configured for one or more of communications, navigation, radio science, and sensors.

A dynamically reconfigurable multi-functional PLL for SRAM-based FPGA in 65nm CMOS technology

NASA Astrophysics Data System (ADS)

Yang, Mingqian; Chen, Lei; Li, Xuewu; Zhang, Yanlong

2018-04-01

Phase-locked loops (PLL) have been widely utilized in FPGA as an important module for clock management. PLL with dynamic reconfiguration capability is always welcomed in FPGA design as it is able to decrease power consumption and simultaneously improve flexibility. In this paper, a multi-functional PLL with dynamic reconfiguration capability for 65nm SRAM-based FPGA is proposed. Firstly, configurable charge pump and loop filter are utilized to optimize the loop bandwidth. Secondly, the PLL incorporates a VCO with dual control voltages to accelerate the adjustment of oscillation frequency. Thirdly, three configurable dividers are presented for flexible frequency synthesis. Lastly, a configuration block with dynamic reconfiguration function is proposed. Simulation results demonstrate that the proposed multi-functional PLL can output clocks with configurable division ratio, phase shift and duty cycle. The PLL can also be dynamically reconfigured without affecting other parts' running or halting the FPGA device.

Dynamic Stall of Finite Span Blades and its Control

NASA Astrophysics Data System (ADS)

Taylor, Keith; Leong, Chia; Amitay, Michael

2013-11-01

An experimental investigational study into a dynamically pitching s809 airfoil at a Reynolds number of 220,000 was conducted. Particle Image Velocimetry was employed to visualize and quantify the flow field around the airfoil. This investigation compares a 2-D configuration with 3-D configuration (i.e., a finite span blade). The difference in the flow field between these two configurations is explored, as the vibrations present in the 3-D configuration (due to the dynamic stall) may contribute to a different apparent flow field than classical results would suggest. In addition, a comparison between lift and drag coefficients, measured on the 2-D and 3-D configurations, is explored, demonstrating how time varying lift and drag forces oscillate at characteristic frequencies associated with the primary vibrational modes of the model. In addition, flow control is applied through the actuation of an array of synthetic jets located near the leading edge of the model, in order to effect changes in the flow field around the model, demonstrating how dynamic stall can be delayed or eliminated during dynamic conditions.

Dynamic positioning configuration and its first-order optimization

NASA Astrophysics Data System (ADS)

Xue, Shuqiang; Yang, Yuanxi; Dang, Yamin; Chen, Wu

2014-02-01

Traditional geodetic network optimization deals with static and discrete control points. The modern space geodetic network is, on the other hand, composed of moving control points in space (satellites) and on the Earth (ground stations). The network configuration composed of these facilities is essentially dynamic and continuous. Moreover, besides the position parameter which needs to be estimated, other geophysical information or signals can also be extracted from the continuous observations. The dynamic (continuous) configuration of the space network determines whether a particular frequency of signals can be identified by this system. In this paper, we employ the functional analysis and graph theory to study the dynamic configuration of space geodetic networks, and mainly focus on the optimal estimation of the position and clock-offset parameters. The principle of the D-optimization is introduced in the Hilbert space after the concept of the traditional discrete configuration is generalized from the finite space to the infinite space. It shows that the D-optimization developed in the discrete optimization is still valid in the dynamic configuration optimization, and this is attributed to the natural generalization of least squares from the Euclidean space to the Hilbert space. Then, we introduce the principle of D-optimality invariance under the combination operation and rotation operation, and propose some D-optimal simplex dynamic configurations: (1) (Semi) circular configuration in 2-dimensional space; (2) the D-optimal cone configuration and D-optimal helical configuration which is close to the GPS constellation in 3-dimensional space. The initial design of GPS constellation can be approximately treated as a combination of 24 D-optimal helixes by properly adjusting the ascending node of different satellites to realize a so-called Walker constellation. In the case of estimating the receiver clock-offset parameter, we show that the circular configuration, the symmetrical cone configuration and helical curve configuration are still D-optimal. It shows that the given total observation time determines the optimal frequency (repeatability) of moving known points and vice versa, and one way to improve the repeatability is to increase the rotational speed. Under the Newton's law of motion, the frequency of satellite motion determines the orbital altitude. Furthermore, we study three kinds of complex dynamic configurations, one of which is the combination of D-optimal cone configurations and a so-called Walker constellation composed of D-optimal helical configuration, the other is the nested cone configuration composed of n cones, and the last is the nested helical configuration composed of n orbital planes. It shows that an effective way to achieve high coverage is to employ the configuration composed of a certain number of moving known points instead of the simplex configuration (such as D-optimal helical configuration), and one can use the D-optimal simplex solutions or D-optimal complex configurations in any combination to achieve powerful configurations with flexile coverage and flexile repeatability. Alternately, how to optimally generate and assess the discrete configurations sampled from the continuous one is discussed. The proposed configuration optimization framework has taken the well-known regular polygons (such as equilateral triangle and quadrangular) in two-dimensional space and regular polyhedrons (regular tetrahedron, cube, regular octahedron, regular icosahedron, or regular dodecahedron) into account. It shows that the conclusions made by the proposed technique are more general and no longer limited by different sampling schemes. By the conditional equation of D-optimal nested helical configuration, the relevance issues of GNSS constellation optimization are solved and some examples are performed by GPS constellation to verify the validation of the newly proposed optimization technique. The proposed technique is potentially helpful in maintenance and quadratic optimization of single GNSS of which the orbital inclination and the orbital altitude change under the precession, as well as in optimally nesting GNSSs to perform global homogeneous coverage of the Earth.

Interaction effects of different drivers of wild bee decline and their influence on host-pathogen dynamics.

PubMed

Meeus, Ivan; Pisman, Matti; Smagghe, Guy; Piot, Niels

2018-04-01

Wild bee decline is a multi-factorial problem, yet it is crucial to understand the impact of a single driver. Hereto the interaction effects of wild bee decline with multiple natural and anthropogenic stressors need to be clear. This is also true for the driver 'pathogens', as stressor induced disturbances of natural host-pathogen dynamics can unbalance settled virulence equilibria. Invasive species, bee domestication, habitat loss, climate changes and insecticides are recognized drivers of wild bee decline, but all influence host-pathogen dynamics as well. Many wild bee pathogens have multiple hosts, which relaxes the host-density limitation of virulence evolution. In conclusion, disturbances of bee-pathogen dynamics can be compared to a game of Russian roulette. Copyright © 2018. Published by Elsevier Inc.

Data-constrained models of quiet and storm-time geosynchronous magnetic field based on observations in the near geospace

NASA Astrophysics Data System (ADS)

Andreeva, V. A.; Tsyganenko, N. A.

2017-12-01

The geosynchronous orbit is unique in that its nightside segment skims along the boundary, separating the inner magnetosphere with a predominantly dipolar configuration from the magnetotail, where the Earth's magnetic field becomes small relative to the contribution from external sources. The ability to accurately reconstruct the magnetospheric configuration at GEO is important to understand the behavior of plasma and energetic particles, which critically affect space weather in the area densely populated by a host of satellites. To that end, we have developed a dynamical empirical model of the geosynchronous magnetic field with forecasting capability, based on a multi-year set of data taken by THEMIS, Polar, Cluster, Geotail, and Van Allen missions. The model's mathematical structure is devised using a new approach [Andreeva and Tsyganenko, 2016, doi:10.1002/2015JA022242], in which the toroidal/poloidal components of the field are represented using the radial and azimuthal basis functions. The model describes the field as a function of solar-magnetic coordinates, geodipole tilt angle, solar wind pressure, and a set of dynamic variables, quantifying the magnetosphere's response to external driving/loading and internal relaxation/dissipation during the disturbance recovery. The response variables are introduced following the approach by Tsyganenko and Sitnov [2005, doi:10.1029/2004JA010798], in which the electric current dynamics was described as a result of competition between the external energy input and the subsequent internal losses of the injected energy. The model's applicability range extends from quiet to moderately disturbed conditions, with peak Sym-H values -150 nT. The obtained results have been validated using independent GOES magnetometer data, taken during the maximum of the 23rd solar cycle and its declining phase.

Test Methods for Telemetry Systems and Subsystems. Volume 5: Test Methods for Digital Recorder/Reproducer Systems and Recorder Memory Modules

DTIC Science & Technology

2016-09-26

serial communications program ( Hyper terminal) Configure METS for PCM 1 Mbps and MIL-STD-1553 10-Hz rate 4 Configure the host software to...Verify recorder stopped 44 Issue . LOOP . Verify recorder goes into record and play in read after write mode 45 Issue .STOP, Verify recorder

The Human Ligase IIIα-XRCC1 Protein Complex Performs DNA Nick Repair after Transient Unwrapping of Nucleosomal DNA*

PubMed Central

Rashid, Ishtiaque; Tomkinson, Alan E.; Pederson, David S.

2017-01-01

Reactive oxygen species generate potentially cytotoxic and mutagenic lesions in DNA, both between and within the nucleosomes that package DNA in chromatin. The vast majority of these lesions are subject to base excision repair (BER). Enzymes that catalyze the first three steps in BER can act at many sites in nucleosomes without the aid of chromatin-remodeling agents and without irreversibly disrupting the host nucleosome. Here we show that the same is true for a protein complex comprising DNA ligase IIIα and the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1), which completes the fourth and final step in (short-patch) BER. Using in vitro assembled nucleosomes containing discretely positioned DNA nicks, our evidence indicates that the ligase IIIα-XRCC1 complex binds to DNA nicks in nucleosomes only when they are exposed by periodic, spontaneous partial unwrapping of DNA from the histone octamer; that the scaffolding protein XRCC1 enhances the ligation; that the ligation occurs within a complex that ligase IIIα-XRCC1 forms with the host nucleosome; and that the ligase IIIα-XRCC1-nucleosome complex decays when ligation is complete, allowing the host nucleosome to return to its native configuration. Taken together, our results illustrate ways in which dynamic properties intrinsic to nucleosomes may contribute to the discovery and efficient repair of base damage in chromatin. PMID:28184006

Aspergillus fumigatus morphology and dynamic host interactions.

PubMed

van de Veerdonk, Frank L; Gresnigt, Mark S; Romani, Luigina; Netea, Mihai G; Latgé, Jean-Paul

2017-11-01

Aspergillus fumigatus is an environmental filamentous fungus that can cause life-threatening disease in immunocompromised individuals. The interactions between A. fumigatus and the host environment are dynamic and complex. The host immune system needs to recognize the distinct morphological forms of A. fumigatus to control fungal growth and prevent tissue invasion, whereas the fungus requires nutrients and needs to adapt to the hostile environment by escaping immune recognition and counteracting host responses. Understanding these highly dynamic interactions is necessary to fully understand the pathogenesis of aspergillosis and to facilitate the design of new therapeutics to overcome the morbidity and mortality caused by A. fumigatus. In this Review, we describe how A. fumigatus adapts to environmental change, the mechanisms of host defence, and our current knowledge of the interplay between the host immune response and the fungus.

Empirical evidence that metabolic theory describes the temperature dependency of within-host parasite dynamics

PubMed Central

Jones, Natalie; Peacock, Stephanie; Phillips, Jessica; Molnár, Péter K.; Krkošek, Martin; Luijckx, Pepijn

2018-01-01

The complexity of host–parasite interactions makes it difficult to predict how host–parasite systems will respond to climate change. In particular, host and parasite traits such as survival and virulence may have distinct temperature dependencies that must be integrated into models of disease dynamics. Using experimental data from Daphnia magna and a microsporidian parasite, we fitted a mechanistic model of the within-host parasite population dynamics. Model parameters comprising host aging and mortality, as well as parasite growth, virulence, and equilibrium abundance, were specified by relationships arising from the metabolic theory of ecology. The model effectively predicts host survival, parasite growth, and the cost of infection across temperature while using less than half the parameters compared to modeling temperatures discretely. Our results serve as a proof of concept that linking simple metabolic models with a mechanistic host–parasite framework can be used to predict temperature responses of parasite population dynamics at the within-host level. PMID:29415043

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity.

PubMed

Frickel, Jens; Theodosiou, Loukas; Becks, Lutz

2017-10-17

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus-host and prey-predator) with a more complex three-species system (virus-host-predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host-virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host-virus coevolution in the complex system and that the virus' effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species.

Between timelessness and historiality: on the dynamics of the epistemic objects of mathematics.

PubMed

Epple, Moritz

2011-09-01

In order to discuss the temporal structure of mathematical research, this essay offers four related definitions of a mathematical object from different times and places. It is argued that in order to appreciate the differences between these definitions, the historian needs to understand that none of them made sense in mathematical practice without a technical framework, referred to but not explained in the definitions themselves (an "epistemic configuration of research"); that the dynamics of the epistemic objects of mathematical research are secondary to the dynamics of these epistemic configurations as a whole; and that the dynamics of epistemic configurations of mathematical research do not follow law-like processes. Very different types of change may happen, and some of them link the dynamics of epistemic configurations with events and developments far beyond the bounds of the research field in question. These insights have historiographical consequences that require us to rethink the kind of temporality ascribed to mathematics.

Supersonic dynamic stability characteristics of the test technique demonstrator NASP configuration

NASA Technical Reports Server (NTRS)

Dress, David A.; Boyden, Richmond P.; Cruz, Christopher I.

1992-01-01

Wind tunnel tests of a National Aero-Space Plane (NASP) configuration were conducted in both test sections of the Langley Unitary Plan Wind Tunnel. The model used is a Langley designed blended body NASP configuration. Dynamic stability characteristics were measured on this configuration at Mach numbers of 2.0, 2.5, 3.5, and 4.5. In addition to tests of the baseline configuration, component buildup tests were conducted. The test results show that the baseline configuration generally has positive damping about all three axes with only isolated exceptions. In addition, there was generally good agreement between the in-pulse dynamic parameters and the corresponding static data which were measured during another series of tests in the Unitary Plan Wind Tunnel. Also included are comparisons of the experimental damping parameters with results from the engineering predictive code APAS (Aerodynamic Preliminary Analysis System). These comparisons show good agreement at low angles of attack; however, the comparisons are generally not as good at the higher angles of attack.

Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation

NASA Technical Reports Server (NTRS)

Afjeh, Abdollah A.; Reed, John A.

2003-01-01

The following reports are presented on this project:A first year progress report on: Development of a Dynamically Configurable,Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; A second year progress report on: Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; An Extensible, Interchangeable and Sharable Database Model for Improving Multidisciplinary Aircraft Design; Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration; and Improving the Aircraft Design Process Using Web-based Modeling and Simulation.

Multi-Model Validation of Currents in the Chesapeake Bay Region in June 2010

DTIC Science & Technology

2012-01-01

host “ DaVinci ” at the Naval Oceanographic Office (NAVOCEANO). The same model configuration also took approximately 1 hr of wall clock time for a 72-hr...comparable to the performance Navy DSRC host DaVinci . Products of water level and horizontal current maps as well as station time series, identical to...DSRC host DaVinci and required approximately 5 hrs of wall-clock time for 72-hr forecasts, including data Figure 10. The Chesapeake Bay Delft3D

Phase stability and dynamics of entangled polymer-nanoparticle composites

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

Mangal, Rahul; Srivastava, Samanvaya; Archer, Lynden A.

Nanoparticle–polymer composites, or polymer–nanoparticle composites (PNCs), exhibit unusual mechanical and dynamical features when the particle size approaches the random coil dimensions of the host polymer. Here, we harness favourable enthalpic interactions between particle-tethered and free, host polymer chains to create model PNCs, in which spherical nanoparticles are uniformly dispersed in high molecular weight entangled polymers. Investigation of the mechanical properties of these model PNCs reveals that the nanoparticles have profound effects on the host polymer motions on all timescales. On short timescales, nanoparticles slow-down local dynamics of the host polymer segments and lower the glass transition temperature. On intermediate timescales,more » where polymer chain motion is typically constrained by entanglements with surrounding molecules, nanoparticles provide additional constraints, which lead to an early onset of entangled polymer dynamics. Finally, on long timescales, nanoparticles produce an apparent speeding up of relaxation of their polymer host.« less

Actively controlling coolant-cooled cold plate configuration

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

Chainer, Timothy J.; Parida, Pritish R.

A method is provided to facilitate active control of thermal and fluid dynamic performance of a coolant-cooled cold plate. The method includes: monitoring a variable associated with at least one of the coolant-cooled cold plate or one or more electronic components being cooled by the cold plate; and dynamically varying, based on the monitored variable, a physical configuration of the cold plate. By dynamically varying the physical configuration, the thermal and fluid dynamic performance of the cold plate are adjusted to, for example, optimally cool the one or more electronic components, and at the same time, reduce cooling power consumptionmore » used in cooling the electronic component(s). The physical configuration can be adjusted by providing one or more adjustable plates within the coolant-cooled cold plate, the positioning of which may be adjusted based on the monitored variable.« less

Non-orthogonal internally contracted multi-configurational perturbation theory (NICPT): Dynamic electron correlation for large, compact active spaces

NASA Astrophysics Data System (ADS)

Kähler, Sven; Olsen, Jeppe

2017-11-01

A computational method is presented for systems that require high-level treatments of static and dynamic electron correlation but cannot be treated using conventional complete active space self-consistent field-based methods due to the required size of the active space. Our method introduces an efficient algorithm for perturbative dynamic correlation corrections for compact non-orthogonal MCSCF calculations. In the algorithm, biorthonormal expansions of orbitals and CI-wave functions are used to reduce the scaling of the performance determining step from quadratic to linear in the number of configurations. We describe a hierarchy of configuration spaces that can be chosen for the active space. Potential curves for the nitrogen molecule and the chromium dimer are compared for different configuration spaces. Already the most compact spaces yield qualitatively correct potentials that with increasing size of configuration spaces systematically approach complete active space results.

Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium

PubMed Central

Grewe, Felix; Zhu, Andan; Mower, Jeffrey P.

2016-01-01

The mitochondrial nad1 gene of seed plants has a complex structure, including four introns in cis or trans configurations and a maturase gene (matR) hosted within the final intron. In the geranium family (Geraniaceae), however, sequencing of representative species revealed that three of the four introns, including one in a trans configuration and another that hosts matR, were lost from the nad1 gene in their common ancestor. Despite the loss of the host intron, matR has been retained as a freestanding gene in most genera of the family, indicating that this maturase has additional functions beyond the splicing of its host intron. In the common ancestor of Pelargonium, matR was transferred to the nuclear genome, where it was split into two unlinked genes that encode either its reverse transcriptase or maturase domain. Both nuclear genes are transcribed and contain predicted mitochondrial targeting signals, suggesting that they express functional proteins that are imported into mitochondria. The nuclear localization and split domain structure of matR in the Pelargonium nuclear genome offers a unique opportunity to assess the function of these two domains using transgenic approaches. PMID:27664178

In-memory interconnect protocol configuration registers

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

Cheng, Kevin Y.; Roberts, David A.

Systems, apparatuses, and methods for moving the interconnect protocol configuration registers into the main memory space of a node. The region of memory used for storing the interconnect protocol configuration registers may also be made cacheable to reduce the latency of accesses to the interconnect protocol configuration registers. Interconnect protocol configuration registers which are used during a startup routine may be prefetched into the host's cache to make the startup routine more efficient. The interconnect protocol configuration registers for various interconnect protocols may include one or more of device capability tables, memory-side statistics (e.g., to support two-level memory data mappingmore » decisions), advanced memory and interconnect features such as repair resources and routing tables, prefetching hints, error correcting code (ECC) bits, lists of device capabilities, set and store base address, capability, device ID, status, configuration, capabilities, and other settings.« less

Exploring the membrane fusion mechanism through force-induced disassembly of HIV-1 six-helix bundle

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

Gao, Kai; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101; University of Chinese Academy of Sciences, Beijing 100049

Enveloped virus, such as HIV-1, employs membrane fusion mechanism to invade into host cell. HIV-1 gp41 ectodomain uses six-helix bundle configuration to accomplish this process. Using molecular dynamic simulations, we confirmed the stability of this six-helix bundle by showing high occupancy of hydrogen bonds and hydrophobic interactions. Key residues and interactions important for the bundle integration were characterized by force-induced unfolding simulations of six-helix bundle, exhibiting the collapse order of these groups of interactions. Moreover, our results in some way concerted with a previous theory that the formation of coiled-coil choose a route which involved cooperative interactions between the N-terminalmore » and C-terminal helix. -- Highlights: •Unfolding of HIV-1 gp41 six-helix bundle is studied by molecular dynamics simulations. •Specific interactions responsible for the stability of HIV-1 envelope post-fusion conformation were identified. •The gp41 six-helix bundle transition inducing membrane fusion might be a cooperative process of the three subunits.« less

Viral antibody dynamics in a chiropteran host

PubMed Central

Baker, Kate S; Suu-Ire, Richard; Barr, Jennifer; Hayman, David T S; Broder, Christopher C; Horton, Daniel L; Durrant, Christopher; Murcia, Pablo R; Cunningham, Andrew A; Wood, James L N

2014-01-01

Bats host many viruses that are significant for human and domestic animal health, but the dynamics of these infections in their natural reservoir hosts remain poorly elucidated. In these, and other, systems, there is evidence that seasonal life-cycle events drive infection dynamics, directly impacting the risk of exposure to spillover hosts. Understanding these dynamics improves our ability to predict zoonotic spillover from the reservoir hosts. To this end, we followed henipavirus antibody levels of >100 individual E. helvum in a closed, captive, breeding population over a 30-month period, using a powerful novel antibody quantitation method. We demonstrate the presence of maternal antibodies in this system and accurately determine their longevity. We also present evidence of population-level persistence of viral infection and demonstrate periods of increased horizontal virus transmission associated with the pregnancy/lactation period. The novel findings of infection persistence and the effect of pregnancy on viral transmission, as well as an accurate quantitation of chiropteran maternal antiviral antibody half-life, provide fundamental baseline data for the continued study of viral infections in these important reservoir hosts. PMID:24111634

Single and multi-band electromagnetic induced transparency-like metamaterials with coupled split ring resonators

NASA Astrophysics Data System (ADS)

Bagci, Fulya; Akaoglu, Baris

2017-08-01

We present a metamaterial configuration exhibiting single and multi-band electromagnetic induced transparency (EIT)-like properties. The unit cell of the single band EIT-like metamaterial consists of a multi-split ring resonator surrounded by a split ring resonator. The multi-split ring resonator acts as a quasi-dark or dark resonator, depending on the polarization of the incident wave, and the split ring resonator serves as the bright resonator. Combination of these two resonators results in a single band EIT-like transmission inside the stop band. EIT-like transmission phenomenon is also clearly observed in the measured transmission spectrum at almost the same frequencies for vertical and horizontal polarized waves, and the numerical results are verified for normal incidence. Moreover, multi-band transmission windows are created within a wide band by combining the two slightly different single band EIT-like metamaterial unit cells that exhibit two different coupling strengths inside a supercell configuration. Group indices as high as 123 for single band and 488 for tri-band transmission, accompanying with high transmission rates (over 80%), are achieved, rendering the metamaterial very suitable for multi-band slow light applications. It is shown that the group delay of the propagating wave can be increased and dynamically controlled by changing the polarization angle. Multi-band EIT-like transmission is also verified experimentally, and a good agreement with simulations is obtained. The proposed novel methodology for obtaining multi-band EIT, which takes advantage of a supercell configuration by hosting slightly different configured unit cells, can be utilized for easily formation and manipulation of multi-band transmission windows inside a stop band.

Host-parasite oscillation dynamics and evolution in a compartmentalized RNA replication system.

PubMed

Bansho, Yohsuke; Furubayashi, Taro; Ichihashi, Norikazu; Yomo, Tetsuya

2016-04-12

To date, various cellular functions have been reconstituted in vitro such as self-replication systems using DNA, RNA, and proteins. The next important challenges include the reconstitution of the interactive networks of self-replicating species and investigating how such interactions generate complex ecological behaviors observed in nature. Here, we synthesized a simple replication system composed of two self-replicating host and parasitic RNA species. We found that the parasitic RNA eradicates the host RNA under bulk conditions; however, when the system is compartmentalized, a continuous oscillation pattern in the population dynamics of the two RNAs emerges. The oscillation pattern changed as replication proceeded mainly owing to the evolution of the host RNA. These results demonstrate that a cell-like compartment plays an important role in host-parasite ecological dynamics and suggest that the origin of the host-parasite coevolution might date back to the very early stages of the evolution of life.

Vector-Borne Pathogen and Host Evolution in a Structured Immuno-Epidemiological System.

PubMed

Gulbudak, Hayriye; Cannataro, Vincent L; Tuncer, Necibe; Martcheva, Maia

2017-02-01

Vector-borne disease transmission is a common dissemination mode used by many pathogens to spread in a host population. Similar to directly transmitted diseases, the within-host interaction of a vector-borne pathogen and a host's immune system influences the pathogen's transmission potential between hosts via vectors. Yet there are few theoretical studies on virulence-transmission trade-offs and evolution in vector-borne pathogen-host systems. Here, we consider an immuno-epidemiological model that links the within-host dynamics to between-host circulation of a vector-borne disease. On the immunological scale, the model mimics antibody-pathogen dynamics for arbovirus diseases, such as Rift Valley fever and West Nile virus. The within-host dynamics govern transmission and host mortality and recovery in an age-since-infection structured host-vector-borne pathogen epidemic model. By considering multiple pathogen strains and multiple competing host populations differing in their within-host replication rate and immune response parameters, respectively, we derive evolutionary optimization principles for both pathogen and host. Invasion analysis shows that the [Formula: see text] maximization principle holds for the vector-borne pathogen. For the host, we prove that evolution favors minimizing case fatality ratio (CFR). These results are utilized to compute host and pathogen evolutionary trajectories and to determine how model parameters affect evolution outcomes. We find that increasing the vector inoculum size increases the pathogen [Formula: see text], but can either increase or decrease the pathogen virulence (the host CFR), suggesting that vector inoculum size can contribute to virulence of vector-borne diseases in distinct ways.

A Comparison of Combustion Dynamics for Multiple 7-Point Lean Direct Injection Combustor Configurations

NASA Technical Reports Server (NTRS)

Tacina, Kathleen M.; Hicks, Yolanda R.

2017-01-01

The combustion dynamics of two 7-point lean direct injection (LDI) combustor configurations are compared. This 7-point LDI configuration has a circular cross section, with a center ("pilot") fuel-air mixer surrounded by six outer ("main") fuel-air mixers. Each fuel-air mixer consists of an axial air swirler followed by a converging-diverging venturi. A simplex fuel injector is inserted through the center of the air swirler, with the fuel injector tip located near the venturi throat. All 7 fuel-air mixers are identical except for the swirler blade angle. In the 'all-60' configuration, the swirler blade angle was 60 deg for all fuel-air mixers. In the '45-60' configuration, the swirler blade angle was 60 deg on the center and 45 deg on the outer fuel-air mixers. Testing was done in a 5-atm flame tube with inlet air temperatures from 630 to 830 F and equivalence ratios from 0.2 to 0.7. Combustion dynamics were measured using a cooled PCB pressure transducer flush-mounted in the wall of the combustor test section. Both configurations had large pressure fluctuations (greater than 2 psi peak-peak) near 730 Hz, the quarter-wave frequency. The all-60 configuration also had large pressure fluctuations near 1170 Hz; the 45-60 configuration did not. The 45-60 configuration had large pressure fluctuations near 480 Hz; the all-60 configuration did not.

A Multicontrolled Enamine Configurational Switch Undergoing Dynamic Constitutional Exchange.

PubMed

Ren, Yansong; Svensson, Per H; Ramström, Olof

2018-05-22

A multiresponsive enamine-based molecular switch is presented, in which forward/backward configurational rotation around the C=C bond could be precisely controlled by the addition of an acid/base or metal ions. Fluorescence turn-on/off effects and large Stokes shifts were observed while regulating the switching process with Cu II . The enamine functionality furthermore enabled double dynamic regimes, in which configurational switching could operate in conjunction with constitutional enamine exchange of the rotor part. This behavior was used to construct a prototypical dynamic covalent switch system through enamine exchange with primary amines. The dynamic exchange process could be readily turned on/off by regulating the switch status with pH. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Critical thresholds in sea lice epidemics: evidence, sensitivity and subcritical estimation

PubMed Central

Frazer, L. Neil; Morton, Alexandra; Krkošek, Martin

2012-01-01

Host density thresholds are a fundamental component of the population dynamics of pathogens, but empirical evidence and estimates are lacking. We studied host density thresholds in the dynamics of ectoparasitic sea lice (Lepeophtheirus salmonis) on salmon farms. Empirical examples include a 1994 epidemic in Atlantic Canada and a 2001 epidemic in Pacific Canada. A mathematical model suggests dynamics of lice are governed by a stable endemic equilibrium until the critical host density threshold drops owing to environmental change, or is exceeded by stocking, causing epidemics that require rapid harvest or treatment. Sensitivity analysis of the critical threshold suggests variation in dependence on biotic parameters and high sensitivity to temperature and salinity. We provide a method for estimating the critical threshold from parasite abundances at subcritical host densities and estimate the critical threshold and transmission coefficient for the two epidemics. Host density thresholds may be a fundamental component of disease dynamics in coastal seas where salmon farming occurs. PMID:22217721

Spatiotemporal model of barley and cereal yellow dwarf virus transmission dynamics with seasonality and plant competition

Treesearch

S.M. Moore; C.A. Manore; V.A. Bokil; E.T. Borer; P.R. Hosseini

2011-01-01

Many generalist pathogens are influenced by the spatial distributions and relative abundances of susceptible host species. The spatial structure of host populations can influence patterns of infection incidence (or disease outbreaks), and the effects of a generalist pathogen on host community dynamics in a spatially heterogeneous community may differ from predictions...

Measurement configuration optimization for dynamic metrology using Stokes polarimetry

NASA Astrophysics Data System (ADS)

Liu, Jiamin; Zhang, Chuanwei; Zhong, Zhicheng; Gu, Honggang; Chen, Xiuguo; Jiang, Hao; Liu, Shiyuan

2018-05-01

As dynamic loading experiments such as a shock compression test are usually characterized by short duration, unrepeatability and high costs, high temporal resolution and precise accuracy of the measurements is required. Due to high temporal resolution up to a ten-nanosecond-scale, a Stokes polarimeter with six parallel channels has been developed to capture such instantaneous changes in optical properties in this paper. Since the measurement accuracy heavily depends on the configuration of the probing beam incident angle and the polarizer azimuth angle, it is important to select an optimal combination from the numerous options. In this paper, a systematic error propagation-based measurement configuration optimization method corresponding to the Stokes polarimeter was proposed. The maximal Frobenius norm of the combinatorial matrix of the configuration error propagating matrix and the intrinsic error propagating matrix is introduced to assess the measurement accuracy. The optimal configuration for thickness measurement of a SiO2 thin film deposited on a Si substrate has been achieved by minimizing the merit function. Simulation and experimental results show a good agreement between the optimal measurement configuration achieved experimentally using the polarimeter and the theoretical prediction. In particular, the experimental result shows that the relative error in the thickness measurement can be reduced from 6% to 1% by using the optimal polarizer azimuth angle when the incident angle is 45°. Furthermore, the optimal configuration for the dynamic metrology of a nickel foil under quasi-dynamic loading is investigated using the proposed optimization method.

Spin-orbital Tidal Dynamics and Tidal Heating in the TRAPPIST-1 Multiplanet System

NASA Astrophysics Data System (ADS)

Makarov, Valeri V.; Berghea, Ciprian T.; Efroimsky, Michael

2018-04-01

We perform numerical simulations of the TRAPPIST-1 system of seven exoplanets orbiting a nearby M dwarf, starting with a previously suggested stable configuration. The long-term stability of this configuration is confirmed, but the motion of planets is found to be chaotic. The eccentricity values are found to vary within finite ranges. The rates of tidal dissipation and tidal evolution of orbits are estimated, assuming an Earth-like rheology for the planets. We find that under this assumption, the planets b, d, and e were captured in the 3:2 or higher spin–orbit resonances during the initial spin-down, but slipped further down into the 1:1 resonance. Depending on its rheology, the innermost planet b may be captured in a stable pseudosynchronous rotation. Nonsynchronous rotation ensures higher levels of tidal dissipation and internal heating. The positive feedback between the viscosity and the dissipation rate—and the ensuing runaway heating—are terminated by a few self-regulation processes. When the temperature is high and the viscosity is low enough, the planet spontaneously leaves the 3:2 resonance. Further heating is stopped either by passing the peak dissipation or by the emergence of partial melt in the mantle. In the post-solidus state, the tidal dissipation is limited to the levels supported by the heat transfer efficiency. The tides on the host star are unlikely to have had a significant dynamical impact. The tides on the synchronized inner planets tend to reduce these planets’ orbital eccentricity, possibly contributing thereby to the system’s stability.

A Scalable, Out-of-Band Diagnostics Architecture for International Space Station Systems Support

NASA Technical Reports Server (NTRS)

Fletcher, Daryl P.; Alena, Rick; Clancy, Daniel (Technical Monitor)

2002-01-01

The computational infrastructure of the International Space Station (ISS) is a dynamic system that supports multiple vehicle subsystems such as Caution and Warning, Electrical Power Systems and Command and Data Handling (C&DH), as well as scientific payloads of varying size and complexity. The dynamic nature of the ISS configuration coupled with the increased demand for payload support places a significant burden on the inherently resource constrained computational infrastructure of the ISS. Onboard system diagnostics applications are hosted on computers that are elements of the avionics network while ground-based diagnostic applications receive only a subset of available telemetry, down-linked via S-band communications. In this paper we propose a scalable, out-of-band diagnostics architecture for ISS systems support that uses a read-only connection for C&DH data acquisition, which provides a lower cost of deployment and maintenance (versus a higher criticality readwrite connection). The diagnostics processing burden is off-loaded from the avionics network to elements of the on-board LAN that have a lower overall cost of operation and increased computational capacity. A superset of diagnostic data, richer in content than the configured telemetry, is made available to Advanced Diagnostic System (ADS) clients running on wireless handheld devices, affording the crew greater mobility for troubleshooting and providing improved insight into vehicle state. The superset of diagnostic data is made available to the ground in near real-time via an out-of band downlink, providing a high level of fidelity between vehicle state and test, training and operational facilities on the ground.

On the Morphology of a Growing City: A Heuristic Experiment Merging Static Economics with Dynamic Geography.

PubMed

Delloye, Justin; Peeters, Dominique; Thomas, Isabelle

2015-01-01

In this paper, we aim at exploring how individual location decisions affect the shape of a growing city and, more precisely, how they may add up to a configuration that diverges from equilibrium configurations formulated ex-ante. To do so, we provide a two-sector city model merging a static equilibrium analysis with agent-based simulations. Results show that under strong agglomeration effects, urban development is monotonic and ends up with circular, monocentric long-term configurations. For low agglomeration effects however, elongated and multicentric urban configurations may emerge. The occurrence and underlying dynamics of these configurations are also discussed regarding commuting costs and the distance-decay of agglomeration economies between firms. To sum up, our paper warns urban planning policy makers against the difference that may stand between appropriate long-term perspectives, represented here by analytic equilibrium configurations, and short-term urban configurations, simulated here by a multi-agent system.

Characterizing rare-event property distributions via replicate molecular dynamics simulations of proteins.

PubMed

Krishnan, Ranjani; Walton, Emily B; Van Vliet, Krystyn J

2009-11-01

As computational resources increase, molecular dynamics simulations of biomolecules are becoming an increasingly informative complement to experimental studies. In particular, it has now become feasible to use multiple initial molecular configurations to generate an ensemble of replicate production-run simulations that allows for more complete characterization of rare events such as ligand-receptor unbinding. However, there are currently no explicit guidelines for selecting an ensemble of initial configurations for replicate simulations. Here, we use clustering analysis and steered molecular dynamics simulations to demonstrate that the configurational changes accessible in molecular dynamics simulations of biomolecules do not necessarily correlate with observed rare-event properties. This informs selection of a representative set of initial configurations. We also employ statistical analysis to identify the minimum number of replicate simulations required to sufficiently sample a given biomolecular property distribution. Together, these results suggest a general procedure for generating an ensemble of replicate simulations that will maximize accurate characterization of rare-event property distributions in biomolecules.

A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host-Pathogen Interaction Networks.

PubMed

Wu, Chia-Chou; Chen, Bor-Sen

2016-01-01

Infected zebrafish coordinates defensive and offensive molecular mechanisms in response to Candida albicans infections, and invasive C. albicans coordinates corresponding molecular mechanisms to interact with the host. However, knowledge of the ensuing infection-activated signaling networks in both host and pathogen and their interspecific crosstalk during the innate and adaptive phases of the infection processes remains incomplete. In the present study, dynamic network modeling, protein interaction databases, and dual transcriptome data from zebrafish and C. albicans during infection were used to infer infection-activated host-pathogen dynamic interaction networks. The consideration of host-pathogen dynamic interaction systems as innate and adaptive loops and subsequent comparisons of inferred innate and adaptive networks indicated previously unrecognized crosstalk between known pathways and suggested roles of immunological memory in the coordination of host defensive and offensive molecular mechanisms to achieve specific and powerful defense against pathogens. Moreover, pathogens enhance intraspecific crosstalk and abrogate host apoptosis to accommodate enhanced host defense mechanisms during the adaptive phase. Accordingly, links between physiological phenomena and changes in the coordination of defensive and offensive molecular mechanisms highlight the importance of host-pathogen molecular interaction networks, and consequent inferences of the host-pathogen relationship could be translated into biomedical applications.

Who acquires infection from whom and how? Disentangling multi-host and multi-mode transmission dynamics in the ‘elimination’ era

PubMed Central

Borlase, Anna; Rudge, James W.

2017-01-01

Multi-host infectious agents challenge our abilities to understand, predict and manage disease dynamics. Within this, many infectious agents are also able to use, simultaneously or sequentially, multiple modes of transmission. Furthermore, the relative importance of different host species and modes can itself be dynamic, with potential for switches and shifts in host range and/or transmission mode in response to changing selective pressures, such as those imposed by disease control interventions. The epidemiology of such multi-host, multi-mode infectious agents thereby can involve a multi-faceted community of definitive and intermediate/secondary hosts or vectors, often together with infectious stages in the environment, all of which may represent potential targets, as well as specific challenges, particularly where disease elimination is proposed. Here, we explore, focusing on examples from both human and animal pathogen systems, why and how we should aim to disentangle and quantify the relative importance of multi-host multi-mode infectious agent transmission dynamics under contrasting conditions, and ultimately, how this can be used to help achieve efficient and effective disease control. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289259

Environment overwhelms both nature and nurture in a model spin glass

NASA Astrophysics Data System (ADS)

Middleton, A. Alan; Yang, Jie

We are interested in exploring what information determines the particular history of the glassy long term dynamics in a disordered material. We study the effect of initial configurations and the realization of stochastic dynamics on the long time evolution of configurations in a two-dimensional Ising spin glass model. The evolution of nearest neighbor correlations is computed using patchwork dynamics, a coarse-grained numerical heuristic for temporal evolution. The dependence of the nearest neighbor spin correlations at long time on both initial spin configurations and noise histories are studied through cross-correlations of long-time configurations and the spin correlations are found to be independent of both. We investigate how effectively rigid bond clusters coarsen. Scaling laws are used to study the convergence of configurations and the distribution of sizes of nearly rigid clusters. The implications of the computational results on simulations and phenomenological models of spin glasses are discussed. We acknowledge NSF support under DMR-1410937 (CMMT program).

Responsive Guest Encapsulation of Dynamic Conjugated Microporous Polymers.

PubMed

Xu, Lai; Li, Youyong

2016-06-30

The host-guest complexes of conjugated microporous polymers encapsulating C60 and dye molecules have been investigated systematically. The orientation of guest molecules inside the cavities, have different terms: inside the open cavities of the polymer, or inside the cavities formed by packing different polymers. The host backbone shows responsive dynamic behavior in order to accommodate the size and shape of incoming guest molecule or guest aggregates. Simulations show that the host-guest binding of conjugated polymers is stronger than that of non-conjugated polymers. This detailed study could provide a clear picture for the host-guest interaction for dynamic conjugated microporous polymers. The mechanism obtained could guide designing new conjugated microporous polymers.

Bacterial effectors target the plant cell nucleus to subvert host transcription.

PubMed

Canonne, Joanne; Rivas, Susana

2012-02-01

In order to promote virulence, Gram-negative bacteria have evolved the ability to inject so-called type III effector proteins into host cells. The plant cell nucleus appears to be a subcellular compartment repeatedly targeted by bacterial effectors. In agreement with this observation, mounting evidence suggests that manipulation of host transcription is a major strategy developed by bacteria to counteract plant defense responses. It has been suggested that bacterial effectors may adopt at least three alternative, although not mutually exclusive, strategies to subvert host transcription. T3Es may (1) act as transcription factors that directly activate transcription in host cells, (2) affect histone packing and chromatin configuration, and/or (3) target host transcription factor activity. Here, we provide an overview on how all these strategies may lead to host transcriptional re-programming and, as a result, to improved bacterial multiplication inside plant cells.

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

Li, Yun; Kouwenhoven, M. B. N.; Stamatellos, D.

The origin of very low-mass hydrogen-burning stars, brown dwarfs (BDs), and planetary-mass objects (PMOs) at the low-mass end of the initial mass function is not yet fully understood. Gravitational fragmentation of circumstellar disks provides a possible mechanism for the formation of such low-mass objects. The kinematic and binary properties of very low-mass objects formed through disk fragmentation at early times (<10 Myr) were discussed in our previous paper. In this paper we extend the analysis by following the long-term evolution of disk-fragmented systems up to an age of 10 Gyr, covering the ages of the stellar and substellar populations inmore » the Galactic field. We find that the systems continue to decay, although the rates at which companions escape or collide with each other are substantially lower than during the first 10 Myr, and that dynamical evolution is limited beyond 1 Gyr. By t = 10 Gyr, about one third of the host stars are single, and more than half have only one companion left. Most of the other systems have two companions left that orbit their host star in widely separated orbits. A small fraction of companions have formed binaries that orbit the host star in a hierarchical triple configuration. The majority of such double-companion systems have internal orbits that are retrograde with respect to their orbits around their host stars. Our simulations allow a comparison between the predicted outcomes of disk fragmentation with the observed low-mass hydrogen-burning stars, BDs, and PMOs in the solar neighborhood. Imaging and radial velocity surveys for faint binary companions among nearby stars are necessary for verification or rejection of the formation mechanism proposed in this paper.« less

Universality of human microbial dynamics

NASA Astrophysics Data System (ADS)

Bashan, Amir; Gibson, Travis E.; Friedman, Jonathan; Carey, Vincent J.; Weiss, Scott T.; Hohmann, Elizabeth L.; Liu, Yang-Yu

2016-06-01

Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies—the Human Microbiome Project and the Student Microbiome Project—we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.

Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales

PubMed Central

Lokmer, Ana; Goedknegt, M. Anouk; Thieltges, David W.; Fiorentino, Dario; Kuenzel, Sven; Baines, John F.; Wegner, K. Mathias

2016-01-01

Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics. PMID:27630625

Performance monitoring for new phase dynamic optimization of instruction dispatch cluster configuration

DOEpatents

Balasubramonian, Rajeev [Sandy, UT; Dwarkadas, Sandhya [Rochester, NY; Albonesi, David [Ithaca, NY

2012-01-24

In a processor having multiple clusters which operate in parallel, the number of clusters in use can be varied dynamically. At the start of each program phase, the configuration option for an interval is run to determine the optimal configuration, which is used until the next phase change is detected. The optimum instruction interval is determined by starting with a minimum interval and doubling it until a low stability factor is reached.

Dynamic intervention: pathogen disarmament of mitochondrial-based immune surveillance.

PubMed

Holland, Robin L; Blanke, Steven R

2014-11-12

In this issue of Cell Host & Microbe, Suzuki et al. (2014) describe a Vibrio cholerae Type-III-secreted effector that targets mitochondrial dynamics to dampen host innate immune signaling. This suggests that mammalian hosts possess surveillance mechanisms to monitor pathogen-mediated alterations in the integrity of normal cellular processes and organelles. Copyright © 2014 Elsevier Inc. All rights reserved.

Advanced Wireless Integrated Navy Network - AWINN

DTIC Science & Technology

2005-09-30

progress report No. 3 on AWINN hardware and software configurations of smart , wideband, multi-function antennas, secure configurable platform, close-in...results to the host PC via a UART soft core. The UART core used is a proprietary Xilinx core which incorporates features described in National...current software uses wheel odometry and visual landmarks to create a map and estimate position on an internal x, y grid . The wheel odometry provides a

Vorticity Dynamics in Single and Multiple Swirling Reacting Jets

NASA Astrophysics Data System (ADS)

Smith, Travis; Aguilar, Michael; Emerson, Benjamin; Noble, David; Lieuwen, Tim

2015-11-01

This presentation describes an analysis of the unsteady flow structures in two multinozzle swirling jet configurations. This work is motivated by the problem of combustion instabilities in premixed flames, a major concern in the development of modern low NOx combustors. The objective is to compare the unsteady flow structures in these two configurations for two separate geometries and determine how certain parameters, primarily distance between jets, influence the flow dynamics. The analysis aims to differentiate between the flow dynamics of single nozzle and triple nozzle configurations. This study looks at how the vorticity in the shear layers of one reacting swirling jet can affect the dynamics of a nearby similar jet. The distance between the swirling jets is found to have an effect on the flow field in determining where swirling jets merge and on the dynamics upstream of the merging location. Graduate Student, School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, GA.

Analytic Patch Configuration (APC) gateway version 1.0 user's guide

NASA Technical Reports Server (NTRS)

Bingel, Bradford D.

1990-01-01

The Analytic Patch Configuration (APC) is an interactive software tool which translates aircraft configuration geometry files from one format into another. This initial release of the APC Gateway accommodates six formats: the four accepted APC formats (89f, 89fd, 89u, and 89ud), the PATRAN 2.x phase 1 neutral file format, and the Integrated Aerodynamic Analysis System (IAAS) General Geometry (GG) format. Written in ANSI FORTRAN 77 and completely self-contained, the APC Gateway is very portable and was already installed on CDC/NOS, VAX/VMS, SUN, SGI/IRIS, CONVEX, and GRAY hosts.

Transonic static and dynamic stability characteristics of a finned projectile configuration

NASA Technical Reports Server (NTRS)

Boyden, R. P.; Brooks, C. W., Jr.; Davenport, E. E.

1978-01-01

Static and dynamic stability tests were made of a finned projectile configuration with the aft-mounted fins arranged in a cruciform pattern. The tests were made at free stream Mach numbers of 0.7, 0.9, 1.1, and 1.2 in the Langley 8-foot transonic pressure tunnel. Some of the parameters measured during the tests were lift, drag, pitching moment, pitch damping, and roll damping. Configurations tested included the body with undeflected fins, the body with various fin deflections for control, and the body with fins removed. Theoretical estimates of the stability derivatives were made for the fins on configuration.

Mathematical modeling of shell configurations made of homogeneous and composite materials experiencing intensive short actions and large displacements

NASA Astrophysics Data System (ADS)

Khairnasov, K. Z.

2018-04-01

The paper presents a mathematical model for solving the problem of behavior of shell configurations under the action of static and dynamic impacts. The problem is solved in geometrically nonlinear statement with regard to the finite element method. The composite structures with different material layers are considered. The obtained equations are used to study the behavior of shell configurations under the action of dynamic loads. The results agree well with the experimental data.

Plague epizootic cycles in Central Asia.

PubMed

Reijniers, Jonas; Begon, Mike; Ageyev, Vladimir S; Leirs, Herwig

2014-06-01

Infection thresholds, widely used in disease epidemiology, may operate on host abundance and, if present, on vector abundance. For wildlife populations, host and vector abundances often vary greatly across years and consequently the threshold may be crossed regularly, both up- and downward. Moreover, vector and host abundances may be interdependent, which may affect the infection dynamics. Theory predicts that if the relevant abundance, or combination of abundances, is above the threshold, then the infection is able to spread; if not, it is bound to fade out. In practice, though, the observed level of infection may depend more on past than on current abundances. Here, we study the temporal dynamics of plague (Yersinia pestis infection), its vector (flea) and its host (great gerbil) in the PreBalkhash region in Kazakhstan. We describe how host and vector abundances interact over time and how this interaction drives the dynamics of the system around the infection threshold, consequently affecting the proportion of plague-infected sectors. We also explore the importance of the interplay between biological and detectability delays in generating the observed dynamics.

The contribution of dynamic visual cues to audiovisual speech perception.

PubMed

Jaekl, Philip; Pesquita, Ana; Alsius, Agnes; Munhall, Kevin; Soto-Faraco, Salvador

2015-08-01

Seeing a speaker's facial gestures can significantly improve speech comprehension, especially in noisy environments. However, the nature of the visual information from the speaker's facial movements that is relevant for this enhancement is still unclear. Like auditory speech signals, visual speech signals unfold over time and contain both dynamic configural information and luminance-defined local motion cues; two information sources that are thought to engage anatomically and functionally separate visual systems. Whereas, some past studies have highlighted the importance of local, luminance-defined motion cues in audiovisual speech perception, the contribution of dynamic configural information signalling changes in form over time has not yet been assessed. We therefore attempted to single out the contribution of dynamic configural information to audiovisual speech processing. To this aim, we measured word identification performance in noise using unimodal auditory stimuli, and with audiovisual stimuli. In the audiovisual condition, speaking faces were presented as point light displays achieved via motion capture of the original talker. Point light displays could be isoluminant, to minimise the contribution of effective luminance-defined local motion information, or with added luminance contrast, allowing the combined effect of dynamic configural cues and local motion cues. Audiovisual enhancement was found in both the isoluminant and contrast-based luminance conditions compared to an auditory-only condition, demonstrating, for the first time the specific contribution of dynamic configural cues to audiovisual speech improvement. These findings imply that globally processed changes in a speaker's facial shape contribute significantly towards the perception of articulatory gestures and the analysis of audiovisual speech. Copyright © 2015 Elsevier Ltd. All rights reserved.

Relative host body condition and food availability influence epidemic dynamics: a Poecilia reticulata-Gyrodactylus turnbulli host-parasite model.

PubMed

Tadiri, Christina P; Dargent, Felipe; Scott, Marilyn E

2013-03-01

Understanding disease transmission is important to species management and human health. Host body condition, nutrition and disease susceptibility interact in a complex manner, and while the individual effects of these variables are well known, our understanding of how they interact and translate to population dynamics is limited. Our objective was to determine whether host relative body condition influences epidemic dynamics, and how this relationship is affected by food availability. Poecilia reticulata (guppies) of roughly similar size were selected and assembled randomly into populations of 10 guppies assigned to 3 different food availability treatments, and the relative condition index (Kn) of each fish was calculated. We infected 1 individual per group ('source' fish) with Gyrodactyus turnbulli and counted parasites on each fish every other day for 10 days. Epidemic parameters for each population were analysed using generalized linear models. High host Kn-particularly that of the 'source' fish-exerted a positive effect on incidence, peak parasite burden, and the degree of parasite aggregation. Low food availability increased the strength of the associations with peak burden and aggregation. Our findings suggest that host Kn and food availability interact to influence epidemic dynamics, and that the condition of the individual that brings the parasite into the host population has a profound impact on the spread of infection.

Networking for large-scale science: infrastructure, provisioning, transport and application mapping

NASA Astrophysics Data System (ADS)

Rao, Nageswara S.; Carter, Steven M.; Wu, Qishi; Wing, William R.; Zhu, Mengxia; Mezzacappa, Anthony; Veeraraghavan, Malathi; Blondin, John M.

2005-01-01

Large-scale science computations and experiments require unprecedented network capabilities in the form of large bandwidth and dynamically stable connections to support data transfers, interactive visualizations, and monitoring and steering operations. A number of component technologies dealing with the infrastructure, provisioning, transport and application mappings must be developed and/or optimized to achieve these capabilities. We present a brief account of the following technologies that contribute toward achieving these network capabilities: (a) DOE UltraScienceNet and NSF CHEETAH network testbeds that provide on-demand and scheduled dedicated network connections; (b) experimental results on transport protocols that achieve close to 100% utilization on dedicated 1Gbps wide-area channels; (c) a scheme for optimally mapping a visualization pipeline onto a network to minimize the end-to-end delays; and (d) interconnect configuration and protocols that provides multiple Gbps flows from Cray X1 to external hosts.

Multiplex PCR-Based Next-Generation Sequencing and Global Diversity of Seoul Virus in Humans and Rats.

PubMed

Kim, Won-Keun; No, Jin Sun; Lee, Seung-Ho; Song, Dong Hyun; Lee, Daesang; Kim, Jeong-Ah; Gu, Se Hun; Park, Sunhye; Jeong, Seong Tae; Kim, Heung-Chul; Klein, Terry A; Wiley, Michael R; Palacios, Gustavo; Song, Jin-Won

2018-02-01

Seoul virus (SEOV) poses a worldwide public health threat. This virus, which is harbored by Rattus norvegicus and R. rattus rats, is the causative agent of hemorrhagic fever with renal syndrome (HFRS) in humans, which has been reported in Asia, Europe, the Americas, and Africa. Defining SEOV genome sequences plays a critical role in development of preventive and therapeutic strategies against the unique worldwide hantavirus. We applied multiplex PCR-based next-generation sequencing to obtain SEOV genome sequences from clinical and reservoir host specimens. Epidemiologic surveillance of R. norvegicus rats in South Korea during 2000-2016 demonstrated that the serologic prevalence of enzootic SEOV infections was not significant on the basis of sex, weight (age), and season. Viral loads of SEOV in rats showed wide dissemination in tissues and dynamic circulation among populations. Phylogenetic analyses showed the global diversity of SEOV and possible genomic configuration of genetic exchanges.

Tidal disruption of fuzzy dark matter subhalo cores

NASA Astrophysics Data System (ADS)

Du, Xiaolong; Schwabe, Bodo; Niemeyer, Jens C.; Bürger, David

2018-03-01

We study tidal stripping of fuzzy dark matter (FDM) subhalo cores using simulations of the Schrödinger-Poisson equations and analyze the dynamics of tidal disruption, highlighting the differences with standard cold dark matter. Mass loss outside of the tidal radius forces the core to relax into a less compact configuration, lowering the tidal radius. As the characteristic radius of a solitonic core scales inversely with its mass, tidal stripping results in a runaway effect and rapid tidal disruption of the core once its central density drops below 4.5 times the average density of the host within the orbital radius. Additionally, we find that the core is deformed into a tidally locked ellipsoid with increasing eccentricities until it is completely disrupted. Using the core mass loss rate, we compute the minimum mass of cores that can survive several orbits for different FDM particle masses and compare it with observed masses of satellite galaxies in the Milky Way.

Head-on collision of multistate ultralight BEC dark matter configurations

NASA Astrophysics Data System (ADS)

Guzmán, F. S.; Avilez, Ana A.

2018-06-01

Density profiles of ultralight Bose-condensate dark matter inferred from numerical simulations of structure formation, ruled by the Gross-Pitaevskii-Poisson (GPP) system of equations, have a core-tail structure. Multistate equilibrium configurations of the GPP system, on the other hand, have a similar core-tail density profile. We now submit these multistate configurations to highly dynamical scenarios and show their potential as providers of appropriate density profiles of structures. We present the simulation of head-on collisions between two equilibrium configurations of the GPP system of equations, including the collision of ground state with multistate configurations. We study the regimes of solitonic and merger behavior and show generic properties of the dynamics of the system, including the relaxation process and attractor density profiles. We show that the merger of multistate configurations has the potential to produce core-tail density profiles, with the core dominated by the ground state and the halo dominated by an additional state.

Fixed-axis electric sail deployment dynamics analysis using hub-mounted momentum control

NASA Astrophysics Data System (ADS)

Fulton, JoAnna; Schaub, Hanspeter

2018-03-01

The deployment dynamics of a spin stabilized electric sail (E-sail) with a hub-mounted control actuator are investigated. Both radial and tangential deployment mechanisms are considered to take the electric sail from a post-launch stowed configuration to a fully deployed configuration. The tangential configuration assumes the multi-kilometer tethers are wound up on the exterior of the spacecraft hub, similar to yo-yo despinner configurations. The deployment speed is controlled through the hub rate. The radial deployment configuration assumes each tether is on its own spool. Here both the hub and spool rate are control variables. The sensitivity of the deployment behavior to E-sail length, maximum rate and tension parameters is investigated. A constant hub rate deployment is compared to a time varying hub rate that maintains a constant tether tension condition. The deployment time can be reduced by a factor of 2 or more by using a tension controlled deployment configuration.

Low-speed static and dynamic force tests of a generic supersonic cruise fighter configuration

NASA Technical Reports Server (NTRS)

Hahne, David E.

1989-01-01

Static and dynamic force tests of a generic fighter configuration designed for sustained supersonic flight were conducted in the Langley 30- by 60-foot tunnel. The baseline configuration had a 65 deg arrow wing, twin wing mounted vertical tails and a canard. Results showed that control was available up to C sub L,max (maximum lift coefficient) from aerodynamic controls about all axes but control in the pitch and yaw axes decreased rapidly in the post-stall angle-of-attack region. The baseline configuration showed stable lateral-directional characteristics at low angles of attack but directional stability occurred near alpha = 25 deg as the wing shielded the vertical tails. The configuration showed positive effective dihedral throughout the test angle-of-attack range. Forced oscillation tests indicated that the baseline configuration had stable damping characteristics about the lateral-directional axes.

Comparison of Rolling Moment Characteristics During Roll Oscillations for a Low and a High Aspect Ratio Configuration

NASA Technical Reports Server (NTRS)

Brandon, Jay M.; Foster, John V.; Shah, Gautam H.; Gato, William; Wilborn, James E.

2004-01-01

Improvements in testing and modeling of nonlinear and unsteady aerodynamic effects for flight dynamics predictions of vehicle performance is critical to enable the design and implementation of new, innovative vehicle concepts. Any configuration which exhibits significant flow separation, nonlinear aerodynamics, control interactions or attempts maneuvering through one or more conditions such as these is, at present, a challenge to test, model or predict flight dynamic responses prior to flight. Even in flight test experiments, adequate models are not available to study and characterize the complex nonlinear and time-dependent flow effects occurring during portions of the maneuvering envelope. Traditionally, airplane designs have been conducted to avoid these areas of the flight envelope. Better understanding and characterization of these flight regimes may not only reduce risk and cost of flight test development programs, but also may pave the way for exploitation of those characteristics that increase airplane capabilities. One of the hurdles is that the nonlinear/unsteady effects appear to be configuration dependent. This paper compares some of the dynamic aerodynamic stability characteristics of two very different configurations - representative of a fighter and a transport airplane - during dynamic body-axis roll wind tunnel tests. The fighter model shows significant effects of oscillation frequency which are not as apparent for the transport configuration.

On the Morphology of a Growing City: A Heuristic Experiment Merging Static Economics with Dynamic Geography

PubMed Central

Delloye, Justin; Peeters, Dominique; Thomas, Isabelle

2015-01-01

In this paper, we aim at exploring how individual location decisions affect the shape of a growing city and, more precisely, how they may add up to a configuration that diverges from equilibrium configurations formulated ex-ante. To do so, we provide a two-sector city model merging a static equilibrium analysis with agent-based simulations. Results show that under strong agglomeration effects, urban development is monotonic and ends up with circular, monocentric long-term configurations. For low agglomeration effects however, elongated and multicentric urban configurations may emerge. The occurrence and underlying dynamics of these configurations are also discussed regarding commuting costs and the distance-decay of agglomeration economies between firms. To sum up, our paper warns urban planning policy makers against the difference that may stand between appropriate long-term perspectives, represented here by analytic equilibrium configurations, and short-term urban configurations, simulated here by a multi-agent system. PMID:26308858

Host-Guest Assembly of a Molecular Reporter with Chiral Cyanohydrins for Assignment of Absolute Stereochemistry.

PubMed

Gholami, Hadi; Anyika, Mercy; Zhang, Jun; Vasileiou, Chrysoula; Borhan, Babak

2016-06-27

The absolute stereochemistry of cyanohydrins, derived from ketones and aldehydes, is obtained routinely, in a microscale and derivatization-free manner, upon their complexation with Zn-MAPOL, a zincated porphyrin host with a binding pocket comprised of a biphenol core. The host-guest complex leads to observable exciton-coupled circular dichroism (ECCD), the sign of which is easily correlated to the absolute stereochemistry of the bound cyanohydrin. A working model, based on the ECCD signal of cyanohydrins with known configuration, is proposed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bias field tunable magnetic configuration and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm length

NASA Astrophysics Data System (ADS)

Adhikari, K.; Choudhury, S.; Mandal, R.; Barman, S.; Otani, Y.; Barman, A.

2017-01-01

Ferromagnetic nano-cross structures promise exotic static magnetic configurations and very rich and tunable magnetization dynamics leading towards potential applications in magnetic logic and communication devices. Here, we report an experimental study of external magnetic field tunable static magnetic configurations and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm lengths (L). Broadband ferromagnetic resonance measurements showed a strong variation in the number of spin-wave (SW) modes and mode frequencies (f) with bias field magnitude (H). Simulated static magnetic configurations and SW mode profiles explain the rich variation of the SW spectra, including mode softening, mode crossover, mode splitting, and mode merging. Such variation of SW spectra is further modified by the size of the nano-cross. Remarkably, with decreasing arm length of nano-cross structures, the onion magnetization ground state becomes more stable. Calculated magnetostatic field distributions support the above observations and revealed the non-collective nature of the dynamics in closely packed nano-cross structures. The latter is useful for their possible applications in magnetic storage and memory devices.

Three-dimensional prominence-hosting magnetic configurations: Creating a helical magnetic flux rope

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

Xia, C.; Keppens, R.; Guo, Y.

2014-01-10

The magnetic configuration hosting prominences and their surrounding coronal structure is a key research topic in solar physics. Recent theoretical and observational studies strongly suggest that a helical magnetic flux rope is an essential ingredient to fulfill most of the theoretical and observational requirements for hosting prominences. To understand flux rope formation details and obtain magnetic configurations suitable for future prominence formation studies, we here report on three-dimensional isothermal magnetohydrodynamic simulations including finite gas pressure and gravity. Starting from a magnetohydrostatic corona with a linear force-free bipolar magnetic field, we follow its evolution when introducing vortex flows around the mainmore » polarities and converging flows toward the polarity inversion line near the bottom of the corona. The converging flows bring the feet of different loops together at the polarity inversion line, where magnetic reconnection and flux cancellation happen. Inflow and outflow signatures of the magnetic reconnection process are identified, and thereby the newly formed helical loops wind around preexisting ones so that a complete flux rope grows and ascends. When a macroscopic flux rope is formed, we switch off the driving flows and find that the system relaxes to a stable state containing a helical magnetic flux rope embedded in an overlying arcade structure. A major part of the formed flux rope is threaded by dipped field lines that can stably support prominence matter, while the total mass of the flux rope is in the order of 4-5× 10{sup 14} g.« less

Microrheology: Structural evolution under static and dynamic conditions by simultaneous analysis of confocal microscopy and diffusing wave spectroscopy

NASA Astrophysics Data System (ADS)

Nicolas, Yves; Paques, Marcel; Knaebel, Alexandra; Steyer, Alain; Munch, Jean-Pierre; Blijdenstein, Theo B. J.; van Aken, George A.

2003-08-01

An oscillatory shear configuration was developed to improve understanding of structural evolution during deformation. It combines an inverted confocal scanning laser microscope (CSLM) and a special sample holder that can apply to the sample specific deformation: oscillatory shear or steady strain. In this configuration, a zero-velocity plane is created in the sample by moving two plates in opposite directions, thereby providing stable observation conditions of the structural behavior under deformation. The configuration also includes diffusion wave spectroscopy (DWS) to monitor the network properties via particle mobility under static and dynamic conditions. CSLM and DWS can be performed simultaneously and three-dimensional images can be obtained under static conditions. This configuration is mainly used to study mechanistic phenomena like particle interaction, aggregation, gelation and network disintegration, interactions at interfaces under static and dynamic conditions in semisolid food materials (desserts, dressings, sauces, dairy products) and in nonfood materials (mineral emulsions, etc.). Preliminary data obtained with this new oscillatory shear configuration are described that demonstrate their capabilities and the potential contribution to other areas of application also.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

Ecology of zoonotic infectious diseases in bats: current knowledge and future directions

USGS Publications Warehouse

Hayman, D.T.; Bowen, R.A.; Cryan, P.M.; McCracken, G.F.; O'Shea, T.J.; Peel, A.J.; Gilbert, A.; Webb, C.T.; Wood, J.L.

2013-01-01

Bats are hosts to a range of zoonotic and potentially zoonotic pathogens. Human activities that increase exposure to bats will likely increase the opportunity for infections to spill over in the future. Ecological drivers of pathogen spillover and emergence in novel hosts, including humans, involve a complex mixture of processes, and understanding these complexities may aid in predicting spillover. In particular, only once the pathogen and host ecologies are known can the impacts of anthropogenic changes be fully appreciated. Cross-disciplinary approaches are required to understand how host and pathogen ecology interact. Bats differ from other sylvatic disease reservoirs because of their unique and diverse lifestyles, including their ability to fly, often highly gregarious social structures, long lifespans and low fecundity rates. We highlight how these traits may affect infection dynamics and how both host and pathogen traits may interact to affect infection dynamics. We identify key questions relating to the ecology of infectious diseases in bats and propose that a combination of field and laboratory studies are needed to create data-driven mechanistic models to elucidate those aspects of bat ecology that are most critical to the dynamics of emerging bat viruses. If commonalities can be found, then predicting the dynamics of newly emerging diseases may be possible. This modelling approach will be particularly important in scenarios when population surveillance data are unavailable and when it is unclear which aspects of host ecology are driving infection dynamics.

Ecology of Zoonotic Infectious Diseases in Bats: Current Knowledge and Future Directions

PubMed Central

Hayman, D T S; Bowen, R A; Cryan, P M; McCracken, G F; O’Shea, T J; Peel, A J; Gilbert, A; Webb, C T; Wood, J L N

2013-01-01

Bats are hosts to a range of zoonotic and potentially zoonotic pathogens. Human activities that increase exposure to bats will likely increase the opportunity for infections to spill over in the future. Ecological drivers of pathogen spillover and emergence in novel hosts, including humans, involve a complex mixture of processes, and understanding these complexities may aid in predicting spillover. In particular, only once the pathogen and host ecologies are known can the impacts of anthropogenic changes be fully appreciated. Cross-disciplinary approaches are required to understand how host and pathogen ecology interact. Bats differ from other sylvatic disease reservoirs because of their unique and diverse lifestyles, including their ability to fly, often highly gregarious social structures, long lifespans and low fecundity rates. We highlight how these traits may affect infection dynamics and how both host and pathogen traits may interact to affect infection dynamics. We identify key questions relating to the ecology of infectious diseases in bats and propose that a combination of field and laboratory studies are needed to create data-driven mechanistic models to elucidate those aspects of bat ecology that are most critical to the dynamics of emerging bat viruses. If commonalities can be found, then predicting the dynamics of newly emerging diseases may be possible. This modelling approach will be particularly important in scenarios when population surveillance data are unavailable and when it is unclear which aspects of host ecology are driving infection dynamics. PMID:22958281

Coupled range dynamics of brood parasites and their hosts responding to climate and vegetation changes.

PubMed

Péron, Guillaume; Altwegg, Res; Jamie, Gabriel A; Spottiswoode, Claire N

2016-09-01

As populations shift their ranges in response to global change, local species assemblages can change, setting the stage for new ecological interactions, community equilibria and evolutionary responses. Here, we focus on the range dynamics of four avian brood parasite species and their hosts in southern Africa, in a context of bush encroachment (increase in woody vegetation density in places previously occupied by savanna-grassland mosaics) favouring some species at the expense of others. We first tested whether hosts and parasites constrained each other's ability to expand or maintain their ranges. Secondly, we investigated whether range shifts represented an opportunity for new host-parasite and parasite-parasite interactions. We used multispecies dynamic occupancy models with interactions, fitted to citizen science data, to estimate the contribution of interspecific interactions to range shifts and to quantify the change in species co-occurrence probability over a 25-year period. Parasites were able to track their hosts' range shifts. We detected no deleterious effect of the parasites' presence on either the local population viability of host species or the hosts' ability to colonize newly suitable areas. In the recently diversified indigobird radiation (Vidua spp.), following bush encroachment, the new assemblages presented more potential opportunities for speciation via host switch, but also more potential for hybridization between extant lineages, also via host switch. Multispecies dynamic occupancy models with interactions brought new insights into the feedbacks between range shifts, biotic interactions and local demography: brood parasitism had little detected impact on extinction or colonization processes, but inversely the latter processes affected biotic interactions via the modification of co-occurrence patterns. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Host and parasite thermal ecology jointly determine the effect of climate warming on epidemic dynamics.

PubMed

Gehman, Alyssa-Lois M; Hall, Richard J; Byers, James E

2018-01-23

Host-parasite systems have intricately coupled life cycles, but each interactor can respond differently to changes in environmental variables like temperature. Although vital to predicting how parasitism will respond to climate change, thermal responses of both host and parasite in key traits affecting infection dynamics have rarely been quantified. Through temperature-controlled experiments on an ectothermic host-parasite system, we demonstrate an offset in the thermal optima for survival of infected and uninfected hosts and parasite production. We combine experimentally derived thermal performance curves with field data on seasonal host abundance and parasite prevalence to parameterize an epidemiological model and forecast the dynamical responses to plausible future climate-warming scenarios. In warming scenarios within the coastal southeastern United States, the model predicts sharp declines in parasite prevalence, with local parasite extinction occurring with as little as 2 °C warming. The northern portion of the parasite's current range could experience local increases in transmission, but assuming no thermal adaptation of the parasite, we find no evidence that the parasite will expand its range northward under warming. This work exemplifies that some host populations may experience reduced parasitism in a warming world and highlights the need to measure host and parasite thermal performance to predict infection responses to climate change.

Nonlinear dynamics behavior analysis of the spatial configuration of a tendril-bearing plant

NASA Astrophysics Data System (ADS)

Feng, Jingjing; Zhang, Qichang; Wang, Wei; Hao, Shuying

2017-03-01

Tendril-bearing plants appear to have a spiraling shape when tendrils climb along a support during growth. The growth characteristics of a tendril-bearer can be simplified to a model of a thin elastic rod with a cylindrical constraint. In this paper, the connection between some typical configuration characteristics of tendrils and complex nonlinear dynamic behavior are qualitatively analyzed. The space configuration problem of tendrils can be explained through the study of the nonlinear dynamic behavior of the thin elastic rod system equation. In this study, the complex non-Z2 symmetric critical orbits in the system equation under critical parameters were presented. A new function transformation method that can effectively maintain the critical orbit properties was proposed, and a new nonlinear differential equations system containing complex nonlinear terms can been obtained to describe the cross section position and direction of a rod during climbing. Numerical simulation revealed that the new system can describe the configuration of a rod with reasonable accuracy. To adequately explain the growing regulation of the rod shape, the critical orbit and configuration of rod are connected in a direct way. The high precision analytical expressions of these complex non-Z2 symmetric critical orbits are obtained by introducing a suitable analytical method, and then these expressions are used to draw the corresponding three-dimensional configuration figures of an elastic thin rod. Combined with actual tendrils on a live plant, the space configuration of the winding knots of tendril is explained by the concept of heteroclinic orbit from the perspective of nonlinear dynamics, and correctness of the theoretical analysis was verified. This theoretical analysis method could also be effectively applied to other similar slender structures.

Combustion Dynamic Characteristics Identification in a 9-point LDI Combustor Under Choked Outlet Boundary Conditions

NASA Technical Reports Server (NTRS)

He, Zhuohui J.; Chang, Clarence T.

2017-01-01

Combustion dynamics data were collected at the NASA Glenn Research Center's CE-5 flame tube test facility under combustor outlet choked conditions. Two 9-point Swirl-Venturi Lean Direct Injection (SV-LDI) configurations were tested in a rectangular cuboid combustor geometry. Combustion dynamic data were measured at different engine operational conditions up to inlet air pressure and temperature of 24.13 bar and 828 K, respectively. In this study, the effects of acoustic cavity resonance, precessing vortex core (PVC), and non-uniform thermal expansion on the dynamic noise spectrum are identified by comparing the dynamic data that collected at various combustor inlet conditions along with combustor geometric calculations. The results show that the acoustic cavity resonance noises were seen in the counter-rotating pilot configuration but not in the co-rotating pilot configuration. Dynamic pressure noise band at around 0.9 kHz was only detected at the P'41 location (9.8 cm after fuel injector face) but not at the P'42 location (29 cm after the fuel injector face); the amplitude of this noise band depended on the thermal expansion ratio (T4/T3). The noise band at around 1.8 kHz was found to depend on the inlet air pressure or the air density inside the combustor. The PVC frequency was not observed in these two configurations.

Seasonal and Spatial Environmental Influence on Opisthorchis viverrini Intermediate Hosts, Abundance, and Distribution: Insights on Transmission Dynamics and Sustainable Control

PubMed Central

Kim, Christina Sunyoung; Echaubard, Pierre; Suwannatrai, Apiporn; Kaewkes, Sasithorn; Wilcox, Bruce A.; Sripa, Banchob

2016-01-01

Background Opisthorchis viverrini (Ov) is a complex-life-cycle trematode affecting 10 million people in SEA (Southeast Asia). Human infection occurs when infected cyprinid fish are consumed raw or undercooked. Ov requires three hosts and presents two free-living parasitic stages. As a consequence Ov transmission and infection in intermediate and human hosts are strongly mediated by environmental factors and understanding how environmental variability influences intermediate host abundance is critical. The objectives of this study were 1) to document water parameters, intermediate hosts abundance and infection spatio-temporal variation, 2) to assess their causal relationships and identify windows of transmission risk. Methodology/Principal Findings Fish and snails were collected monthly for one year at 12 sites in Lawa Lake, an Ov-endemic region of Khon Kaen Province in Northeast Thailand. Physicochemical water parameters [pH, temperature (Tp), dissolved oxygen (DO), Salinity, electrical conductivity (EC), total dissolved solid (TDS), nitrite nitrogen (NO2-N), lead (Pb), total coliform bacteria (TCB) and fecal coliform bacteria (FCB)] were measured. Multivariate analyses, linear models and kriging were used to characterize water parameter variation and its influence on host abundance and infection prevalence. We found that sampling sites could be grouped in three clusters and discriminated along a nitrogen-salinity gradient where higher levels in the lake’s southern region predicted higher Bithynia relative abundance (P<0.05) and lower snail and fish species diversity (P<0.05). Highest Bithynia abundance occurred during rainy season (P<0.001), independently of site influence. Cyprinids were the most abundant fish family and higher cyprinid relative abundance was found in areas with higher Bithynia relative abundance (P<0.05). Ov infection in snails was anecdotal while Ov infection in fish was higher in the southern region (P<0.001) at sites showing high FCB. Conclusions/Significance Our results indicate that water contamination and waterways configuration can influence freshwater communities’ assemblages possibly creating ideal conditions for sustained transmission. Sustainable control may require a better appreciation of the system’s ecology with wise governance and development planning particularly in the current context of SEA agricultural intensification and landscape modification. PMID:27880787

Seasonal and Spatial Environmental Influence on Opisthorchis viverrini Intermediate Hosts, Abundance, and Distribution: Insights on Transmission Dynamics and Sustainable Control.

PubMed

Kim, Christina Sunyoung; Echaubard, Pierre; Suwannatrai, Apiporn; Kaewkes, Sasithorn; Wilcox, Bruce A; Sripa, Banchob

2016-11-01

Opisthorchis viverrini (Ov) is a complex-life-cycle trematode affecting 10 million people in SEA (Southeast Asia). Human infection occurs when infected cyprinid fish are consumed raw or undercooked. Ov requires three hosts and presents two free-living parasitic stages. As a consequence Ov transmission and infection in intermediate and human hosts are strongly mediated by environmental factors and understanding how environmental variability influences intermediate host abundance is critical. The objectives of this study were 1) to document water parameters, intermediate hosts abundance and infection spatio-temporal variation, 2) to assess their causal relationships and identify windows of transmission risk. Fish and snails were collected monthly for one year at 12 sites in Lawa Lake, an Ov-endemic region of Khon Kaen Province in Northeast Thailand. Physicochemical water parameters [pH, temperature (Tp), dissolved oxygen (DO), Salinity, electrical conductivity (EC), total dissolved solid (TDS), nitrite nitrogen (NO2-N), lead (Pb), total coliform bacteria (TCB) and fecal coliform bacteria (FCB)] were measured. Multivariate analyses, linear models and kriging were used to characterize water parameter variation and its influence on host abundance and infection prevalence. We found that sampling sites could be grouped in three clusters and discriminated along a nitrogen-salinity gradient where higher levels in the lake's southern region predicted higher Bithynia relative abundance (P<0.05) and lower snail and fish species diversity (P<0.05). Highest Bithynia abundance occurred during rainy season (P<0.001), independently of site influence. Cyprinids were the most abundant fish family and higher cyprinid relative abundance was found in areas with higher Bithynia relative abundance (P<0.05). Ov infection in snails was anecdotal while Ov infection in fish was higher in the southern region (P<0.001) at sites showing high FCB. Our results indicate that water contamination and waterways configuration can influence freshwater communities' assemblages possibly creating ideal conditions for sustained transmission. Sustainable control may require a better appreciation of the system's ecology with wise governance and development planning particularly in the current context of SEA agricultural intensification and landscape modification.

The effects of host-feeding on stability of discrete-time host-parasitoid population dynamic models.

PubMed

Emerick, Brooks; Singh, Abhyudai

2016-02-01

Discrete-time models are the traditional approach for capturing population dynamics of a host-parasitoid system. Recent work has introduced a semi-discrete framework for obtaining model update functions that connect host-parasitoid population levels from year-to-year. In particular, this framework uses differential equations to describe the host-parasitoid interaction during the time of year when they come in contact, allowing specific behaviors to be mechanistically incorporated. We use the semi-discrete approach to study the effects of host-feeding, which occurs when a parasitoid consumes a potential host larva without ovipositing. We find that host-feeding by itself cannot stabilize the system, and both populations exhibit behavior similar to the Nicholson-Bailey model. However, when combined with stabilizing mechanisms such as density-dependent host mortality, host-feeding contracts the region of parameter space that allows for a stable host-parasitoid equilibrium. In contrast, when combined with a density-dependent parasitoid attack rate, host-feeding expands the non-zero equilibrium stability region. Our results show that host-feeding causes inefficiency in the parasitoid population, which yields a higher population of hosts per generation. This suggests that host-feeding may have limited long-term impact in terms of suppressing host levels for biological control applications. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative assessment of erbium fiber ring lasers and reflective SOA linear lasers for fiber Bragg grating dynamic strain sensing.

PubMed

Wei, Heming; Krishnaswamy, Sridhar

2017-05-01

Fiber Bragg grating (FBG) dynamic strain sensors using both an erbium-based fiber ring laser configuration and a reflective semiconductor optical amplifier (RSOA)-based linear laser configuration are investigated theoretically and experimentally. Fiber laser models are first presented to analyze the output characteristics of both fiber laser configurations when the FBG sensor is subjected to dynamic strains at high frequencies. Due to differences in the transition times of erbium and the semiconductor (InP/InGaAsP), erbium-doped fiber amplifier (EDFA)- and RSOA-based fiber lasers exhibit different responses and regimes of stability when the FBG is subjected to dynamic strains. The responses of both systems are experimentally verified using an adaptive photorefractive two-wave mixing (TWM) spectral demodulation technique. The experimental results show that the RSOA-FBG fiber linear cavity laser is stable and can stably respond to dynamic strains at high frequencies. An example application using a multiplexed TWM interferometer to demodulate multiple FBG sensors is also discussed.

Emulating a flexible space structure: Modeling

NASA Technical Reports Server (NTRS)

Waites, H. B.; Rice, S. C.; Jones, V. L.

1988-01-01

Control Dynamics, in conjunction with Marshall Space Flight Center, has participated in the modeling and testing of Flexible Space Structures. Through the series of configurations tested and the many techniques used for collecting, analyzing, and modeling the data, many valuable insights have been gained and important lessons learned. This paper discusses the background of the Large Space Structure program, Control Dynamics' involvement in testing and modeling of the configurations (especially the Active Control Technique Evaluation for Spacecraft (ACES) configuration), the results from these two processes, and insights gained from this work.

The evolution of parasite manipulation of host dispersal

PubMed Central

Lion, Sébastien; van Baalen, Minus; Wilson, William G

2006-01-01

We investigate the evolution of manipulation of host dispersal behaviour by parasites using spatially explicit individual-based simulations. We find that when dispersal is local, parasites always gain from increasing their hosts' dispersal rate, although the evolutionary outcome is determined by the costs-to-benefits ratio. However, when dispersal can be non-local, we show that parasites investing in an intermediate dispersal distance of their hosts are favoured even when the manipulation is not costly, due to the intrinsic spatial dynamics of the host–parasite interaction. Our analysis highlights the crucial importance of ecological spatial dynamics in evolutionary processes and reveals the theoretical possibility that parasites could manipulate their hosts' dispersal. PMID:16600882

Low driving voltage simplified tandem organic light-emitting devices by using exciplex-forming hosts

NASA Astrophysics Data System (ADS)

Zhou, Dong-Ying; Cui, Lin-Song; Zhang, Ying-Jie; Liao, Liang-Sheng; Aziz, Hany

2014-10-01

Tandem organic light-emitting devices (OLEDs), i.e., OLEDs containing multiple electroluminescence (EL) units that are vertically stacked, are attracting significant interest because of their ability to realize high current efficiency and long operational lifetime. However, stacking multiple EL units in tandem OLEDs increases driving voltage and complicates fabrication process relative to their standard single unit counterparts. In this paper, we demonstrate low driving voltage tandem OLEDs via utilizing exciplex-forming hosts in the EL units instead of conventional host materials. The use of exciplex-forming hosts reduces the charge injection barriers and the trapping of charges on guest molecules, resulting in the lower driving voltage. The use of exciplex-forming hosts also allows using fewer layers, hence simpler EL configuration which is beneficial for reducing the fabrication complexity of tandem OLEDs.

Merging mechanical and electromechanical bandgaps in locally resonant metamaterials and metastructures

NASA Astrophysics Data System (ADS)

Sugino, C.; Ruzzene, M.; Erturk, A.

2018-07-01

Locally resonant metamaterials are characterized by bandgaps at wavelengths much larger than the lattice size. Such locally resonant bandgaps can be formed using mechanical or electromechanical resonators. However, the nature of bandgap formation in mechanical and electromechanical (particularly piezoelectric) metamaterials is fundamentally different since the former is associated with a dynamic modal mass, while the latter is due to a dynamic modal stiffness. Next-generation metamaterials and resulting metastructures (i.e. finite configurations with specified boundary conditions) hosting mechanical resonators as well as piezoelectric interfaces connected to resonating circuits can enable the formation of two bandgaps, right above and below the design frequency of the mechanical and electrical resonators, respectively, yielding a wider bandgap and enhanced design flexibility as compared to using a purely mechanical, or a purely electromechanical configuration. In this work, we establish a fully coupled framework for hybrid mechanical-electromechanical metamaterials and finite metastructures. Combined bandgap size is approximated in closed form as a function of the added mass ratio of the resonators and the system-level electromechanical coupling for the infinite resonators approximation. Case studies are presented for a hybrid metamaterial cantilever under bending vibration to understand the interaction of these two locally resonant metamaterial domains in bandgap formation. Specifically, it is shown that the mechanical and electromechanical bandgaps do not fully merge for a finite number of resonators in an undamped setting. However, the presence of even light damping in the resonators suppresses the intermediate resonances emerging within the combined bandgap, enabling seamless merging of the two bandgaps in real-world structures that have damping. The overall concept of combining mechanical and electromechanical bandgaps in the same single metastructure can be leveraged in more complex topologies of piezoelectric metamaterial-based solids and structures.

Tool for a configurable integrated circuit that uses determination of dynamic power consumption

NASA Technical Reports Server (NTRS)

Davoodi, Azadeh (Inventor); French, Matthew C. (Inventor); Agarwal, Deepak (Inventor); Wang, Li (Inventor)

2011-01-01

A configurable logic tool that allows minimization of dynamic power within an FPGA design without changing user-entered specifications. The minimization of power may use minimized clock nets as a first order operation, and a second order operation that minimizes other factors, such as area of placement, area of clocks and/or slack.

Stackable Form-Factor Peripheral Component Interconnect Device and Assembly

NASA Technical Reports Server (NTRS)

Somervill, Kevin M. (Inventor); Ng, Tak-kwong (Inventor); Torres-Pomales, Wilfredo (Inventor); Malekpour, Mahyar R. (Inventor)

2013-01-01

A stackable form-factor Peripheral Component Interconnect (PCI) device can be configured as a host controller or a master/target for use on a PCI assembly. PCI device may comprise a multiple-input switch coupled to a PCI bus, a multiplexor coupled to the switch, and a reconfigurable device coupled to one of the switch and multiplexor. The PCI device is configured to support functionality from power-up, and either control function or add-in card function.

Control of forward swept wing configurations dominated by flight-dynamic/aeroelastic interactions

NASA Technical Reports Server (NTRS)

Rimer, M.; Chipman, R.; Muniz, B.

1984-01-01

An active control system concept for an aeroelastic wind-tunnel model of a statically unstable FSW configuration with wing-mounted stores is developed to provide acceptable longitudinal flying qualities while maintaining adequate flutter speed margin. On FSW configurations, the inherent aeroelastic wing divergence tendency causes strong flight-dynamic/aeroelastic interactions that in certain cases can produce a dynamic instability known as body-freedom flutter (BFF). The carriage of wing-mounted stores is shown to severely aggravate this problem. The control system developed combines a canard-based SAS with an Active Divergence/Flutter Suppression (ADFS) system which relies on wing-mounted sensors and a trailing-edge device (flaperon). Synergism between these two systems is exploited to obtain the flying qualities and flutter speed objectives.

Global Culture: A Noise Induced Transition in Finite Systems

NASA Astrophysics Data System (ADS)

Klemm, Konstantin; Eguíluz, Victor M.; Toral, Raúl; San Miguel, Maxi

2003-04-01

We analyze Axelrod's model for the unbiased transmission of culture in the presence of noise. In a one-dimensional lattice, the dynamics is described in terms of a Lyapunov potential, where the disordered configurations are metastable states of the dynamics. In a two-dimensional lattice the dynamics is governed by the average relaxation time T for perturbations to the homogeneous configuration. If the noise rate is smaller than 1/T, the perturbations drive the system to a completely ordered configuration, whereas the system remains disordered for larger noise rates. Based on a mean-field approximation we obtain the average relaxation time T(N) = Nln(N) for system size N. Thus in the limit of infinite system size the system is disordered for any finite noise rate.

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

PubMed

Cooke, Ben; Schmidler, Scott C

2008-10-28

We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

The Problem of Auto-Correlation in Parasitology

PubMed Central

Pollitt, Laura C.; Reece, Sarah E.; Mideo, Nicole; Nussey, Daniel H.; Colegrave, Nick

2012-01-01

Explaining the contribution of host and pathogen factors in driving infection dynamics is a major ambition in parasitology. There is increasing recognition that analyses based on single summary measures of an infection (e.g., peak parasitaemia) do not adequately capture infection dynamics and so, the appropriate use of statistical techniques to analyse dynamics is necessary to understand infections and, ultimately, control parasites. However, the complexities of within-host environments mean that tracking and analysing pathogen dynamics within infections and among hosts poses considerable statistical challenges. Simple statistical models make assumptions that will rarely be satisfied in data collected on host and parasite parameters. In particular, model residuals (unexplained variance in the data) should not be correlated in time or space. Here we demonstrate how failure to account for such correlations can result in incorrect biological inference from statistical analysis. We then show how mixed effects models can be used as a powerful tool to analyse such repeated measures data in the hope that this will encourage better statistical practices in parasitology. PMID:22511865

Postprandial remodeling of the gut microbiota in Burmese pythons

PubMed Central

Costello, Elizabeth K.; Gordon, Jeffrey I.; Secor, Stephen M.; Knight, Rob

2014-01-01

The vertebrate gut microbiota evolved in an environment typified by periodic fluctuations in nutrient availability, yet little is known about its responses to host feeding and fasting. Because many model species (e.g., mice) are adapted to lifestyles of frequent small meals, we turned to the Burmese python, a sit-and-wait foraging snake that consumes large prey at long intervals (>1 month), to examine the effects of a dynamic nutrient milieu on the gut microbiota. We employed multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities harvested from the intestines of fasted and digesting snakes, and from their rodent meal. In this unprecedented survey of a reptilian host, we found that Bacteroidetes and Firmicutes numerically dominated the python gut. In the large intestine, fasting was associated with increased abundances of the genera Bacteroides, Rikenella, Synergistes, and Akkermansia, and reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12 hours and 3 days after feeding, Firmicutes, including the taxa Clostridium, Lactobacillus, and Peptostreptococcaceae, gradually outnumbered the fasting-dominant Bacteroidetes, and overall ‘species’-level diversity increased significantly. Most lineages appeared to be indigenous to the python rather than ingested with the meal, but a dietary source of Lactobacillus could not be ruled out. Thus, the observed large-scale alterations of the gut microbiota that accompany the Burmese python's own dramatic physiological and morphological changes during feeding and fasting emphasize the need to consider both microbial and host cellular responses to nutrient flux. The Burmese python may provide a unique model for dissecting these interrelationships. PMID:20520652

Moment measurements in dynamic and quasi-static spine segment testing using eccentric compression are susceptible to artifacts based on loading configuration.

PubMed

Van Toen, Carolyn; Carter, Jarrod W; Oxland, Thomas R; Cripton, Peter A

2014-12-01

The tolerance of the spine to bending moments, used for evaluation of injury prevention devices, is often determined through eccentric axial compression experiments using segments of the cadaver spine. Preliminary experiments in our laboratory demonstrated that eccentric axial compression resulted in "unexpected" (artifact) moments. The aim of this study was to evaluate the static and dynamic effects of test configuration on bending moments during eccentric axial compression typical in cadaver spine segment testing. Specific objectives were to create dynamic equilibrium equations for the loads measured inferior to the specimen, experimentally verify these equations, and compare moment responses from various test configurations using synthetic (rubber) and human cadaver specimens. The equilibrium equations were verified by performing quasi-static (5 mm/s) and dynamic experiments (0.4 m/s) on a rubber specimen and comparing calculated shear forces and bending moments to those measured using a six-axis load cell. Moment responses were compared for hinge joint, linear slider and hinge joint, and roller joint configurations tested at quasi-static and dynamic rates. Calculated shear force and bending moment curves had similar shapes to those measured. Calculated values in the first local minima differed from those measured by 3% and 15%, respectively, in the dynamic test, and these occurred within 1.5 ms of those measured. In the rubber specimen experiments, for the hinge joint (translation constrained), quasi-static and dynamic posterior eccentric compression resulted in flexion (unexpected) moments. For the slider and hinge joints and the roller joints (translation unconstrained), extension ("expected") moments were measured quasi-statically and initial flexion (unexpected) moments were measured dynamically. In the cadaver experiments with roller joints, anterior and posterior eccentricities resulted in extension moments, which were unexpected and expected, for those configurations, respectively. The unexpected moments were due to the inertia of the superior mounting structures. This study has shown that eccentric axial compression produces unexpected moments due to translation constraints at all loading rates and due to the inertia of the superior mounting structures in dynamic experiments. It may be incorrect to assume that bending moments are equal to the product of compression force and eccentricity, particularly where the test configuration involves translational constraints and where the experiments are dynamic. In order to reduce inertial moment artifacts, the mass, and moment of inertia of any loading jig structures that rotate with the specimen should be minimized. Also, the distance between these structures and the load cell should be reduced.

Environmental conditions and Puumala virus transmission in Belgium

PubMed Central

Linard, Catherine; Tersago, Katrien; Leirs, Herwig; Lambin, Eric F

2007-01-01

Background Non-vector-borne zoonoses such as Puumala hantavirus (PUUV) can be transmitted directly, by physical contact between infected and susceptible hosts, or indirectly, with the environment as an intermediate. The objective of this study is to better understand the causal link between environmental features and PUUV prevalence in bank vole population in Belgium, and hence with transmission risk to humans. Our hypothesis was that environmental conditions controlling the direct and indirect transmission paths differ, such that the risk of transmission to humans is not only determined by host abundance. We explored the relationship between, on one hand, environmental variables and, on the other hand, host abundance, PUUV prevalence in the host, and human cases of nephropathia epidemica (NE). Statistical analyses were carried out on 17 field sites situated in Belgian broadleaf forests. Results Linear regressions showed that landscape attributes, particularly landscape configuration, influence the abundance of hosts in broadleaf forests. Based on logistic regressions, we show that PUUV prevalence among bank voles is more linked to variables favouring the survival of the virus in the environment, and thus the indirect transmission: low winter temperatures are strongly linked to prevalence among bank voles, and high soil moisture is linked to the number of NE cases among humans. The transmission risk to humans therefore depends on the efficiency of the indirect transmission path. Human risk behaviours, such as the propensity for people to go in forest areas that best support the virus, also influence the number of human cases. Conclusion The transmission risk to humans of non-vector-borne zoonoses such as PUUV depends on a combination of various environmental factors. To understand the complex causal pathways between the environment and disease risk, one should distinguish between environmental factors related to the abundance of hosts such as land-surface attributes, landscape configuration, and climate – i.e., host ecology, – and environmental factors related to PUUV prevalence, mainly winter temperatures and soil moisture – i.e., virus ecology. Beyond a threshold abundance of hosts, environmental factors favouring the indirect transmission path (soil and climate) can better predict the number of NE cases among humans than factors influencing the abundance of hosts. PMID:18078526

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly

PubMed Central

Hanski, Ilkka A.

2011-01-01

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time. PMID:21788506

Optimal foraging in seasonal environments: implications for residency of Australian flying foxes in food-subsidized urban landscapes.

PubMed

Páez, David J; Restif, Olivier; Eby, Peggy; Plowright, Raina K

2018-05-05

Bats provide important ecosystem services such as pollination of native forests; they are also a source of zoonotic pathogens for humans and domestic animals. Human-induced changes to native habitats may have created more opportunities for bats to reside in urban settings, thus decreasing pollination services to native forests and increasing opportunities for zoonotic transmission. In Australia, fruit bats ( Pteropus spp. flying foxes) are increasingly inhabiting urban areas where they feed on anthropogenic food sources with nutritional characteristics and phenology that differ from native habitats. We use optimal foraging theory to investigate the relationship between bat residence time in a patch, the time it takes to search for a new patch (simulating loss of native habitat) and seasonal resource production. We show that it can be beneficial to reside in a patch, even when food productivity is low, as long as foraging intensity is low and the expected searching time is high. A small increase in the expected patch searching time greatly increases the residence time, suggesting nonlinear associations between patch residence and loss of seasonal native resources. We also found that sudden increases in resource consumption due to an influx of new bats has complex effects on patch departure times that again depend on expected searching times and seasonality. Our results suggest that the increased use of urban landscapes by bats may be a response to new spatial and temporal configurations of foraging opportunities. Given that bats are reservoir hosts of zoonotic diseases, our results provide a framework to study the effects of foraging ecology on disease dynamics.One contribution of 14 to a theme isssue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'. © 2018 The Author(s).

[Dynamics of parasite communities in an age series of Arctic Cisco Coregonus migratorius (Georgi, 1775)].

PubMed

Dugarov, Zh N; Pronin, N M

2013-01-01

Parasite communities of Arctic cisco from Chivyrkui Bay of Lake Baikal have been analyzed at levels of a host individual (infracommunity), a individual age group of a host-(assemblages of infracommunities), and a host population (component community). Significant positive correlations of parameters of species richness (number of parasite species, Margalef and Menhinick indices) with the age of Arctic cisco were recorded only at the level of parasite inffacommunities. The absence of linear positive correlations between the parameters of species richness and the age of Arctic cisco at the level of assemblages of parasite infracommunities were revealed for the first time for fish of Lake Baikal. The peculiarity of the dynamics of parasite communities of. Arctic cisco is determined by specific features of the host physiology and ecology, primarily by the age dynamics of the feeding spectrum.

Transience after disturbance: Obligate species recovery dynamics depend on disturbance duration.

PubMed

Singer, Alexander; Johst, Karin

2017-06-01

After a disturbance event, population recovery becomes an important species response that drives ecosystem dynamics. Yet, it is unclear how interspecific interactions impact species recovery from a disturbance and which role the disturbance duration (pulse or press) plays. Here, we analytically derive conditions that govern the transient recovery dynamics from disturbance of a host and its obligately dependent partner in a two-species metapopulation model. We find that, after disturbance, species recovery dynamics depend on the species' role (i.e. host or obligately dependent species) as well as the duration of disturbance. Host recovery starts immediately after the disturbance. In contrast, for obligate species, recovery depends on disturbance duration. After press disturbance, which allows dynamics to equilibrate during disturbance, obligate species immediately start to recover. Yet, after pulse disturbance, obligate species continue declining although their hosts have already begun to increase. Effectively, obligate species recovery is delayed until a necessary host threshold occupancy is reached. Obligates' delayed recovery arises solely from interspecific interactions independent of dispersal limitations, which contests previous explanations. Delayed recovery exerts a two-fold negative effect, because populations continue declining to even smaller population sizes and the phase of increased risk from demographic stochastic extinction in small populations is prolonged. We argue that delayed recovery and its determinants -species interactions and disturbance duration - have to be considered in biodiversity management. Copyright © 2017 Elsevier Inc. All rights reserved.

Predators indirectly control vector-borne disease: linking predator-prey and host-pathogen models.

PubMed

Moore, Sean M; Borer, Elizabeth T; Hosseini, Parviez R

2010-01-06

Pathogens transmitted by arthropod vectors are common in human populations, agricultural systems and natural communities. Transmission of these vector-borne pathogens depends on the population dynamics of the vector species as well as its interactions with other species within the community. In particular, predation may be sufficient to control pathogen prevalence indirectly via the vector. To examine the indirect effect of predators on vectored-pathogen dynamics, we developed a theoretical model that integrates predator-prey and host-pathogen theory. We used this model to determine whether predation can prevent pathogen persistence or alter the stability of host-pathogen dynamics. We found that, in the absence of predation, pathogen prevalence in the host increases with vector fecundity, whereas predation on the vector causes pathogen prevalence to decline, or even become extinct, with increasing vector fecundity. We also found that predation on a vector may drastically slow the initial spread of a pathogen. The predator can increase host abundance indirectly by reducing or eliminating infection in the host population. These results highlight the importance of studying interactions that, within the greater community, may alter our predictions when studying disease dynamics. From an applied perspective, these results also suggest situations where an introduced predator or the natural enemies of a vector may slow the rate of spread of an emerging vector-borne pathogen.

Positive train control interoperability and networking research : final report.

DOT National Transportation Integrated Search

2015-12-01

This document describes the initial development of an ITC PTC Shared Network (IPSN), a hosted : environment to support the distribution, configuration management, and IT governance of Interoperable : Train Control (ITC) Positive Train Control (PTC) s...

Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.

PubMed

Chong, Song-Ho; Ham, Sihyun

2015-10-01

Quantifying how the rugged nature of the underlying free-energy landscape determines the entropic cost a protein must incur upon folding and ligand binding is a challenging problem. Here, we present a novel computational approach that dissects the protein configurational entropy on the basis of the classification of protein dynamics on the landscape into two separate components: short-term vibrational dynamics related to individual free-energy wells and long-term conformational dynamics associated with transitions between wells. We apply this method to separate the configurational entropy of the protein villin headpiece subdomain into its conformational and vibrational components. We find that the change in configurational entropy upon folding is dominated by the conformational entropy despite the fact that the magnitude of the vibrational entropy is the significantly larger component in each of the folded and unfolded states, which is in accord with the previous empirical estimations. The straightforward applicability of our method to unfolded proteins promises a wide range of applications, including those related to intrinsically disordered proteins.

Stalking as paranoid attachment: a typological and dynamic model.

PubMed

Wilson, John S; Ermshar, Annette L; Welsh, Robert K

2006-06-01

Stalking encompasses a wide range of behavioral patterns, risk factors, interpersonal dynamics, and dangerousness. To account for these diverse phenomena, we propose that stalking behavior is best conceptualized by a dynamic interaction of attachment styles and psychodynamic phenomena. This paper articulates a model that explains stalking behavior within the framework of attachment theory. Four prototypical configurations of stalkers and their victims are developed. Each configuration is discussed in terms of a pattern of internal representations, affective constellations, combinations of aggression and narcissism, and potential for future violence. The four configurations proposed here are maintained through stalkers' over ideational linkage fantasies and projective identifications, which range from shame-prone and needy idealization to malevolent torment of the victim. Our model arrays erotomanic, jealous, and persecutory attachments along a continuum of increasingly paranoid and pathological identifications. We argue that these prototypical attachment configurations provide a theoretically driven means of differentiating phases of stalking, and as such provide useful leads in the empirical study and clinical assessment, treatment, and management of stalkers.

General-Purpose Serial Interface For Remote Control

NASA Technical Reports Server (NTRS)

Busquets, Anthony M.; Gupton, Lawrence E.

1990-01-01

Computer controls remote television camera. General-purpose controller developed to serve as interface between host computer and pan/tilt/zoom/focus functions on series of automated video cameras. Interface port based on 8251 programmable communications-interface circuit configured for tristated outputs, and connects controller system to any host computer with RS-232 input/output (I/O) port. Accepts byte-coded data from host, compares them with prestored codes in read-only memory (ROM), and closes or opens appropriate switches. Six output ports control opening and closing of as many as 48 switches. Operator controls remote television camera by speaking commands, in system including general-purpose controller.

Imaging host cell-Leishmania interaction dynamics implicates parasite motility, lysosome recruitment, and host cell wounding in the infection process.

PubMed

Forestier, Claire-Lise; Machu, Christophe; Loussert, Celine; Pescher, Pascale; Späth, Gerald F

2011-04-21

Leishmania donovani causes human visceral leishmaniasis. The parasite infectious cycle comprises extracellular flagellated promastigotes that proliferate inside the insect vector, and intracellular nonmotile amastigotes that multiply within infected host cells. Using primary macrophages infected with virulent metacyclic promastigotes and high spatiotemporal resolution microscopy, we dissect the dynamics of the early infection process. We find that motile promastigotes enter macrophages in a polarized manner through their flagellar tip and are engulfed into host lysosomal compartments. Persistent intracellular flagellar activity leads to reorientation of the parasite flagellum toward the host cell periphery and results in oscillatory parasite movement. The latter is associated with local lysosomal exocytosis and host cell plasma membrane wounding. These findings implicate lysosome recruitment followed by lysosome exocytosis, consistent with parasite-driven host cell injury, as key cellular events in Leishmania host cell infection. This work highlights the role of promastigote polarity and motility during parasite entry. Copyright © 2011 Elsevier Inc. All rights reserved.

Parasite transmission among relatives halts Red Queen dynamics.

PubMed

Greenspoon, Philip B; Mideo, Nicole

2017-03-01

The theory that coevolving hosts and parasites create a fluctuating selective environment for one another (i.e., produce Red Queen dynamics) has deep roots in evolutionary biology; yet empirical evidence for Red Queen dynamics remains scarce. Fluctuating coevolutionary dynamics underpin the Red Queen hypothesis for the evolution of sex, as well as hypotheses explaining the persistence of genetic variation under sexual selection, local parasite adaptation, the evolution of mutation rate, and the evolution of nonrandom mating. Coevolutionary models that exhibit Red Queen dynamics typically assume that hosts and parasites encounter one another randomly. However, if related individuals aggregate into family groups or are clustered spatially, related hosts will be more likely to encounter parasites transmitted by genetically similar individuals. Using a model that incorporates familial parasite transmission, we show that a slight degree of familial parasite transmission is sufficient to halt coevolutionary fluctuations. Our results predict that evidence for Red Queen dynamics, and its evolutionary consequences, are most likely to be found in biological systems in which hosts and parasites mix mainly at random, and are less likely to be found in systems with familial aggregation. This presents a challenge to the Red Queen hypothesis and other hypotheses that depend on coevolutionary cycling. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Dynamics of Quantum Adiabatic Evolution Algorithm for Number Partitioning

NASA Technical Reports Server (NTRS)

Smelyanskiy, V. N.; Toussaint, U. V.; Timucin, D. A.

2002-01-01

We have developed a general technique to study the dynamics of the quantum adiabatic evolution algorithm applied to random combinatorial optimization problems in the asymptotic limit of large problem size n. We use as an example the NP-complete Number Partitioning problem and map the algorithm dynamics to that of an auxiliary quantum spin glass system with the slowly varying Hamiltonian. We use a Green function method to obtain the adiabatic eigenstates and the minimum excitation gap. g min, = O(n 2(exp -n/2), corresponding to the exponential complexity of the algorithm for Number Partitioning. The key element of the analysis is the conditional energy distribution computed for the set of all spin configurations generated from a given (ancestor) configuration by simultaneous flipping of a fixed number of spins. For the problem in question this distribution is shown to depend on the ancestor spin configuration only via a certain parameter related to 'the energy of the configuration. As the result, the algorithm dynamics can be described in terms of one-dimensional quantum diffusion in the energy space. This effect provides a general limitation of a quantum adiabatic computation in random optimization problems. Analytical results are in agreement with the numerical simulation of the algorithm.

A method of demand-driven and data-centric Web service configuration for flexible business process implementation

NASA Astrophysics Data System (ADS)

Xu, Boyi; Xu, Li Da; Fei, Xiang; Jiang, Lihong; Cai, Hongming; Wang, Shuai

2017-08-01

Facing the rapidly changing business environments, implementation of flexible business process is crucial, but difficult especially in data-intensive application areas. This study aims to provide scalable and easily accessible information resources to leverage business process management. In this article, with a resource-oriented approach, enterprise data resources are represented as data-centric Web services, grouped on-demand of business requirement and configured dynamically to adapt to changing business processes. First, a configurable architecture CIRPA involving information resource pool is proposed to act as a scalable and dynamic platform to virtualise enterprise information resources as data-centric Web services. By exposing data-centric resources as REST services in larger granularities, tenant-isolated information resources could be accessed in business process execution. Second, dynamic information resource pool is designed to fulfil configurable and on-demand data accessing in business process execution. CIRPA also isolates transaction data from business process while supporting diverse business processes composition. Finally, a case study of using our method in logistics application shows that CIRPA provides an enhanced performance both in static service encapsulation and dynamic service execution in cloud computing environment.

Dynamics of Quantum Adiabatic Evolution Algorithm for Number Partitioning

NASA Technical Reports Server (NTRS)

Smelyanskiy, Vadius; vonToussaint, Udo V.; Timucin, Dogan A.; Clancy, Daniel (Technical Monitor)

2002-01-01

We have developed a general technique to study the dynamics of the quantum adiabatic evolution algorithm applied to random combinatorial optimization problems in the asymptotic limit of large problem size n. We use as an example the NP-complete Number Partitioning problem and map the algorithm dynamics to that of an auxiliary quantum spin glass system with the slowly varying Hamiltonian. We use a Green function method to obtain the adiabatic eigenstates and the minimum exitation gap, gmin = O(n2(sup -n/2)), corresponding to the exponential complexity of the algorithm for Number Partitioning. The key element of the analysis is the conditional energy distribution computed for the set of all spin configurations generated from a given (ancestor) configuration by simultaneous flipping of a fixed number of spins. For the problem in question this distribution is shown to depend on the ancestor spin configuration only via a certain parameter related to the energy of the configuration. As the result, the algorithm dynamics can be described in terms of one-dimensional quantum diffusion in the energy space. This effect provides a general limitation of a quantum adiabatic computation in random optimization problems. Analytical results are in agreement with the numerical simulation of the algorithm.

Evolution and selection of river networks: Statics, dynamics, and complexity

PubMed Central

Rinaldo, Andrea; Rigon, Riccardo; Banavar, Jayanth R.; Maritan, Amos; Rodriguez-Iturbe, Ignacio

2014-01-01

Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics—every spanning tree is exactly a local minimum of total energy dissipation. It is remarkable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features explain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept. PMID:24550264

Local random configuration-tree theory for string repetition and facilitated dynamics of glass

NASA Astrophysics Data System (ADS)

Lam, Chi-Hang

2018-02-01

We derive a microscopic theory of glassy dynamics based on the transport of voids by micro-string motions, each of which involves particles arranged in a line hopping simultaneously displacing one another. Disorder is modeled by a random energy landscape quenched in the configuration space of distinguishable particles, but transient in the physical space as expected for glassy fluids. We study the evolution of local regions with m coupled voids. At a low temperature, energetically accessible local particle configurations can be organized into a random tree with nodes and edges denoting configurations and micro-string propagations respectively. Such trees defined in the configuration space naturally describe systems defined in two- or three-dimensional physical space. A micro-string propagation initiated by a void can facilitate similar motions by other voids via perturbing the random energy landscape, realizing path interactions between voids or equivalently string interactions. We obtain explicit expressions of the particle diffusion coefficient and a particle return probability. Under our approximation, as temperature decreases, random trees of energetically accessible configurations exhibit a sequence of percolation transitions in the configuration space, with local regions containing fewer coupled voids entering the non-percolating immobile phase first. Dynamics is dominated by coupled voids of an optimal group size, which increases as temperature decreases. Comparison with a distinguishable-particle lattice model (DPLM) of glass shows very good quantitative agreements using only two adjustable parameters related to typical energy fluctuations and the interaction range of the micro-strings.

Thermal Change and the Dynamics of Multi-Host Parasite Life Cycles in Aquatic Ecosystems.

PubMed

Barber, Iain; Berkhout, Boris W; Ismail, Zalina

2016-10-01

Altered thermal regimes associated with climate change are impacting significantly on the physical, chemical, and biological characteristics of the Earth's natural ecosystems, with important implications for the biology of aquatic organisms. As well as impacting the biology of individual species, changing thermal regimes have the capacity to mediate ecological interactions between species, and the potential for climate change to impact host-parasite interactions in aquatic ecosystems is now well recognized. Predicting what will happen to the prevalence and intensity of infection of parasites with multiple hosts in their life cycles is especially challenging because the addition of each additional host dramatically increases the potential permutations of response. In this short review, we provide an overview of the diverse routes by which altered thermal regimes can impact the dynamics of multi-host parasite life cycles in aquatic ecosystems. In addition, we examine how experimentally amenable host-parasite systems are being used to determine the consequences of changing environmental temperatures for these different types of mechanism. Our overarching aim is to examine the potential of changing thermal regimes to alter not only the biology of hosts and parasites, but also the biology of interactions between hosts and parasites. We also hope to illustrate the complexity that is likely to be involved in making predictions about the dynamics of infection by multi-host parasites in thermally challenged aquatic ecosystems. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.

Flight dynamic investigations of flying wing with winglet configured unmanned aerial vehicle

NASA Astrophysics Data System (ADS)

Ro, Kapseong

2006-05-01

A swept wing tailless vehicle platform is well known in the radio control (RC) and sailing aircraft community for excellent spiral stability during soaring or thermaling, while exhibiting no Dutch roll behavior at high speed. When an unmanned aerial vehicle (UAV) is subjected to fly a mission in a rugged mountainous terrain where air current or thermal up-drift is frequently present, this is great aerodynamic benefit over the conventional cross-tailed aircraft which requires careful balance between lateral and directional stability. Such dynamic characteristics can be studied through vehicle dynamic modeling and simulation, but it requires configuration aerodynamic data through wind tunnel experiments. Obtaining such data is very costly and time consuming, and it is not feasible especially for low cost and dispensable UAVs. On the other hand, the vehicle autonomy is quite demanding which requires substantial understanding of aircraft dynamic characteristics. In this study, flight dynamics of an UAV platform based on flying wing with a large winglet was investigated through analytical modeling and numerical simulation. Flight dynamic modeling software and experimental formulae were used to obtain essential configuration aerodynamic characteristics, and linear flight dynamic analysis was carried out to understand the effect of wing sweep angle and winglet size on the vehicle dynamic characteristics.

Pseudo-random dynamic address configuration (PRDAC) algorithm for mobile ad hoc networks

NASA Astrophysics Data System (ADS)

Wu, Shaochuan; Tan, Xuezhi

2007-11-01

By analyzing all kinds of address configuration algorithms, this paper provides a new pseudo-random dynamic address configuration (PRDAC) algorithm for mobile ad hoc networks. Based on PRDAC, the first node that initials this network randomly chooses a nonlinear shift register that can generates an m-sequence. When another node joins this network, the initial node will act as an IP address configuration sever to compute an IP address according to this nonlinear shift register, and then allocates this address and tell the generator polynomial of this shift register to this new node. By this means, when other node joins this network, any node that has obtained an IP address can act as a server to allocate address to this new node. PRDAC can also efficiently avoid IP conflicts and deal with network partition and merge as same as prophet address (PA) allocation and dynamic configuration and distribution protocol (DCDP). Furthermore, PRDAC has less algorithm complexity, less computational complexity and more sufficient assumption than PA. In addition, PRDAC radically avoids address conflicts and maximizes the utilization rate of IP addresses. Analysis and simulation results show that PRDAC has rapid convergence, low overhead and immune from topological structures.

Mortality and Population Dynamics of Bemisia tabaci within a Multi-Crop System

USDA-ARS?s Scientific Manuscript database

The population dynamics of mobile polyphagous pests is governed by a complex set of interacting factors that involve multiple host-plants, seasonality, movement and demography. Bemisia tabaci is a multivoltine insect with no diapause that maintains population continuity by moving from one host to a...

The role of host sex in parasite dynamics: individual based model simulations of host-parasite interactions in a semi-enclosed embayment.

NASA Astrophysics Data System (ADS)

Velo Suarez, L.; Arancio, M.; Sourisseau, M.

2016-02-01

Parasitic dinoflagellates of the genus Amoebophrya infect free-living dinoflagellates, some of which can cause harmful algal blooms (HABs). During a field study in Salt Pond (MA, USA), we found a significant influence of Amoebophrya spp. on populations of Alexandrium fundyense. Parasitism appeared to exhibit a significant top down influence on A. fundyense populations and a dramatic life-cycle transition from vegetative division to sexual fusion was recorded. Despite our intensive sampling in Salt Pond, host-parasite interactions were undersampled owing to the very short time scales relevant to host-Amoebophrya spp. dynamics. In the present work, we explored the role of sexual reproduction and excystment/encystment processes using an Individual Based Model (IBM). The model was parameterized using published data and laboratory experiments carried out to analyze Amoebophrya spp. functional response. Observed-simulated differences in host-parasite dynamics support the hypothesis of parasite-host simultaneous dormancy, and further excystment months later to propagate both species. Results suggest that coexistence of A. fundyense and Amoebophrya spp. and their annual persistence in Salt Pond might rely on a sexual response/encystment. Understanding host-parasite interactions and coexistence strategies will improve our knowledge of Alexandrium spp. blooms and assess the impact of parasites on natural plankton assemblages in coastal systems.

Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence

PubMed Central

Clerc, Melanie; Ebert, Dieter; Hall, Matthew D.

2015-01-01

How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite Pasteuria ramosa infecting the crustacean Daphnia magna. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence. PMID:25761710

The application of high efficient yellow phosphorescent material to white OLEDs

NASA Astrophysics Data System (ADS)

Lin, Jin-Sheng; Ku, Chun-Neng; Huang, Pang-Chi; Wu, Cheng-An; Chang, Meng-Hao; Liou, Jia-Lun; Tseng, Mei-Rurng

2014-10-01

A new type of thiopyridinyl-based iridium molecule (POT) was used as the yellow phosphorescent material in our research. On fabricating a yellow PHOLED by doping POT-02 with host as the emitter, the device achieved a high power efficiency of 66.0 lm/W and an external quantum efficiency of 23.2%. On the other hand, a white organic lightemitting diode (WOLED) with a high power efficiency has been demonstrated by dispersing a host-free, yellow phosphorescent material in-between double blue phosphorescent emitters. In this study, we introduce a simple process for generating yellow emission of a WOLED by using the B/Y/B EML configuration. The B/Y/B EML configuration can achieve a higher efficiency and a smaller color shift with various operational brightness values. Based on the concept of this device, the molecular engineering of the blue phosphorescent host material as well as the light-extraction film, a WOLED with a power efficiency of 103 lm/W and an external quantum efficiency of 38.2% at a practical brightness of 1000 cd/m2 with CIE coordinates (CIEx, y) of (0.36, 0.48) can be achieved.

Selective predation and productivity jointly drive complex behavior in host-parasite systems.

PubMed

Hall, Spencer R; Duffy, Meghan A; Cáceres, Carla E

2005-01-01

Successful invasion of a parasite into a host population and resulting host-parasite dynamics can depend crucially on other members of a host's community such as predators. We do not fully understand how predation intensity and selectivity shape host-parasite dynamics because the interplay between predator density, predator foraging behavior, and ecosystem productivity remains incompletely explored. By modifying a standard susceptible-infected model, we show how productivity can modulate complex behavior induced by saturating and selective foraging behavior of predators in an otherwise stable host-parasite system. When predators strongly prefer parasitized hosts, the host-parasite system can oscillate, but predators can also create alternative stable states, Allee effects, and catastrophic extinction of parasites. In the latter three cases, parasites have difficulty invading and/or persisting in ecosystems. When predators are intermediately selective, these more complex behaviors become less important, but the host-parasite system can switch from stable to oscillating and then back to stable states along a gradient of predator control. Surprisingly, at higher productivity, predators that neutrally select or avoid parasitized hosts can catalyze extinction of both hosts and parasites. Thus, synergy between two enemies can end disastrously for the host. Such diverse outcomes underscore the crucial importance of the community and ecosystem context in which host-parasite interactions occur.

The dynamics of the de Sitter resonance

NASA Astrophysics Data System (ADS)

Celletti, Alessandra; Paita, Fabrizio; Pucacco, Giuseppe

2018-02-01

We study the dynamics of the de Sitter resonance, namely the stable equilibrium configuration of the first three Galilean satellites. We clarify the relation between this family of configurations and the more general Laplace resonant states. In order to describe the dynamics around the de Sitter stable equilibrium, a one-degree-of-freedom Hamiltonian normal form is constructed and exploited to identify initial conditions leading to the two families. The normal form Hamiltonian is used to check the accuracy in the location of the equilibrium positions. Besides, it gives a measure of how sensitive it is with respect to the different perturbations acting on the system. By looking at the phase plane of the normal form, we can identify a Laplace-like configuration, which highlights many substantial aspects of the observed one.

Robotic intelligence kernel

DOEpatents

Bruemmer, David J [Idaho Falls, ID

2009-11-17

A robot platform includes perceptors, locomotors, and a system controller. The system controller executes a robot intelligence kernel (RIK) that includes a multi-level architecture and a dynamic autonomy structure. The multi-level architecture includes a robot behavior level for defining robot behaviors, that incorporate robot attributes and a cognitive level for defining conduct modules that blend an adaptive interaction between predefined decision functions and the robot behaviors. The dynamic autonomy structure is configured for modifying a transaction capacity between an operator intervention and a robot initiative and may include multiple levels with at least a teleoperation mode configured to maximize the operator intervention and minimize the robot initiative and an autonomous mode configured to minimize the operator intervention and maximize the robot initiative. Within the RIK at least the cognitive level includes the dynamic autonomy structure.

Low-speed Aerodynamic Investigations of a Hybrid Wing Body Configuration

NASA Technical Reports Server (NTRS)

Vicroy, Dan D.; Gatlin, Gregory M.; Jenkins, Luther N.; Murphy, Patrick C.; Carter, Melissa B.

2014-01-01

Two low-speed static wind tunnel tests and a water tunnel static and dynamic forced-motion test have been conducted on a hybrid wing-body (HWB) twinjet configuration. These tests, in addition to computational fluid dynamics (CFD) analysis, have provided a comprehensive dataset of the low-speed aerodynamic characteristics of this nonproprietary configuration. In addition to force and moment measurements, the tests included surface pressures, flow visualization, and off-body particle image velocimetry measurements. This paper will summarize the results of these tests and highlight the data that is available for code comparison or additional analysis.

Systems and methods for performing wireless financial transactions

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

McCown, Steven Harvey

2012-07-03

A secure computing module (SCM) is configured for connection with a host device. The SCM includes a processor for performing secure processing operations, a host interface for coupling the processor to the host device, and a memory connected to the processor wherein the processor logically isolates at least some of the memory from access by the host device. The SCM also includes a proximate-field wireless communicator connected to the processor to communicate with another SCM associated with another host device. The SCM generates a secure digital signature for a financial transaction package and communicates the package and the signature tomore » the other SCM using the proximate-field wireless communicator. Financial transactions are performed from person to person using the secure digital signature of each person's SCM and possibly message encryption. The digital signatures and transaction details are communicated to appropriate financial organizations to authenticate the transaction parties and complete the transaction.« less

Host polymer influence on dilute polystyrene segmental dynamics

NASA Astrophysics Data System (ADS)

Lutz, T. R.

2005-03-01

We have utilized deuterium NMR to investigate the segmental dynamics of dilute (2%) d3-polystyrene (PS) chains in miscible polymer blends with polybutadiene, poly(vinyl ethylene), polyisoprene, poly(vinyl methylether) and poly(methyl methacrylate). In the dilute limit, we find qualitative differences depending upon whether the host polymer has dynamics that are faster or slower than that of pure PS. In blends where PS is the fast (low Tg) component, segmental dynamics are slowed upon blending and can be fit by the Lodge-McLeish model. When PS is the slow (high Tg) component, PS segmental dynamics speed up upon blending, but cannot be fit by the Lodge-McLeish model unless a temperature dependent self-concentration is employed. These results are qualitatively consistent with a recent suggestion by Kant, Kumar and Colby (Macromolecules, 2003, 10087), based upon data at higher concentrations. Furthermore, as the slow component, we find the segmental dynamics of PS has a temperature dependence similar to that of its host. This suggests viewing the high Tg component dynamics in a miscible blend as similar to a polymer in a low molecular weight solvent.

Git Replacement for the

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

Robinson, P.

2014-09-23

GRAPE is a tool for managing software project workflows for the Git version control system. It provides a suite of tools to simplify and configure branch based development, integration with a project's testing suite, and integration with the Atlassian Stash repository hosting tool.

Control of Dual-Opposed Stirling Convertors with Active Power Factor Correction Controllers

NASA Technical Reports Server (NTRS)

Regan, Timothy F.; Lewandowski, Edward J.; Schreiber, Jeffrey G.

2007-01-01

When using recently-developed active power factor correction (APFC) controllers in power systems comprised of dual-opposed free-piston Stirling convertors, a variety of configurations of the convertors and controller(s) can be considered, with configuration ultimately selected based on benefits of efficiency, reliability, and robust operation. The configuration must not only achieve stable control of the two convertors, but also synchronize and regulate motion of the pistons to minimize net dynamic forces. The NASA Glenn Research Center (GRC) System Dynamic Model (SDM) was used to study ten configurations of dual-opposed convertor systems. These configurations considered one controller with the alternators connected in series or in parallel, and two controllers with the alternators not connected (isolated). For the configurations where the alternators were not connected, several different approaches were evaluated to synchronize the two convertors. In addition, two thermodynamic configurations were considered: two convertors with isolated working spaces and convertors with a shared expansion space. Of the ten configurations studied, stable operating modes were found for four. Three of those four had a common expansion space. One stable configuration was found for the dual-opposed convertors with separate working spaces. That configuration required isochronous control of both convertors, and two APFC controllers were used to accomplish this. A frequency/phase control loop was necessary to allow each APFC controller to synchronize its associated convertor with a common frequency.

Control of Dual-Opposed Stirling Convertors with Active Power Factor Correction Controllers

NASA Technical Reports Server (NTRS)

Regan, Timothy F.; Lewandowski, Edward J.; Schreiber, Jeffrey G.

2006-01-01

When using recently-developed active power factor correction (APFC) controllers in power systems comprised of dual-opposed free-piston Stirling convertors, a variety of configurations of the convertors and controller(s) can be considered, with configuration ultimately selected based on benefits of efficiency, reliability, and robust operation. The configuration must not only achieve stable control of the two convertors, but also synchronize and regulate motion of the pistons to minimize net dynamic forces. The NASA Glenn Research Center (GRC) System Dynamic Model (SDM) was used to study ten configurations of dual-opposed convertor systems. These configurations considered one controller with the alternators connected in series or in parallel, and two controllers with the alternators not connected (isolated). For the configurations where the alternators were not connected, several different approaches were evaluated to synchronize the two convertors. In addition, two thermodynamic configurations were considered: two convertors with isolated working spaces and convertors with a shared expansion space. Of the ten configurations studied, stable operating modes were found for four. Three of those four had a common expansion space. One stable configuration was found for the dual-opposed convertors with separate working spaces. That configuration required isochronous control of both convertors, and two APFC controllers were used to accomplish this. A frequency/phase control loop was necessary to allow each APFC controller to synchronize its associated convertor with a common frequency.

Atomic Data and Spectral Line Intensities for Be-like Ions

NASA Technical Reports Server (NTRS)

Bhatia, Anand; Landi, E.

2008-01-01

Atomic data and collision rates are needed to model the spectrum of optically thin astrophysical sources. Recent observations from solar instrumentation such as SOH0 and Hinode have revealed the presence of hosts of lines emitted by high-energy configurations from ions belonging to the Be-like to the 0-like isoelectronic sequences. Data for such configurations are often unavailable in the literature. We have started a program to calculate the atomic parameters and rates for the high-energy configurations of Be-like ions of the type ls2.21.nl' where n=3,4,5. We report on the results of this project and on the diagnostic application of the predicted spectral lines.

Environment-Dependent Guest Exchange in Supramolecular Hosts

PubMed Central

2015-01-01

Dynamic exchange of guest molecules, encapsulated in host assemblies, is a phenomenon in supramolecular chemistry that has important implications in several applications. While the mechanism of exchange in micellar assemblies has been previously investigated, the effect of host and guest environment upon the guest-exchange dynamics has received little attention, if any. In this paper, we study the guest-exchange mechanism in pH-sensitive nanogels along with pH-insensitive nanogels as a control. By systematically comparing the behavior of these nanogels, we show that size, concentration, and hydrophobicity can all play a critical role in guest-exchange dynamics. More importantly, these studies reveal that the dominant mechanism of guest exchange can intimately depend on environmental factors. PMID:25244305

Modeling the within-host dynamics of cholera: bacterial-viral interaction.

PubMed

Wang, Xueying; Wang, Jin

2017-08-01

Novel deterministic and stochastic models are proposed in this paper for the within-host dynamics of cholera, with a focus on the bacterial-viral interaction. The deterministic model is a system of differential equations describing the interaction among the two types of vibrios and the viruses. The stochastic model is a system of Markov jump processes that is derived based on the dynamics of the deterministic model. The multitype branching process approximation is applied to estimate the extinction probability of bacteria and viruses within a human host during the early stage of the bacterial-viral infection. Accordingly, a closed-form expression is derived for the disease extinction probability, and analytic estimates are validated with numerical simulations. The local and global dynamics of the bacterial-viral interaction are analysed using the deterministic model, and the result indicates that there is a sharp disease threshold characterized by the basic reproduction number [Formula: see text]: if [Formula: see text], vibrios ingested from the environment into human body will not cause cholera infection; if [Formula: see text], vibrios will grow with increased toxicity and persist within the host, leading to human cholera. In contrast, the stochastic model indicates, more realistically, that there is always a positive probability of disease extinction within the human host.

Evolution in action: climate change, biodiversity dynamics and emerging infectious disease

PubMed Central

Hoberg, Eric P.; Brooks, Daniel R.

2015-01-01

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host–parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)—phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference—provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. PMID:25688014

Co-infection does not predict disease signs in Gopherus tortoises

PubMed Central

Gov, Ryan; Sandmeier, Franziska C.; Snyder, Sarah J.; Tracy, C. Richard

2017-01-01

In disease ecology, the host immune system interacts with environmental conditions and pathogen properties to affect the impact of disease on the host. Within the host, pathogens may interact to facilitate or inhibit each other's growth, and pathogens interact with different hosts differently. We investigated co-infection of two Mycoplasma and the association of infection with clinical signs of upper respiratory tract disease in four congeneric tortoise host species (Gopherus) in the United States to detect differences in infection risk and disease dynamics in these hosts. Mojave Desert tortoises had greater prevalence of Mycoplasma agassizii than Texas tortoises and gopher tortoises, while there were no differences in Mycoplasma testudineum prevalence among host species. In some host species, the presence of each pathogen influenced the infection intensity of the other; hence, these two mycoplasmas interact differently within different hosts, and our results may indicate facilitation of these bacteria. Neither infection nor co-infection was associated with clinical signs of disease, which tend to fluctuate across time. From M. agassizii DNA sequences, we detected no meaningful differentiation of haplotypes among hosts. Experimental inoculation studies and recurrent resampling of wild individuals could help to decipher the underlying mechanisms of disease dynamics in this system. PMID:29134096

The Worm Propagation Model with Dual Dynamic Quarantine Strategy

NASA Astrophysics Data System (ADS)

Yao, Yu; Xie, Xiao-Wu; Guo, Hao; Gao, Fu-Xiang; Yu, Ge

Internet worms are becoming more and more harmful with the rapid development of the Internet. Due to the extremely fast spread and great destructive power of network worms, strong dynamic quarantine strategies are necessary. Inspired by the real-world approach to the prevention and treatment of infectious diseases, this paper proposes a quarantine strategy based on dynamic worm propagation model: the SIQRV dual quarantine model. This strategy uses dynamic quarantine method to make the vulnerable host and infected host quarantined, and then release them after a certain period of time, regardless of whether quarantined host security is checked. Through mathematic modeling, it has been found that when the basic reproduction number R0 is less than a critical value, the system will stabilize in the disease-free equilibrium, that is, in theory, the infected hosts will be completely immune. Finally, by comparing the simulation results and numerical analysis, the basic agreement between the two curves supports the validity of the mathematical model. Our future work will be focusing on taking both the delay and double-quarantine strategy into account and further expanding the scale of our simulation work.

Mycobacterium ulcerans dynamics in aquatic ecosystems are driven by a complex interplay of abiotic and biotic factors

PubMed Central

Garchitorena, Andrés; Guégan, Jean-François; Léger, Lucas; Eyangoh, Sara; Marsollier, Laurent; Roche, Benjamin

2015-01-01

Host–parasite interactions are often embedded within complex host communities and can be influenced by a variety of environmental factors, such as seasonal variations in climate or abiotic conditions in water and soil, which confounds our understanding of the main drivers of many multi-host pathogens. Here, we take advantage of a combination of large environmental data sets on Mycobacterium ulcerans (MU), an environmentally persistent microorganism associated to freshwater ecosystems and present in a large variety of aquatic hosts, to characterize abiotic and biotic factors driving the dynamics of this pathogen in two regions of Cameroon. We find that MU dynamics are largely driven by seasonal climatic factors and certain physico-chemical conditions in stagnant and slow-flowing ecosystems, with an important role of pH as limiting factor. Furthermore, water conditions can modify the effect of abundance and diversity of aquatic organisms on MU dynamics, which suggests a different contribution of two MU transmission routes for aquatic hosts (trophic vs environmental transmission) depending on local abiotic factors. DOI: http://dx.doi.org/10.7554/eLife.07616.001 PMID:26216042

Topographically induced internal solitary waves in a pycnocline: Ultrasonic probes and stereo-correlation measurements

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

Dossmann, Yvan, E-mail: yvan.dossmann@anu.edu.au; CNRM-GAME, UMR3589 METEO-FRANCE and CNRS, 42 avenue Gaspard Coriolis, 31057 Toulouse Cedex 01; Laboratoire d’Aérologie, 14 avenue Edouard Belin, 31400 Toulouse

Internal solitary waves (ISWs) are large amplitude stable waves propagating in regions of high density gradients such as the ocean pycnocline. Their dynamics has often been investigated in two-dimensional approaches, however, their three-dimensional evolution is still poorly known. Experiments have been conducted in the large stratified water tank of CNRM-GAME to study the generation of ISWs in two academic configurations inspired by oceanic regimes. First, ultrasonic probes are used to measure the interfacial displacement in the two configurations. In the primary generation case for which the two layers are of constant density, the generation of ISWs is investigated in twomore » series of experiments with varying amplitude and forcing frequency. In the secondary generation case for which the lower layer is stratified, the generation of ISWs from the impact of an internal wave beam on the pycnocline and their subsequent dynamics is studied. The dynamics of ISWs in these two regimes accords well with analytical approaches and numerical simulations performed in analogous configurations. Then, recent developments of a stereo correlation technique are used to describe the three-dimensional structure of propagating ISWs. In the primary generation configuration, small transverse effects are observed in the course of the ISW propagation. In the secondary generation configuration, larger transverse structures are observed in the interfacial waves dynamics. The interaction between interfacial troughs and internal waves propagating in the lower stratified layer are a possible cause for the generation of these structures. The magnitude of these transverse structures is quantified with a nondimensional parameter in the two configurations. They are twice as large in the secondary generation case as in the primary generation case.« less

From Within Host Dynamics to the Epidemiology of Infectious Disease: Scientific Overview and Challenges

PubMed Central

Gutierrez, Juan B.; Galinski, Mary R.; Cantrell, Stephen; Voit, Eberhard O.

2015-01-01

Since their earliest days, humans have been struggling with infectious diseases. Caused by viruses, bacteria, protozoa, or even higher organisms like worms, these diseases depend critically on numerous intricate interactions between parasites and hosts, and while we have learned much about these interactions, many details are still obscure. It is evident that the combined host-parasite dynamics constitutes a complex system that involves components and processes at multiple scales of time, space, and biological organization. At one end of this hierarchy we know of individual molecules that play crucial roles for the survival of a parasite or for the response and survival of its host. At the other end, one realizes that the spread of infectious diseases by far exceeds specific locales and, due to today's easy travel of hosts carrying a multitude of organisms, can quickly reach global proportions. The community of mathematical modelers has been addressing specific aspects of infectious diseases for a long time. Most of these efforts have focused on one or two select scales of a multi-level disease and used quite different computational approaches. This restriction to a molecular, physiological, or epidemiological level was prudent, as it has produced solid pillars of a foundation from which it might eventually be possible to launch comprehensive, multi-scale modeling efforts that make full use of the recent advances in biology and, in particular, the various high-throughput methodologies accompanying the emerging –omics revolution. This special issue contains contributions from biologists and modelers, most of whom presented and discussed their work at the workshop From within Host Dynamics to the Epidemiology of Infectious Disease, which was held at the Mathematical Biosciences Institute at Ohio State University in April 2014. These contributions highlight some of the forays into a deeper understanding of the dynamics between parasites and their hosts, and the consequences of this dynamics for the spread and treatment of infectious diseases. PMID:26474512

Alternate space station freedom configuration considerations to accommodate solar dynamic power

NASA Technical Reports Server (NTRS)

Deryder, L. J.; Cruz, J. N.; Heck, M. L.; Robertson, B. P.; Troutman, P. A.

1989-01-01

The results of a technical audit of the Space Station Freedom Program conducted by the Program Director was announced in early 1989 and included a proposal to use solar dynamic power generation systems to provide primary electrical energy for orbital flight operations rather than photovoltaic solar array systems. To generate the current program baseline power of 75 kW, two or more solar concentrators approximately 50 feet in diameter would be required to replace four pairs of solar arrays whose rectangular blanket size is approximately 200 feet by 30 feet. The photovoltaic power system concept uses solar arrays to generate electricity that is stored in nickel-hydrogen batteries. The proposed concept uses the solar concentrator dishes to reflect and focus the Sun's energy to heat helium-xenon gas to drive electricity generating turbines. The purpose here is to consider the station configuration issues for incorporation of solar dynamic power system components. Key flight dynamic configuration geometry issues are addressed and an assembly sequence scenario is developed.

Macroscopic damping model for structural dynamics with random polycrystalline configurations

NASA Astrophysics Data System (ADS)

Yang, Yantao; Cui, Junzhi; Yu, Yifan; Xiang, Meizhen

2018-06-01

In this paper the macroscopic damping model for dynamical behavior of the structures with random polycrystalline configurations at micro-nano scales is established. First, the global motion equation of a crystal is decomposed into a set of motion equations with independent single degree of freedom (SDOF) along normal discrete modes, and then damping behavior is introduced into each SDOF motion. Through the interpolation of discrete modes, the continuous representation of damping effects for the crystal is obtained. Second, from energy conservation law the expression of the damping coefficient is derived, and the approximate formula of damping coefficient is given. Next, the continuous damping coefficient for polycrystalline cluster is expressed, the continuous dynamical equation with damping term is obtained, and then the concrete damping coefficients for a polycrystalline Cu sample are shown. Finally, by using statistical two-scale homogenization method, the macroscopic homogenized dynamical equation containing damping term for the structures with random polycrystalline configurations at micro-nano scales is set up.

Host-virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: survival of the fattest.

PubMed

Pagarete, António; Allen, Michael J; Wilson, William H; Kimmance, Susan A; de Vargas, Colomban

2009-11-01

The interactions between viruses and phytoplankton play a key role in shaping the ecological and evolutionary dynamics of oceanic ecosystems. One of the most fascinating examples of horizontal gene transfer between a eukaryotic host and its virus is a de novo sphingolipid biosynthesis pathway (SBP) found in the genomes of both Emiliania huxleyi and its coccolithovirus EhV-86. Here, we focus on a natural E. huxleyi/coccolithovirus system off the coast of Norway and investigate the dynamics of host and virus homologous gene expression for two of the most important sphingolipid biosynthesis enzymes, serine palmitoyl transferase (SPT) and dihydroceramide desaturase (DCD). Transcriptional dynamics display three defined stages along E. huxleyi bloom formation and decline, with the coccolithovirus transcripts taking over and controlling the SBP in stages 2 and 3. The observed patterns fit the hypothesis according to which viral sphingolipids are involved in the timing and physical processes of virion release from the host cells. This study provides a unique insight into the transcriptional interplay of homologous metabolic pathways between virus and host during temporal progression of oceanic E. huxleyi blooms.

Lymph Node Cellular and Viral Dynamics in Natural Hosts and Impact for HIV Cure Strategies.

PubMed

Huot, Nicolas; Bosinger, Steven E; Paiardini, Mirko; Reeves, R Keith; Müller-Trutwin, Michaela

2018-01-01

Combined antiretroviral therapies (cARTs) efficiently control HIV replication leading to undetectable viremia and drastic increases in lifespan of people living with HIV. However, cART does not cure HIV infection as virus persists in cellular and anatomical reservoirs, from which the virus generally rebounds soon after cART cessation. One major anatomical reservoir are lymph node (LN) follicles, where HIV persists through replication in follicular helper T cells and is also trapped by follicular dendritic cells. Natural hosts of SIV, such as African green monkeys and sooty mangabeys, generally do not progress to disease although displaying persistently high viremia. Strikingly, these hosts mount a strong control of viral replication in LN follicles shortly after peak viremia that lasts throughout infection. Herein, we discuss the potential interplay between viral control in LNs and the resolution of inflammation, which is characteristic for natural hosts. We furthermore detail the differences that exist between non-pathogenic SIV infection in natural hosts and pathogenic HIV/SIV infection in humans and macaques regarding virus target cells and replication dynamics in LNs. Several mechanisms have been proposed to be implicated in the strong control of viral replication in natural host's LNs, such as NK cell-mediated control, that will be reviewed here, together with lessons and limitations of in vivo cell depletion studies that have been performed in natural hosts. Finally, we discuss the impact that these insights on viral dynamics and host responses in LNs of natural hosts have for the development of strategies toward HIV cure.

Further studies on criteria for the onset of dynamical instability in general three-body systems

NASA Technical Reports Server (NTRS)

Pendleton, Y. J.; Black, D. C.

1983-01-01

Numerical experiments designed for the elucidation of the conditions under which self-gravitating, three-body systems become dynamically unstable are examined of the cases of four orbital configuration types: circular, prograde, and coplanar; circular, retrograde, and coplanar; circular, direct, and inclined; and eccentric, direct, and coplanar. Results indicate that orbital inclination does not significantly affect stability in 'outer planet' configurations, while the stability of 'inner planet' configurations, where the tertiary is in close orbit about one member of the binary, is markedly less affected, once the relative orbital inclination is greater than 50 deg. It is found that the onset of dynamical instability is only weakly dependent on the eccentricity of either the binary or tertiary orbit, as long as the mass of the tertiary is comparable to the reduced mass of the binary.

Dynamic/Jitter Assessment of Multiple Potential HabEx Structural Designs

NASA Technical Reports Server (NTRS)

Knight, J. Brent; Stahl, H. Philip; Singleton, Andy; Hunt, Ron; Therrell, Melissa; Caldwell, Kate; Garcia, Jay; Baysinger, Mike

2017-01-01

One of the driving structural requirements of the Habitable Exo-Planet (HabEx) telescope is to maintain Line Of Sight (LOS) stability between the Primary Mirror (PM) and Secondary Mirror (SM) of = 5 mas. Dynamic analyses of two configurations of a proposed (HabEx) 4 meter off-axis telescope structure were performed to predict effects of jitter on primary/secondary mirror alignment. The dynamic disturbance used as the forcing function was the James Webb Space Telescope reaction wheel assembly vibration emission specification level. The objective of these analyses was to predict "order-of-magnitude" performance for various structural configurations which will roll into efforts to define the HabEx structural design's global architecture. Two variations of the basic architectural design were analyzed. Relative motion between the PM and the SM for each design configuration are reported.

Dynamic/jitter assessment of multiple potential HabEx structural designs

NASA Astrophysics Data System (ADS)

Knight, J. Brent; Stahl, H. Philip; Singleton, Andy; Hunt, Ron; Therrell, Melissa; Caldwell, Kate; Garcia, Jay; Baysinger, Mike

2017-09-01

One of the driving structural requirements of the Habitable Exo-Planet (HabEx) telescope is to maintain Line Of Sight (LOS) stability between the Primary Mirror (PM) and Secondary Mirror (SM) of <= 5 milli-arc seconds (mas). Dynamic analyses of two configurations of a proposed HabEx 4 meter off-axis telescope structure were performed to predict effects of a vibration input on primary/secondary mirror alignment. The dynamic disturbance used as the forcing function was the James Webb Space Telescope reaction wheel assembly vibration emission specification level. The objective of these analyses was to predict "order-of-magnitude" performance for various structural configurations which contribute to efforts in defining the HabEx structural design's global architecture. Two variations of the basic architectural design were analyzed. Relative motion between the PM and the SM for each design configuration are reported.

Effect of Air Swirler Configuration on Lean Direct Injector Flow Structure and Combustion Performance with a 7-Point Lean Direct Injector Array

NASA Technical Reports Server (NTRS)

Hicks, Yolanda R.; Tacina, Kathleen M.; Anderson, Robert C.

2017-01-01

Studies of various injector configurations in a 7-point Lean Direct Injector (LDI) array are reported for both non-reacting (cold) flow and for Jet-A/air reacting flows. For cold flow, central recirculation zone (CRZ) formation is investigated and for reacting flows, combustor operability and dynamics are of interest. 2D Particle Image Velocimetry (PIV) measurements are described for the cold flow experiments and flame chemiluminescence imaging and dynamic pressure results are discussed for the reacting flow cases. PIV results indicate that for this configuration the close spacing between swirler elements leads to strong interaction that affects whether a CRZ forms, and pilot recess and counter-swirl helps to isolate swirlers from one another. Dynamics results focus on features identified near 500-Hz.

On reliable control system designs. Ph.D. Thesis; [actuators

NASA Technical Reports Server (NTRS)

Birdwell, J. D.

1978-01-01

A mathematical model for use in the design of reliable multivariable control systems is discussed with special emphasis on actuator failures and necessary actuator redundancy levels. The model consists of a linear time invariant discrete time dynamical system. Configuration changes in the system dynamics are governed by a Markov chain that includes transition probabilities from one configuration state to another. The performance index is a standard quadratic cost functional, over an infinite time interval. The actual system configuration can be deduced with a one step delay. The calculation of the optimal control law requires the solution of a set of highly coupled Riccati-like matrix difference equations. Results can be used for off-line studies relating the open loop dynamics, required performance, actuator mean time to failure, and functional or identical actuator redundancy, with and without feedback gain reconfiguration strategies.

Influence of Multiple Infection and Relatedness on Virulence: Disease Dynamics in an Experimental Plant Population and Its Castrating Parasite

PubMed Central

Buono, Lorenza; López-Villavicencio, Manuela; Shykoff, Jacqui A.; Snirc, Alodie; Giraud, Tatiana

2014-01-01

The level of parasite virulence, i.e., the decrease in host's fitness due to a pathogen, is expected to depend on several parameters, such as the type of the disease (e.g., castrating or host-killing) and the prevalence of multiple infections. Although these parameters have been extensively studied theoretically, few empirical data are available to validate theoretical predictions. Using the anther smut castrating disease on Silene latifolia caused by Microbotryum lychnidis-dioicae, we studied the dynamics of multiple infections and of different components of virulence (host death, non-recovery and percentage of castrated stems) during the entire lifespan of the host in an experimental population. We monitored the number of fungal genotypes within plants and their relatedness across five years, using microsatellite markers, as well as the rates of recovery and host death in the population. The mean relatedness among genotypes within plants remained at a high level throughout the entire host lifespan despite the dynamics of the disease, with recurrent new infections. Recovery was lower for plants with multiple infections compared to plants infected by a single genotype. As expected for castrating parasites, M. lychnidis-dioicae did not increase host mortality. Mortality varied across years but was generally lower for plants that had been diseased the preceding year. This is one of the few studies to have empirically verified theoretical expectations for castrating parasites, and to show particularly i) that castrated hosts live longer, suggesting that parasites can redirect resources normally used in reproduction to increase host lifespan, lengthening their transmission phase, and ii) that multiple infections increase virulence, here in terms of non-recovery and host castration. PMID:24892951

A synthetic eicosanoid LX-mimetic unravels host-donor interactions in allogeneic BMT-induced GvHD to reveal an early protective role for host neutrophils.

PubMed

Devchand, Pallavi R; Schmidt, Birgitta A; Primo, Valeria C; Zhang, Qing-yin; Arnaout, M Amin; Serhan, Charles N; Nikolic, Boris

2005-02-01

Lipoxin A(4) (LXA(4)) and aspirin-triggered 15-epi-LXA(4) are potent endogenous lipid mediators thought to define the inflammatory set-point. We used single prophylactic administrations of a synthetic aspirin-triggered lipoxin A(4) signal mimetic, ATLa, to probe dynamics of early host-donor interactions in a mouse model for the inflammation-associated multifactorial disease of allogeneic bone marrow transplant (BMT) -induced graft-vs.-host disease (GvHD). We first demonstrated that both host and donor are responsive to the ATLa signals. The simple and restricted regimen of a single prophylactic administration of ATLa [100 ng/mL to donor cells or 1 microg (approximately 50 microg/kg) i.v. to host] was sufficient to delay death. Clinical indicators of weight, skin lesions, diarrhea and eye inflammation were monitored. Histological analyses on day 45 post-BMT showed that the degree of cellular trafficking, particularly neutrophil infiltrate, and protection of end-organ target pathology are different, depending on whether the host or donor was treated with ATLa. Taken together, these results chart some ATLa protective effects on GvHD cellular dynamics over time and identify a previously unrecognized effect of host neutrophils in the early phase post-BMT as important determinants in the dynamics of GvHD onset and progression.-Devchand, P. R., Schmidt, B. A., Primo, V. C., Zhang, Q.-y., Arnaout, M. A., Serhan, C. N., Nikolic, B. A synthetic eicosanoid LX-mimetic unravels host-donor interactions in allogeneic BMT-induced GvHD to reveal an early protective role for host neutrophils.

Multi-stage Vector-Borne Zoonoses Models: A Global Analysis.

PubMed

Bichara, Derdei; Iggidr, Abderrahman; Smith, Laura

2018-04-25

A class of models that describes the interactions between multiple host species and an arthropod vector is formulated and its dynamics investigated. A host-vector disease model where the host's infection is structured into n stages is formulated and a complete global dynamics analysis is provided. The basic reproduction number acts as a sharp threshold, that is, the disease-free equilibrium is globally asymptotically stable (GAS) whenever [Formula: see text] and that a unique interior endemic equilibrium exists and is GAS if [Formula: see text]. We proceed to extend this model with m host species, capturing a class of zoonoses where the cross-species bridge is an arthropod vector. The basic reproduction number of the multi-host-vector, [Formula: see text], is derived and shown to be the sum of basic reproduction numbers of the model when each host is isolated with an arthropod vector. It is shown that the disease will persist in all hosts as long as it persists in one host. Moreover, the overall basic reproduction number increases with respect to the host and that bringing the basic reproduction number of each isolated host below unity in each host is not sufficient to eradicate the disease in all hosts. This is a type of "amplification effect," that is, for the considered vector-borne zoonoses, the increase in host diversity increases the basic reproduction number and therefore the disease burden.

The specificity of host-bat fly interaction networks across vegetation and seasonal variation.

PubMed

Zarazúa-Carbajal, Mariana; Saldaña-Vázquez, Romeo A; Sandoval-Ruiz, César A; Stoner, Kathryn E; Benitez-Malvido, Julieta

2016-10-01

Vegetation type and seasonality promote changes in the species composition and abundance of parasite hosts. However, it is poorly known how these variables affect host-parasite interaction networks. This information is important to understand the dynamics of parasite-host relationships according to biotic and abiotic changes. We compared the specialization of host-bat fly interaction networks, as well as bat fly and host species composition between upland dry forest and riparian forest and between dry and rainy seasons in a tropical dry forest in Jalisco, Mexico. Bat flies were surveyed by direct collection from bats. Our results showed that host-bat fly interaction networks were more specialized in upland dry forest compared to riparian forest. Bat fly species composition was different between the dry and rainy seasons, while host species composition was different between upland dry forest and riparian forest. The higher specialization in upland dry forest could be related to the differences in bat host species composition and their respective roosting habits. Variation in the composition of bat fly species between dry and rainy seasons coincides with the seasonal shifts in their species richness. Our study confirms the high specialization of host-bat fly interactions and shows the importance of biotic and abiotic factors to understand the dynamics of parasite-host interactions.

Evolution in action: climate change, biodiversity dynamics and emerging infectious disease.

PubMed

Hoberg, Eric P; Brooks, Daniel R

2015-04-05

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host-parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)--phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference--provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Conformational changes in intact dengue virus reveal serotype-specific expansion

PubMed Central

Lim, Xin-Xiang; Chandramohan, Arun; Lim, Xin Ying Elisa; Bag, Nirmalya; Sharma, Kamal Kant; Wirawan, Melissa; Wohland, Thorsten; Lok, Shee-Mei; Anand, Ganesh S.

2017-01-01

Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37 °C (associated with host entry), despite high sequence and structural homology among the four known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of two serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Förster Resonance Energy Transfer. Our results show temperature-dependent dynamics hotspots on DENV2 and DENV1 particles with DENV1 showing expansion at 40 °C but not at 37 °C. HDXMS measurement of virion dynamics in solution offers a powerful approach to identify potential epitopes, map virus-antibody complex structure and dynamics, and test effects of multiple host-specific perturbations on viruses and virus-antibody complexes. PMID:28186093

Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence.

PubMed

Clerc, Melanie; Ebert, Dieter; Hall, Matthew D

2015-04-07

How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite Pasteuria ramosa infecting the crustacean Daphnia magna. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Automated Tetrahedral Mesh Generation for CFD Analysis of Aircraft in Conceptual Design

NASA Technical Reports Server (NTRS)

Ordaz, Irian; Li, Wu; Campbell, Richard L.

2014-01-01

The paper introduces an automation process of generating a tetrahedral mesh for computational fluid dynamics (CFD) analysis of aircraft configurations in early conceptual design. The method was developed for CFD-based sonic boom analysis of supersonic configurations, but can be applied to aerodynamic analysis of aircraft configurations in any flight regime.

Dynamics of a gravity-gradient stabilized flexible spacecraft

NASA Technical Reports Server (NTRS)

Meirovitch, L.; Juang, J. N.

1974-01-01

The dynamics of gravity-gradient stabilized flexible satellite in the neighborhood of a deformed equilibrium configuration are discussed. First the equilibrium configuration was determined by solving a set of nonlinear differential equations. Then stability of motion about the deformed equilibrium was tested by means of the Liapunov direct method. The natural frequencies of oscillation of the complete structure were calculated. The analysis is applicable to the RAE/B satellite.

Programmable superpositions of Ising configurations

NASA Astrophysics Data System (ADS)

Sieberer, Lukas M.; Lechner, Wolfgang

2018-05-01

We present a framework to prepare superpositions of bit strings, i.e., many-body spin configurations, with deterministic programmable probabilities. The spin configurations are encoded in the degenerate ground states of the lattice-gauge representation of an all-to-all connected Ising spin glass. The ground-state manifold is invariant under variations of the gauge degrees of freedom, which take the form of four-body parity constraints. Our framework makes use of these degrees of freedom by individually tuning them to dynamically prepare programmable superpositions. The dynamics combines an adiabatic protocol with controlled diabatic transitions. We derive an effective model that allows one to determine the control parameters efficiently even for large system sizes.

Exciton intrachain transport induced by interchain packing configurations in conjugated polymers.

PubMed

Meng, Ruixuan; Gao, Kun; Zhang, Gaiyan; Han, Shixuan; Yang, Fujiang; Li, Yuan; Xie, Shijie

2015-07-28

Based on a tight binding model combined with a nonadiabatic dynamics approach, we theoretically investigate the exciton intrachain transport in conjugated polymers with different interchain packing configurations. We construct two different interchain packing configurations, i.e. linear and exponential forms, and simulate the dynamical processes of the exciton transport in these systems. We find that, in both cases, there exists a distribution of driving force for exciton transport, which stems from the gradient of the exciton creation energy along the chains. This finding enriches the picture of exciton transport in polymers and provides a new idea to improve the exciton transport length in polymeric photovoltaic devices.

Mixed-Fidelity Approach for Design of Low-Boom Supersonic Aircraft

NASA Technical Reports Server (NTRS)

Li, Wu; Shields, Elwood; Geiselhart, Karl

2011-01-01

This paper documents a mixed-fidelity approach for the design of low-boom supersonic aircraft with a focus on fuselage shaping.A low-boom configuration that is based on low-fidelity analysis is used as the baseline. The fuselage shape is modified iteratively to obtain a configuration with an equivalent-area distribution derived from computational fluid dynamics analysis that attempts to match a predetermined low-boom target area distribution and also yields a low-boom ground signature. The ground signature of the final configuration is calculated by using a state-of-the-art computational-fluid-dynamics-based boom analysis method that generates accurate midfield pressure distributions for propagation to the ground with ray tracing. The ground signature that is propagated from a midfield pressure distribution has a shaped ramp front, which is similar to the ground signature that is propagated from the computational fluid dynamics equivalent-area distribution. This result supports the validity of low-boom supersonic configuration design by matching a low-boom equivalent-area target, which is easier to accomplish than matching a low-boom midfield pressure target.

A Comparison of Combustion Dynamics for Multiple 7-Point Lean Direct Injection Combustor Configurations

NASA Technical Reports Server (NTRS)

Tacina, K. M.; Hicks, Y. R.

2017-01-01

The combustion dynamics of multiple 7-point lean direct injection (LDI) combustor configurations are compared. LDI is a fuel-lean combustor concept for aero gas turbine engines in which multiple small fuel-air mixers replace one traditionally-sized fuel-air mixer. This 7-point LDI configuration has a circular cross section, with a center (pilot) fuel-air mixer surrounded by six outer (main) fuel-air mixers. Each fuel-air mixer consists of an axial air swirler followed by a converging-diverging venturi. A simplex fuel injector is inserted through the center of the air swirler, with the fuel injector tip located near the venturi throat. All 7 fuel-air mixers are identical except for the swirler blade angle, which varies with the configuration. Testing was done in a 5-atm flame tube with inlet air temperatures from 600 to 800 F and equivalence ratios from 0.4 to 0.7. Combustion dynamics were measured using a cooled PCB pressure transducer flush-mounted in the wall of the combustor test section.

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

Mittal, Sparsh; Zhang, Zhao

With each CMOS technology generation, leakage energy consumption has been dramatically increasing and hence, managing leakage power consumption of large last-level caches (LLCs) has become a critical issue in modern processor design. In this paper, we present EnCache, a novel software-based technique which uses dynamic profiling-based cache reconfiguration for saving cache leakage energy. EnCache uses a simple hardware component called profiling cache, which dynamically predicts energy efficiency of an application for 32 possible cache configurations. Using these estimates, system software reconfigures the cache to the most energy efficient configuration. EnCache uses dynamic cache reconfiguration and hence, it does not requiremore » offline profiling or tuning the parameter for each application. Furthermore, EnCache optimizes directly for the overall memory subsystem (LLC and main memory) energy efficiency instead of the LLC energy efficiency alone. The experiments performed with an x86-64 simulator and workloads from SPEC2006 suite confirm that EnCache provides larger energy saving than a conventional energy saving scheme. For single core and dual-core system configurations, the average savings in memory subsystem energy over a shared baseline configuration are 30.0% and 27.3%, respectively.« less

The Merger-Free Growth of Galaxies and Supermassive Black Holes

NASA Astrophysics Data System (ADS)

Simmons, Brooke; Smethurst, Rebecca; Lintott, Chris; Martin, Garreth; Kaviraj, Sugata; Devriendt, Julien; Galaxy Zoo Team

2018-01-01

There is now clear evidence that the merger-driven pathway to black hole and galaxy growth is only half the story. Merger-free evolution contributes roughly equally to the overall growth of black holes in the Universe and is also responsible for a significant amount of galaxy growth over cosmic time. A recent study examining the growth of black holes in unambiguously disk-dominated galaxies shows these black holes reach quasar-like luminosities and black hole masses typical of those hosted in bulge-dominated and elliptical galaxies with major mergers in their evolutionary histories. However, while there appears to be no correlation between the size of the black hole and upper limits on the host galaxy bulges, the fitted correlation between black hole mass and total galaxy stellar mass in these merger-free systems is fully consistent with the canonical relationship based on merger-driven systems. There is further evidence via comparison between observed populations and cosmological simulations confirming that bulgeless systems are generally consistent with having merger-free histories. If bulgeless and disk-dominated galaxies are indeed signatures of systems with no violent mergers in their formation histories, the same correlation between black hole and galaxy in these systems versus that seen in elliptical galaxy samples indicates the black hole-galaxy connection must originate with a process more fundamental than the dynamical configuration of a galaxy's stars.

Assessment of optimal strategies in a two-patch dengue transmission model with seasonality.

PubMed

Kim, Jung Eun; Lee, Hyojung; Lee, Chang Hyeong; Lee, Sunmi

2017-01-01

Emerging and re-emerging dengue fever has posed serious problems to public health officials in many tropical and subtropical countries. Continuous traveling in seasonally varying areas makes it more difficult to control the spread of dengue fever. In this work, we consider a two-patch dengue model that can capture the movement of host individuals between and within patches using a residence-time matrix. A previous two-patch dengue model without seasonality is extended by adding host demographics and seasonal forcing in the transmission rates. We investigate the effects of human movement and seasonality on the two-patch dengue transmission dynamics. Motivated by the recent Peruvian dengue data in jungle/rural areas and coast/urban areas, our model mimics the seasonal patterns of dengue outbreaks in two patches. The roles of seasonality and residence-time configurations are highlighted in terms of the seasonal reproduction number and cumulative incidence. Moreover, optimal control theory is employed to identify and evaluate patch-specific control measures aimed at reducing dengue prevalence in the presence of seasonality. Our findings demonstrate that optimal patch-specific control strategies are sensitive to seasonality and residence-time scenarios. Targeting only the jungle (or endemic) is as effective as controlling both patches under weak coupling or symmetric mobility. However, focusing on intervention for the city (or high density areas) turns out to be optimal when two patches are strongly coupled with asymmetric mobility.

Joint  effects of habitat configuration and temporal stochasticity on population dynamics

Treesearch

Jennifer M. Fraterrigo; Scott M. Pearson; Monica G. Turner

2009-01-01

Habitat configuration and temporal stochasticity in the environment are recognized as important drivers of population structure, yet few studies have examined the combined influence of these factors....

MULTISCALE MODEL OF CRISPR-INDUCED COEVOLUTIONARY DYNAMICS: DIVERSIFICATION AT THE INTERFACE OF LAMARCK AND DARWIN

PubMed Central

Childs, Lauren M; Held, Nicole L; Young, Mark J; Whitaker, Rachel J; Weitz, Joshua S

2012-01-01

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multiscale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of existent strains, such that populations have very low similarity compared over the long term. However, in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains (as single strains and coalitions) and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active. PMID:22759281

Dynamics of a feline virus with two transmission modes within exponentially growing host populations.

PubMed Central

Berthier, K; Langlais, M; Auger, P; Pontier, D

2000-01-01

Feline panleucopenia virus (FPLV) was introduced in 1977 on Marion Island (in the southern Indian Ocean) with the aim of eradicating the cat population and provoked a huge decrease in the host population within six years. The virus can be transmitted either directly through contacts between infected and healthy cats or indirectly between a healthy cat and the contaminated environment: a specific feature of the virus is its high rate of survival outside the host. In this paper, a model was designed in order to take these two modes of transmission into account. The results showed that a mass-action incidence assumption was more appropriate than a proportionate mixing one in describing the dynamics of direct transmission. Under certain conditions the virus was able to control the host population at a low density. The indirect transmission acted as a reservoir supplying the host population with a low but sufficient density of infected individuals which allowed the virus to persist. The dynamics of the infection were more affected by the demographic parameters of the healthy hosts than by the epidemiological ones. Thus, demographic parameters should be precisely measured in field studies in order to obtain accurate predictions. The predicted results of our model were in good agreement with observations. PMID:11416908

Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

PubMed

Burdon, J J; Thrall, P H; Ericson, L

2013-08-01

Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evolutionary dynamics of host-plant specialization: a case study of the tribe Nymphalini.

PubMed

Janz, N; Nyblom, K; Nylin, S

2001-04-01

Two general patterns that have emerged from the intense studies on insect-host plant associations are a predominance of specialists over generalists and a taxonomic conservatism in host-plant use. In most insect-host plant systems, explanations for these patterns must be based on biases in the processes of host colonizations, host shifts, and specialization, rather than cospeciation. In the present paper, we investigate changes in host range in the nymphalid butterfly tribe Nymphalini, using parsimony optimizations of host-plant data on the butterfly phylogeny. In addition, we performed larval establishment tests to search for larval capacity to feed and survive on plants that have been lost from the female egg-laying repertoire. Optimizations suggested an ancestral association with Urticaceae, and most of the tested species showed a capacity to feed on Urtica dioica regardless of actual host-plant use. In addition, there was a bias among the successful establishments on nonhosts toward plants that are used as hosts by other species in the Nymphalini. An increased likelihood of colonizing ancestral or related plants could also provide an alternative explanation for the observed pattern that some plant families appear to have been colonized independently several times in the tribe. We also show that there is no directionality in host range evolution toward increased specialization, that is, specialization is not a dead end. Instead, changes in host range show a very dynamic pattern.

A new approach to barrier-top fission dynamics

NASA Astrophysics Data System (ADS)

Bertsch, G. F.; Mehlhaff, J. M.

2016-06-01

We proposed a calculational framework for describing induced fission that avoids the Bohr-Wheeler assumption of well-defined fission channels. The building blocks of our approach are configurations that form a discrete, orthogonal basis and can be characterized by both energy and shape. The dynamics is to be determined by interaction matrix elements between the states rather than by a Hill-Wheeler construction of a collective coordinate. Within our approach, several simple limits can be seen: diffusion; quantized conductance; and ordinary decay through channels. The specific proposal for the discrete basis is to use the Kπ quantum numbers of the axially symmetric Hartree-Fock approximation to generate the configurations. Fission paths would be determined by hopping from configuration to configuration via the residual interaction. We show as an example the configurations needed to describe a fictitious fission decay 32S → 16 O + 16 O. We also examine the geometry of the path for fission of 236U, measuring distances by the number of jumps needed to go to a new Kπ partition.

Dynamic axial crushing of bitubular tubes with curvy polygonal inner-tube sections

NASA Astrophysics Data System (ADS)

Ahmed, Naveed; Xue, Pu; Zafar, Naeem

Bitubular structural configurations, where the outer tube is circular, square and curvy square in shape while the inner-tube section is curvy triangular, square and hexagonal in different proposed configurations, are numerically crushed under dynamic axial loading. The crashworthiness effectiveness for changing inner-tube polygonal cross-section for each of the outer tube sections is studied and compared with changing outer tube shape. The deformation plots and energy absorption (EA) parameters such as peak crushing force (PCF) mean crushing force (MCF), energy absorption and crush force efficiency for each case are evaluated. Most of the configurations showed ovalization with low PCF and MCF and moderate crush force efficiency. Afterwards, effects of L/D and t/R on deformation modes and EA are demonstrated by selecting one of the configurations from each group using published experimental results.

Comparing Methods for Dynamic Airspace Configuration

NASA Technical Reports Server (NTRS)

Zelinski, Shannon; Lai, Chok Fung

2011-01-01

This paper compares airspace design solutions for dynamically reconfiguring airspace in response to nominal daily traffic volume fluctuation. Airspace designs from seven algorithmic methods and a representation of current day operations in Kansas City Center were simulated with two times today's demand traffic. A three-configuration scenario was used to represent current day operations. Algorithms used projected unimpeded flight tracks to design initial 24-hour plans to switch between three configurations at predetermined reconfiguration times. At each reconfiguration time, algorithms used updated projected flight tracks to update the subsequent planned configurations. Compared to the baseline, most airspace design methods reduced delay and increased reconfiguration complexity, with similar traffic pattern complexity results. Design updates enabled several methods to as much as half the delay from their original designs. Freeform design methods reduced delay and increased reconfiguration complexity the most.

Separate Flow Nozzle Test Status Meeting

NASA Technical Reports Server (NTRS)

Saiyed, Naseem H. (Editor)

2000-01-01

NASA Glenn, in partnership with US industry, completed an exhaustive experimental study on jet noise reduction from separate flow nozzle exhaust systems. The study developed a data base on various bypass ratio nozzles, screened quietest configurations and acquired pertinent data for predicting the plume behavior and ultimately its corresponding jet noise. Several exhaust system configurations provided over 2.5 EPNdB jet noise reduction at take-off power. These data were disseminated to US aerospace industry in a conference hosted by NASA GRC whose proceedings are shown in this report.

The instrumental principles of MST radars and incoherent scatter radars and the configuration of radar system hardware

NASA Technical Reports Server (NTRS)

Roettger, Juergen

1989-01-01

The principle of pulse modulation used in the case of coherent scatter radars (MST radars) is discussed. Coherent detection and the corresponding system configuration is delineated. Antenna requirements and design are outlined and the phase-coherent transmitter/receiver system is described. Transmit/receive duplexers, transmitters, receivers, and quadrature detectors are explained. The radar controller, integrator, decoder and correlator design as well as the data transfer and the control and monitoring by the host computer are delineated. Typical operation parameters of some well-known radars are summarized.

Effect of Dynamic Rolling Oscillations on Twin Tail Buffet Response

NASA Technical Reports Server (NTRS)

Sheta, Essam F.; Kandil, Osama A.

1999-01-01

The effect of dynamic rolling oscillations of delta-wing/twin-tail configuration on twin-tail buffet response is investigated. The computational model consists of a sharp-edged delta wing of aspect ratio one and swept-back flexible twin tail with taper ratio of 0.23. The configuration model is statically pitched at 30 deg. angle of attack and then forced to oscillate in roll around the symmetry axis at a constant amplitude of 4 deg. and reduced frequency of pi and 2(pi). The freestream Mach number and Reynolds number are 0.3 and 1.25 million, respectively. This multidisciplinary problem is solved using three sets of equations on a dynamic multi-block grid structure. The first set is the unsteady, full Navier-Stokes equations, the second set is the aeroelastic equations for coupled bending and torsion vibrations of the tails, and the third set is the grid-displacement equations. The configuration is investigated for inboard position of the twin tails which corresponds to a separation distance between the twin tails of 33% wing span. The computed results are compared with the results of stationary configuration, which previously have been validated using experimental data. The results conclusively showed that the rolling oscillations of the configuration have led to higher loads, higher deflections, and higher excitation peaks than those of the stationary configuration. Moreover, increasing the reduced frequency has led to higher loads and excitation peaks and lower bending and torsion deflections and acceleration.

Probing Massive Black Hole Populations and Their Environments with LISA

NASA Astrophysics Data System (ADS)

Katz, Michael; Larson, Shane

2018-01-01

With the adoption of the LISA Mission Proposal by the European Space Agency in response to its call for L3 mission concepts, gravitational wave measurements from space are on the horizon. With data from the Illustris large-scale cosmological simulation, we provide analysis of LISA detection rates accompanied by characterization of the merging Massive Black Holes (MBH) and their host galaxies. MBHs of total mass $\\sim10^6-10^9 M_\\odot$ are the main focus of this study. Using a precise treatment of the dynamical friction evolutionary process prior to gravitational wave emission, we evolve MBH simulation particle mergers from $\\sim$kpc scales until coalescence to achieve a merger distribution. Using the statistical basis of the Illustris output, we Monte-carlo synthesize many realizations of the merging massive black hole population across space and time. We use those realizations to build mock LISA detection catalogs to understand the impact of LISA mission configurations on our ability to probe massive black hole merger populations and their environments throughout the visible Universe.

A uniform approach for programming distributed heterogeneous computing systems

PubMed Central

Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas

2014-01-01

Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater’s performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations. PMID:25844015

Featured Image: A Gap in TW Hydrae

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2016-04-01

This remarkable image (click for the full view!) is a high-resolution map of the 870 m light emitted by the protoplanetary disk surrounding the young solar analog TW Hydrae. A recent study led by Sean Andrews (Harvard-Smithsonian Center for Astrophysics) presents these observations, obtained with the long-baseline configuration of the Atacama Large Millimeter/submillimeter Array (ALMA) at an unprecedented spatial resolution of ~1 AU. The data represent the distribution of millimeter-sized dust grains in this disk, revealing a beautiful concentric ring structure out to a radial distance of 60 AU from the host star. The apparent gaps in the disk could have anyof three origins:Chemical: apparent gaps can becaused by condensation fronts of volatilesMagnetic: apparent gaps can becaused by radial magnetic pressure variationsDynamic: actual gaps can becaused by the clearing of dust by young planets.For more information, check out the paper below!CitationSean M. Andrews et al 2016 ApJ 820 L40. doi:10.3847/2041-8205/820/2/L40

Methodology for analysis and simulation of large multidisciplinary problems

NASA Technical Reports Server (NTRS)

Russell, William C.; Ikeda, Paul J.; Vos, Robert G.

1989-01-01

The Integrated Structural Modeling (ISM) program is being developed for the Air Force Weapons Laboratory and will be available for Air Force work. Its goal is to provide a design, analysis, and simulation tool intended primarily for directed energy weapons (DEW), kinetic energy weapons (KEW), and surveillance applications. The code is designed to run on DEC (VMS and UNIX), IRIS, Alliant, and Cray hosts. Several technical disciplines are included in ISM, namely structures, controls, optics, thermal, and dynamics. Four topics from the broad ISM goal are discussed. The first is project configuration management and includes two major areas: the software and database arrangement and the system model control. The second is interdisciplinary data transfer and refers to exchange of data between various disciplines such as structures and thermal. Third is a discussion of the integration of component models into one system model, i.e., multiple discipline model synthesis. Last is a presentation of work on a distributed processing computing environment.

A uniform approach for programming distributed heterogeneous computing systems.

PubMed

Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas

2014-12-01

Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater's performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations.

GIS Application System Design Applied to Information Monitoring

NASA Astrophysics Data System (ADS)

Qun, Zhou; Yujin, Yuan; Yuena, Kang

Natural environment information management system involves on-line instrument monitoring, data communications, database establishment, information management software development and so on. Its core lies in collecting effective and reliable environmental information, increasing utilization rate and sharing degree of environment information by advanced information technology, and maximizingly providing timely and scientific foundation for environmental monitoring and management. This thesis adopts C# plug-in application development and uses a set of complete embedded GIS component libraries and tools libraries provided by GIS Engine to finish the core of plug-in GIS application framework, namely, the design and implementation of framework host program and each functional plug-in, as well as the design and implementation of plug-in GIS application framework platform. This thesis adopts the advantages of development technique of dynamic plug-in loading configuration, quickly establishes GIS application by visualized component collaborative modeling and realizes GIS application integration. The developed platform is applicable to any application integration related to GIS application (ESRI platform) and can be as basis development platform of GIS application development.

Past and future perspectives on mathematical models of tick-borne pathogens.

PubMed

Norman, R A; Worton, A J; Gilbert, L

2016-06-01

Ticks are vectors of pathogens which are important both with respect to human health and economically. They have a complex life cycle requiring several blood meals throughout their life. These blood meals take place on different individual hosts and potentially on different host species. Their life cycle is also dependent on environmental conditions such as the temperature and habitat type. Mathematical models have been used for the more than 30 years to help us understand how tick dynamics are dependent on these environmental factors and host availability. In this paper, we review models of tick dynamics and summarize the main results. This summary is split into two parts, one which looks at tick dynamics and one which looks at tick-borne pathogens. In general, the models of tick dynamics are used to determine when the peak in tick densities is likely to occur in the year and how that changes with environmental conditions. The models of tick-borne pathogens focus more on the conditions under which the pathogen can persist and how host population densities might be manipulated to control these pathogens. In the final section of the paper, we identify gaps in the current knowledge and future modelling approaches. These include spatial models linked to environmental information and Geographic Information System maps, and development of new modelling techniques which model tick densities per host more explicitly.

Global culture: A noise-induced transition in finite systems

NASA Astrophysics Data System (ADS)

Klemm, Konstantin; Eguíluz, Víctor M.; Toral, Raúl; Miguel, Maxi San

2003-04-01

We analyze the effect of cultural drift, modeled as noise, in Axelrod’s model for the dissemination of culture. The disordered multicultural frozen configurations are found not to be stable. This general result is proven rigorously in d=1, where the dynamics is described in terms of a Lyapunov potential. In d=2, the dynamics is governed by the average relaxation time T of perturbations. Noise at a rate r≲T-1 induces monocultural configurations, whereas r≳T-1 sustains disorder. In the thermodynamic limit, the relaxation time diverges and global polarization persists in spite of a dynamics of local convergence.

Towards a new paradigm for species association dynamics

USDA-ARS?s Scientific Manuscript database

Parasite-host and insect-plant research have very divergent traditions despite the fact that many phytophagous insects live parasitically on their host plants. In parasitology it is a traditional assumption that parasites are typically highly specialized. Cospeciation between parasites and hosts is ...

Mapping the microbiome of Ictalurid catfish: tissue and species-specific community composition

USDA-ARS?s Scientific Manuscript database

Host mucosal immunity is regulated by the complex interplay between environmental factors, host genetics, and commensal and pathogen dynamics. Microbial imbalances due to physiological stressors, changes in nutrition, and/or antibiotic application can potentiate over-exuberant host immune responses ...

Intraspecific competition: the role of lags between attack and death in host-parasitoid interactions.

PubMed

Cameron, T C; Metcalfe, D; Beckerman, A P; Sait, S M

2007-05-01

Many natural enemies do not immediately kill their host, and the lag this creates between attack and host death results in mixed populations of uninfected and infected hosts. Both competition and parasitism are known to be major structuring forces in ecological communities; however, surprisingly little is known about how the competitive nature of infected hosts could affect the survival and dynamics of remaining uninfected host populations. Using a laboratory system comprising the Indian meal moth, Plodia interpunctella, and a solitary koinobiont parasitoid, Venturia canescens, we address this question by conducting replicated competition experiments between the unparasitized and parasitized classes of host larvae. For varying proportions of parasitized host larvae and competitor densities, we consider the effects of competition within (intraclass) and between (interclass) unparasitized and parasitized larvae on the survival, development time, and size of adult moths and parasitoid wasps. The greatest effects were on survival: increased competitor densities reduced survival of both parasitized and unparasitized larvae. However, unparasitized larvae survival, but not parasitized larvae survival, was reduced by increasing interclass competition. To our knowledge, this is the first experimental demonstration of the competitive superiority of parasitized over unparasitized hosts for limiting resources. We discuss possible mechanisms for this phenomenon, why it may have evolved, and its possible influence on the stability of host-parasite dynamics.

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

Desjardins, Tiffany; Schmidt, Derek William; Di Stefano, Carlos

These experiments are the first experiments in the Mshock campaign at the National Ignition Facility. The experiment is scheduled to be conducted on Dec. 14, 2017. The goal of the Mshock campaign is to study feedthrough dynamics of the Richtmyer- Meshkov instability in a thin layer. These dynamics will be studied in both a reshock configuration (initially) and then in a multi-shock configuration where it is planned to reshock the RM instability up to 3 times (four shocks total).

Overview of Sensitivity Analysis and Shape Optimization for Complex Aerodynamic Configurations

NASA Technical Reports Server (NTRS)

Newman, Perry A.; Newman, James C., III; Barnwell, Richard W.; Taylor, Arthur C., III; Hou, Gene J.-W.

1998-01-01

This paper presents a brief overview of some of the more recent advances in steady aerodynamic shape-design sensitivity analysis and optimization, based on advanced computational fluid dynamics. The focus here is on those methods particularly well- suited to the study of geometrically complex configurations and their potentially complex associated flow physics. When nonlinear state equations are considered in the optimization process, difficulties are found in the application of sensitivity analysis. Some techniques for circumventing such difficulties are currently being explored and are included here. Attention is directed to methods that utilize automatic differentiation to obtain aerodynamic sensitivity derivatives for both complex configurations and complex flow physics. Various examples of shape-design sensitivity analysis for unstructured-grid computational fluid dynamics algorithms are demonstrated for different formulations of the sensitivity equations. Finally, the use of advanced, unstructured-grid computational fluid dynamics in multidisciplinary analyses and multidisciplinary sensitivity analyses within future optimization processes is recommended and encouraged.

Self-Organization of Metal Nanoparticles in Light: Electrodynamics-Molecular Dynamics Simulations and Optical Binding Experiments.

PubMed

McCormack, Patrick; Han, Fei; Yan, Zijie

2018-02-01

Light-driven self-organization of metal nanoparticles (NPs) can lead to unique optical matter systems, yet simulation of such self-organization (i.e., optical binding) is a complex computational problem that increases nonlinearly with system size. Here we show that a combined electrodynamics-molecular dynamics simulation technique can simulate the trajectories and predict stable configurations of silver NPs in optical fields. The simulated dynamic equilibrium of a two-NP system matches the probability density of oscillations for two optically bound NPs obtained experimentally. The predicted stable configurations for up to eight NPs are further compared to experimental observations of silver NP clusters formed by optical binding in a Bessel beam. All configurations are confirmed to form in real systems, including pentagonal clusters with five-fold symmetry. Our combined simulations and experiments have revealed a diverse optical matter system formed by anisotropic optical binding interactions, providing a new strategy to discover artificial materials.

Dynamic Airspace Configuration

NASA Technical Reports Server (NTRS)

Bloem, Michael J.

2014-01-01

In air traffic management systems, airspace is partitioned into regions in part to distribute the tasks associated with managing air traffic among different systems and people. These regions, as well as the systems and people allocated to each, are changed dynamically so that air traffic can be safely and efficiently managed. It is expected that new air traffic control systems will enable greater flexibility in how airspace is partitioned and how resources are allocated to airspace regions. In this talk, I will begin by providing an overview of some previous work and open questions in Dynamic Airspace Configuration research, which is concerned with how to partition airspace and assign resources to regions of airspace. For example, I will introduce airspace partitioning algorithms based on clustering, integer programming optimization, and computational geometry. I will conclude by discussing the development of a tablet-based tool that is intended to help air traffic controller supervisors configure airspace and controllers in current operations.

Catenaries in Drag

NASA Astrophysics Data System (ADS)

Chakrabarti, Brato; Hanna, James

2014-11-01

Dynamical equilibria of towed cables and sedimenting filaments have been the targets of much numerical work; here, we provide analytical expressions for the configurations of a translating and axially moving string subjected to a uniform body force and local, linear, anisotropic drag forces. Generically, these configurations comprise a five-parameter family of planar shapes determined by the ratio of tangential (axial) and normal drag coefficients, the angle between the translational velocity and the body force, the relative magnitudes of translational and axial drag forces with respect to the body force, and a scaling parameter. This five-parameter family of shapes is, in fact, a degenerate six-parameter family of equilibria in which inertial forces rescale the tension in the string without affecting its shape. Each configuration is represented by a first order dynamical system for the tangential angle of the body. Limiting cases include the dynamic catenaries with or without drag, and purely sedimenting or towed strings.

Method and system to estimate variables in an integrated gasification combined cycle (IGCC) plant

DOEpatents

Kumar, Aditya; Shi, Ruijie; Dokucu, Mustafa

2013-09-17

System and method to estimate variables in an integrated gasification combined cycle (IGCC) plant are provided. The system includes a sensor suite to measure respective plant input and output variables. An extended Kalman filter (EKF) receives sensed plant input variables and includes a dynamic model to generate a plurality of plant state estimates and a covariance matrix for the state estimates. A preemptive-constraining processor is configured to preemptively constrain the state estimates and covariance matrix to be free of constraint violations. A measurement-correction processor may be configured to correct constrained state estimates and a constrained covariance matrix based on processing of sensed plant output variables. The measurement-correction processor is coupled to update the dynamic model with corrected state estimates and a corrected covariance matrix. The updated dynamic model may be configured to estimate values for at least one plant variable not originally sensed by the sensor suite.

Modelling Parasite Transmission in a Grazing System: The Importance of Host Behaviour and Immunity

PubMed Central

Fox, Naomi J.; Marion, Glenn; Davidson, Ross S.; White, Piran C. L.; Hutchings, Michael R.

2013-01-01

Parasitic helminths present one of the most pervasive challenges to grazing herbivores. Many macro-parasite transmission models focus on host physiological defence strategies, omitting more complex interactions between hosts and their environments. This work represents the first model that integrates both the behavioural and physiological elements of gastro-intestinal nematode transmission dynamics in a managed grazing system. A spatially explicit, individual-based, stochastic model is developed, that incorporates both the hosts’ immunological responses to parasitism, and key grazing behaviours including faecal avoidance. The results demonstrate that grazing behaviour affects both the timing and intensity of parasite outbreaks, through generating spatial heterogeneity in parasite risk and nutritional resources, and changing the timing of exposure to the parasites’ free-living stages. The influence of grazing behaviour varies with the host-parasite combination, dependent on the development times of different parasite species and variations in host immune response. Our outputs include the counterintuitive finding that under certain conditions perceived parasite avoidance behaviours (faecal avoidance) can increase parasite risk, for certain host-parasite combinations. Through incorporating the two-way interaction between infection dynamics and grazing behaviour, the potential benefits of parasite-induced anorexia are also demonstrated. Hosts with phenotypic plasticity in grazing behaviour, that make grazing decisions dependent on current parasite burden, can reduce infection with minimal loss of intake over the grazing season. This paper explores how both host behaviours and immunity influence macro-parasite transmission in a spatially and temporally heterogeneous environment. The magnitude and timing of parasite outbreaks is influenced by host immunity and behaviour, and the interactions between them; the incorporation of both regulatory processes is required to fully understand transmission dynamics. Understanding of both physiological and behavioural defence strategies will aid the development of novel approaches for control. PMID:24223133

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

Stochastic processes constrain the within and between host evolution of influenza virus.

PubMed

McCrone, John T; Woods, Robert J; Martin, Emily T; Malosh, Ryan E; Monto, Arnold S; Lauring, Adam S

2018-05-03

The evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define influenza virus dynamics in human hosts through sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected from individuals in a prospective community-based cohort, they are broadly representative of natural infections with seasonal viruses. Consistent with a neutral model of evolution, sequence data from 49 serially sampled individuals illustrated the dynamic turnover of synonymous and nonsynonymous single nucleotide variants and provided little evidence for positive selection of antigenic variants. We also identified 43 genetically-validated transmission pairs in this cohort. Maximum likelihood optimization of multiple transmission models estimated an effective transmission bottleneck of 1-2 genomes. Our data suggest that positive selection is inefficient at the level of the individual host and that stochastic processes dominate the host-level evolution of influenza viruses. © 2018, McCrone et al.

Single-cell transcriptional dynamics of flavivirus infection

PubMed Central

Bekerman, Elena

2018-01-01

Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage and shock or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level. PMID:29451494

Viral control of phytoplankton populations--a review.

PubMed

Brussaard, Corina P D

2004-01-01

Phytoplankton population dynamics are the result of imbalances between reproduction and losses. Losses include grazing, sinking, and natural mortality. As the importance of microbes in aquatic ecology has been recognized, so has the potential significance of viruses as mortality agents for phytoplankton. The field of algal virus ecology is steadily changing and advancing as new viruses are isolated and new methods are developed for quantifying the impact of viruses on phytoplankton dynamics and diversity. With this development, evidence is accumulating that viruses can control phytoplankton dynamics through reduction of host populations, or by preventing algal host populations from reaching high levels. The identification of highly specific host ranges of viruses is changing our understanding of population dynamics. Viral-mediated mortality may not only affect algal species succession, but may also affect intraspecies succession. Through cellular lysis, viruses indirectly affect the fluxes of energy, nutrients, and organic matter, especially during algal bloom events when biomass is high. Although the importance of viruses is presently recognized, it is apparent that many aspects of viral-mediated mortality of phytoplankton are still poorly understood. It is imperative that future research addresses the mechanisms that regulate virus infectivity, host resistance, genotype richness, abundance, and the fate of viruses over time and space.

Phosphor suspended in silicone, molded/formed and used in a remote phosphor configuration

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

Kolodin, Boris; Deshpande, Anirudha R

A light emitting package comprising a support hosting at least one light emitting diode. A light transmissive dome comprised of a silicone including a phosphor material positioned to receive light emitted by the diode. A glass cap overlies said dome.

How do humans affect wildlife nematodes?

USGS Publications Warehouse

Weinstein, Sara B.; Lafferty, Kevin D.

2015-01-01

Human actions can affect wildlife and their nematode parasites. Species introductions and human-facilitated range expansions can create new host–parasite interactions. Novel hosts can introduce parasites and have the potential to both amplify and dilute nematode transmission. Furthermore, humans can alter existing nematode dynamics by changing host densities and the abiotic conditions that affect larval parasite survival. Human impacts on wildlife might impair parasites by reducing the abundance of their hosts; however, domestic animal production and complex life cycles can maintain transmission even when wildlife becomes rare. Although wildlife nematodes have many possible responses to human actions, understanding host and parasite natural history, and the mechanisms behind the changing disease dynamics might improve disease control in the few cases where nematode parasitism impacts wildlife.

Visualizing viral transport and host infection

NASA Astrophysics Data System (ADS)

Son, Kwangmin; Guasto, Jeffrey; Cubillos-Ruiz, Andres; Sullivan, Matthew; Stocker, Roman; MIT Team

2013-11-01

A virus is a non-motile infectious agent that can only replicate inside a living host. They consist of a <100 nm diameter capsid which houses their DNA, and a <20 nm diameter tail used to inject DNA to the host, which are classified into three different morphologies by the tail type: short tail (~ 10 nm, podovirus), rigid contractile tail (~ 100 nm, myovirus), or flexible noncontractile tail (~ 300 nm, siphovirus). Combining microfluidics with epifluorescent microscopy, we studied the simultaneous diffusive transport governing the initial encounter and ultimately the infection of a non-motile cyanobacteria host (~ 1 μm prochlorococcus) and their viral (phage) counterparts in real time. This methodology allows us to quantify the virus-host encounter/adsorption dynamics and subsequently the effectiveness of various tail morphologies for viral infection. Viral transport and the role of viral morphology in host-virus interactions are critical to our understanding of both ecosystem dynamics and human health, as well as to the evolution of virus morphology.

Cryptic disease-induced mortality may cause host extinction in an apparently stable host-parasite system.

PubMed

Valenzuela-Sánchez, Andrés; Schmidt, Benedikt R; Uribe-Rivera, David E; Costas, Francisco; Cunningham, Andrew A; Soto-Azat, Claudio

2017-09-27

The decline of wildlife populations due to emerging infectious disease often shows a common pattern: the parasite invades a naive host population, producing epidemic disease and a population decline, sometimes with extirpation. Some susceptible host populations can survive the epidemic phase and persist with endemic parasitic infection. Understanding host-parasite dynamics leading to persistence of the system is imperative to adequately inform conservation practice. Here we combine field data, statistical and mathematical modelling to explore the dynamics of the apparently stable Rhinoderma darwinii - Batrachochytrium dendrobatidis (Bd) system. Our results indicate that Bd-induced population extirpation may occur even in the absence of epidemics and where parasite prevalence is relatively low. These empirical findings are consistent with previous theoretical predictions showing that highly pathogenic parasites are able to regulate host populations even at extremely low prevalence, highlighting that disease threats should be investigated as a cause of population declines even in the absence of an overt increase in mortality. © 2017 The Author(s).

Selective predation and rapid evolution can jointly dampen effects of virulent parasites on Daphnia populations.

PubMed

Duffy, Meghan A; Hall, Spencer R

2008-04-01

Parasites are ubiquitous and often highly virulent, yet clear examples of parasite-driven changes in host density in natural populations are surprisingly scarce. Here, we illustrate an example of this phenomenon and offer a theoretically reasonable resolution. We document the effects of two parasites, the bacterium Spirobacillus cienkowskii and the yeast Metschnikowia bicuspidata, on a common freshwater invertebrate, Daphnia dentifera. We show that while both parasites were quite virulent to individual hosts, only bacterial epidemics were associated with significant changes in host population dynamics and density. Our theoretical results may help explain why yeast epidemics did not significantly affect population dynamics. Using a model parameterized with data we collected, we argue that two prominent features of this system, rapid evolution of host resistance to the parasite and selective predation on infected hosts, both decrease peak infection prevalence and can minimize decline in host density during epidemics. Taken together, our results show that understanding the outcomes of host-parasite interactions in this Daphnia-microparasite system may require consideration of ecological context and evolutionary processes and their interaction.

An Ada programming support environment

NASA Technical Reports Server (NTRS)

Tyrrill, AL; Chan, A. David

1986-01-01

The toolset of an Ada Programming Support Environment (APSE) being developed at North American Aircraft Operations (NAAO) of Rockwell International, is described. The APSE is resident on three different hosts and must support developments for the hosts and for embedded targets. Tools and developed software must be freely portable between the hosts. The toolset includes the usual editors, compilers, linkers, debuggers, configuration magnagers, and documentation tools. Generally, these are being supplied by the host computer vendors. Other tools, for example, pretty printer, cross referencer, compilation order tool, and management tools were obtained from public-domain sources, are implemented in Ada and are being ported to the hosts. Several tools being implemented in-house are of interest, these include an Ada Design Language processor based on compilable Ada. A Standalone Test Environment Generator facilitates test tool construction and partially automates unit level testing. A Code Auditor/Static Analyzer permits the Ada programs to be evaluated against measures of quality. An Ada Comment Box Generator partially automates generation of header comment boxes.

Influence of an amorphous wall on the distribution of localized excitations in a colloidal glass-forming liquid

NASA Astrophysics Data System (ADS)

Gokhale, Shreyas; Hima Nagamanasa, K.; Sood, A. K.; Ganapathy, Rajesh

2016-07-01

Elucidating the nature of the glass transition has been the holy grail of condensed matter physics and statistical mechanics for several decades. A phenomenological aspect that makes glass formation a conceptually formidable problem is that structural and dynamic correlations in glass-forming liquids are too subtle to be captured at the level of conventional two-point functions. As a consequence, a host of theoretical techniques, such as quenched amorphous configurations of particles, have been devised and employed in simulations and colloid experiments to gain insights into the mechanisms responsible for these elusive correlations. Very often, though, the analysis of spatio-temporal correlations is performed in the context of a single theoretical framework, and critical comparisons of microscopic predictions of competing theories are thereby lacking. Here, we address this issue by analysing the distribution of localized excitations, which are building blocks of relaxation as per the dynamical facilitation (DF) theory, in the presence of an amorphous wall, a construct motivated by the random first-order transition theory (RFOT). We observe that spatial profiles of the concentration of excitations exhibit complex features such as non-monotonicity and oscillations. Moreover, the smoothly varying part of the concentration profile yields a length scale {ξc} , which we compare with a previously computed length scale {ξ\\text{dyn}} . Our results suggest a method to assess the role of dynamical facilitation in governing structural relaxation in glass-forming liquids.

Vector-virus interactions and transmission dynamics of West Nile virus.

PubMed

Ciota, Alexander T; Kramer, Laura D

2013-12-09

West Nile virus (WNV; Flavivirus; Flaviviridae) is the cause of the most widespread arthropod-borne viral disease in the world and the largest outbreak of neuroinvasive disease ever observed. Mosquito-borne outbreaks are influenced by intrinsic (e.g., vector and viral genetics, vector and host competence, vector life-history traits) and extrinsic (e.g., temperature, rainfall, human land use) factors that affect virus activity and mosquito biology in complex ways. The concept of vectorial capacity integrates these factors to address interactions of the virus with the arthropod host, leading to a clearer understanding of their complex interrelationships, how they affect transmission of vector-borne disease, and how they impact human health. Vertebrate factors including host competence, population dynamics, and immune status also affect transmission dynamics. The complexity of these interactions are further exacerbated by the fact that not only can divergent hosts differentially alter the virus, but the virus also can affect both vertebrate and invertebrate hosts in ways that significantly alter patterns of virus transmission. This chapter concentrates on selected components of the virus-vector-vertebrate interrelationship, focusing specifically on how interactions between vector, virus, and environment shape the patterns and intensity of WNV transmission.

Trees wanted--dead or alive! Host selection and population dynamics in tree-killing bark beetles.

PubMed

Kausrud, Kyrre L; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between "endemic" and "epidemic" regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics.

Vector-Virus Interactions and Transmission Dynamics of West Nile Virus

PubMed Central

Ciota, Alexander T.; Kramer, Laura D.

2013-01-01

West Nile virus (WNV; Flavivirus; Flaviviridae) is the cause of the most widespread arthropod-borne viral disease in the world and the largest outbreak of neuroinvasive disease ever observed. Mosquito-borne outbreaks are influenced by intrinsic (e.g., vector and viral genetics, vector and host competence, vector life-history traits) and extrinsic (e.g., temperature, rainfall, human land use) factors that affect virus activity and mosquito biology in complex ways. The concept of vectorial capacity integrates these factors to address interactions of the virus with the arthropod host, leading to a clearer understanding of their complex interrelationships, how they affect transmission of vector-borne disease, and how they impact human health. Vertebrate factors including host competence, population dynamics, and immune status also affect transmission dynamics. The complexity of these interactions are further exacerbated by the fact that not only can divergent hosts differentially alter the virus, but the virus also can affect both vertebrate and invertebrate hosts in ways that significantly alter patterns of virus transmission. This chapter concentrates on selected components of the virus-vector-vertebrate interrelationship, focusing specifically on how interactions between vector, virus, and environment shape the patterns and intensity of WNV transmission. PMID:24351794

Hybrid Configuration of Darrieus and Savonius Rotors for Stand-alone Power Systems

NASA Astrophysics Data System (ADS)

Wakui, Tetsuya; Tanzawa, Yoshiaki; Hashizume, Takumi; Nagao, Toshio

The suitable hybrid configuration of Darrieus lift-type and Savonius drag-type rotors for stand-alone wind turbine-generator systems is discussed using our dynamic simulation model. Two types of hybrid configurations are taken up: Type-A installs the Savonius rotor inside the Darrieus rotor and Type-B installs the Savonius rotor outside the Darrieus rotor. The computed results of the output characteristics and the dynamic behaviors of the system operated at the maximum power coefficient points show that Type-A, which has fine operating behavior to wind speed changes and can be compactly designed because of a shorter rotational shaft, is an effective way for self-controlled stand-alone small-scale systems.

Host identity matters in the amphibian-Batrachochytrium dendrobatidis system: fine-scale patterns of variation in responses to a multi-host pathogen

Treesearch

Stephanie Gervasi; Carmen Gondhalekar; Deanna H. Olson; Andrew R. Blaustein

2013-01-01

Species composition within ecological assemblages can drive disease dynamics including pathogen invasion, spread, and persistence. In multi-host pathogen systems, interspecific variation in responses to infection creates important context dependency when predicting the outcome of disease. Here, we examine the responses of three sympatric host species to a single fungal...

The Impact of Prophage on the Equilibria and Stability of Phage and Host

NASA Astrophysics Data System (ADS)

Yu, Pei; Nadeem, Alina; Wahl, Lindi M.

2017-06-01

In this paper, we present a bacteriophage model that includes prophage, that is, phage genomes that are incorporated into the host cell genome. The general model is described by an 18-dimensional system of ordinary differential equations. This study focuses on asymptotic behaviour of the model, and thus the system is reduced to a simple six-dimensional model, involving uninfected host cells, infected host cells and phage. We use dynamical system theory to explore the dynamic behaviour of the model, studying in particular the impact of prophage on the equilibria and stability of phage and host. We employ bifurcation and stability theory, centre manifold and normal form theory to show that the system has multiple equilibrium solutions which undergo a series of bifurcations, finally leading to oscillating motions. Numerical simulations are presented to illustrate and confirm the analytical predictions. The results of this study indicate that in some parameter regimes, the host cell population may drive the phage to extinction through diversification, that is, if multiple types of host emerge; this prediction holds even if the phage population is likewise diverse. This parameter regime is restricted, however, if infecting phage are able to recombine with prophage sequences in the host cell genome.

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut

PubMed Central

Reese, Aspen T; Cho, Eugenia H; Klitzman, Bruce; Nichols, Scott P; Wisniewski, Natalie A; Villa, Max M; Durand, Heather K; Jiang, Sharon; Midani, Firas S; Nimmagadda, Sai N; O'Connell, Thomas M; Wright, Justin P; Deshusses, Marc A

2018-01-01

How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration. PMID:29916366

Molecular dynamics simulation of low-energy recoil events in titanate pyrochlores

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

Dong, Liyuan; Setyawan, Wahyu; Li, Yuhong

2017-01-01

Molecular dynamics simulations of low-energy displacements in titanate pyrochlores have been carried out along three main directions, to determineE dfor A, Ti and O, corresponding defect configurations, and defect formation dynamics.

Biophysical synaptic dynamics in an analog VLSI network of Hodgkin-Huxley neurons.

PubMed

Yu, Theodore; Cauwenberghs, Gert

2009-01-01

We study synaptic dynamics in a biophysical network of four coupled spiking neurons implemented in an analog VLSI silicon microchip. The four neurons implement a generalized Hodgkin-Huxley model with individually configurable rate-based kinetics of opening and closing of Na+ and K+ ion channels. The twelve synapses implement a rate-based first-order kinetic model of neurotransmitter and receptor dynamics, accounting for NMDA and non-NMDA type chemical synapses. The implemented models on the chip are fully configurable by 384 parameters accounting for conductances, reversal potentials, and pre/post-synaptic voltage-dependence of the channel kinetics. We describe the models and present experimental results from the chip characterizing single neuron dynamics, single synapse dynamics, and multi-neuron network dynamics showing phase-locking behavior as a function of synaptic coupling strength. The 3mm x 3mm microchip consumes 1.29 mW power making it promising for applications including neuromorphic modeling and neural prostheses.

Dynamics of Water Associated with Lithium Ions Distributed in Polyethylene Oxide

DOE PAGES

Zhang, Zhe; Ohl, Michael; Diallo, Souleymane O.; ...

2015-11-03

We studied the dynamics of water in polyethylene oxide (PEO)/LiCl solution with quasielastic neutron scattering experiments and molecular dynamics (MD) simulations. Two different time scales of water diffusion representing interfacial water and bulk water dynamics have been identified. Furthermore, the measured diffusion coefficient of interfacial water remained 5–10 times smaller than that of bulk water, but both were slowed by approximately 50% in the presence of Li +. Detailed analysis of MD trajectories suggests that Li + is favorably found at the surface of the hydration layer, and the probability to find the caged Li + configuration formed by themore » PEO is lower than for the noncaged Li +-PEO configuration. In both configurations, however, the slowing down of water molecules is driven by reorienting water molecules and creating water-Li + hydration complexes. Moreover, performing the MD simulation with different ions (Na + and K +) revealed that smaller ionic radius of the ions is a key factor in disrupting the formation of PEO cages by allowing spaces for water molecules to come in between the ion and PEO.« less

Dynamics of Water Associated with Lithium Ions Distributed in Polyethylene Oxide

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Ohl, Michael; Diallo, Souleymane O.; Jalarvo, Niina H.; Hong, Kunlun; Han, Youngkyu; Smith, Gregory S.; Do, Changwoo

2015-11-01

The dynamics of water in polyethylene oxide (PEO)/LiCl solution has been studied with quasielastic neutron scattering experiments and molecular dynamics (MD) simulations. Two different time scales of water diffusion representing interfacial water and bulk water dynamics have been identified. The measured diffusion coefficient of interfacial water remained 5-10 times smaller than that of bulk water, but both were slowed by approximately 50% in the presence of Li+ . Detailed analysis of MD trajectories suggests that Li+ is favorably found at the surface of the hydration layer, and the probability to find the caged Li+ configuration formed by the PEO is lower than for the noncaged Li+-PEO configuration. In both configurations, however, the slowing down of water molecules is driven by reorienting water molecules and creating water-Li+ hydration complexes. Performing the MD simulation with different ions (Na+ and K+ ) revealed that smaller ionic radius of the ions is a key factor in disrupting the formation of PEO cages by allowing spaces for water molecules to come in between the ion and PEO.

Dynamics of Water Associated with Lithium Ions Distributed in Polyethylene Oxide.

PubMed

Zhang, Zhe; Ohl, Michael; Diallo, Souleymane O; Jalarvo, Niina H; Hong, Kunlun; Han, Youngkyu; Smith, Gregory S; Do, Changwoo

2015-11-06

The dynamics of water in polyethylene oxide (PEO)/LiCl solution has been studied with quasielastic neutron scattering experiments and molecular dynamics (MD) simulations. Two different time scales of water diffusion representing interfacial water and bulk water dynamics have been identified. The measured diffusion coefficient of interfacial water remained 5-10 times smaller than that of bulk water, but both were slowed by approximately 50% in the presence of Li(+). Detailed analysis of MD trajectories suggests that Li(+) is favorably found at the surface of the hydration layer, and the probability to find the caged Li(+) configuration formed by the PEO is lower than for the noncaged Li(+)-PEO configuration. In both configurations, however, the slowing down of water molecules is driven by reorienting water molecules and creating water-Li(+) hydration complexes. Performing the MD simulation with different ions (Na(+) and K(+)) revealed that smaller ionic radius of the ions is a key factor in disrupting the formation of PEO cages by allowing spaces for water molecules to come in between the ion and PEO.

Analytical study of inside-out Gimbal dynamics. Volume 2: Appendix

NASA Technical Reports Server (NTRS)

Rybak, S. C.

1976-01-01

Stability data, eigenvalue data, and instrument pointing system earth point tracking time histories at various orbital altitudes are presented. These data apply to the inside-out Gimbal system configuration and the coincident Gimbal system configuration.

Development of gas-to-gas lift pad dynamic seals, volumes 1 and 2

NASA Technical Reports Server (NTRS)

Pope, A. N.; Pugh, D. W.

1987-01-01

Dynamic tests were performed on self acting (hydrodynamic) carbon face rotary shaft seals to assess their potential, relative to presently used labyrinth seals, for improving performance of aircraft gas turbine engines by reducing air leakage flow rate at compressor end seal locations. Three self acting bearing configurations, designed to supply load support at the interface of the stationary carbon seal and rotating seal race, were tested. Two configurations, the shrouded taper and shrouded flat step, were incorporated on the face of the stationary carbon seal element. The third configuration, inward pumping spiral grooves, was incorporated on the hard faced surface of the rotating seal race. Test results demonstrated seal leakage air flow rates from 75 to 95% lower that can be achieved with best state-of-the-art labyrinth designs and led to identification of the need for a more geometrically stable seal design configuration which is presently being manufactured for subsequent test evaluation.

Structural dynamic and thermal stress analysis of nuclear reactor vessel support system

NASA Technical Reports Server (NTRS)

Chi-Diango, J.

1972-01-01

A nuclear reactor vessel is supported by a Z-ring and a box ring girder. The two proposed structural configurations to transmit the loads from the Z-ring and the box ring girder to the foundation are shown. The cantilever concrete ledge transmitting the load from the Z-ring and the box girder via the cavity wall to the foundation is shown, along with the loads being transmitted through one of the six steel columns. Both of these two supporting systems were analyzed by using rigid format 9 of NASTRAN for dynamic loads, and the thermal stresses were analyzed by AXISOL. The six column configuration was modeled by a combination of plate and bar elements, and the concrete cantilever ledge configuration was modeled by plate elements. Both configurations were found structurally satisfactory; however, nonstructural considerations favored the concrete cantilever ledge.

The effect of engine spin direction on the dynamics of powered two wheelers

NASA Astrophysics Data System (ADS)

Massaro, Matteo; Marconi, Edoardo

2018-04-01

The effect of engine spin direction on the dynamics of powered two wheelers is investigated in terms of steady-state points (equilibria), vibration modes (stability), manoeuvre time (performance/manoeuvrability) and handling. The goal is to assess and quantify the advantage sometimes claimed for the 'counter-rotating' engine configuration, where the engine spins in the opposite direction with respect to wheels, against the 'conventional' configuration, where the engine spins in the same direction of wheels.

Do Optomechanical Metasurfaces Run Out of Time?

PubMed

Viaene, Sophie; Ginis, Vincent; Danckaert, Jan; Tassin, Philippe

2018-05-11

Artificially structured metasurfaces make use of specific configurations of subwavelength resonators to efficiently manipulate electromagnetic waves. Additionally, optomechanical metasurfaces have the desired property that their actual configuration may be tuned by adjusting the power of a pump beam, as resonators move to balance pump-induced electromagnetic forces with forces due to elastic filaments or substrates. Although the reconfiguration time of optomechanical metasurfaces crucially determines their performance, the transient dynamics of unit cells from one equilibrium state to another is not understood. Here, we make use of tools from nonlinear dynamics to analyze the transient dynamics of generic optomechanical metasurfaces based on a damped-resonator model with one configuration parameter. We show that the reconfiguration time of optomechanical metasurfaces is not only limited by the elastic properties of the unit cell but also by the nonlinear dependence of equilibrium states on the pump power. For example, when switching is enabled by hysteresis phenomena, the reconfiguration time is seen to increase by over an order of magnitude. To illustrate these results, we analyze the nonlinear dynamics of a bilayer cross-wire metasurface whose optical activity is tuned by an electromagnetic torque. Moreover, we provide a lower bound for the configuration time of generic optomechanical metasurfaces. This lower bound shows that optomechanical metasurfaces cannot be faster than state-of-the-art switches at reasonable powers, even at optical frequencies.

Do Optomechanical Metasurfaces Run Out of Time?

NASA Astrophysics Data System (ADS)

Viaene, Sophie; Ginis, Vincent; Danckaert, Jan; Tassin, Philippe

2018-05-01

Artificially structured metasurfaces make use of specific configurations of subwavelength resonators to efficiently manipulate electromagnetic waves. Additionally, optomechanical metasurfaces have the desired property that their actual configuration may be tuned by adjusting the power of a pump beam, as resonators move to balance pump-induced electromagnetic forces with forces due to elastic filaments or substrates. Although the reconfiguration time of optomechanical metasurfaces crucially determines their performance, the transient dynamics of unit cells from one equilibrium state to another is not understood. Here, we make use of tools from nonlinear dynamics to analyze the transient dynamics of generic optomechanical metasurfaces based on a damped-resonator model with one configuration parameter. We show that the reconfiguration time of optomechanical metasurfaces is not only limited by the elastic properties of the unit cell but also by the nonlinear dependence of equilibrium states on the pump power. For example, when switching is enabled by hysteresis phenomena, the reconfiguration time is seen to increase by over an order of magnitude. To illustrate these results, we analyze the nonlinear dynamics of a bilayer cross-wire metasurface whose optical activity is tuned by an electromagnetic torque. Moreover, we provide a lower bound for the configuration time of generic optomechanical metasurfaces. This lower bound shows that optomechanical metasurfaces cannot be faster than state-of-the-art switches at reasonable powers, even at optical frequencies.

Quality status display for a vibration welding process

DOEpatents

Spicer, John Patrick; Abell, Jeffrey A.; Wincek, Michael Anthony; Chakraborty, Debejyo; Bracey, Jennifer; Wang, Hui; Tavora, Peter W.; Davis, Jeffrey S.; Hutchinson, Daniel C.; Reardon, Ronald L.; Utz, Shawn

2017-03-28

A system includes a host machine and a status projector. The host machine is in electrical communication with a collection of sensors and with a welding controller that generates control signals for controlling the welding horn. The host machine is configured to execute a method to thereby process the sensory and control signals, as well as predict a quality status of a weld that is formed using the welding horn, including identifying any suspect welds. The host machine then activates the status projector to illuminate the suspect welds. This may occur directly on the welds using a laser projector, or on a surface of the work piece in proximity to the welds. The system and method may be used in the ultrasonic welding of battery tabs of a multi-cell battery pack in a particular embodiment. The welding horn and welding controller may also be part of the system.

Prevalence of Buggy Creek Virus (Togaviridae: Alphavirus) in Insect Vectors Increases Over Time in the Presence of an Invasive Avian Host

PubMed Central

Moore, Amy T.; O'Brien, Valerie A.

2012-01-01

Abstract Invasive species can disrupt natural disease dynamics by altering pathogen transmission among native hosts and vectors. The relatively recent occupancy of cliff swallow (Petrochelidon pyrrhonota) nesting colonies in western Nebraska by introduced European house sparrows (Passer domesticus) has led to yearly increases in the prevalence of an endemic arbovirus, Buggy Creek virus (BCRV), in its native swallow bug (Oeciacus vicarius) vector at sites containing both the invasive sparrow host and the native swallow host. At sites without the invasive host, no long-term changes in prevalence have occurred. The percentage of BCRV isolates exhibiting cytopathicity in Vero-cell culture assays increased significantly with year at sites with sparrows but not at swallow-only sites, suggesting that the virus is becoming more virulent to vertebrates in the presence of the invasive host. Increased BCRV prevalence in bug vectors at mixed-species colonies may reflect high virus replication rates in house sparrow hosts, resulting in frequent virus transmission between sparrows and swallow bugs. This case represents a rare empirical example of a pathogen effectively switching to an invasive host, documented in the early phases of the host's arrival in a specialized ecosystem and illustrating how an invasive species can promote long-term changes in host–parasite transmission dynamics. PMID:21923265

Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection

PubMed Central

Huang, Yongsheng; Zaas, Aimee K.; Rao, Arvind; Dobigeon, Nicolas; Woolf, Peter J.; Veldman, Timothy; Øien, N. Christine; McClain, Micah T.; Varkey, Jay B.; Nicholson, Bradley; Carin, Lawrence; Kingsmore, Stephen; Woods, Christopher W.; Ginsburg, Geoffrey S.; Hero, Alfred O.

2011-01-01

Exposure to influenza viruses is necessary, but not sufficient, for healthy human hosts to develop symptomatic illness. The host response is an important determinant of disease progression. In order to delineate host molecular responses that differentiate symptomatic and asymptomatic Influenza A infection, we inoculated 17 healthy adults with live influenza (H3N2/Wisconsin) and examined changes in host peripheral blood gene expression at 16 timepoints over 132 hours. Here we present distinct transcriptional dynamics of host responses unique to asymptomatic and symptomatic infections. We show that symptomatic hosts invoke, simultaneously, multiple pattern recognition receptors-mediated antiviral and inflammatory responses that may relate to virus-induced oxidative stress. In contrast, asymptomatic subjects tightly regulate these responses and exhibit elevated expression of genes that function in antioxidant responses and cell-mediated responses. We reveal an ab initio molecular signature that strongly correlates to symptomatic clinical disease and biomarkers whose expression patterns best discriminate early from late phases of infection. Our results establish a temporal pattern of host molecular responses that differentiates symptomatic from asymptomatic infections and reveals an asymptomatic host-unique non-passive response signature, suggesting novel putative molecular targets for both prognostic assessment and ameliorative therapeutic intervention in seasonal and pandemic influenza. PMID:21901105

Technical evaluation report on the fluid dynamics panel Symposium on High Angle of attack aerodynamics. [slender wings, bodies of revolution, and body-wing configurations

NASA Technical Reports Server (NTRS)

Polhamus, E. C.

1979-01-01

An overview is presented of 32 formal papers and 7 open session papers. Topics covered include: (1) studies of configurations of practical interest; (2) mathematical modelling and supporting investigations of slender wings, bodies of revolution, and body-wing configurations; (3) design methods; and (4) air intakes.

Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking.

PubMed

Martínez, José Mario; Martínez, Leandro

2003-05-01

Molecular Dynamics is a powerful methodology for the comprehension at molecular level of many chemical and biochemical systems. The theories and techniques developed for structural and thermodynamic analyses are well established, and many software packages are available. However, designing starting configurations for dynamics can be cumbersome. Easily generated regular lattices can be used when simple liquids or mixtures are studied. However, for complex mixtures, polymer solutions or solid adsorbed liquids (for example) this approach is inefficient, and it turns out to be very hard to obtain an adequate coordinate file. In this article, the problem of obtaining an adequate initial configuration is treated as a "packing" problem and solved by an optimization procedure. The initial configuration is chosen in such a way that the minimum distance between atoms of different molecules is greater than a fixed tolerance. The optimization uses a well-known algorithm for box-constrained minimization. Applications are given for biomolecule solvation, many-component mixtures, and interfaces. This approach can reduce the work of designing starting configurations from days or weeks to few minutes or hours, in an automated fashion. Packing optimization is also shown to be a powerful methodology for space search in docking of small ligands to proteins. This is demonstrated by docking of the thyroid hormone to its nuclear receptor. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 819-825, 2003

The cloud services innovation platform- enabling service-based environmental modelling using infrastructure-as-a-service cloud computing

USDA-ARS?s Scientific Manuscript database

Service oriented architectures allow modelling engines to be hosted over the Internet abstracting physical hardware configuration and software deployments from model users. Many existing environmental models are deployed as desktop applications running on user's personal computers (PCs). Migration ...

Host age modulates parasite infectivity, virulence and reproduction.

PubMed

Izhar, Rony; Ben-Ami, Frida

2015-07-01

Host age is one of the most striking differences among hosts within most populations, but there is very little data on how age-dependent effects impact ecological and evolutionary dynamics of both the host and the parasite. Here, we examined the influence of host age (juveniles, young and old adults) at parasite exposure on host susceptibility, fecundity and survival as well as parasite transmission, using two clones of the water flea Daphnia magna and two clones of its bacterial parasite Pasteuria ramosa. Younger D. magna were more susceptible to infection than older ones, regardless of host or parasite clone. Also, younger-infected D. magna became castrated faster than older hosts, but host and parasite clone effects contributed to this trait as well. Furthermore, the early-infected D. magna produced considerably more parasite transmission stages than late-infected ones, while host age at exposure did not affect virulence as it is defined in models (host mortality). When virulence is defined more broadly as the negative effects of infection on host fitness, by integrating the parasitic effects on host fecundity and mortality, then host age at exposure seems to slide along a negative relationship between host and parasite fitness. Thus, the virulence-transmission trade-off differs strongly among age classes, which in turn affects predictions of optimal virulence. Age-dependent effects on host susceptibility, virulence and parasite transmission could pose an important challenge for experimental and theoretical studies of infectious disease dynamics and disease ecology. Our results present a call for a more explicit stage-structured theory for disease, which will incorporate age-dependent epidemiological parameters. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

An Assessment of Combustion Dynamics in a Low-Nox, Second-Generation Swirl-Venturi Lean Direct Injection Combustion Concept

NASA Technical Reports Server (NTRS)

Tacina, K. M.; Chang, C. T.; Lee, P.; Mongia, H.; Podboy, D. P.; Dam, B.

2015-01-01

Dynamic pressure measurements were taken during flame-tube emissions testing of three second-generation swirl-venturi lean direct injection (SV-LDI) combustor configurations. These measurements show that combustion dynamics were typically small. However, a small number of points showed high combustion dynamics, with peak-to-peak dynamic pressure fluctuations above 0.5 psi. High combustion dynamics occurred at low inlet temperatures in all three SV-LDI configurations, so combustion dynamics were explored further at low temperature conditions. A point with greater than 1.5 psi peak-to-peak dynamic pressure fluctuations was identified at an inlet temperature of 450!F, a pressure of 100 psia, an air pressure drop of 3%, and an overall equivalence ratio of 0.35. This is an off design condition: the temperature and pressure are typical of 7% power conditions, but the equivalence ratio is high. At this condition, the combustion dynamics depended strongly on the fuel staging. Combustion dynamics could be reduced significantly without changing the overall equivalence ratio by shifting the fuel distribution between stages. Shifting the fuel distribution also decreased NOx emissions.

Embed dynamic content in your poster.

PubMed

Hutchins, B Ian

2013-01-29

A new technology has emerged that will facilitate the presentation of dynamic or otherwise inaccessible data on posters at scientific meetings. Video, audio, or other digital files hosted on mobile-friendly sites can be linked to through a quick response (QR) code, a two-dimensional barcode that can be scanned by smartphones, which then display the content. This approach is more affordable than acquiring tablet computers for playing dynamic content and can reach many users at large conferences. This resource details how to host videos, generate QR codes, and view the associated files on mobile devices.

Structure, dynamics and bifurcations of discrete solitons in trapped ion crystals

NASA Astrophysics Data System (ADS)

Landa, H.; Reznik, B.; Brox, J.; Mielenz, M.; Schaetz, T.

2013-09-01

We study discrete solitons (kinks) accessible in the state-of-the-art trapped ion experiments, considering zigzag crystals and quasi-three-dimensional configurations, both theoretically and experimentally. We first extend the theoretical understanding of different phenomena predicted and recently experimentally observed in the structure and dynamics of these topological excitations. Employing tools from topological degree theory, we analyze bifurcations of crystal configurations in dependence on the trapping parameters, and investigate the formation of kink configurations and the transformations of kinks between different structures. This allows us to accurately define and calculate the effective potential experienced by solitons within the Wigner crystal, and study how this (so-called Peierls-Nabarro) potential gets modified to a non-periodic globally trapping potential in certain parameter regimes. The kinks' rest mass (energy) and spectrum of modes are computed and the dynamics of linear and nonlinear kink oscillations are analyzed. We also present novel, experimentally observed, configurations of kinks incorporating a large-mass defect realized by an embedded molecular ion, and of pairs of interacting kinks stable for long times, offering the perspective for exploring and exploiting complex collective nonlinear excitations, controllable on the quantum level.

Experimental and analytical transonic flutter characteristics of a geared-elevator configuration

NASA Technical Reports Server (NTRS)

Ruhlin, C. L.; Doggett, R. V., Jr.; Gregory, R. A.

1980-01-01

The flutter model represented the aft fuselage and empennage of a proposed supersonic transport airplane and had an all movable horizontal tail with a geared elevator. It was tested mounted from a sting in the transonic dynamics tunnel. Symmetric flutter boundaries were determined experimentally at Mach numbers from 0.7 to 1.14 for a geared elevator configuration (gear ratio of 2.8 to 1.0) and an ungeared elevator configuration (gear ratio of 1.0 to 1.0). Gearing the elevator increased the experimental flutter dynamic pressures about 20 percent. Flutter calculations were made for the geared elevator configuration by using two analytical methods based on subsonic lifting surface theory. Both methods analyzed the stabilizer and elevator as a single, deforming surface, but one method also allowed the elevator to be analyzed as hinged from the stabilizer. All analyses predicted lower flutter dynamic pressures than experiment with best agreement (within 12 percent) for the hinged elevator method. Considering the model as mounted from a flexible rather than rigid sting in the analyses, had only a slight effect on the flutter results but was significant in that a sting related vibration mode was identified as a potentially flutter critical mode.

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

PubMed

Chen, Yunjie; Roux, Benoît

2015-08-11

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up to 21 times for polyalanine and (AAQAA)3 in water.

A graph based algorithm for adaptable dynamic airspace configuration for NextGen

NASA Astrophysics Data System (ADS)

Savai, Mehernaz P.

The National Airspace System (NAS) is a complicated large-scale aviation network, consisting of many static sectors wherein each sector is controlled by one or more controllers. The main purpose of the NAS is to enable safe and prompt air travel in the U.S. However, such static configuration of sectors will not be able to handle the continued growth of air travel which is projected to be more than double the current traffic by 2025. Under the initiative of the Next Generation of Air Transportation system (NextGen), the main objective of Adaptable Dynamic Airspace Configuration (ADAC) is that the sectors should change to the changing traffic so as to reduce the controller workload variance with time while increasing the throughput. Change in the resectorization should be such that there is a minimal increase in exchange of air traffic among controllers. The benefit of a new design (improvement in workload balance, etc.) should sufficiently exceed the transition cost, in order to deserve a change. This leads to the analysis of the concept of transition workload which is the cost associated with a transition from one sectorization to another. Given two airspace configurations, a transition workload metric which considers the air traffic as well as the geometry of the airspace is proposed. A solution to reduce this transition workload is also discussed. The algorithm is specifically designed to be implemented for the Dynamic Airspace Configuration (DAC) Algorithm. A graph model which accurately represents the air route structure and air traffic in the NAS is used to formulate the airspace configuration problem. In addition, a multilevel graph partitioning algorithm is developed for Dynamic Airspace Configuration which partitions the graph model of airspace with given user defined constraints and hence provides the user more flexibility and control over various partitions. In terms of air traffic management, vertices represent airports and waypoints. Some of the major (busy) airports need to be given more importance and hence treated separately. Thus the algorithm takes into account the air route structure while finding a balance between sector workloads. The performance of the proposed algorithms and performance metrics is validated with the Enhanced Traffic Management System (ETMS) air traffic data.

Absorbing phase transitions in deterministic fixed-energy sandpile models

NASA Astrophysics Data System (ADS)

Park, Su-Chan

2018-03-01

We investigate the origin of the difference, which was noticed by Fey et al. [Phys. Rev. Lett. 104, 145703 (2010), 10.1103/PhysRevLett.104.145703], between the steady state density of an Abelian sandpile model (ASM) and the transition point of its corresponding deterministic fixed-energy sandpile model (DFES). Being deterministic, the configuration space of a DFES can be divided into two disjoint classes such that every configuration in one class should evolve into one of absorbing states, whereas no configurations in the other class can reach an absorbing state. Since the two classes are separated in terms of toppling dynamics, the system can be made to exhibit an absorbing phase transition (APT) at various points that depend on the initial probability distribution of the configurations. Furthermore, we show that in general the transition point also depends on whether an infinite-size limit is taken before or after the infinite-time limit. To demonstrate, we numerically study the two-dimensional DFES with Bak-Tang-Wiesenfeld toppling rule (BTW-FES). We confirm that there are indeed many thresholds. Nonetheless, the critical phenomena at various transition points are found to be universal. We furthermore discuss a microscopic absorbing phase transition, or a so-called spreading dynamics, of the BTW-FES, to find that the phase transition in this setting is related to the dynamical isotropic percolation process rather than self-organized criticality. In particular, we argue that choosing recurrent configurations of the corresponding ASM as an initial configuration does not allow for a nontrivial APT in the DFES.

Absorbing phase transitions in deterministic fixed-energy sandpile models.

PubMed

Park, Su-Chan

2018-03-01

We investigate the origin of the difference, which was noticed by Fey et al. [Phys. Rev. Lett. 104, 145703 (2010)PRLTAO0031-900710.1103/PhysRevLett.104.145703], between the steady state density of an Abelian sandpile model (ASM) and the transition point of its corresponding deterministic fixed-energy sandpile model (DFES). Being deterministic, the configuration space of a DFES can be divided into two disjoint classes such that every configuration in one class should evolve into one of absorbing states, whereas no configurations in the other class can reach an absorbing state. Since the two classes are separated in terms of toppling dynamics, the system can be made to exhibit an absorbing phase transition (APT) at various points that depend on the initial probability distribution of the configurations. Furthermore, we show that in general the transition point also depends on whether an infinite-size limit is taken before or after the infinite-time limit. To demonstrate, we numerically study the two-dimensional DFES with Bak-Tang-Wiesenfeld toppling rule (BTW-FES). We confirm that there are indeed many thresholds. Nonetheless, the critical phenomena at various transition points are found to be universal. We furthermore discuss a microscopic absorbing phase transition, or a so-called spreading dynamics, of the BTW-FES, to find that the phase transition in this setting is related to the dynamical isotropic percolation process rather than self-organized criticality. In particular, we argue that choosing recurrent configurations of the corresponding ASM as an initial configuration does not allow for a nontrivial APT in the DFES.

The coevolutionary dynamics of obligate ant social parasite systems--between prudence and antagonism.

PubMed

Brandt, Miriam; Foitzik, Susanne; Fischer-Blass, Birgit; Heinze, Jürgen

2005-05-01

In this synthesis we apply coevolutionary models to the interactions between socially parasitic ants and their hosts. Obligate social parasite systems are ideal models for coevolution, because the close phylogenetic relationship between these parasites and their hosts results in similar evolutionary potentials, thus making mutual adaptations in a stepwise fashion especially likely to occur. The evolutionary dynamics of host-parasite interactions are influenced by a number of parameters, for example the parasite's transmission mode and rate, the genetic structure of host and parasite populations, the antagonists' migration rates, and the degree of mutual specialisation. For the three types of obligate ant social parasites, queen-tolerant and queen-intolerant inquilines and slavemakers, several of these parameters, and thus the evolutionary trajectory, are likely to differ. Because of the fundamental differences in lifestyle between these social parasite systems, coevolution should further select for different traits in the parasites and their hosts. Queen-tolerant inquilines are true parasites that exert a low selection pressure on their host, because of their rarity and the fact that they do not conduct slave raids to replenish their labour force. Due to their high degree of specialisation and the potential for vertical transmission, coevolutionary theory would predict interactions between these workerless parasites and their hosts to become even more benign over time. Queen-intolerant inquilines that kill the host queen during colony take-over are best described as parasitoids, and their reproductive success is limited by the existing worker force of the invaded host nest. These parasites should therefore evolve strategies to best exploit this fixed resource. Slavemaking ants, by contrast, act as parasites only during colony foundation, while their frequent slave raids follow a predator prey dynamic. They often exploit a number of host species at a given site, and theory predicts that their associations are best described in terms of a highly antagonistic coevolutionary arms race.

Quantitative Investigation of the Role of Intra-/Intercellular Dynamics in Bacterial Quorum Sensing.

PubMed

Leaman, Eric J; Geuther, Brian Q; Behkam, Bahareh

2018-04-20

Bacteria utilize diffusible signals to regulate population density-dependent coordinated gene expression in a process called quorum sensing (QS). While the intracellular regulatory mechanisms of QS are well-understood, the effect of spatiotemporal changes in the population configuration on the sensitivity and robustness of the QS response remains largely unexplored. Using a microfluidic device, we quantitatively characterized the emergent behavior of a population of swimming E. coli bacteria engineered with the lux QS system and a GFP reporter. We show that the QS activation time follows a power law with respect to bacterial population density, but this trend is disrupted significantly by microscale variations in population configuration and genetic circuit noise. We then developed a computational model that integrates population dynamics with genetic circuit dynamics to enable accurate (less than 7% error) quantitation of the bacterial QS activation time. Through modeling and experimental analyses, we show that changes in spatial configuration of swimming bacteria can drastically alter the QS activation time, by up to 22%. The integrative model developed herein also enables examination of the performance robustness of synthetic circuits with respect to growth rate, circuit sensitivity, and the population's initial size and spatial structure. Our framework facilitates quantitative tuning of microbial systems performance through rational engineering of synthetic ribosomal binding sites. We have demonstrated this through modulation of QS activation time over an order of magnitude. Altogether, we conclude that predictive engineering of QS-based bacterial systems requires not only the precise temporal modulation of gene expression (intracellular dynamics) but also accounting for the spatiotemporal changes in population configuration (intercellular dynamics).

Gut immune system: a new frontier for nutritional modulation of gut health

USDA-ARS?s Scientific Manuscript database

The gut represents a continuously evolving ecosystem consisting of trillions of commensal bacteria living in symbiosis with the host. The host-microbe interplay plays a crucial role in physiological development and health of the host. There is increasing evidence that shows a dynamic interaction be...

Physics-informed machine learning for inorganic scintillator discovery

NASA Astrophysics Data System (ADS)

Pilania, G.; McClellan, K. J.; Stanek, C. R.; Uberuaga, B. P.

2018-06-01

Applications of inorganic scintillators—activated with lanthanide dopants, such as Ce and Eu—are found in diverse fields. As a strict requirement to exhibit scintillation, the 4f ground state (with the electronic configuration of [Xe]4fn 5d0) and 5d1 lowest excited state (with the electronic configuration of [Xe]4fn-1 5d1) levels induced by the activator must lie within the host bandgap. Here we introduce a new machine learning (ML) based search strategy for high-throughput chemical space explorations to discover and design novel inorganic scintillators. Building upon well-known physics-based chemical trends for the host dependent electron binding energies within the 4f and 5d1 energy levels of lanthanide ions and available experimental data, the developed ML model—coupled with knowledge of the vacuum referred valence and conduction band edges computed from first principles—can rapidly and reliably estimate the relative positions of the activator's energy levels relative to the valence and conduction band edges of any given host chemistry. Using perovskite oxides and elpasolite halides as examples, the presented approach has been demonstrated to be able to (i) capture systematic chemical trends across host chemistries and (ii) effectively screen promising compounds in a high-throughput manner. While a number of other application-specific performance requirements need to be considered for a viable scintillator, the scheme developed here can be a practically useful tool to systematically down-select the most promising candidate materials in a first line of screening for a subsequent in-depth investigation.

Stable configurations in social networks

NASA Astrophysics Data System (ADS)

Bronski, Jared C.; DeVille, Lee; Ferguson, Timothy; Livesay, Michael

2018-06-01

We present and analyze a model of opinion formation on an arbitrary network whose dynamics comes from a global energy function. We study the global and local minimizers of this energy, which we call stable opinion configurations, and describe the global minimizers under certain assumptions on the friendship graph. We show a surprising result that the number of stable configurations is not necessarily monotone in the strength of connection in the social network, i.e. the model sometimes supports more stable configurations when the interpersonal connections are made stronger.

The Role of Clonal Interference in the Evolutionary Dynamics of Plasmid-Host Adaptation

PubMed Central

Hughes, Julie M.; Lohman, Brian K.; Deckert, Gail E.; Nichols, Eric P.; Settles, Matt; Abdo, Zaid; Top, Eva M.

2012-01-01

ABSTRACT Promiscuous plasmids replicate in a wide range of bacteria and therefore play a key role in the dissemination of various host-beneficial traits, including antibiotic resistance. Despite the medical relevance, little is known about the evolutionary dynamics through which drug resistance plasmids adapt to new hosts and thereby persist in the absence of antibiotics. We previously showed that the incompatibility group P-1 (IncP-1) minireplicon pMS0506 drastically improved its stability in novel host Shewanella oneidensis MR-1 after 1,000 generations under antibiotic selection for the plasmid. The only mutations found were those affecting the N terminus of the plasmid replication initiation protein TrfA1. Our aim in this study was to gain insight into the dynamics of plasmid evolution. Changes in stability and genotype frequencies of pMS0506 were monitored in evolving populations of MR-1 (pMS0506). Genotypes were determined by sequencing trfA1 amplicons from individual clones and by 454 pyrosequencing of whole plasmids from entire populations. Stability of pMS0506 drastically improved by generation 200. Many evolved plasmid genotypes with point mutations as well as in-frame and frameshift deletions and duplications in trfA1 were observed in all lineages with both sequencing methods. Strikingly, multiple genotypes were simultaneously present at high frequencies (>10%) in each population. Their relative abundances changed over time, but after 1,000 generations only one or two genotypes dominated the populations. This suggests that hosts with different plasmid genotypes were competing with each other, thus affecting the evolutionary trajectory. Plasmids can thus rapidly improve their stability, and clonal interference plays a significant role in plasmid-host adaptation dynamics. PMID:22761390

Preliminary Numerical Simulations of Nozzle Formation in the Host Rock of Supersonic Volcanic Jets

NASA Astrophysics Data System (ADS)

Wohletz, K. H.; Ogden, D. E.; Glatzmaier, G. A.

2006-12-01

Recognizing the difficulty in quantitatively predicting how a vent changes during an explosive eruption, Kieffer (Kieffer, S.W., Rev. Geophys. 27, 1989) developed the theory of fluid dynamic nozzles for volcanism, utilizing a highly developed predictive scheme used extensively in aerodynamics for design of jet and rocket nozzles. Kieffer's work shows that explosive eruptions involve flow from sub to supersonic conditions through the vent and that these conditions control the erosion of the vent to nozzle shapes and sizes that maximize mass flux. The question remains how to predict the failure and erosion of vent host rocks by a high-speed, multiphase, compressible fluid that represents an eruption column. Clearly, in order to have a quantitative model of vent dynamics one needs a robust computational method for a turbulent, compressible, multiphase fluid. Here we present preliminary simulations of fluid flowing from a high-pressure reservoir through an eroding conduit and into the atmosphere. The eruptive fluid is modeled as an ideal gas, the host rock as a simple incompressible fluid with sandstone properties. Although these simulations do not yet include the multiphase dynamics of the eruptive fluid or the solid mechanics of the host rock, the evolution of the host rock into a supersonic nozzle is clearly seen. Our simulations show shock fronts both above the conduit, where the gas has expanded into the atmosphere, and within the conduit itself, thereby influencing the dynamics of the jet decompression.

Multiscale System for Environmentally-Driven Infectious Disease with Threshold Control Strategy

NASA Astrophysics Data System (ADS)

Sun, Xiaodan; Xiao, Yanni

A multiscale system for environmentally-driven infectious disease is proposed, in which control measures at three different scales are implemented when the number of infected hosts exceeds a certain threshold. Our coupled model successfully describes the feedback mechanisms of between-host dynamics on within-host dynamics by employing one-scale variable guided enhancement of interventions on other scales. The modeling approach provides a novel idea of how to link the large-scale dynamics to small-scale dynamics. The dynamic behaviors of the multiscale system on two time-scales, i.e. fast system and slow system, are investigated. The slow system is further simplified to a two-dimensional Filippov system. For the Filippov system, we study the dynamics of its two subsystems (i.e. free-system and control-system), the sliding mode dynamics, the boundary equilibrium bifurcations, as well as the global behaviors. We prove that both subsystems may undergo backward bifurcations and the sliding domain exists. Meanwhile, it is possible that the pseudo-equilibrium exists and is globally stable, or the pseudo-equilibrium, the disease-free equilibrium and the real equilibrium are tri-stable, or the pseudo-equilibrium and the real equilibrium are bi-stable, or the pseudo-equilibrium and disease-free equilibrium are bi-stable, which depends on the threshold value and other parameter values. The global stability of the pseudo-equilibrium reveals that we may maintain the number of infected hosts at a previously given value. Moreover, the bi-stability and tri-stability indicate that whether the number of infected individuals tends to zero or a previously given value or other positive values depends on the parameter values and the initial states of the system. These results highlight the challenges in the control of environmentally-driven infectious disease.

Dynamic two-photon imaging of the immune response to Toxoplasma gondii infection.

PubMed

Luu, L; Coombes, J L

2015-03-01

Toxoplasma gondii is a highly successful parasite that can manipulate host immune responses to optimize its persistence and spread. As a result, a highly complex relationship exists between T. gondii and the immune system of the host. Advances in imaging techniques, and in particular, the application of two-photon microscopy to mouse infection models, have made it possible to directly visualize interactions between parasites and the host immune system as they occur in living tissues. Here, we will discuss how dynamic imaging techniques have provided unexpected new insight into (i) how immune responses are dynamically regulated by cells and structures in the local tissue environment, (ii) how protective responses to T. gondii are generated and (iii) how the parasite exploits the immune system for its own benefit. © 2014 John Wiley & Sons Ltd.

Uncertainty Quantification and Certification Prediction of Low-Boom Supersonic Aircraft Configurations

NASA Technical Reports Server (NTRS)

West, Thomas K., IV; Reuter, Bryan W.; Walker, Eric L.; Kleb, Bil; Park, Michael A.

2014-01-01

The primary objective of this work was to develop and demonstrate a process for accurate and efficient uncertainty quantification and certification prediction of low-boom, supersonic, transport aircraft. High-fidelity computational fluid dynamics models of multiple low-boom configurations were investigated including the Lockheed Martin SEEB-ALR body of revolution, the NASA 69 Delta Wing, and the Lockheed Martin 1021-01 configuration. A nonintrusive polynomial chaos surrogate modeling approach was used for reduced computational cost of propagating mixed, inherent (aleatory) and model-form (epistemic) uncertainty from both the computation fluid dynamics model and the near-field to ground level propagation model. A methodology has also been introduced to quantify the plausibility of a design to pass a certification under uncertainty. Results of this study include the analysis of each of the three configurations of interest under inviscid and fully turbulent flow assumptions. A comparison of the uncertainty outputs and sensitivity analyses between the configurations is also given. The results of this study illustrate the flexibility and robustness of the developed framework as a tool for uncertainty quantification and certification prediction of low-boom, supersonic aircraft.

Configuration maintaining control of three-body ring tethered system based on thrust compensation

NASA Astrophysics Data System (ADS)

Huang, Panfeng; Liu, Binbin; Zhang, Fan

2016-06-01

Space multi-tethered systems have shown broad prospects in remote observation missions. This paper mainly focuses on the dynamics and configuration maintaining control of space spinning three-body ring tethered system for such mission. Firstly, we establish the spinning dynamic model of the three-body ring tethered system considering the elasticity of the tether using Newton-Euler method, and then validate the suitability of this model by numerical simulation. Subsequently, LP (Likins-Pringle) initial equilibrium conditions for the tethered system are derived based on rigid body's equilibrium theory. Simulation results show that tether slack, snapping and interaction between the tethers exist in the three-body ring system, and its' configuration can not be maintained without control. Finally, a control strategy based on thrust compensation, namely thrust to simulate tether compression under LP initial equilibrium conditions is designed to solve the configuration maintaining control problem. Control effects are verified by numerical simulation compared with uncontrolled situation. Simulation results show that the configuration of the three-body ring tethered system could maintain under this active control strategy.

Beech Fructification and Bank Vole Population Dynamics - Combined Analyses of Promoters of Human Puumala Virus Infections in Germany

PubMed Central

Reil, Daniela; Imholt, Christian; Eccard, Jana Anja; Jacob, Jens

2015-01-01

The transmission of wildlife zoonoses to humans depends, amongst others, on complex interactions of host population ecology and pathogen dynamics within host populations. In Europe, the Puumala virus (PUUV) causes nephropathia epidemica in humans. In this study we investigated complex interrelations within the epidemic system of PUUV and its rodent host, the bank vole (Myodes glareolus). We suggest that beech fructification and bank vole abundance are both decisive factors affecting human PUUV infections. While rodent host dynamics are expected to be directly linked to human PUUV infections, beech fructification is a rather indirect predictor by serving as food source for PUUV rodent hosts. Furthermore, we examined the dependence of bank vole abundance on beech fructification. We analysed a 12-year (2001-2012) time series of the parameters: beech fructification (as food resource for the PUUV host), bank vole abundance and human incidences from 7 Federal States of Germany. For the first time, we could show the direct interrelation between these three parameters involved in human PUUV epidemics and we were able to demonstrate on a large scale that human PUUV infections are highly correlated with bank vole abundance in the present year, as well as beech fructification in the previous year. By using beech fructification and bank vole abundance as predictors in one model we significantly improved the degree of explanation of human PUUV incidence. Federal State was included as random factor because human PUUV incidence varies considerably among states. Surprisingly, the effect of rodent abundance on human PUUV infections is less strong compared to the indirect effect of beech fructification. Our findings are useful to facilitate the development of predictive models for host population dynamics and the related PUUV infection risk for humans and can be used for plant protection and human health protection purposes. PMID:26214509

Beech Fructification and Bank Vole Population Dynamics--Combined Analyses of Promoters of Human Puumala Virus Infections in Germany.

PubMed

Reil, Daniela; Imholt, Christian; Eccard, Jana Anja; Jacob, Jens

2015-01-01

The transmission of wildlife zoonoses to humans depends, amongst others, on complex interactions of host population ecology and pathogen dynamics within host populations. In Europe, the Puumala virus (PUUV) causes nephropathia epidemica in humans. In this study we investigated complex interrelations within the epidemic system of PUUV and its rodent host, the bank vole (Myodes glareolus). We suggest that beech fructification and bank vole abundance are both decisive factors affecting human PUUV infections. While rodent host dynamics are expected to be directly linked to human PUUV infections, beech fructification is a rather indirect predictor by serving as food source for PUUV rodent hosts. Furthermore, we examined the dependence of bank vole abundance on beech fructification. We analysed a 12-year (2001-2012) time series of the parameters: beech fructification (as food resource for the PUUV host), bank vole abundance and human incidences from 7 Federal States of Germany. For the first time, we could show the direct interrelation between these three parameters involved in human PUUV epidemics and we were able to demonstrate on a large scale that human PUUV infections are highly correlated with bank vole abundance in the present year, as well as beech fructification in the previous year. By using beech fructification and bank vole abundance as predictors in one model we significantly improved the degree of explanation of human PUUV incidence. Federal State was included as random factor because human PUUV incidence varies considerably among states. Surprisingly, the effect of rodent abundance on human PUUV infections is less strong compared to the indirect effect of beech fructification. Our findings are useful to facilitate the development of predictive models for host population dynamics and the related PUUV infection risk for humans and can be used for plant protection and human health protection purposes.

Simulation of generation and dynamics of polarization singularities with circular Airy beams.

PubMed

Ye, Dong; Peng, Xinyu; Zhou, Muchun; Xin, Yu; Song, Minmin

2017-11-01

The generation and dynamics of polarization singularities have been underresearched for years, while the focusing property of the topological configuration has not been explored much. In this paper, we simulated the generation of low-order polarization singularities with a circular Airy beam and explored the focusing property of the synthetic light field during propagation due to the autofocusing of the component. Our work researched the focusing properties of the polarization singularity configuration, which may help to develop its application prospect.

System dynamics and simulation of LSS

NASA Technical Reports Server (NTRS)

Ryan, R. F.

1978-01-01

Large Space Structures have many unique problems arising from mission objectives and the resulting configuration. Inherent in these configurations is a strong coupling among several of the designing disciplines. In particular, the coupling between structural dynamics and control is a key design consideration. The solution to these interactive problems requires efficient and accurate analysis, simulation and test techniques, and properly planned and conducted design trade studies. The discussion presented deals with these subjects and concludes with a brief look at some NASA capabilities which can support these technology studies.

Dynamic stall: An example of strong interaction between viscous and inviscid flows

NASA Technical Reports Server (NTRS)

Philippe, J. J.

1978-01-01

A study was done of the phenomena concerning profiles in dynamic stall configuration, and more specially those related to pitch oscillations. The most characteristic experimental results on flow separations with a vortex character, and their repercussions on local pressures and total forces were analyzed. Some aspects of the methods for predicting flows with the presence (or not) of boundary layer separation are examined, as well as the main simplified methods available to date for the calculation of total forces in such configurations.

Signal Processing Methods for Liquid Rocket Engine Combustion Stability Assessments

NASA Technical Reports Server (NTRS)

Kenny, R. Jeremy; Lee, Erik; Hulka, James R.; Casiano, Matthew

2011-01-01

The J2X Gas Generator engine design specifications include dynamic, spontaneous, and broadband combustion stability requirements. These requirements are verified empirically based high frequency chamber pressure measurements and analyses. Dynamic stability is determined with the dynamic pressure response due to an artificial perturbation of the combustion chamber pressure (bomb testing), and spontaneous and broadband stability are determined from the dynamic pressure responses during steady operation starting at specified power levels. J2X Workhorse Gas Generator testing included bomb tests with multiple hardware configurations and operating conditions, including a configuration used explicitly for engine verification test series. This work covers signal processing techniques developed at Marshall Space Flight Center (MSFC) to help assess engine design stability requirements. Dynamic stability assessments were performed following both the CPIA 655 guidelines and a MSFC in-house developed statistical-based approach. The statistical approach was developed to better verify when the dynamic pressure amplitudes corresponding to a particular frequency returned back to pre-bomb characteristics. This was accomplished by first determining the statistical characteristics of the pre-bomb dynamic levels. The pre-bomb statistical characterization provided 95% coverage bounds; these bounds were used as a quantitative measure to determine when the post-bomb signal returned to pre-bomb conditions. The time for post-bomb levels to acceptably return to pre-bomb levels was compared to the dominant frequency-dependent time recommended by CPIA 655. Results for multiple test configurations, including stable and unstable configurations, were reviewed. Spontaneous stability was assessed using two processes: 1) characterization of the ratio of the peak response amplitudes to the excited chamber acoustic mode amplitudes and 2) characterization of the variability of the peak response's frequency over the test duration. This characterization process assists in evaluating the discreteness of a signal as well as the stability of the chamber response. Broadband stability was assessed using a running root-mean-square evaluation. These techniques were also employed, in a comparative analysis, on available Fastrac data, and these results are presented here.

Unix Security Cookbook

NASA Astrophysics Data System (ADS)

Rehan, S. C.

This document has been written to help Site Managers secure their Unix hosts from being compromised by hackers. I have given brief introductions to the security tools along with downloading, configuring and running information. I have also included a section on my recommendations for installing these security tools starting from an absolute minimum security requirement.

Ada Compiler Validation Summary Report: Certificate Number: 900121S1. 10251 Computer Sciences Corporation MC Ada V1.2.Beta/Concurrent Computer Corporation Concurrent/Masscomp 5600 Host To Concurrent/Masscomp 5600 (Dual 68020 Processor Configuration) Target

DTIC Science & Technology

1990-04-23

developed Ada Real - Time Operating System (ARTOS) for bare machine environments(Target), ACW 1.1I0. " ; - -M.UIECTTERMS Ada programming language, Ada...configuration) Operating System: CSC developed Ada Real - Time Operating System (ARTOS) for bare machine environments Memory Size: 4MB 2.2...Test Method Testing of the MC Ado V1.2.beta/ Concurrent Computer Corporation compiler and the CSC developed Ada Real - Time Operating System (ARTOS) for

A continuum model for dynamic analysis of the Space Station

NASA Technical Reports Server (NTRS)

Thomas, Segun

1989-01-01

Dynamic analysis of the International Space Station using MSC/NASTRAN had 1312 rod elements, 62 beam elements, 489 nodes and 1473 dynamic degrees of freedom. A realtime, man-in-the-loop simulation of such a model is impractical. This paper discusses the mathematical model for realtime dynamic simulation of the Space Station. Several key questions in structures and structural dynamics are addressed. First, to achieve a significant reduction in the number of dynamic degrees of freedom, a continuum equivalent representation of the Space Station truss structure which accounted for the unsymmetry of the basic configuration and resulted in the coupling of extensional and transverse deformation, is developed. Next, dynamic equations for the continuum equivalent of the Space Station truss structure are formulated using a matrix version of Kane's dynamical equations. Flexibility is accounted for by using a theory that accommodates extension, bending in two principal planes and shear displacement. Finally, constraint equations suitable for dynamic analysis of flexible bodies with closed loop configuration are developed and solution of the resulting system of equations is based on the zero eigenvalue theorem.

Probing how initial retinal configuration controls photochemical dynamics in retinal proteins

NASA Astrophysics Data System (ADS)

Wand, A.; Rozin, R.; Eliash, T.; Friedman, N.; Jung, K. H.; Sheves, M.; Ruhman, S.

2013-03-01

The effects of the initial retinal configuration and the active isomerization coordinate on the photochemistry of retinal proteins (RPs) are assessed by comparing photochemical dynamics of two stable retinal ground state configurations (all-trans,15-anti vs. 13-cis,15-syn), within two RPs: Bacteriorhodopsin (BR) and Anabaena Sensory Rhodopsin (ASR). Hyperspectral pump-probe spectroscopy shows that photochemistry starting from 13-cis retinal in both proteins is 3-10 times faster than when started in the all-trans state, suggesting that the hastening is ubiquitous to microbial RPs, regardless of their different biological functions and origin. This may also relate to the known disparity of photochemical rates between microbial RPs and visual pigments. Importance and possible underlying mechanisms are discussed as well.

Structure and Dynamics of Polymer/Polymer grafted nanoparticle composite

NASA Astrophysics Data System (ADS)

Archer, Lynden

Addition of nanoparticles to polymers is a well-practiced methodology for augmenting various properties of the polymer host, including mechanical strength, thermal stability, barrier properties, dimensional stability and wear resistance. Many of these property changes are known to arise from nanoparticle-induced modification of polymer structure and chain dynamics, which are strong functions of the dispersion state of the nanoparticles' and on their relative size (D) to polymer chain dimensions (e.g. Random coil radius Rg or entanglement mesh size a) . This talk will discuss polymer nanocomposites (PNCs) comprised of Polyethylene Glycol (PEG) tethered silica nanoparticles (SiO2-PEG) dispersed in polymers as model systems for investigating phase stability and dynamics of PNCs. On the basis of small-angle X-ray Scattering, it will be shown that favorable enthalpic interactions between particle-tethered chains and a polymer host provides an important mechanism for creating PNCs in which particle aggregation is avoided. The talk will report on polymer and particle scale dynamics in these materials and will show that grafted nanoparticles well dispersed in a polymer host strongly influence the host polymer relaxation dynamics on all timescales and the polymers in turn produce dramatic changes in the nature (from diffusive to hyperdiffusive) and speed of nano particle decorrelation dynamics at the polymer entanglement threshold. A local viscosity model capable of explaining these observations is discussed and the results compared with scaling theories for NP motions in polymers This material is based on work supported by the National Science Foundation Award Nos. DMR-1609125 and CBET-1512297.

BRIDGING SCALES IN THE EVOLUTION OF INFECTIOUS DISEASE LIFE HISTORIES: APPLICATION

PubMed Central

Mideo, Nicole; Nelson, William A.; Reece, Sarah E.; Bell, Andrew S.; Read, Andrew F.; Day, Troy

2014-01-01

Within- and between-host disease processes occur on the same timescales, therefore changes in the within-host dynamics of parasites, resources, and immunity can interact with changes in the epidemiological dynamics to affect evolutionary outcomes. Consequently, studies of the evolution of disease life histories, that is, infection-age-specific patterns of transmission and virulence, have been constrained by the need for a mechanistic understanding of within-host disease dynamics. In a companion paper (Day et al. 2011), we develop a novel approach that quantifies the relevant within-host aspects of disease through genetic covariance functions. Here, we demonstrate how to apply this theory to data. Using two previously published datasets from rodent malaria infections, we show how to translate experimental measures into disease life-history traits, and how to quantify the covariance in these traits. Our results show how patterns of covariance can interact with epidemiological dynamics to affect evolutionary predictions for disease life history. We also find that the selective constraints on disease life-history evolution can vary qualitatively, and that “simple” virulence-transmission trade-offs that are often the subject of experimental investigation can be obscured by trade-offs within one trait alone. Finally, we highlight the type and quality of data required for future applications. PMID:22023593

Inferring infection hazard in wildlife populations by linking data across individual and population scales.

PubMed

Pepin, Kim M; Kay, Shannon L; Golas, Ben D; Shriner, Susan S; Gilbert, Amy T; Miller, Ryan S; Graham, Andrea L; Riley, Steven; Cross, Paul C; Samuel, Michael D; Hooten, Mevin B; Hoeting, Jennifer A; Lloyd-Smith, James O; Webb, Colleen T; Buhnerkempe, Michael G

2017-03-01

Our ability to infer unobservable disease-dynamic processes such as force of infection (infection hazard for susceptible hosts) has transformed our understanding of disease transmission mechanisms and capacity to predict disease dynamics. Conventional methods for inferring FOI estimate a time-averaged value and are based on population-level processes. Because many pathogens exhibit epidemic cycling and FOI is the result of processes acting across the scales of individuals and populations, a flexible framework that extends to epidemic dynamics and links within-host processes to FOI is needed. Specifically, within-host antibody kinetics in wildlife hosts can be short-lived and produce patterns that are repeatable across individuals, suggesting individual-level antibody concentrations could be used to infer time since infection and hence FOI. Using simulations and case studies (influenza A in lesser snow geese and Yersinia pestis in coyotes), we argue that with careful experimental and surveillance design, the population-level FOI signal can be recovered from individual-level antibody kinetics, despite substantial individual-level variation. In addition to improving inference, the cross-scale quantitative antibody approach we describe can reveal insights into drivers of individual-based variation in disease response, and the role of poorly understood processes such as secondary infections, in population-level dynamics of disease. © 2017 John Wiley & Sons Ltd/CNRS.

Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus

PubMed Central

Weber de Melo, Vanessa; Sheikh Ali, Hanan; Freise, Jona; Kühnert, Denise; Essbauer, Sandra; Mertens, Marc; Wanka, Konrad M; Drewes, Stephan; Ulrich, Rainer G; Heckel, Gerald

2015-01-01

Many viruses significantly impact human and animal health. Understanding the population dynamics of these viruses and their hosts can provide important insights for epidemiology and virus evolution. Puumala virus (PUUV) is a European hantavirus that may cause regional outbreaks of hemorrhagic fever with renal syndrome in humans. Here, we analyzed the spatiotemporal dynamics of PUUV circulating in local populations of its rodent reservoir host, the bank vole (Myodes glareolus) during eight years. Phylogenetic and population genetic analyses of all three genome segments of PUUV showed strong geographical structuring at a very local scale. There was a high temporal turnover of virus strains in the local bank vole populations, but several virus strains persisted through multiple years. Phylodynamic analyses showed no significant changes in the local effective population sizes of PUUV, although vole numbers and virus prevalence fluctuated widely. Microsatellite data demonstrated also a temporally persisting subdivision between local vole populations, but these groups did not correspond to the subdivision in the virus strains. We conclude that restricted transmission between vole populations and genetic drift play important roles in shaping the genetic structure and temporal dynamics of PUUV in its natural host which has several implications for zoonotic risks of the human population. PMID:26136821

Inferring infection hazard in wildlife populations by linking data across individual and population scales

USGS Publications Warehouse

Pepin, Kim M.; Kay, Shannon L.; Golas, Ben D.; Shriner, Susan A.; Gilbert, Amy T.; Miller, Ryan S.; Graham, Andrea L.; Riley, Steven; Cross, Paul C.; Samuel, Michael D.; Hooten, Mevin B.; Hoeting, Jennifer A.; Lloyd-Smith, James O.; Webb, Colleen T.; Buhnerkempe, Michael G.

2017-01-01

Our ability to infer unobservable disease-dynamic processes such as force of infection (infection hazard for susceptible hosts) has transformed our understanding of disease transmission mechanisms and capacity to predict disease dynamics. Conventional methods for inferring FOI estimate a time-averaged value and are based on population-level processes. Because many pathogens exhibit epidemic cycling and FOI is the result of processes acting across the scales of individuals and populations, a flexible framework that extends to epidemic dynamics and links within-host processes to FOI is needed. Specifically, within-host antibody kinetics in wildlife hosts can be short-lived and produce patterns that are repeatable across individuals, suggesting individual-level antibody concentrations could be used to infer time since infection and hence FOI. Using simulations and case studies (influenza A in lesser snow geese and Yersinia pestis in coyotes), we argue that with careful experimental and surveillance design, the population-level FOI signal can be recovered from individual-level antibody kinetics, despite substantial individual-level variation. In addition to improving inference, the cross-scale quantitative antibody approach we describe can reveal insights into drivers of individual-based variation in disease response, and the role of poorly understood processes such as secondary infections, in population-level dynamics of disease.

Modelling variability in lymphatic filariasis: macrofilarial dynamics in the Brugia pahangi--cat model.

PubMed

Michael, E; Grenfell, B T; Isham, V S; Denham, D A; Bundy, D A

1998-01-22

A striking feature of lymphatic filariasis is the considerable heterogeneity in infection burden observed between hosts, which greatly complicates the analysis of the population dynamics of the disease. Here, we describe the first application of the moment closure equation approach to model the sources and the impact of this heterogeneity for macrofilarial population dynamics. The analysis is based on the closest laboratory equivalent of the life cycle and immunology of infection in humans--cats chronically infected with the filarial nematode Brugia pahangi. Two sets of long-term experiments are analysed: hosts given either single primary infections or given repeat infections. We begin by quantifying changes in the mean and aggregation of adult parasites (inversely measured by the negative binomial parameter, kappa in cohorts of hosts using generalized linear models. We then apply simple stochastic models to interpret observed patterns. The models and empirical data indicate that parasite aggregation tracks the decline in the mean burden with host age in primary infections. Conversely, in repeat infections, aggregation increases as the worm burden declines with experience of infection. The results show that the primary infection variability is consistent with heterogeneities in parasite survival between hosts. By contrast, the models indicate that the reduction in parasite variability with time in repeat infections is most likely due to the 'filtering' effect of a strong, acquired immune response, which gradually acts to remove the initial variability generated by heterogeneities in larval mortality. We discuss this result in terms of the homogenizing effect of host immunity-driven density-dependence on macrofilarial burden in older hosts.

The Upper Atmosphere Research Satellite In-Flight Dynamics

NASA Technical Reports Server (NTRS)

Woodard, Stanley E.

1997-01-01

Upper Atmosphere Research Satellite flight data from the first 737 days after launch (September 1991) was used to investigate spacecraft disturbances and responses. The investigation included two in-flight dynamics experiments (approximately three orbits each). Orbital and configuration influences on spacecraft dynamic response were also examined. Orbital influences were due to temperature variation from crossing the Earth's terminator and variation of the solar incident energy as the orbit precessed. During the terminator crossing, the rapid ambient temperature change caused the spacecraft's two flexible appendages to experience thermal elastic bending (thermal snap). The resulting response was dependent upon the orientation of the solar array and the solar incident energy. Orbital influences were also caused by on-board and environmental disturbances and spacecraft configuration changes resulting in dynamic responses which were repeated each orbit. Configuration influences were due to solar array rotation changing spacecraft modal properties. The investigation quantified the spacecraft dynamic response produced by the solar array and high gain antenna harmonic drive disturbances. The solar array's harmonic drive output resonated two solar array modes. Friction in the solar array gear drive provided sufficient energy dissipation which prevented the solar panels from resonating catastrophically; however, the solar array vibration amplitude was excessively large. The resulting vibration had a latitude-specific pattern.

Computer symbiosis: Emergence of symbiotic behavior through evolution

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

Ikegami, Takashi; Kaneko, Kunihiko

Symbiosis is altruistic cooperation between distinct species. It is one of the most effective evolutionary processes, but its dynamics are not well understood as yet. A simple model of symbiosis is introduced, where we consider interactions between hosts and parasites and also mutations of hosts and parasites. It is found that a symbiotic state emerges for a suitable range of mutation rates. The symbiotic state is not static, but dynamically oscillates. Harmful parasites violating symbiosis appear periodically, but are rapidly extinguished by hosts and other parasites, and the symbiotic state is recovered. The emergence of ''Tit for Tat'' strategy tomore » maintain symbiosis is discussed. 4 figs.« less

Parasites and phytoplankton, with special emphasis on dinoflagellate infections.

PubMed

Park, Myung Gil; Yih, Wonho; Coats, D Wayne

2004-01-01

Planktonic members of most algal groups are known to harbor intracellular symbionts, including viruses, bacteria, fungi, and protozoa. Among the dinoflagellates, viral and bacterial associations were recognized a quarter century ago, yet their impact on host populations remains largely unresolved. By contrast, fungal and protozoan infections of dinoflagellates are well documented and generally viewed as playing major roles in host population dynamics. Our understanding of fungal parasites is largely based on studies for freshwater diatoms and dinoflagellates, although fungal infections are known for some marine phytoplankton. In freshwater systems, fungal chytrids have been linked to mass mortalities of host organisms, suppression or retardation of phytoplankton blooms, and selective effects on species composition leading to successional changes in plankton communities. Parasitic dinoflagellates of the genus Amoebophrya and the newly described Perkinsozoa, Parvilucifera infectans, are widely distributed in coastal waters of the world where they commonly infect photosynthetic and heterotrophic dinoflagellates. Recent work indicates that these parasites can have significant impacts on host physiology, behavior, and bloom dynamics. Thus, parasitism needs to be carefully considered in developing concepts about plankton dynamics and the flow of material in marine food webs.

The effect of host cluster gravitational tidal forces on the internal dynamics of spiral galaxies

NASA Astrophysics Data System (ADS)

Mayer, Alexander

2013-04-01

New empirical observation by Bidin, Carraro, Mendez & Smith finds ``a lack of dark matter in the Solar neighborhood" (2012 ApJ 751, 30). This, and the discovery of a vast polar structure of Milky Way satellites by Pawlowski, Pflamm-Altenburg & Kroupa (2012 MNRAS 423, 1109), conflict with the prevailing interpretation of the measured Galactic rotation curve. Simulating the dynamical effects of host cluster tidal forces on galaxy disks reveals radial migration in a spiral structure and an orbital velocity that accelerates with increasing galactocentric radial coordinate. A virtual ``toy model,'' which is based on an Earth-orbiting system of particles and is physically realizable in principle, is available at GravitySim.net. Given the perturbing gravitational effect of the host cluster on a spiral galaxy disk and that a similar effect does not exist for the Solar System, the two systems represent distinct classes of gravitational dynamical systems. The observed `flat' and accelerating rotation curves of spiral galaxies can be attributed to gravitational interaction with the host cluster; no `dark matter halo' is required to explain the observable.

Environmental Nutrient Supply Directly Alters Plant Traits but Indirectly Determines Virus Growth Rate

PubMed Central

Lacroix, Christelle; Seabloom, Eric W.; Borer, Elizabeth T.

2017-01-01

Ecological stoichiometry and resource competition theory both predict that nutrient rates and ratios can alter infectious disease dynamics. Pathogens such as viruses hijack nutrient rich host metabolites to complete multiple steps of their epidemiological cycle. As the synthesis of these molecules requires nitrogen (N) and phosphorus (P), environmental supply rates, and ratios of N and P to hosts can directly limit disease dynamics. Environmental nutrient supplies also may alter virus epidemiology indirectly by changing host phenotype or the dynamics of coinfecting pathogens. We tested whether host nutrient supplies and coinfection control pathogen growth within hosts and transmission to new hosts, either directly or through modifications of plant tissue chemistry (i.e., content and stoichiometric ratios of nutrients), host phenotypic traits, or among-pathogen interactions. We examined two widespread plant viruses (BYDV-PAV and CYDV-RPV) in cultivated oats (Avena sativa) grown along a range of N and of P supply rates. N and P supply rates altered plant tissue chemistry and phenotypic traits; however, environmental nutrient supplies and plant tissue content and ratios of nutrients did not directly alter virus titer. Infection with CYDV-RPV altered plant traits and resulted in thicker plant leaves (i.e., higher leaf mass per area) and there was a positive correlation between CYDV-RPV titer and leaf mass per area. CYDV-RPV titer was reduced by the presence of a competitor, BYDV-PAV, and higher CYDV-RPV titer led to more severe chlorotic symptoms. In our experimental conditions, virus transmission was unaffected by nutrient supply rates, co-infection, plant stoichiometry, or plant traits, although nutrient supply rates have been shown to increase infection and coinfection rates. This work provides a robust test of the role of plant nutrient content and ratios in the dynamics of globally important pathogens and reveals a more complex relationship between within-host virus growth and alterations of plant traits. A deeper understanding of the differential effects of environmental nutrient supplies on virus epidemiology and ecology is particularly relevant given the rapid increase of nutrients flowing into Earth's ecosystems as a result of human activities. PMID:29163408

Fungal Iron Availability during Deep Seated Candidiasis Is Defined by a Complex Interplay Involving Systemic and Local Events

PubMed Central

Potrykus, Joanna; Stead, David; MacCallum, Donna M.; Urgast, Dagmar S.; Raab, Andrea; van Rooijen, Nico; Feldmann, Jörg; Brown, Alistair J. P.

2013-01-01

Nutritional immunity – the withholding of nutrients by the host – has long been recognised as an important factor that shapes bacterial-host interactions. However, the dynamics of nutrient availability within local host niches during fungal infection are poorly defined. We have combined laser ablation-inductively coupled plasma mass spectrometry (LA-ICP MS), MALDI imaging and immunohistochemistry with microtranscriptomics to examine iron homeostasis in the host and pathogen in the murine model of systemic candidiasis. Dramatic changes in the renal iron landscape occur during disease progression. The infection perturbs global iron homeostasis in the host leading to iron accumulation in the renal medulla. Paradoxically, this is accompanied by nutritional immunity in the renal cortex as iron exclusion zones emerge locally around fungal lesions. These exclusion zones correlate with immune infiltrates and haem oxygenase 1-expressing host cells. This local nutritional immunity decreases iron availability, leading to a switch in iron acquisition mechanisms within mature fungal lesions, as revealed by laser capture microdissection and qRT-PCR analyses. Therefore, a complex interplay of systemic and local events influences iron homeostasis and pathogen-host dynamics during disease progression. PMID:24146619

Molecular dynamics simulation of low dielectric constant polymer electrolytes

NASA Astrophysics Data System (ADS)

Wheatle, Bill; Lynd, Nathaniel; Ganesan, Venkat

Recent experimental studies measured the ionic conductivities of a series of poly(glycidyl ether)s with varying neat dielectric constants (ɛ), viscosities (η), and glass transition temperatures (Tg), as hosts for lithium bistrifluoromethanesulfonimide (LiTFSI) salt. In such a context, it was demonstrated that the ionic conductivity of these polymer electrolytes was a function of ɛ rather than Tg or η, suggesting that there may exist regimes in which ionic conductivity is not limited by slow segmental dynamics but rather by low ionic dissociation. Motivated by such results, we used atomistic molecular dynamics to study the structure and transport characteristics of the same set of host polymers. We found that the coordination number of TFSI- about Li+ in the first solvation shell and the total fraction of free ions increased as a function of ɛ, implying the polymer hosts enhanced ion dissociation. In addition, we found that increasing the dielectric constant of the host polymer enhanced self-correlated ion transport, as evidenced by an increase in the diffusion coefficients of each ion species. Overall, we confirmed that limited ion dissociation in low- ɛ polymer electrolyte hosts hampers ionic conductivity. We would like to thank the National Science Foundation Graduate Research Fellowship Program for funding this research endeavor.

Temporal dynamics of Puumala hantavirus infection in cyclic populations of bank voles.

PubMed

Voutilainen, Liina; Kallio, Eva R; Niemimaa, Jukka; Vapalahti, Olli; Henttonen, Heikki

2016-02-18

Understanding the dynamics of zoonotic pathogens in their reservoir host populations is a prerequisite for predicting and preventing human disease epidemics. The human infection risk of Puumala hantavirus (PUUV) is highest in northern Europe, where populations of the rodent host (bank vole, Myodes glareolus) undergo cyclic fluctuations. We conducted a 7-year capture-mark-recapture study to monitor seasonal and multiannual patterns of the PUUV infection rate in bank vole populations exhibiting a 3-year density cycle. Infected bank voles were most abundant in mid-winter months during years of increasing or peak host density. Prevalence of PUUV infection in bank voles exhibited a regular, seasonal pattern reflecting the annual population turnover and accumulation of infections within each year cohort. In autumn, the PUUV transmission rate tracked increasing host abundance, suggesting a density-dependent transmission. However, prevalence of PUUV infection was similar during the increase and peak years of the density cycle despite a twofold difference in host density. This may result from the high proportion of individuals carrying maternal antibodies constraining transmission during the cycle peak years. Our exceptionally intensive and long-term dataset provides a solid basis on which to develop models to predict the dynamic public health threat posed by PUUV in northern Europe.

Pathogen dynamics during invasion and establishment of white-nose syndrome explain mechanisms of host persistence.

PubMed

Frick, Winifred F; Cheng, Tina L; Langwig, Kate E; Hoyt, Joseph R; Janicki, Amanda F; Parise, Katy L; Foster, Jeffrey T; Kilpatrick, A Marm

2017-03-01

Disease dynamics during pathogen invasion and establishment determine the impacts of disease on host populations and determine the mechanisms of host persistence. Temporal progression of prevalence and infection intensity illustrate whether tolerance, resistance, reduced transmission, or demographic compensation allow initially declining populations to persist. We measured infection dynamics of the fungal pathogen Pseudogymnoascus destructans that causes white-nose syndrome in bats by estimating pathogen prevalence and load in seven bat species at 167 hibernacula over a decade as the pathogen invaded, became established, and some host populations stabilized. Fungal loads increased rapidly and prevalence rose to nearly 100% at most sites within 2 yr of invasion in six of seven species. Prevalence and loads did not decline over time despite huge reductions in colony sizes, likely due to an extensive environmental reservoir. However, there was substantial variation in fungal load among sites with persisting colonies, suggesting that both tolerance and resistance developed at different sites in the same species. In contrast, one species disappeared from hibernacula within 3 yr of pathogen invasion. Variable host responses to pathogen invasion require different management strategies to prevent disease-induced extinction and to facilitate evolution of tolerance or resistance in persisting populations. © 2016 by the Ecological Society of America.

Trees Wanted—Dead or Alive! Host Selection and Population Dynamics in Tree-Killing Bark Beetles

PubMed Central

Kausrud, Kyrre L.; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr.

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between “endemic” and “epidemic” regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics. PMID:21647433

A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host–Pathogen Interaction Networks

PubMed Central

Wu, Chia-Chou; Chen, Bor-Sen

2016-01-01

Infected zebrafish coordinates defensive and offensive molecular mechanisms in response to Candida albicans infections, and invasive C. albicans coordinates corresponding molecular mechanisms to interact with the host. However, knowledge of the ensuing infection-activated signaling networks in both host and pathogen and their interspecific crosstalk during the innate and adaptive phases of the infection processes remains incomplete. In the present study, dynamic network modeling, protein interaction databases, and dual transcriptome data from zebrafish and C. albicans during infection were used to infer infection-activated host–pathogen dynamic interaction networks. The consideration of host–pathogen dynamic interaction systems as innate and adaptive loops and subsequent comparisons of inferred innate and adaptive networks indicated previously unrecognized crosstalk between known pathways and suggested roles of immunological memory in the coordination of host defensive and offensive molecular mechanisms to achieve specific and powerful defense against pathogens. Moreover, pathogens enhance intraspecific crosstalk and abrogate host apoptosis to accommodate enhanced host defense mechanisms during the adaptive phase. Accordingly, links between physiological phenomena and changes in the coordination of defensive and offensive molecular mechanisms highlight the importance of host–pathogen molecular interaction networks, and consequent inferences of the host–pathogen relationship could be translated into biomedical applications. PMID:26881892

Laser-induced electron dynamics including photoionization: A heuristic model within time-dependent configuration interaction theory.

PubMed

Klinkusch, Stefan; Saalfrank, Peter; Klamroth, Tillmann

2009-09-21

We report simulations of laser-pulse driven many-electron dynamics by means of a simple, heuristic extension of the time-dependent configuration interaction singles (TD-CIS) approach. The extension allows for the treatment of ionizing states as nonstationary states with a finite, energy-dependent lifetime to account for above-threshold ionization losses in laser-driven many-electron dynamics. The extended TD-CIS method is applied to the following specific examples: (i) state-to-state transitions in the LiCN molecule which correspond to intramolecular charge transfer, (ii) creation of electronic wave packets in LiCN including wave packet analysis by pump-probe spectroscopy, and, finally, (iii) the effect of ionization on the dynamic polarizability of H(2) when calculated nonperturbatively by TD-CIS.

Investigation of dynamic noise affecting geodynamics information in a tethered subsatellite

NASA Technical Reports Server (NTRS)

Gullahorn, G. E.

1984-01-01

The effects of a tethered satellite system's internal dynamics on the subsatellite were calculated including both overall motions (libration and attitude oscillations) and internal tether oscillations. The SKYHOOK tether simulation program was modified to operate with atmospheric density variations and to output quantities of interest. Techniques and software for analyzing the results were developed including noise spectral analysis. A program was begun for computing a stable configuration of a tether system subject to air drag. These configurations will be of use as initial conditions for SKYHOOK and, through linearized analysis, directly for stability and dynamical studies. A case study in which the subsatellite traverses an atmospheric density enhancement confirmed some theoretical calculations, and pointed out some aspects of the interaction with the tether system dynamics.

Computational fluid dynamics evaluation of the cross-limb stent graft configuration for endovascular aneurysm repair.

PubMed

Shek, Tina L T; Tse, Leonard W; Nabovati, Aydin; Amon, Cristina H

2012-12-01

The technique of crossing the limbs of bifurcated modular stent grafts for endovascular aneurysm repair (EVAR) is often employed in the face of splayed aortic bifurcations to facilitate cannulation and prevent device kinking. However, little has been reported about the implications of cross-limb EVAR, especially in comparison to conventional EVAR. Previous computational fluid dynamics studies of conventional EVAR grafts have mostly utilized simplified planar stent graft geometries. We herein examined the differences between conventional and cross-limb EVAR by comparing their hemodynamic flow fields (i.e., in the "direct" and "cross" configurations, respectively). We also added a "planar" configuration, which is commonly found in the literature, to identify how well this configuration compares to out-of-plane stent graft configurations from a hemodynamic perspective. A representative patient's cross-limb stent graft geometry was segmented using computed tomography imaging in Mimics software. The cross-limb graft geometry was used to build its direct and planar counterparts in SolidWorks. Physiologic velocity and mass flow boundary conditions and blood properties were implemented for steady-state and pulsatile transient simulations in ANSYS CFX. Displacement forces, wall shear stress (WSS), and oscillatory shear index (OSI) were all comparable between the direct and cross configurations, whereas the planar geometry yielded very different predictions of hemodynamics compared to the out-of-plane stent graft configurations, particularly for displacement forces. This single-patient study suggests that the short-term hemodynamics involved in crossing the limbs is as safe as conventional EVAR. Higher helicity and improved WSS distribution of the cross-limb configuration suggest improved flow-related thrombosis resistance in the short term. However, there may be long-term fatigue implications to stent graft use in the cross configuration when compared to the direct configuration.

The plant host pathogen interface: cell wall and membrane dynamics of pathogen-induced responses.

PubMed

Day, Brad; Graham, Terry

2007-10-01

Perception of pathogens by their hosts is the outcome of a highly coordinated and sophisticated surveillance network, tightly regulated by both host and pathogen elicitors, effectors, and signaling processes. In this article, we focus on two relatively well-studied host-pathogens systems, one involving a bacterial-plant interaction (Pseudomonas syringae-Arabidopsis) and the other involving an oomycete-plant interaction (Phytophthora sojae-soybean). We discuss the status of current research related to events occurring at the host-pathogen interface in these two systems, and how these events influence the organization and activation of resistance responses in the respective hosts. This recent research has revealed that in addition to the previously identified resistance machinery (R-proteins, molecular chaperones, etc.), the dynamics of the cell wall, membrane trafficking, and the actin cytoskeleton are intimately associated with the activation of resistance in plants. Specifically, in Arabidopsis, a possible connection between the actin machinery and R-protein- mediated induction of disease resistance is described. In the case of the P. sojae-soybean interaction, we describe the fact that a classical basal resistance elicitor, the cell wall glucan elicitor from the pathogen, can directly activate host hypersensitive cell death, which is apparently modulated in a race-specific manner by the presence of R genes in the host.

Inflammatory phenotypes in the intestine of poultry: Not all inflammation is created equally

USDA-ARS?s Scientific Manuscript database

The intestinal tract harbors a diverse community of microbes that have co-evolved with the host immune system. Although many of these microbes execute functions that are critical for host physiology, the host immune system must control the microbial community so that the dynamics of this interdepen...

Various antibiotic alternative strategies to reduce pathogen-induced inflammation and to maintain gut homeostasis in broiler chickens

USDA-ARS?s Scientific Manuscript database

The gut represents a continuously evolving ecosystem consisting of trillions of commensal bacteria living in symbiosis with the host. This host-microbe interplay plays a crucial role in physiological development and health of the host. There is increasing evidence that shows a dynamic interaction b...

Bridging scales in the evolution of infectious disease life histories: theory.

PubMed

Day, Troy; Alizon, Samuel; Mideo, Nicole

2011-12-01

A significant goal of recent theoretical research on pathogen evolution has been to develop theory that bridges within- and between-host dynamics. The main approach used to date is one that nests within-host models of pathogen replication in models for the between-host spread of infectious diseases. Although this provides an elegant approach, it nevertheless suffers from some practical difficulties. In particular, the information required to satisfactorily model the mechanistic details of the within-host dynamics is not often available. Here, we present a theoretical approach that circumvents these difficulties by quantifying the relevant within-host factors in an empirically tractable way. The approach is closely related to quantitative genetic models for function-valued traits, and it also allows for the prediction of general characteristics of disease life history, including the timing of virulence, transmission, and host recovery. In a companion paper, we illustrate the approach by applying it to data from a model system of malaria. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Side-chain mobility in the folded state of Myoglobin

NASA Astrophysics Data System (ADS)

Lammert, Heiko; Onuchic, Jose

We study the accessibility of alternative side-chain rotamer configurations in the native state of Myoglobin, using an all-atom structure-based model. From long, unbiased simulation trajectories we determine occupancies of rotameric states and also estimate configurational and vibrational entropies. Direct sampling of the full native-state dynamics, enabled by the simple model, reveals facilitation of side-chain motions by backbone dynamics. Correlations between different dihedral angles are quantified and prove to be weak. We confirm global trends in the mobilities of side-chains, following burial and also the chemical character of residues. Surface residues loose little configurational entropy upon folding; side-chains contribute significantly to the entropy of the folded state. Mobilities of buried side-chains vary strongly with temperature. At ambient temperature, individual side-chains in the core of the protein gain substantial access to alternative rotamers, with occupancies that are likely observable experimentally. Finally, the dynamics of buried side-chains may be linked to the internal pockets, available to ligand gas molecules in Myoglobin.

Controlling multiple security robots in a warehouse environment

NASA Technical Reports Server (NTRS)

Everett, H. R.; Gilbreath, G. A.; Heath-Pastore, T. A.; Laird, R. T.

1994-01-01

The Naval Command Control and Ocean Surveillance Center (NCCOSC) has developed an architecture to provide coordinated control of multiple autonomous vehicles from a single host console. The multiple robot host architecture (MRHA) is a distributed multiprocessing system that can be expanded to accommodate as many as 32 robots. The initial application will employ eight Cybermotion K2A Navmaster robots configured as remote security platforms in support of the Mobile Detection Assessment and Response System (MDARS) Program. This paper discusses developmental testing of the MRHA in an operational warehouse environment, with two actual and four simulated robotic platforms.

Wilderness in the 'city' revisited: different urbes shape transmission of Echinococcus multilocularis by altering predator and prey communities.

PubMed

Liccioli, Stefano; Giraudoux, Patrick; Deplazes, Peter; Massolo, Alessandro

2015-07-01

The urbanization of Echinococcus multilocularis, the agent of alveolar echinococcosis (AE), is a public health concern worldwide. Here we propose to consider 'urban' habitats under a broad ecological perspective and discuss the effects of human settlements (urbes) on host communities and the process of parasite urbanization. We argue that interactions between landscape features (i.e., landscape composition and configuration) and host communities can shape the heterogeneity of transmission gradients observed within and across different types of human settlement. Due to unique ecological characteristics and public health management priorities, we envisage urban landscapes as a model system to further increase our understanding of host-parasite interactions shaping the circulation of E. multilocularis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method [Non-Adiabatic Ab Initio Molecular Dynamics with Floating Occupation Molecular Orbitals CASCI Method

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

Hollas, Daniel; Sistik, Lukas; Hohenstein, Edward G.

Here, we show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest thatmore » the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.« less

Helminths as vectors of pathogens in vertebrate hosts: a theoretical approach.

PubMed

Perkins, Sarah E; Fenton, Andy

2006-07-01

Pathogens frequently use vectors to facilitate transmission between hosts and, for vertebrate hosts, the vectors are typically ectoparasitic arthropods. However, other parasites that are intimately associated with their hosts may also be ideal candidate vectors; namely the parasitic helminths. Here, we present empirical evidence that helminth vectoring of pathogens occurs in a range of vertebrate systems by a variety of helminth taxa. Using a novel theoretical framework we explore the dynamics of helminth vectoring and determine which host-helminth-pathogen characteristics may favour the evolution of helminth vectoring. We use two theoretical models: the first is a population dynamic model amalgamated from standard macro- and microparasite models, which serves as a framework for investigation of within-host interactions between co-infecting pathogens and helminths. The second is an evolutionary model, which we use to predict the ecological conditions under which we would expect helminth vectoring to evolve. We show that, like arthropod vectors, helminth vectors increase pathogen fitness. However, unlike arthropod vectors, helminth vectoring increases the pathogenic impact on the host and may allow the evolution of high pathogen virulence. We show that concomitant infection of a host with a helminth and pathogen are not necessarily independent of one another, due to helminth vectoring of microparasites, with profound consequences for pathogen persistence and the impact of disease on the host population.

Perspectives on the role of mobility, behavior, and time scales in the spread of diseases.

PubMed

Castillo-Chavez, Carlos; Bichara, Derdei; Morin, Benjamin R

2016-12-20

The dynamics, control, and evolution of communicable and vector-borne diseases are intimately connected to the joint dynamics of epidemiological, behavioral, and mobility processes that operate across multiple spatial, temporal, and organizational scales. The identification of a theoretical explanatory framework that accounts for the pattern regularity exhibited by a large number of host-parasite systems, including those sustained by host-vector epidemiological dynamics, is but one of the challenges facing the coevolving fields of computational, evolutionary, and theoretical epidemiology. Host-parasite epidemiological patterns, including epidemic outbreaks and endemic recurrent dynamics, are characteristic to well-identified regions of the world; the result of processes and constraints such as strain competition, host and vector mobility, and population structure operating over multiple scales in response to recurrent disturbances (like El Niño) and climatological and environmental perturbations over thousands of years. It is therefore important to identify and quantify the processes responsible for observed epidemiological macroscopic patterns: the result of individual interactions in changing social and ecological landscapes. In this perspective, we touch on some of the issues calling for the identification of an encompassing theoretical explanatory framework by identifying some of the limitations of existing theory, in the context of particular epidemiological systems. Fostering the reenergizing of research that aims at disentangling the role of epidemiological and socioeconomic forces on disease dynamics, better understood as complex adaptive systems, is a key aim of this perspective.

NASA Docking System (NDS) Interface Definitions Document (IDD). Revision C, Nov. 2010

NASA Technical Reports Server (NTRS)

2010-01-01

The NASA Docking System (NDS) mating system supports low approach velocity docking and provides a modular and reconfigurable standard interface, supporting crewed and autonomous vehicles during mating and assembly operations. The NDS is NASA's implementation for the emerging International Docking System Standard (IDSS) using low impact docking technology. All NDS configurations can mate with the configuration specified in the IDSS Interface Definition Document (IDD) released September 21, 2010. The NDS evolved from the Low Impact Docking System (LIDS). The acronym international Low Impact Docking System (iLIDS) is also used to describe this system. NDS and iLIDS may be used interchangeability. Some of the heritage documentation and implementations (e.g., software command names) used on NDS will continue to use the LIDS acronym. The NDS IDD defines the interface characteristics and performance capability of the NDS, including uses ranging from crewed to autonomous space vehicles and from low earth orbit to deep space exploration. The responsibility for developing space vehicles and for making them technically and operationally compatible with the NDS rests with the vehicle providers. Host vehicle examples include crewed/uncrewed spacecraft, space station modules, elements, etc. Within this document, any docking space vehicle will be referred to as the host vehicle. This document defines the NDS-to-NDS interfaces, as well as the NDS-to-host vehicle interfaces and performance capability.

Mealybugs with distinct endosymbiotic systems living on the same host plant.

PubMed

Koga, Ryuichi; Nikoh, Naruo; Matsuura, Yu; Meng, Xian-Ying; Fukatsu, Takema

2013-01-01

Mealybugs (Homoptera: Coccoidea: Pseudococcidae) possess a large bacteriome consisting of a number of bacteriocytes whose cytoplasm is populated by endosymbiotic bacteria. In many mealybugs of the subfamily Pseudococcinae, a peculiar endosymbiotic configuration has been identified: within the bacteriocytes, the primary betaproteobacterial endosymbiont Tremblaya princeps endocellularly harbor secondary gammaproteobacterial endosymbionts in a nested manner. Meanwhile, some mealybugs of the subfamily Phenacoccinae are associated only with a betaproteobacterial endosymbiont, designated as Tremblaya phenacola, which constitutes a distinct sister clade of T. princeps. However, cytological configuration of the endosymbiotic system in the phenacoccine mealybugs has not been established. Here, we investigated the endosymbiotic systems of the azalea mealybugs Crisicoccus azaleae (Pseudococcinae) and Phenacoccus azaleae (Phenacoccinae) living on the same host plants. Crisicoccus azaleae possessed a nested endosymbiotic system with T. princeps within the bacteriocyte cytoplasm and itself endocellularly harboring gammaproteobacterial cells, whereas P. azaleae exhibited a simple endosymbiotic system in which T. phenacola cells are localized within the bacteriocytes without additional gammaproteobacterial associates. Considering that these mealybugs live on the identical plant phloem sap, these different endosymbiotic consortia likely play similar biological roles for their host insects. The findings presented here should be helpful for future functional and comparative genomics toward elucidating evolutionary pathways of mealybugs and their endosymbionts. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Dynamical Stability and Long-term Evolution of Rotating Stellar Systems

NASA Astrophysics Data System (ADS)

Varri, Anna L.; Vesperini, E.; McMillan, S. L. W.; Bertin, G.

2011-05-01

We present the first results of an extensive survey of N-body simulations designed to investigate the dynamical stability and the long-term evolution of two new families of self-consistent stellar dynamical models, characterized by the presence of internal rotation. The first family extends the well-known King models to the case of axisymmetric systems flattened by solid-body rotation while the second family is characterized by differential rotation. The equilibrium configurations thus obtained can be described in terms of two dimensionless parameters, which measure the concentration and the amount of rotation, respectively. Slowly rotating configurations are found to be dynamically stable and we followed their long-term evolution, in order to evaluate the interplay between collisional relaxation and angular momentum transport. We also studied the stability of rapidly rotating models, which are characterized by the presence of a toroidal core embedded in an otherwise quasi-spherical configuration. In both cases, a description in terms of the radial and global properties, such as the ratio between the ordered kinetic energy and the gravitational energy of the system, is provided. Because the role of angular momentum in the process of cluster formation is only partly understood, we also undertook a preliminary investigation of the violent relaxation of simple systems initially characterized by approximate solid-body rotation. The properties of the final equilibrium configurations thus obtained are compared with those of the above-described family of differentially rotating models.

Long-term dynamics of Mycoplasma conjunctivae at the wildlife-livestock interface in the Pyrenees

PubMed Central

Cabezón, Oscar; Frey, Joachim; Velarde, Roser; Serrano, Emmanuel; Colom-Cadena, Andreu; Gelormini, Giuseppina; Marco, Ignasi; Mentaberre, Gregorio; Lavín, Santiago; López-Olvera, Jorge Ramón

2017-01-01

Functional roles of domestic and wild host populations in infectious keratoconjunctivitis (IKC) epidemiology have been extensively discussed claiming a domestic reservoir for the more susceptible wild hosts, however, based on limited data. With the aim to better assess IKC epidemiology in complex host-pathogen alpine systems, the long-term infectious dynamics and molecular epidemiology of Mycoplasma conjunctivae was investigated in all host populations from six study areas in the Pyrenees and one in the Cantabrian Mountains (Northern Spain). Detection of M. conjunctivae was performed by qPCR on 3600 eye swabs collected during seven years from hunted wild ungulates and sympatric domestic sheep (n = 1800 animals), and cluster analyses of the strains were performed including previous reported local strains. Mycoplasma conjunctivae was consistently detected in three Pyrenean chamois (Rupicapra p. pyrenaica) populations, as well as in sheep flocks (17.0% of sheep) and occasionally in mouflon (Ovis aries musimon) from the Pyrenees (22.2% in one year/area); statistically associated with ocular clinical signs only in chamois. Chamois populations showed different infection dynamics with low but steady prevalence (4.9%) and significant yearly fluctuations (0.0%– 40.0%). Persistence of specific M. conjunctivae strain clusters in wild host populations is demonstrated for six and nine years. Cross-species transmission between chamois and sheep and chamois and mouflon were also sporadically evidenced. Overall, independent M. conjunctivae sylvatic and domestic cycles occurred at the wildlife-livestock interface in the alpine ecosystems from the Pyrenees with sheep and chamois as the key host species for each cycle, and mouflon as a spill-over host. Host population characteristics and M. conjunctivae strains resulted in different epidemiological scenarios in chamois, ranging from the fading out of the mycoplasma to the epidemic and endemic long-term persistence. These findings highlight the capacity of M. conjunctivae to establish diverse interactions and persist in host populations, also with different transmission conditions. PMID:29016676

Assessment of optimal strategies in a two-patch dengue transmission model with seasonality

PubMed Central

Lee, Chang Hyeong; Lee, Sunmi

2017-01-01

Emerging and re-emerging dengue fever has posed serious problems to public health officials in many tropical and subtropical countries. Continuous traveling in seasonally varying areas makes it more difficult to control the spread of dengue fever. In this work, we consider a two-patch dengue model that can capture the movement of host individuals between and within patches using a residence-time matrix. A previous two-patch dengue model without seasonality is extended by adding host demographics and seasonal forcing in the transmission rates. We investigate the effects of human movement and seasonality on the two-patch dengue transmission dynamics. Motivated by the recent Peruvian dengue data in jungle/rural areas and coast/urban areas, our model mimics the seasonal patterns of dengue outbreaks in two patches. The roles of seasonality and residence-time configurations are highlighted in terms of the seasonal reproduction number and cumulative incidence. Moreover, optimal control theory is employed to identify and evaluate patch-specific control measures aimed at reducing dengue prevalence in the presence of seasonality. Our findings demonstrate that optimal patch-specific control strategies are sensitive to seasonality and residence-time scenarios. Targeting only the jungle (or endemic) is as effective as controlling both patches under weak coupling or symmetric mobility. However, focusing on intervention for the city (or high density areas) turns out to be optimal when two patches are strongly coupled with asymmetric mobility. PMID:28301523

Verifying the secure setup of UNIX client/servers and detection of network intrusion

NASA Astrophysics Data System (ADS)

Feingold, Richard; Bruestle, Harry R.; Bartoletti, Tony; Saroyan, R. A.; Fisher, John M.

1996-03-01

This paper describes our technical approach to developing and delivering Unix host- and network-based security products to meet the increasing challenges in information security. Today's global `Infosphere' presents us with a networked environment that knows no geographical, national, or temporal boundaries, and no ownership, laws, or identity cards. This seamless aggregation of computers, networks, databases, applications, and the like store, transmit, and process information. This information is now recognized as an asset to governments, corporations, and individuals alike. This information must be protected from misuse. The Security Profile Inspector (SPI) performs static analyses of Unix-based clients and servers to check on their security configuration. SPI's broad range of security tests and flexible usage options support the needs of novice and expert system administrators alike. SPI's use within the Department of Energy and Department of Defense has resulted in more secure systems, less vulnerable to hostile intentions. Host-based information protection techniques and tools must also be supported by network-based capabilities. Our experience shows that a weak link in a network of clients and servers presents itself sooner or later, and can be more readily identified by dynamic intrusion detection techniques and tools. The Network Intrusion Detector (NID) is one such tool. NID is designed to monitor and analyze activity on the Ethernet broadcast Local Area Network segment and product transcripts of suspicious user connections. NID's retrospective and real-time modes have proven invaluable to security officers faced with ongoing attacks to their systems and networks.

Investigating the internal structure of galaxies and clusters through strong gravitational lensing

NASA Astrophysics Data System (ADS)

Jigish Gandhi, Pratik; Grillo, Claudio; Bonamigo, Mario

2018-01-01

Gravitational lensing studies have radically improved our understanding of the internal structure of galaxies and cluster-scale systems. In particular, the combination of strong lensing and stellar dynamics or stellar population synthesis models have made it possible to characterize numerous fundamental properties of the galaxies as well as dark matter halos and subhalos with unprecedented robustness and accuracy. Here we demonstrate the usefulness and accuracy of strong lensing as a probe for characterising the properties of cluster members as well as dark matter halos, to show that such characterisation carried out via lensing analyses alone is as viable as those carried out through a combination of spectroscopy and lensing analyses.Our study uses focuses on the early-type galaxy cluster MACS J1149.5+2223 at redshift 0.54 in the Hubble Frontier Fields (HFF) program, where the first magnified and spatially resolved multiple images of supernova (SN) “Refsdal” and its late-type host galaxy at redshift 1.489 were detected. The Refsdal system is unique in being the first ever multiply-imaged supernova, with it’s first four images appearing in an Einstein Cross configuration around one of the cluster members in 2015. In our lensing analyses we use HST data of the multiply-imaged SN Refsdal to constrain the dynamical masses, velocity dispersions, and virial radii of individual galaxies and dark matter halos in the MACS J1149.5+2223 cluster. For our lensing models we select a sample of 300 cluster members within approximately 500 kpc from the BCG, and a set of reliable multiple images associated with 18 distinct knots in the SN host spiral galaxy, as well as multiple images of the supernova itself. Our results provide accurate measurements of the masses, velocity dispersions, and radii of the cluster’s dark matter halo as well as three chosen members galaxies, in strong agreement with those obtained by Grillo et al 2015, demonstrating the usefulness of strong lensing in characterising the properties of cluster-scale systems.

Life history determines genetic structure and evolutionary potential of host-parasite interactions.

PubMed

Barrett, Luke G; Thrall, Peter H; Burdon, Jeremy J; Linde, Celeste C

2008-12-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.

Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: Wave-vector space analysis

NASA Astrophysics Data System (ADS)

Separdar, L.; Davatolhagh, S.

2016-12-01

Molecular dynamics simulations at constant (N , V , T) are used to study the mutual effects of gold nanoparticles on the structure and dynamics of Kob-Andersen binary Lennard-Jones (BLJ) liquid within the framework of mode coupling theory of dynamic glass transition in the reciprocal space. The results show the 'softening' effect of the gold nanoparticles on the liquid dynamics in terms of (i) reducing the mode coupling crossover temperature Tc with respect to that of the bulk BLJ (i.e. BLJ without nanoparticles), (ii) decreasing the time interval of β-relaxation, and (iii) decreasing the exponent γ characterizing the power-law behavior of the α-relaxation time. This softening effect is explained in terms of the van der Waals attraction between the gold atoms comprising the nanoparticle and the BLJ host atoms, such that adsorption of host atoms onto the nanoparticle surface creates more space or free-volume for the other atoms to diffuse. By the same token interactions of purely excluded-volume-type are expected to result in the opposite effect. It is also noted that, much unlike BLJ host particles, the dynamics of gold nanoparticles is much less dependent on the wave-vector and that it exhibits a nearly exponential behavior in the α-relaxation regime.

Measuring Tissue Perfusion During Pressure Relief Maneuvers: Insights Into Preventing Pressure Ulcers

PubMed Central

Makhsous, Mohsen; Priebe, Michael; Bankard, James; Rowles, Diana; Zeigler, Mary; Chen, David; Lin, Fang

2007-01-01

Background/Objective: To study the effect on tissue perfusion of relieving interface pressure using standard wheelchair pushups compared with a mechanical automated dynamic pressure relief system. Design: Repeated measures in 2 protocols on 3 groups of subjects. Participants: Twenty individuals with motor-complete paraplegia below T4, 20 with motor-complete tetraplegia, and 20 able-bodied subjects. Methods: Two 1-hour sitting protocols: dynamic protocol, sitting configuration alternated every 10 minutes between a normal sitting configuration and an off-loading configuration; wheelchair pushup protocol, normal sitting configuration with standard wheelchair pushup once every 20 minutes. Main Outcome Measures: Transcutaneous partial pressures of oxygen and carbon dioxide measured from buttock overlying the ischial tuberosity and interface pressure measured at the seat back and buttocks. Perfusion deterioration and recovery times were calculated during changes in interface pressures. Results: In the off-loading configuration, concentrated interface pressure during the normal sitting configuration was significantly diminished, and tissue perfusion was significantly improved. Wheelchair pushups showed complete relief of interface pressure but incomplete recovery of tissue perfusion. Conclusions: Interface pressure analysis does not provide complete information about the effectiveness of pressure relief maneuvers. Measures of tissue perfusion may help establish more effective strategies. Relief achieved by standard wheelchair pushups may not be sufficient to recover tissue perfusion compromised during sitting; alternate maneuvers may be necessary. The dynamic seating system provided effective pressure relief with sustained reduction in interface pressure adequate for complete recovery of tissue perfusion. Differences in perfusion recovery times between subjects with spinal cord injury (SCI) and controls raise questions about the importance of changes in vascular responses to pressure after SCI. PMID:18092567

Aerodynamic Analysis of a Canard Missile Configuration using ANSYS-CFX

DTIC Science & Technology

2011-12-01

OF A CANARD MISSILE CONFIGURATION USING ANSYS - CFX by Hong Chuan Wee December 2011 Thesis Advisor: Maximilian Platzer Second Reader...DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE Aerodynamic Analysis of a Canard Missile Configuration using ANSYS - CFX 5. FUNDING NUMBERS 6...distribution is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This study used the Computational Fluid Dynamics code, ANSYS - CFX to

Emerging methods to study bacteriophage infection at the single-cell level.

PubMed

Dang, Vinh T; Sullivan, Matthew B

2014-01-01

Bacteria and their viruses (phages) are abundant across diverse ecosystems and their interactions influence global biogeochemical cycles and incidence of disease. Problematically, both classical and metagenomic methods insufficiently assess the host specificity of phages and phage-host infection dynamics in nature. Here we review emerging methods to study phage-host interaction and infection dynamics with a focus on those that offer resolution at the single-cell level. These methods leverage ever-increasing sequence data to identify virus signals from single-cell amplified genome datasets or to produce primers/probes to target particular phage-bacteria pairs (digital PCR and phageFISH), even in complex communities. All three methods enable study of phage infection of uncultured bacteria from environmental samples, while the latter also discriminates between phage-host interaction outcomes (e.g., lytic, chronic, lysogenic) in model systems. Together these techniques enable quantitative, spatiotemporal studies of phage-bacteria interactions from environmental samples of any ecosystem, which will help elucidate and predict the ecological and evolutionary impacts of specific phage-host pairings in nature.

Characterizing the next-generation matrix and basic reproduction number in ecological epidemiology.

PubMed

Roberts, M G; Heesterbeek, J A P

2013-03-01

We address the interaction of ecological processes, such as consumer-resource relationships and competition, and the epidemiology of infectious diseases spreading in ecosystems. Modelling such interactions seems essential to understand the dynamics of infectious agents in communities consisting of interacting host and non-host species. We show how the usual epidemiological next-generation matrix approach to characterize invasion into multi-host communities can be extended to calculate R₀, and how this relates to the ecological community matrix. We then present two simple examples to illustrate this approach. The first of these is a model of the rinderpest, wildebeest, grass interaction, where our inferred dynamics qualitatively matches the observed phenomena that occurred after the eradication of rinderpest from the Serengeti ecosystem in the 1980s. The second example is a prey-predator system, where both species are hosts of the same pathogen. It is shown that regions for the parameter values exist where the two host species are only able to coexist when the pathogen is present to mediate the ecological interaction.

Separation of plastic waste via the hydraulic separator Multidune under different geometric configurations.

PubMed

La Marca, Floriana; Moroni, Monica; Cherubini, Lorenzo; Lupo, Emanuela; Cenedese, Antonio

2012-07-01

The recovery of high-quality plastic materials is becoming an increasingly challenging issue for the recycling sector. Technologies for plastic recycling have to guarantee high-quality secondary raw material, complying with specific standards, for use in industrial applications. The variability in waste plastics does not always correspond to evident differences in physical characteristics, making traditional methodologies ineffective for plastic separation. The Multidune separator is a hydraulic channel allowing the sorting of solid particles on the basis of differential transport mechanisms by generating particular fluid dynamic conditions due to its geometric configuration and operational settings. In this paper, the fluid dynamic conditions were investigated by an image analysis technique, allowing the reconstruction of velocity fields generated inside the Multidune, considering two different geometric configurations of the device, Configuration A and Configuration B. Furthermore, tests on mono- and bi-material samples were completed with varying operational conditions under both configurations. In both series of experiments, the bi-material samples were composed of differing proportions (85% vs. 15%) to simulate real conditions in an industrial plant for the purifying of a useful fraction from a contaminating fraction. The separation results were evaluated in terms of grade and recovery of the useful fraction. Copyright © 2012 Elsevier Ltd. All rights reserved.

Hydrodynamically Lubricated Rotary Shaft Having Twist Resistant Geometry

DOEpatents

Dietle, Lannie; Gobeli, Jeffrey D.

1993-07-27

A hydrodynamically lubricated squeeze packing type rotary shaft with a cross-sectional geometry suitable for pressurized lubricant retention is provided which, in the preferred embodiment, incorporates a protuberant static sealing interface that, compared to prior art, dramatically improves the exclusionary action of the dynamic sealing interface in low pressure and unpressurized applications by achieving symmetrical deformation of the seal at the static and dynamic sealing interfaces. In abrasive environments, the improved exclusionary action results in a dramatic reduction of seal and shaft wear, compared to prior art, and provides a significant increase in seal life. The invention also increases seal life by making higher levels of initial compression possible, compared to prior art, without compromising hydrodynamic lubrication; this added compression makes the seal more tolerant of compression set, abrasive wear, mechanical misalignment, dynamic runout, and manufacturing tolerances, and also makes hydrodynamic seals with smaller cross-sections more practical. In alternate embodiments, the benefits enumerated above are achieved by cooperative configurations of the seal and the gland which achieve symmetrical deformation of the seal at the static and dynamic sealing interfaces. The seal may also be configured such that predetermined radial compression deforms it to a desired operative configuration, even through symmetrical deformation is lacking.

Punctuated equilibrium and shock waves in molecular models of biological evolution.

PubMed

Saakian, David B; Ghazaryan, Makar H; Hu, Chin-Kun

2014-08-01

We consider the dynamics in infinite population evolution models with a general symmetric fitness landscape. We find shock waves, i.e., discontinuous transitions in the mean fitness, in evolution dynamics even with smooth fitness landscapes, which means that the search for the optimal evolution trajectory is more complicated. These shock waves appear in the case of positive epistasis and can be used to represent punctuated equilibria in biological evolution during long geological time scales. We find exact analytical solutions for discontinuous dynamics at the large-genome-length limit and derive optimal mutation rates for a fixed fitness landscape to send the population from the initial configuration to some final configuration in the fastest way.

Correlation of ground tests and analyses of a dynamically scaled Space Station model configuration

NASA Technical Reports Server (NTRS)

Javeed, Mehzad; Edighoffer, Harold H.; Mcgowan, Paul E.

1993-01-01

Verification of analytical models through correlation with ground test results of a complex space truss structure is demonstrated. A multi-component, dynamically scaled space station model configuration is the focus structure for this work. Previously established test/analysis correlation procedures are used to develop improved component analytical models. Integrated system analytical models, consisting of updated component analytical models, are compared with modal test results to establish the accuracy of system-level dynamic predictions. Design sensitivity model updating methods are shown to be effective for providing improved component analytical models. Also, the effects of component model accuracy and interface modeling fidelity on the accuracy of integrated model predictions is examined.

Simulated Pitot tube designed to detect blockage by ice, volcanic dust, sand, insects and to clear it: phase 1

NASA Astrophysics Data System (ADS)

Jackson, David A.

2014-05-01

A simulated coaxial Pitot tube has been developed using fibre optic sensors combined with actuators to monitor and maintain its correct operation under different environmental conditions. Experiments are reported showing that the dynamic and static tubes can be cleared of ice. It is also demonstrated that the dynamic tube can be cleared of dust and sand which is not the case for the static tube in the coaxial configuration. An approach is proposed to overcome this problem involving a conventional configuration where the static tube is operated independently orthogonal to the dynamic tube with a second set of sensors and actuators.

The Dynamic Community of Interest and Its Realization in ZODIAC

DTIC Science & Technology

2009-10-01

the ZODIAC project. ZODIAC is a network architecture that puts security first and foremost, with security broken down into confidentiality, integrity...hosts, a unified solution for MANETs will work for hosts or routers as well. DYNAMIC COMMUNITIES OF INTEREST The basis of the ZODIAC design is a new dis...narrow scope of each DCoI limits attack propagation, and supports confidentiality ABSTRACT The ZODIAC project has been exploring a security first

Lytic to temperate switching of viral communities

NASA Astrophysics Data System (ADS)

Knowles, B.; Silveira, C. B.; Bailey, B. A.; Barott, K.; Cantu, V. A.; Cobián-Güemes, A. G.; Coutinho, F. H.; Dinsdale, E. A.; Felts, B.; Furby, K. A.; George, E. E.; Green, K. T.; Gregoracci, G. B.; Haas, A. F.; Haggerty, J. M.; Hester, E. R.; Hisakawa, N.; Kelly, L. W.; Lim, Y. W.; Little, M.; Luque, A.; McDole-Somera, T.; McNair, K.; de Oliveira, L. S.; Quistad, S. D.; Robinett, N. L.; Sala, E.; Salamon, P.; Sanchez, S. E.; Sandin, S.; Silva, G. G. Z.; Smith, J.; Sullivan, C.; Thompson, C.; Vermeij, M. J. A.; Youle, M.; Young, C.; Zgliczynski, B.; Brainard, R.; Edwards, R. A.; Nulton, J.; Thompson, F.; Rohwer, F.

2016-03-01

Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in diverse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities; thus ‘more microbes, fewer viruses’.

Molecular Dynamics Simulations and XAFS (MD-XAFS)

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

Schenter, Gregory K.; Fulton, John L.

2017-01-20

MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.

Measurements of Pressure Distributions and Force Coefficients in a Squeeze Film Damper. Part 1: Fully Open Ended Configuration

NASA Technical Reports Server (NTRS)

Jung, S. Y.; Sanandres, Luis A.; Vance, J. M.

1991-01-01

Measurements of pressure distributions and force coefficients were carried out in two types of squeeze film dampers, executing a circular centered orbit, an open-ended configuration, and a partially sealed one, in order to investigate the effect of fluid inertia and cavitation on pressure distributions and force coefficients. Dynamic pressure measurements were carried out for two orbit radii, epsilon 0.5 and 0.8. It was found that the partially sealed configuration was less influenced by fluid inertia than the open ended configuration.

Dynamically re-configurable CMOS imagers for an active vision system

NASA Technical Reports Server (NTRS)

Yang, Guang (Inventor); Pain, Bedabrata (Inventor)

2005-01-01

A vision system is disclosed. The system includes a pixel array, at least one multi-resolution window operation circuit, and a pixel averaging circuit. The pixel array has an array of pixels configured to receive light signals from an image having at least one tracking target. The multi-resolution window operation circuits are configured to process the image. Each of the multi-resolution window operation circuits processes each tracking target within a particular multi-resolution window. The pixel averaging circuit is configured to sample and average pixels within the particular multi-resolution window.

Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

PubMed

Bell, David R; Qi, Rui; Jing, Zhifeng; Xiang, Jin Yu; Mejias, Christopher; Schnieders, Michael J; Ponder, Jay W; Ren, Pengyu

2016-11-09

Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.

BSM (+BMM) Data Emulator Dynamic Interrogative Data Capture (DIDC) Assessment Report: Impacts of DIDC

DOT National Transportation Integrated Search

2016-04-01

The objective of the Dynamic Interrogative Data Capture (DIDC) algorithms and software is to optimize the capture and transmission of vehicle-based data under a range of dynamically configurable messaging strategies. The key hypothesis of DIDC is tha...

A Second β-Hexosaminidase Encoded in the Streptococcus pneumoniae Genome Provides an Expanded Biochemical Ability to Degrade Host Glycans*

PubMed Central

Robb, Melissa; Robb, Craig S.; Higgins, Melanie A.; Hobbs, Joanne K.; Paton, James C.; Boraston, Alisdair B.

2015-01-01

An important facet of the interaction between the pathogen Streptococcus pneumoniae (pneumococcus) and its human host is the ability of this bacterium to process host glycans. To achieve cleavage of the glycosidic bonds in host glycans, S. pneumoniae deploys a wide array of glycoside hydrolases. Here, we identify and characterize a new family 20 glycoside hydrolase, GH20C, from S. pneumoniae. Recombinant GH20C possessed the ability to hydrolyze the β-linkages joining either N-acetylglucosamine or N-acetylgalactosamine to a wide variety of aglycon residues, thus revealing this enzyme to be a generalist N-acetylhexosaminidase in vitro. X-ray crystal structures were determined for GH20C in a ligand-free form, in complex with the N-acetylglucosamine and N-acetylgalactosamine products of catalysis and in complex with both gluco- and galacto-configured inhibitors O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino N-phenyl carbamate (PUGNAc), O-(2-acetamido-2-deoxy-d-galactopyranosylidene)amino N-phenyl carbamate (GalPUGNAc), N-acetyl-d-glucosamine-thiazoline (NGT), and N-acetyl-d-galactosamine-thiazoline (GalNGT) at resolutions from 1.84 to 2.7 Å. These structures showed N-acetylglucosamine and N-acetylgalactosamine to be recognized via identical sets of molecular interactions. Although the same sets of interaction were maintained with the gluco- and galacto-configured inhibitors, the inhibition constants suggested preferred recognition of the axial O4 when an aglycon moiety was present (Ki for PUGNAc > GalPUGNAc) but preferred recognition of an equatorial O4 when the aglycon was absent (Ki for GalNGT > NGT). Overall, this study reveals GH20C to be another tool that is unique in the arsenal of S. pneumoniae and that it may implement the effort of the bacterium to utilize and/or destroy the wide array of host glycans that it may encounter. PMID:26491009

Effect of Configuration Pitching Motion on Twin Tail Buffet Response

NASA Technical Reports Server (NTRS)

Sheta, Essam F.; Kandil, Osama A.

1998-01-01

The effect of dynamic pitch-up motion of delta wing on twin-tail buffet response is investigated. The computational model consists of a delta wing-twin tail configuration. The computations are carried out on a dynamic multi-block grid structure. This multidisciplinary problem is solved using three sets of equations which consists of the unsteady Navier-Stokes equations, the aeroelastic equations, and the grid displacement equations. The configuration is pitched-up from zero up to 60 deg. angle of attack, and the freestream Mach number and Reynolds number are 0.3 and 1.25 million, respectively. With the twin tail fixed as rigid surfaces and with no-forced pitch-up motion, the problem is solved for the initial flow conditions. Next, the problem is solved for the twin-tail response for uncoupled bending and torsional vibrations due to the unsteady loads on the twin tail and due to the forced pitch-up motion. The dynamic pitch-up problem is also solved for the flow response with the twin tail kept rigid. The configuration is investigated for inboard position of the twin tail which corresponds to a separation distance between the twin tail of 33% wing chord. The computed results are compared with the available experimental data.

Test of the ``radical-like polymerization'' scheme in molecular dynamics on the behavior of polymers under shock loading

NASA Astrophysics Data System (ADS)

Lemarchand, Claire; Bousquet, David; Schnell, Benoît; Pineau, Nicolas

2017-06-01

The behavior of polymer melts under shock loading is a question attracting more and more attention because of applications such as polymer-bonded explosives, light-weight armor and civilian protective equipment, like sports and car equipment. Molecular dynamics (MD) simulations are a very good tool to characterize the microscopic response of the polymer to a shock wave. To do so, the initial configuration of the polymer melt needs to be realistic. The ``radical-like polymerization'' scheme is a method to obtain near equilibrium configurations of a melt of long polymer chains. It consists in adding one neighboring monomer at a time to each growing chain. Between each polymerization step an MD run is performed to relax the new configuration. We test how details of our implementation of the ``radical-like polymerization'' scheme can impact or not Hugoniot curves and changes of chain configuration under shock. We compare our results to other simulation and experimental results on reference polymers.

Dynamic configuration management of a multi-standard and multi-mode reconfigurable multi-ASIP architecture for turbo decoding

NASA Astrophysics Data System (ADS)

Lapotre, Vianney; Gogniat, Guy; Baghdadi, Amer; Diguet, Jean-Philippe

2017-12-01

The multiplication of connected devices goes along with a large variety of applications and traffic types needing diverse requirements. Accompanying this connectivity evolution, the last years have seen considerable evolutions of wireless communication standards in the domain of mobile telephone networks, local/wide wireless area networks, and Digital Video Broadcasting (DVB). In this context, intensive research has been conducted to provide flexible turbo decoder targeting high throughput, multi-mode, multi-standard, and power consumption efficiency. However, flexible turbo decoder implementations have not often considered dynamic reconfiguration issues in this context that requires high speed configuration switching. Starting from this assessment, this paper proposes the first solution that allows frame-by-frame run-time configuration management of a multi-processor turbo decoder without compromising the decoding performances.

Investigations of High Pressure Acoustic Waves in Resonators with Seal-like Features

NASA Technical Reports Server (NTRS)

Daniels, Christopher; Steinetz, Bruce; Finkbeiner, Joshua

2003-01-01

A conical resonator (having a dissonant acoustic design) was tested in four configurations: (1) baseline resonator with closed ends and no blockage, (2) closed resonator with internal blockage, (3) ventilated resonator with no blockage, and (4) ventilated resonator with an applied pressure differential. These tests were conducted to investigate the effects of blockage and ventilation holes on dynamic pressurization. Additionally, the investigation was to determine the ability of acoustic pressurization to impede flow through the resonator. In each of the configurations studied, the entire resonator was oscillated at the gas resonant frequency while dynamic pressure, static pressure, and temperature of the fluid were measured. In the final configuration, flow through the resonator was recorded for three oscillation conditions. Ambient condition air was used as the working fluid.

Evaluation of Federated Searching Options for the School Library

ERIC Educational Resources Information Center

Abercrombie, Sarah E.

2008-01-01

Three hosted federated search tools, Follett One Search, Gale PowerSearch Plus, and WebFeat Express, were configured and implemented in a school library. Databases from five vendors and the OPAC were systematically searched. Federated search results were compared with each other and to the results of the same searches in the database's native…

Survival of planets around shrinking stellar binaries

PubMed Central

Muñoz, Diego J.; Lai, Dong

2015-01-01

The discovery of transiting circumbinary planets by the Kepler mission suggests that planets can form efficiently around binary stars. None of the stellar binaries currently known to host planets has a period shorter than 7 d, despite the large number of eclipsing binaries found in the Kepler target list with periods shorter than a few days. These compact binaries are believed to have evolved from wider orbits into their current configurations via the so-called Lidov–Kozai migration mechanism, in which gravitational perturbations from a distant tertiary companion induce large-amplitude eccentricity oscillations in the binary, followed by orbital decay and circularization due to tidal dissipation in the stars. Here we explore the orbital evolution of planets around binaries undergoing orbital decay by this mechanism. We show that planets may survive and become misaligned from their host binary, or may develop erratic behavior in eccentricity, resulting in their consumption by the stars or ejection from the system as the binary decays. Our results suggest that circumbinary planets around compact binaries could still exist, and we offer predictions as to what their orbital configurations should be like. PMID:26159412

Survival of planets around shrinking stellar binaries.

PubMed

Muñoz, Diego J; Lai, Dong

2015-07-28

The discovery of transiting circumbinary planets by the Kepler mission suggests that planets can form efficiently around binary stars. None of the stellar binaries currently known to host planets has a period shorter than 7 d, despite the large number of eclipsing binaries found in the Kepler target list with periods shorter than a few days. These compact binaries are believed to have evolved from wider orbits into their current configurations via the so-called Lidov-Kozai migration mechanism, in which gravitational perturbations from a distant tertiary companion induce large-amplitude eccentricity oscillations in the binary, followed by orbital decay and circularization due to tidal dissipation in the stars. Here we explore the orbital evolution of planets around binaries undergoing orbital decay by this mechanism. We show that planets may survive and become misaligned from their host binary, or may develop erratic behavior in eccentricity, resulting in their consumption by the stars or ejection from the system as the binary decays. Our results suggest that circumbinary planets around compact binaries could still exist, and we offer predictions as to what their orbital configurations should be like.

Coupling fluid dynamics and host-rock deformation associated with magma intrusion in the crust: Insights from analogue experiments

NASA Astrophysics Data System (ADS)

Kavanagh, J. L.; Dennis, D. J.

2014-12-01

Models of magma ascent in the crust tend to either consider the dynamics of fluid flow within intrusions or the associated host-rock deformation. However, these processes are coupled in nature, and so to develop a more complete understanding of magma ascent dynamics in the crust both need to be taken into account. We present a series of gelatine analogue experiments that use both Particle Image Velocimentry (PIV) and Digital Image Correlation (DIC) techniques to characterise the dynamics of fluid flow within intrusions and to quantify the associated deformation of the intruded media. Experiments are prepared by filling a 40x40x30 cm3 clear-Perspex tank with a low-concentration gelatine mixture (2-5 wt%) scaled to be of comparable stiffness to crustal strata. Fluorescent seeding particles are added to the gelatine mixture during its preparation and to the magma analogue prior to injection. Two Dantec CCD cameras are positioned outside the tank and a vertical high-power laser sheet positioned along the centre line is triggered to illuminate the seeding particles with short intense pulses. Dyed water (the magma analogue) injected into the solid gelatine from below causes a vertically propagating penny-shaped crack (dike) to form. Incremental and cumulative displacement vectors are calculated by cross-correlation between successive images at a defined time interval. Spatial derivatives map the fluid flow within the intrusion and associated strain and stress evolution of the host, both during dike propagation and on to eruption. As the gelatine deforms elastically at the experimental conditions, strain calculations correlate with stress. Models which couple fluid dynamics and host deformation make an important step towards improving our understanding of the dynamics of magma transport through the crust and to help constrain the tendency for eruption.

Contributions of Transonic Dynamics Tunnel Testing to Airplane Flutter Clearance

NASA Technical Reports Server (NTRS)

Rivera, Jose A.; Florance, James R.

2000-01-01

The Transonic Dynamics Tunnel (TDT) became in operational in 1960, and since that time has achieved the status of the world's premier wind tunnel for testing large in aeroelastically scaled models at transonic speeds. The facility has many features that contribute to its uniqueness for aeroelastic testing. This paper will briefly describe these capabilities and features, and their relevance to aeroelastic testing. Contributions to specific airplane configurations and highlights from the flutter tests performed in the TDT aimed at investigating the aeroelastic characteristics of these configurations are presented.

Supersonic dynamic stability characteristics of a space shuttle orbiter. [wind tunnel tests of scale models

NASA Technical Reports Server (NTRS)

Freeman, D. C., Jr.; Boyden, R. P.; Davenport, E. E.

1976-01-01

Supersonic forced-oscillation tests of a 0.0165-scale model of a modified 089B Rockwell International shuttle orbiter were conducted in a wind tunnel for several configurations over a Mach range from 1.6 to 4.63. The tests covered angles of attack up to 30 deg. The period and damping of the basic unaugmented vehicle were calculated along the entry trajectory using the measured damping results. Some parameter analysis was made with the measured dynamic derivatives. Photographs of the test configurations and test equipment are shown.

Solar dynamic heat receiver thermal characteristics in low earth orbit

NASA Technical Reports Server (NTRS)

Wu, Y. C.; Roschke, E. J.; Birur, G. C.

1988-01-01

A simplified system model is under development for evaluating the thermal characteristics and thermal performance of a solar dynamic spacecraft energy system's heat receiver. Results based on baseline orbit, power system configuration, and operational conditions, are generated for three basic receiver concepts and three concentrator surface slope errors. Receiver thermal characteristics and thermal behavior in LEO conditions are presented. The configuration in which heat is directly transferred to the working fluid is noted to generate the best system and thermal characteristics. as well as the lowest performance degradation with increasing slope error.

H_Hyd_Shktub_Mshock_III, JJJ, KKK (S01,S02,S03) on the National Ignition Facility

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

Desjardins, Tiffany; Schmidt, Derek William; Di Stefano, Carlos

2017-12-15

These experiments are the first experiments in the Mshock campaign at the National Ignition Facility. The experiment is scheduled to be conducted on Dec. 14, 2017. The goal of the Mshock campaign is to study feedthrough dynamics of the Richtmyer- Meshkov instability in a thin layer. These dynamics will be studied in both a reshock configuration (initially) and then in a multi-shock configuration where it is planned to reshock the RM instability up to 3 times (four shocks total).

Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis.

PubMed

Seal, John B; Alverdy, John C; Zaborina, Olga; An, Gary

2011-09-19

There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis. An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed--i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data--i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design--i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses. Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research.

Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis

PubMed Central

2011-01-01

Background There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis. Methodology/Principal Findings An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed - i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data - i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design - i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses. Conclusions/Significance Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research. PMID:21929759

Results of complex annual parasitological monitoring in the coastal area of Kola Bay

NASA Astrophysics Data System (ADS)

Kuklin, V. V.; Kuklina, M. M.; Kisova, N. E.; Maslich, M. A.

2009-12-01

The results of annual parasitological monitoring in the coastal area near the Abram-mys (Kola Bay, Barents Sea) are presented. The studies were performed in 2006-2007 and included complex examination of the intermediate hosts (mollusks and crustaceans) and definitive hosts (marine fish and birds) of the helminths. The biodiversity of the parasite fauna, seasonal dynamics, and functioning patterns of the parasite systems were investigated. The basic regularities in parasite circulation were assessed in relation to their life cycle strategies and the ecological features of the intermediate and definitive hosts. The factors affecting the success of parasite circulation in the coastal ecosystems were revealed through analysis of parasite biodiversity and abundance dynamics.

Spatial evolutionary epidemiology of spreading epidemics.

PubMed

Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

Modelling the effects of phylogeny and body size on within-host pathogen replication and immune response.

PubMed

Banerjee, Soumya; Perelson, Alan S; Moses, Melanie

2017-11-01

Understanding how quickly pathogens replicate and how quickly the immune system responds is important for predicting the epidemic spread of emerging pathogens. Host body size, through its correlation with metabolic rates, is theoretically predicted to impact pathogen replication rates and immune system response rates. Here, we use mathematical models of viral time courses from multiple species of birds infected by a generalist pathogen (West Nile Virus; WNV) to test more thoroughly how disease progression and immune response depend on mass and host phylogeny. We use hierarchical Bayesian models coupled with nonlinear dynamical models of disease dynamics to incorporate the hierarchical nature of host phylogeny. Our analysis suggests an important role for both host phylogeny and species mass in determining factors important for viral spread such as the basic reproductive number, WNV production rate, peak viraemia in blood and competency of a host to infect mosquitoes. Our model is based on a principled analysis and gives a quantitative prediction for key epidemiological determinants and how they vary with species mass and phylogeny. This leads to new hypotheses about the mechanisms that cause certain taxonomic groups to have higher viraemia. For example, our models suggest that higher viral burst sizes cause corvids to have higher levels of viraemia and that the cellular rate of virus production is lower in larger species. We derive a metric of competency of a host to infect disease vectors and thereby sustain the disease between hosts. This suggests that smaller passerine species are highly competent at spreading the disease compared with larger non-passerine species. Our models lend mechanistic insight into why some species (smaller passerine species) are pathogen reservoirs and some (larger non-passerine species) are potentially dead-end hosts for WNV. Our techniques give insights into the role of body mass and host phylogeny in the spread of WNV and potentially other zoonotic diseases. The major contribution of this work is a computational framework for infectious disease modelling at the within-host level that leverages data from multiple species. This is likely to be of interest to modellers of infectious diseases that jump species barriers and infect multiple species. Our method can be used to computationally determine the competency of a host to infect mosquitoes that will sustain WNV and other zoonotic diseases. We find that smaller passerine species are more competent in spreading the disease than larger non-passerine species. This suggests the role of host phylogeny as an important determinant of within-host pathogen replication. Ultimately, we view our work as an important step in linking within-host viral dynamics models to between-host models that determine spread of infectious disease between different hosts. © 2017 The Author(s).

Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop

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

Miner, Jacob Carlson; Garcia, Angel Enrique

Monovalent salt solutions have strongly coupled interactions with biopolymers, from large polyelectrolytes to small RNA oligomers. High salt concentrations have been known to induce transitions in the structure of RNA, producing non-canonical configurations and even driving RNA to precipitate out of solution. Using all-atom molecular dynamics simulations, we model a monovalent salt species (KCL) at high concentrations (0.1–3m) and calculate the equilibrium distributions of water and ions around a small tetraloop-forming RNA oligomer in a variety of structural arrangements: folded A-RNA (canonical) and Z-RNA (non-canonical) tetraloops and unfolded configurations. From these data, we calculate the ion preferential binding coefficients andmore » Donnan coefficients for the RNA oligomer as a function of concentration and structure. We find that cation accumulation is highest around non-canonical Z-RNA configurations at concentrations below 0.5m, while unfolded configurations accumulate the most co-ions in all concentrations. By contrast, canonical A-RNA structures consistently show the lowest accumulations for all ion species. Water distributions vary markedly with RNA configuration but show little dependency on KCL concentration. Based on Donnan coefficient calculations, the net charge of the solution at the surface of the RNA decreases linearly as a function of salt concentration and becomes net-neutral near 2.5–3m KCL for folded configurations, while unfolded configurations still show a positive solution charge. Our findings show that all-atom molecular dynamics can describe the equilibrium distributions of monovalent salt in the presence of small RNA oligomers at KCL concentrations where ion correlation effects become important. Furthermore, these results provide valuable insights into the distributions of water and ions near the RNA oligomer surface as a function of structural configuration.« less

Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop

DOE PAGES

Miner, Jacob Carlson; Garcia, Angel Enrique

2018-05-29

Monovalent salt solutions have strongly coupled interactions with biopolymers, from large polyelectrolytes to small RNA oligomers. High salt concentrations have been known to induce transitions in the structure of RNA, producing non-canonical configurations and even driving RNA to precipitate out of solution. Using all-atom molecular dynamics simulations, we model a monovalent salt species (KCL) at high concentrations (0.1–3m) and calculate the equilibrium distributions of water and ions around a small tetraloop-forming RNA oligomer in a variety of structural arrangements: folded A-RNA (canonical) and Z-RNA (non-canonical) tetraloops and unfolded configurations. From these data, we calculate the ion preferential binding coefficients andmore » Donnan coefficients for the RNA oligomer as a function of concentration and structure. We find that cation accumulation is highest around non-canonical Z-RNA configurations at concentrations below 0.5m, while unfolded configurations accumulate the most co-ions in all concentrations. By contrast, canonical A-RNA structures consistently show the lowest accumulations for all ion species. Water distributions vary markedly with RNA configuration but show little dependency on KCL concentration. Based on Donnan coefficient calculations, the net charge of the solution at the surface of the RNA decreases linearly as a function of salt concentration and becomes net-neutral near 2.5–3m KCL for folded configurations, while unfolded configurations still show a positive solution charge. Our findings show that all-atom molecular dynamics can describe the equilibrium distributions of monovalent salt in the presence of small RNA oligomers at KCL concentrations where ion correlation effects become important. Furthermore, these results provide valuable insights into the distributions of water and ions near the RNA oligomer surface as a function of structural configuration.« less

Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop

NASA Astrophysics Data System (ADS)

Miner, Jacob Carlson; García, Angel Enrique

2018-06-01

Monovalent salt solutions have strongly coupled interactions with biopolymers, from large polyelectrolytes to small RNA oligomers. High salt concentrations have been known to induce transitions in the structure of RNA, producing non-canonical configurations and even driving RNA to precipitate out of solution. Using all-atom molecular dynamics simulations, we model a monovalent salt species (KCL) at high concentrations (0.1-3m) and calculate the equilibrium distributions of water and ions around a small tetraloop-forming RNA oligomer in a variety of structural arrangements: folded A-RNA (canonical) and Z-RNA (non-canonical) tetraloops and unfolded configurations. From these data, we calculate the ion preferential binding coefficients and Donnan coefficients for the RNA oligomer as a function of concentration and structure. We find that cation accumulation is highest around non-canonical Z-RNA configurations at concentrations below 0.5m, while unfolded configurations accumulate the most co-ions in all concentrations. By contrast, canonical A-RNA structures consistently show the lowest accumulations for all ion species. Water distributions vary markedly with RNA configuration but show little dependency on KCL concentration. Based on Donnan coefficient calculations, the net charge of the solution at the surface of the RNA decreases linearly as a function of salt concentration and becomes net-neutral near 2.5-3m KCL for folded configurations, while unfolded configurations still show a positive solution charge. Our findings show that all-atom molecular dynamics can describe the equilibrium distributions of monovalent salt in the presence of small RNA oligomers at KCL concentrations where ion correlation effects become important. Furthermore, these results provide valuable insights into the distributions of water and ions near the RNA oligomer surface as a function of structural configuration.

Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop.

PubMed

Miner, Jacob Carlson; García, Angel Enrique

2018-06-14

Monovalent salt solutions have strongly coupled interactions with biopolymers, from large polyelectrolytes to small RNA oligomers. High salt concentrations have been known to induce transitions in the structure of RNA, producing non-canonical configurations and even driving RNA to precipitate out of solution. Using all-atom molecular dynamics simulations, we model a monovalent salt species (KCL) at high concentrations (0.1-3m) and calculate the equilibrium distributions of water and ions around a small tetraloop-forming RNA oligomer in a variety of structural arrangements: folded A-RNA (canonical) and Z-RNA (non-canonical) tetraloops and unfolded configurations. From these data, we calculate the ion preferential binding coefficients and Donnan coefficients for the RNA oligomer as a function of concentration and structure. We find that cation accumulation is highest around non-canonical Z-RNA configurations at concentrations below 0.5m, while unfolded configurations accumulate the most co-ions in all concentrations. By contrast, canonical A-RNA structures consistently show the lowest accumulations for all ion species. Water distributions vary markedly with RNA configuration but show little dependency on KCL concentration. Based on Donnan coefficient calculations, the net charge of the solution at the surface of the RNA decreases linearly as a function of salt concentration and becomes net-neutral near 2.5-3m KCL for folded configurations, while unfolded configurations still show a positive solution charge. Our findings show that all-atom molecular dynamics can describe the equilibrium distributions of monovalent salt in the presence of small RNA oligomers at KCL concentrations where ion correlation effects become important. Furthermore, these results provide valuable insights into the distributions of water and ions near the RNA oligomer surface as a function of structural configuration.

Dynamics of a "low-enrichment high-retention" upwelling center over the southern Senegal shelf

NASA Astrophysics Data System (ADS)

Ndoye, Siny; Capet, Xavier; Estrade, Philippe; Sow, Bamol; Machu, Eric; Brochier, Timothée.; Döring, Julian; Brehmer, Patrice

2017-05-01

Senegal is the southern tip of the Canary upwelling system. Its coastal ocean hosts an upwelling center which shapes sea surface temperatures between latitudes 12° and 15°N. Near this latter latitude, the Cape Verde headland and a sudden change in shelf cross-shore profile are major sources of heterogeneity in the southern Senegal upwelling sector (SSUS). SSUS dynamics is investigated by means of Regional Ocean Modeling System simulations. Configuration realism and resolution (Δx≈ 2 km) are sufficient to reproduce the SSUS frontal system. Our main focus is on the 3-D upwelling circulation which turns out to be profoundly different from 2-D theory: cold water injection onto the shelf and upwelling are strongly concentrated within a few tens of kilometers south of Cape Verde and largely arise from flow divergence in the alongshore direction; a significant fraction of the upwelled waters are retained nearshore over long distances while travelling southward under the influence of northerly winds. Another source of complexity, regional-scale alongshore pressure gradients, also contributes to the overall retention of upwelled waters over the shelf. Varying the degree of realism of atmospheric and oceanic forcings does not appreciably change these conclusions. This study sheds light on the dynamics and circulation underlying the recurrent sea surface temperature pattern observed during the upwelling season and offers new perspectives on the connections between the SSUS physical environment and its ecosystems. It also casts doubt on the validity of upwelling intensity estimations based on simple Ekman upwelling indices at such local scales.

General purpose computer program for interacting supersonic configurations: Programmer's manual

NASA Technical Reports Server (NTRS)

Crill, W.; Dale, B.

1977-01-01

The program ISCON (Interacting Supersonic Configuration) is described. The program is in support of the problem to generate a numerical procedure for determining the unsteady dynamic forces on interacting wings and tails in supersonic flow. Subroutines are presented along with the complete FORTRAN source listing.

Factors Impacting School Closure and Configuration

ERIC Educational Resources Information Center

Corrales, Antonio

2017-01-01

Newly implemented state policy dealing with school finance created several consequences in a school district to include school configuration and restructuring of educational programs. This case describes how a new school finance law changes the entire dynamic of a school district and its newly appointed superintendent. The superintendent…

The analysis and large-angle control of a flexible beam using an adaptive truss

NASA Technical Reports Server (NTRS)

Warrington, Thomas J.; Clark, William W.; Robertshaw, Harry H.; Horner, C. Garnett

1991-01-01

This preliminary study of an adaptive truss slewing problem investigates the static positioning of an adaptive truss at slewed orientations and the dynamic vibrations of an attached flexible beam. A nonlinear model of an adaptive truss and flexible beam is derived. Linear control laws are developed and simulated for various truss configurations. Results show the linear control laws developed at a slewed configuration perform best at that configuration.

Coupled elasticity–diffusion model for the effects of cytoskeleton deformation on cellular uptake of cylindrical nanoparticles

PubMed Central

Wang, Jizeng; Li, Long

2015-01-01

Molecular dynamic simulations and experiments have recently demonstrated how cylindrical nanoparticles (CNPs) with large aspect ratios penetrate animal cells and inevitably deform cytoskeletons. Thus, a coupled elasticity–diffusion model was adopted to elucidate this interesting biological phenomenon by considering the effects of elastic deformations of cytoskeleton and membrane, ligand–receptor binding and receptor diffusion. The mechanism by which the binding energy drives the CNPs with different orientations to enter host cells was explored. This mechanism involved overcoming the resistance caused by cytoskeleton and membrane deformations and the change in configurational entropy of the ligand–receptor bonds and free receptors. Results showed that deformation of the cytoskeleton significantly influenced the engulfing process by effectively slowing down and even hindering the entry of the CNPs. Additionally, the engulfing depth was determined quantitatively. CNPs preferred or tended to vertically attack target cells until they were stuck in the cytoskeleton as implied by the speed of vertically oriented CNPs that showed much faster initial engulfing speeds than horizontally oriented CNPs. These results elucidated the most recent molecular dynamics simulations and experimental observations on the cellular uptake of carbon nanotubes and phagocytosis of filamentous Escherichia coli bacteria. The most efficient engulfment showed the stiffness-dependent optimal radius of the CNPs. Cytoskeleton stiffness exhibited more significant influence on the optimal sizes of the vertical uptake than the horizontal uptake. PMID:25411410

An open-source, FireWire camera-based, Labview-controlled image acquisition system for automated, dynamic pupillometry and blink detection.

PubMed

de Souza, John Kennedy Schettino; Pinto, Marcos Antonio da Silva; Vieira, Pedro Gabrielle; Baron, Jerome; Tierra-Criollo, Carlos Julio

2013-12-01

The dynamic, accurate measurement of pupil size is extremely valuable for studying a large number of neuronal functions and dysfunctions. Despite tremendous and well-documented progress in image processing techniques for estimating pupil parameters, comparatively little work has been reported on practical hardware issues involved in designing image acquisition systems for pupil analysis. Here, we describe and validate the basic features of such a system which is based on a relatively compact, off-the-shelf, low-cost FireWire digital camera. We successfully implemented two configurable modes of video record: a continuous mode and an event-triggered mode. The interoperability of the whole system is guaranteed by a set of modular software components hosted on a personal computer and written in Labview. An offline analysis suite of image processing algorithms for automatically estimating pupillary and eyelid parameters were assessed using data obtained in human subjects. Our benchmark results show that such measurements can be done in a temporally precise way at a sampling frequency of up to 120 Hz and with an estimated maximum spatial resolution of 0.03 mm. Our software is made available free of charge to the scientific community, allowing end users to either use the software as is or modify it to suit their own needs. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Integrating multiple scientific computing needs via a Private Cloud infrastructure

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Brunetti, R.; Lusso, S.; Vallero, S.

2014-06-01

In a typical scientific computing centre, diverse applications coexist and share a single physical infrastructure. An underlying Private Cloud facility eases the management and maintenance of heterogeneous use cases such as multipurpose or application-specific batch farms, Grid sites catering to different communities, parallel interactive data analysis facilities and others. It allows to dynamically and efficiently allocate resources to any application and to tailor the virtual machines according to the applications' requirements. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques; for example, rolling updates can be performed easily and minimizing the downtime. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 site and a dynamically expandable PROOF-based Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The Private Cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem (used in two different configurations for worker- and service-class hypervisors) and the OpenWRT Linux distribution (used for network virtualization). A future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and by using mainstream contextualization tools like CloudInit.

Spin-diffusions and diffusive molecular dynamics

NASA Astrophysics Data System (ADS)

Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon

2017-12-01

Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.

Applying Reflective Middleware Techniques to Optimize a QoS-enabled CORBA Component Model Implementation

NASA Technical Reports Server (NTRS)

Wang, Nanbor; Kircher, Michael; Schmidt, Douglas C.

2000-01-01

Although existing CORBA specifications, such as Real-time CORBA and CORBA Messaging, address many end-to-end quality-of-service (QoS) properties, they do not define strategies for configuring these properties into applications flexibly, transparently, and adaptively. Therefore, application developers must make these configuration decisions manually and explicitly, which is tedious, error-prone, and often sub-optimal. Although the recently adopted CORBA Component Model (CCM) does define a standard configuration frame-work for packaging and deploying software components, conventional CCM implementations focus on functionality rather than adaptive quality-of service, which makes them unsuitable for next-generation applications with demanding QoS requirements. This paper presents three contributions to the study of middleware for QoS-enabled component-based applications. It outlines reflective middleware techniques designed to adaptively: (1) select optimal communication mechanisms, (2) man- age QoS properties of CORBA components in their containers, and (3) (re)configure selected component executors dynamically. Based on our ongoing research on CORBA and the CCM, we believe the application of reflective techniques to component middleware will provide a dynamically adaptive and (re)configurable framework for COTS software that is well-suited for the QoS demands of next-generation applications.

Dynamic analysis of the large deployable reflector

NASA Technical Reports Server (NTRS)

Calleson, Robert E.; Scott, A. Don

1987-01-01

The Large Deployable Reflector (LDR) is to be an astronomical observatory orbiting above Earth's obscuring atmosphere and operating in the spectral range between 30 microns and 1000 microns wavelength. The LDR will be used to study such astronomical phenomena as stellar and galactic formation, cosmology, and planetary atmospheres. The LDR will be the first observatory to be erected and assembled in space. This distinction brings with it several major technological challenges such as the development of ultra-lightweight deployable mirrors, advanced mirror fabrication techniques, advanced structures, and control of vibrations due to various sources of excitation. The purpose of this analysis is to provide an assessment of the vibrational response due to secondary mirror chopping and LDR slewing. The dynamic response of two 20-m LDR configurations was studied. Two mirror support configurations were investigated for the Ames concept, the first employs a six-strut secondary mirror support structure, while the second uses a triple-bipod support design. All three configurations were modeled using a tetrahedral truss design for the primary mirror support structure. Response resulting from secondary mirror chopping was obtained for the two Ames configurations, and the response of the primary mirror from slewing was obtained for all three configurations.

Bridging scales in the evolution of infectious disease life histories: application.

PubMed

Mideo, Nicole; Nelson, William A; Reece, Sarah E; Bell, Andrew S; Read, Andrew F; Day, Troy

2011-11-01

Within- and between-host disease processes occur on the same timescales, therefore changes in the within-host dynamics of parasites, resources, and immunity can interact with changes in the epidemiological dynamics to affect evolutionary outcomes. Consequently, studies of the evolution of disease life histories, that is, infection-age-specific patterns of transmission and virulence, have been constrained by the need for a mechanistic understanding of within-host disease dynamics. In a companion paper (Day et al. 2011), we develop a novel approach that quantifies the relevant within-host aspects of disease through genetic covariance functions. Here, we demonstrate how to apply this theory to data. Using two previously published datasets from rodent malaria infections, we show how to translate experimental measures into disease life-history traits, and how to quantify the covariance in these traits. Our results show how patterns of covariance can interact with epidemiological dynamics to affect evolutionary predictions for disease life history. We also find that the selective constraints on disease life-history evolution can vary qualitatively, and that "simple" virulence-transmission trade-offs that are often the subject of experimental investigation can be obscured by trade-offs within one trait alone. Finally, we highlight the type and quality of data required for future applications. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Modelling the host-pathogen interactions of macrophages and Candida albicans using Game Theory and dynamic optimization.

PubMed

Dühring, Sybille; Ewald, Jan; Germerodt, Sebastian; Kaleta, Christoph; Dandekar, Thomas; Schuster, Stefan

2017-07-01

The release of fungal cells following macrophage phagocytosis, called non-lytic expulsion, is reported for several fungal pathogens. On one hand, non-lytic expulsion may benefit the fungus in escaping the microbicidal environment of the phagosome. On the other hand, the macrophage could profit in terms of avoiding its own lysis and being able to undergo proliferation. To analyse the causes of non-lytic expulsion and the relevance of macrophage proliferation in the macrophage- Candida albicans interaction, we employ Evolutionary Game Theory and dynamic optimization in a sequential manner. We establish a game-theoretical model describing the different strategies of the two players after phagocytosis. Depending on the parameter values, we find four different Nash equilibria and determine the influence of the systems state of the host upon the game. As our Nash equilibria are a direct consequence of the model parameterization, we can depict several biological scenarios. A parameter region, where the host response is robust against the fungal infection, is determined. We further apply dynamic optimization to analyse whether macrophage mitosis is relevant in the host-pathogen interaction of macrophages and C. albicans For this, we study the population dynamics of the macrophage- C. albicans interactions and the corresponding optimal controls for the macrophages, indicating the best macrophage strategy of switching from proliferation to attacking fungal cells. © 2017 The Author(s).

In Vitro Quantification of Gutter Formation and Chimney Graft Compression in Chimney EVAR Stent-Graft Configurations Using Electrocardiography-Gated Computed Tomography.

PubMed

Overeem, Simon P; Donselaar, Esmé J; Boersen, Jorrit T; Groot Jebbink, Erik; Slump, Cornelis H; de Vries, Jean-Paul P M; Reijnen, Michel M P J

2018-03-01

To assess the dynamic behavior of chimney grafts during the cardiac cycle. Three chimney endovascular aneurysm repair (EVAR) stent-graft configurations (Endurant and Advanta V12, Endurant and Viabahn, and Endurant and BeGraft) were placed in silicone aneurysm models and subjected to physiologic flow. Electrocardiography (ECG)-gated contrast-enhanced computed tomography was used to visualize geometric changes during the cardiac cycle. Endograft and chimney graft surface, gutter volume, chimney graft angulation over the center lumen line, and the D-ratio (the ratio between the lengths of the major and minor axes) were independently assessed by 2 observers at 10 time points in the cardiac cycle. Both gutter volumes and chimney graft geometry changed significantly during the cardiac cycle in all 3 configurations (p<0.001). Gutters and endoleaks were observed in all configurations. The largest gutter volume (232.8 mm 3 ) and change in volume (20.7 mm 3 ) between systole and diastole were observed in the Endurant-Advanta configuration. These values were 2.7- and 3.0-fold higher, respectively, compared to the Endurant-Viabahn configuration and 1.7- and 1.6-fold higher as observed in the Endurant-BeGraft configuration. The Endurant-Viabahn configuration had the highest D-ratio (right, 1.26-1.35; left, 1.33-1.48), while the Endurant-BeGraft configuration had the lowest (right, 1.11-1.17; left, 1.08-1.15). Assessment of the interobserver variability showed a high correlation (intraclass correlation >0.935) between measurements. Gutter volumes and stent compression are dynamic phenomena that reshape during the cardiac cycle. Compelling differences were observed during the cardiac cycle in all configurations, with the self-expanding (Endurant-Viabahn) chimney EVAR configurations having smaller gutters and less variation in gutter volume during the cardiac cycle yet more stent compression without affecting the chimney graft surface.

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

2015-08-01

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli

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

Liu Jun, E-mail: Jun.Liu.1@uth.tmc.edu; Chen Chengyen; Shiomi, Daisuke

2011-09-01

Bacteriophage P1 has a contractile tail that targets the conserved lipopolysaccharide on the outer membrane surface of the host for initial adsorption. The mechanism by which P1 DNA enters the host cell is not well understood, mainly because the transient molecular interactions between bacteriophage and bacteria have been difficult to study by conventional approaches. Here, we engineered tiny E. coli host cells so that the initial stages of P1-host interactions could be captured in unprecedented detail by cryo-electron tomography. Analysis of three-dimensional reconstructions of frozen-hydrated specimens revealed three predominant configurations: an extended tail stage with DNA present in the phagemore » head, a contracted tail stage with DNA, and a contracted tail stage without DNA. Comparative analysis of various conformations indicated that there is uniform penetration of the inner tail tube into the E. coli periplasm and a significant movement of the baseplate away from the outer membrane during tail contraction.« less

Early-Life Food Nutrition, Microbiota Maturation and Immune Development Shape Life-Long Health.

PubMed

Zhou, Xiaoli; Du, Lina; Shi, Ronghua; Chen, Zhidong; Zhou, Yiming; Li, Zongjie

2018-06-06

The current knowledge about early-life nutrition and environmental factors that affect the interaction between the symbiotic microbiota and the host immune system has demonstrated novel regulatory target for treating allergic diseases, autoimmune disorders and metabolic syndrome. Various kinds of food nutrients (such as dietary fiber, starch, polyphenols and proteins) can provide energy resources for both intestinal microbiota and the host. The indigestible food components are fermented by the indigenous gut microbiota to produce diverse metabolites, including short-chain fatty acids, bile acids and trimethylamine-N-oxide, which can regulate the host metabolized physiology, immunity homeostasis and health state. Therefore it is commonly believed early-life perturbation of the microbial community structure and the dietary nutrition interference on the child mucosal immunity contribute to the whole life susceptibility to chronic diseases. In all, the combined interrelationship between food ingredients nutrition, intestinal microbiota configurations and host system immunity provides new therapeutic targets to treat various kinds of pathogenic inflammations and chronic diseases.

Transition-metal doped sulfide, selenide, and telluride laser crystal and lasers

DOEpatents

Krupke, W.F.; Page, R.H.; DeLoach, L.D.; Payne, S.A.

1996-07-30

A new class of solid state laser crystals and lasers are formed of transition metal doped sulfide, selenide, and telluride host crystals which have four fold coordinated substitutional sites. The host crystals include II-VI compounds. The host crystal is doped with a transition metal laser ion, e.g., chromium, cobalt or iron. In particular, Cr{sup 2+}-doped ZnS and ZnSe generate laser action near 2.3 {micro}m. Oxide, chloride, fluoride, bromide and iodide crystals with similar structures can also be used. Important aspects of these laser materials are the tetrahedral site symmetry of the host crystal, low excited state absorption losses and high luminescence efficiency, and the d{sup 4} and d{sup 6} electronic configurations of the transition metal ions. The same materials are also useful as saturable absorbers for passive Q-switching applications. The laser materials can be used as gain media in amplifiers and oscillators; these gain media can be incorporated into waveguides and semiconductor lasers. 18 figs.

Transition-metal doped sulfide, selenide, and telluride laser crystal and lasers

DOEpatents

Krupke, William F.; Page, Ralph H.; DeLoach, Laura D.; Payne, Stephen A.

1996-01-01

A new class of solid state laser crystals and lasers are formed of transition metal doped sulfide, selenide, and telluride host crystals which have four fold coordinated substitutional sites. The host crystals include II-VI compounds. The host crystal is doped with a transition metal laser ion, e.g., chromium, cobalt or iron. In particular, Cr.sup.2+ -doped ZnS and ZnSe generate laser action near 2.3 .mu.m. Oxide, chloride, fluoride, bromide and iodide crystals with similar structures can also be used. Important aspects of these laser materials are the tetrahedral site symmetry of the host crystal, low excited state absorption losses and high luminescence efficiency, and the d.sup.4 and d.sup.6 electronic configurations of the transition metal ions. The same materials are also useful as saturable absorbers for passive Q-switching applications. The laser materials can be used as gain media in amplifiers and oscillators; these gain media can be incorporated into waveguides and semiconductor lasers.

Host persistence or extinction from emerging infectious disease: insights from white-nose syndrome in endemic and invading regions.

PubMed

Hoyt, Joseph R; Langwig, Kate E; Sun, Keping; Lu, Guanjun; Parise, Katy L; Jiang, Tinglei; Frick, Winifred F; Foster, Jeffrey T; Feng, Jiang; Kilpatrick, A Marm

2016-03-16

Predicting species' fates following the introduction of a novel pathogen is a significant and growing problem in conservation. Comparing disease dynamics between introduced and endemic regions can offer insight into which naive hosts will persist or go extinct, with disease acting as a filter on host communities. We examined four hypothesized mechanisms for host-pathogen persistence by comparing host infection patterns and environmental reservoirs for Pseudogymnoascus destructans (the causative agent of white-nose syndrome) in Asia, an endemic region, and North America, where the pathogen has recently invaded. Although colony sizes of bats and hibernacula temperatures were very similar, both infection prevalence and fungal loads were much lower on bats and in the environment in Asia than North America. These results indicate that transmission intensity and pathogen growth are lower in Asia, likely due to higher host resistance to pathogen growth in this endemic region, and not due to host tolerance, lower transmission due to smaller populations, or lower environmentally driven pathogen growth rate. Disease filtering also appears to be favouring initially resistant species in North America. More broadly, determining the mechanisms allowing species persistence in endemic regions can help identify species at greater risk of extinction in introduced regions, and determine the consequences for disease dynamics and host-pathogen coevolution. © 2016 The Author(s).

Invasion and Persistence of Infectious Agents in Fragmented Host Populations

PubMed Central

Jesse, Marieke; Mazzucco, Rupert; Dieckmann, Ulf; Heesterbeek, Hans; Metz, Johan A. J.

2011-01-01

One of the important questions in understanding infectious diseases and their prevention and control is how infectious agents can invade and become endemic in a host population. A ubiquitous feature of natural populations is that they are spatially fragmented, resulting in relatively homogeneous local populations inhabiting patches connected by the migration of hosts. Such fragmented population structures are studied extensively with metapopulation models. Being able to define and calculate an indicator for the success of invasion and persistence of an infectious agent is essential for obtaining general qualitative insights into infection dynamics, for the comparison of prevention and control scenarios, and for quantitative insights into specific systems. For homogeneous populations, the basic reproduction ratio plays this role. For metapopulations, defining such an ‘invasion indicator’ is not straightforward. Some indicators have been defined for specific situations, e.g., the household reproduction number . However, these existing indicators often fail to account for host demography and especially host migration. Here we show how to calculate a more broadly applicable indicator for the invasion and persistence of infectious agents in a host metapopulation of equally connected patches, for a wide range of possible epidemiological models. A strong feature of our method is that it explicitly accounts for host demography and host migration. Using a simple compartmental system as an example, we illustrate how can be calculated and expressed in terms of the key determinants of epidemiological dynamics. PMID:21980339

Ecological dynamics of emerging bat virus spillover

PubMed Central

Plowright, Raina K.; Eby, Peggy; Hudson, Peter J.; Smith, Ina L.; Westcott, David; Bryden, Wayne L.; Middleton, Deborah; Reid, Peter A.; McFarlane, Rosemary A.; Martin, Gerardo; Tabor, Gary M.; Skerratt, Lee F.; Anderson, Dale L.; Crameri, Gary; Quammen, David; Jordan, David; Freeman, Paul; Wang, Lin-Fa; Epstein, Jonathan H.; Marsh, Glenn A.; Kung, Nina Y.; McCallum, Hamish

2015-01-01

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility. PMID:25392474

Space Shuttle Main Engine Low Pressure Oxidizer Turbo-Pump Inducer Dynamic Environment Characterization through Water Model and Hot-Fire Testing

NASA Technical Reports Server (NTRS)

Arellano, Patrick; Patton, Marc; Schwartz, Alan; Stanton, David

2006-01-01

The Low Pressure Oxidizer Turbopump (LPOTP) inducer on the Block II configuration Space Shuttle Main Engine (SSME) experienced blade leading edge ripples during hot firing. This undesirable condition led to a minor redesign of the inducer blades. This resulted in the need to evaluate the performance and the dynamic environment of the redesign, relative to the current configuration, as part of the design acceptance process. Sub-scale water model tests of the two inducer configurations were performed, with emphasis on the dynamic environment due to cavitation induced vibrations. Water model tests were performed over a wide range of inlet flow coefficient and pressure conditions, representative of the scaled operating envelope of the Block II SSME, both in flight and in ground hot-fire tests, including all power levels. The water test hardware, facility set-up, type and placement of instrumentation, the scope of the test program, specific test objectives, data evaluation process and water test results that characterize and compare the two SSME LPOTP inducers are discussed. In addition, dynamic characteristics of the two water models were compared to hot fire data from specially instrumented ground tests. In general, good agreement between the water model and hot fire data was found, which confirms the value of water model testing for dynamic characterization of rocket engine turbomachinery.

Instantaneous Normal Modes and the Protein Glass Transition

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

Schulz, Roland; Krishnan, Marimuthu; Daidone, Isabella

2009-01-01

In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at ~ 220more » K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.« less

Instantaneous Normal Modes and the Protein Glass Transition

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

Schultz, Roland; Krishnan, Marimuthu; Daidone, Isabella

2009-01-01

In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at 220 K.more » The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.« less

Repercussion of geometric and dynamic constraints on the 3D rendering quality in structurally adaptive multi-view shooting systems

NASA Astrophysics Data System (ADS)

Ali-Bey, Mohamed; Moughamir, Saïd; Manamanni, Noureddine

2011-12-01

in this paper a simulator of a multi-view shooting system with parallel optical axes and structurally variable configuration is proposed. The considered system is dedicated to the production of 3D contents for auto-stereoscopic visualization. The global shooting/viewing geometrical process, which is the kernel of this shooting system, is detailed and the different viewing, transformation and capture parameters are then defined. An appropriate perspective projection model is afterward derived to work out a simulator. At first, this latter is used to validate the global geometrical process in the case of a static configuration. Next, the simulator is used to show the limitations of a static configuration of this shooting system type by considering the case of dynamic scenes and then a dynamic scheme is achieved to allow a correct capture of this kind of scenes. After that, the effect of the different geometrical capture parameters on the 3D rendering quality and the necessity or not of their adaptation is studied. Finally, some dynamic effects and their repercussions on the 3D rendering quality of dynamic scenes are analyzed using error images and some image quantization tools. Simulation and experimental results are presented throughout this paper to illustrate the different studied points. Some conclusions and perspectives end the paper. [Figure not available: see fulltext.

Dynamic microbiome evolution in social bees

PubMed Central

Kwong, Waldan K.; Medina, Luis A.; Koch, Hauke; Sing, Kong-Wah; Soh, Eunice Jia Yu; Ascher, John S.; Jaffé, Rodolfo; Moran, Nancy A.

2017-01-01

The highly social (eusocial) corbiculate bees, comprising the honey bees, bumble bees, and stingless bees, are ubiquitous insect pollinators that fulfill critical roles in ecosystem services and human agriculture. Here, we conduct wide sampling across the phylogeny of these corbiculate bees and reveal a dynamic evolutionary history behind their microbiota, marked by multiple gains and losses of gut associates, the presence of generalist as well as host-specific strains, and patterns of diversification driven, in part, by host ecology (for example, colony size). Across four continents, we found that different host species have distinct gut communities, largely independent of geography or sympatry. Nonetheless, their microbiota has a shared heritage: The emergence of the eusocial corbiculate bees from solitary ancestors appears to coincide with the acquisition of five core gut bacterial lineages, supporting the hypothesis that host sociality facilitates the development and maintenance of specialized microbiomes. PMID:28435856

Evolutionary and ecological forces that shape the bacterial communities of the human gut

PubMed Central

Messer, Jeannette S.; Liechty, Emma R; Vogel, Olivia A.; Chang, Eugene B.

2017-01-01

Since microbes were first described in the mid-1600's, we have come to appreciate that they live all around and within us with both beneficial and detrimental effects on nearly every aspect of our lives. The human gastrointestinal tract is inhabited by a dynamic community of trillions of bacteria that constantly interact with each other and their human host. The acquisition of these bacteria is not stochastic, but determined by circumstance (environment), host rules (genetics, immune state, mucus, etc), and dynamic self-selection among microbes to form stable, resilient communities that are in balance with the host. In this review, we will discuss how these factors lead to formation of the gut bacterial community and influence its interactions with the host. We will also address how gut bacteria contribute to disease and how they could potentially be targeted to prevent and treat a variety of human ailments. PMID:28145439

Caste-specific differences in hindgut microbial communities of honey bees (Apis mellifera).

PubMed

Kapheim, Karen M; Rao, Vikyath D; Yeoman, Carl J; Wilson, Brenda A; White, Bryan A; Goldenfeld, Nigel; Robinson, Gene E

2015-01-01

Host-symbiont dynamics are known to influence host phenotype, but their role in social behavior has yet to be investigated. Variation in life history across honey bee (Apis mellifera) castes may influence community composition of gut symbionts, which may in turn influence caste phenotypes. We investigated the relationship between host-symbiont dynamics and social behavior by characterizing the hindgut microbiome among distinct honey bee castes: queens, males and two types of workers, nurses and foragers. Despite a shared hive environment and mouth-to-mouth food transfer among nestmates, we detected separation among gut microbiomes of queens, workers, and males. Gut microbiomes of nurses and foragers were similar to previously characterized honey bee worker microbiomes and to each other, despite differences in diet, activity, and exposure to the external environment. Queen microbiomes were enriched for bacteria that may enhance metabolic conversion of energy from food to egg production. We propose that the two types of workers, which have the highest diversity of operational taxonomic units (OTUs) of bacteria, are central to the maintenance of the colony microbiome. Foragers may introduce new strains of bacteria to the colony from the environment and transfer them to nurses, who filter and distribute them to the rest of the colony. Our results support the idea that host-symbiont dynamics influence microbiome composition and, reciprocally, host social behavior.

Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle.

PubMed

Jupe, Julietta; Stam, Remco; Howden, Andrew J M; Morris, Jenny A; Zhang, Runxuan; Hedley, Pete E; Huitema, Edgar

2013-06-25

Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome sequences of both hosts and microbes, little is known about the signal interplay between them during infection. In particular, accurate descriptions of coordinate relationships between host and microbe transcriptional programs are lacking. Here, we explore the molecular interaction between the hemi-biotrophic broad host range pathogen Phytophthora capsici and tomato. Infection assays and use of a composite microarray allowed us to unveil distinct changes in both P. capsici and tomato transcriptomes, associated with biotrophy and the subsequent switch to necrotrophy. These included two distinct transcriptional changes associated with early infection and the biotrophy to necrotrophy transition that may contribute to infection and completion of the P. capsici lifecycle Our results suggest dynamic but highly regulated transcriptional programming in both host and pathogen that underpin P. capsici disease and hemi-biotrophy. Dynamic expression changes of both effector-coding genes and host factors involved in immunity, suggests modulation of host immune signaling by both host and pathogen. With new unprecedented detail on transcriptional reprogramming, we can now explore the coordinate relationships that drive host-microbe interactions and the basic processes that underpin pathogen lifestyles. Deliberate alteration of lifestyle-associated transcriptional changes may allow prevention or perhaps disruption of hemi-biotrophic disease cycles and limit damage caused by epidemics.

Mode of transmission, host switching, and escape from the Red Queen by viviparous gyrodactylids (Monogenoidea).

PubMed

Boeger, Walter A; Kritsky, Delane C; Pie, Marcio R; Engers, Kerlen B

2005-10-01

Compared to other monogenoidean groups, viviparous gyrodactylids exhibit extraordinary species diversity and broad host range. It has been suggested that this evolutionary success is associated with a suite of morphological and life-history traits that include, in part, continuous transmission (i.e., ability to infect new hosts throughout the gyrodactylid life cycle). Experiments were conducted to explore the putative adaptive advantage of continuous transmission within viviparous gyrodactylids during colonization of new host resources. Differences in infrapopulation growth, such as abundance, prevalence, and duration of the infection, of Gyrodactylus anisopharynx on 3 species of fish--Corydoras paleatus and Corydoras ehrhardti (both natural hosts) as well as Corydoras schwartzi (a host not known to harbor G. anisopharynx)--held under isolated and grouped conditions were determined. Results showed that infrapopulations of G. anisopharynx on C. paleatus and C. schwartzi had higher growth when the parasite had the opportunity for host transfer (grouped hosts). Infrapopulations of G. anisopharynx on isolated and grouped C. ehrhardti showed an opposite trend, although differences in mean duration and maximum abundance were not statistically different. Results obtained from experiments with C. paleatus and C. schwartzi support the hypothesis that continuous transmission in viviparous gyrodactylids enhances colonization success, probably by allowing initial avoidance of Red Queen dynamics. The absence of statistical differences between infrapopulations on isolated and grouped C. ehrhardti suggests that parasite dynamics may be influenced by factors other than continuous transmission in this host.

Host-pathogen dynamics under sterilizing pathogens and fecundity-longevity trade-off in hosts.

PubMed

Janoušková, Eva; Berec, Luděk

2018-08-07

Infectious diseases are known to regulate population dynamics, an observation that underlies the use of pathogens as control agents of unwanted populations. Sterilizing rather than lethal pathogens are often suggested so as to avoid unnecessary suffering of the infected hosts. Until recently, models used to assess plausibility of pathogens as potential pest control agents have not included a possibility that reduced fecundity of the infected individuals may save their energy expenditure on reproduction and thus increase their longevity relative to the susceptible ones. Here, we develop a model of host-pathogen interaction that builds on this idea. We analyze the model for a variety of infection transmission functions, revealing that the indirect effect of sterilizing pathogens on mortality of the infected hosts, mediated by a fecundity-longevity trade-off, may cause hosts at endemic equilibria to attain densities higher than when there is no effect of pathogens on host mortality. On the other hand, an opposite outcome occurs when the fecundity-longevity trade-off is concave or when the degree of fecundity reduction by the pathogen is high enough. This points to a possibility that using sterilizing pathogens as agents of pest control may actually be less effective than previously thought, the more so since we also suggest that if sexual selection acts on the host species then the presence of sterilizing pathogens may even enhance host densities above the levels achieved without infection. Copyright © 2018 Elsevier Ltd. All rights reserved.

Cancer dormancy and criticality from a game theory perspective.

PubMed

Wu, Amy; Liao, David; Kirilin, Vlamimir; Lin, Ke-Chih; Torga, Gonzalo; Qu, Junle; Liu, Liyu; Sturm, James C; Pienta, Kenneth; Austin, Robert

2018-01-01

The physics of cancer dormancy, the time between initial cancer treatment and re-emergence after a protracted period, is a puzzle. Cancer cells interact with host cells via complex, non-linear population dynamics, which can lead to very non-intuitive but perhaps deterministic and understandable progression dynamics of cancer and dormancy. We explore here the dynamics of host-cancer cell populations in the presence of (1) payoffs gradients and (2) perturbations due to cell migration. We determine to what extent the time-dependence of the populations can be quantitively understood in spite of the underlying complexity of the individual agents and model the phenomena of dormancy.

Local interactions lead to pathogen-driven change to host population dynamics.

PubMed

Boots, Michael; Childs, Dylan; Reuman, Daniel C; Mealor, Michael

2009-10-13

Individuals tend to interact more strongly with nearby individuals or within particular social groups. Recent theoretical advances have demonstrated that these within-population relationships can have fundamental implications for ecological and evolutionary dynamics. In particular, contact networks are crucial to the spread and evolution of disease. However, the theory remains largely untested experimentally. Here, we manipulate habitat viscosity and thereby the frequency of local interactions in an insect-pathogen model system in which the virus had previously been shown to have little effect on host population dynamics. At high viscosity, the pathogen caused the collapse of dominant and otherwise stable host generation cycles. Modeling shows that this collapse can be explained by an increase in the frequency of intracohort interactions relative to intercohort interactions, leading to more disease transmission. Our work emphasizes that spatial structure can subtly mediate intraspecific competition and the effects of natural enemies. A decrease in dispersal in a population may actually (sometimes rather counterintuitively) intensify the effects of parasites. Broadly, because anthropological and environmental change often cause changes in population mixing, our work highlights the potential for dramatic changes in the effects of parasites on host populations.

Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche

PubMed Central

2010-01-01

Background Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner. Results We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks. Conclusions These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not sufficient to fully reproduce root SCN organization and genetic profiles. We then highlight some experimental holes that remain to be studied and postulate some novel gene interactions. Finally, we suggest the existence of a generic dynamical motif that can be involved in both plant and animal SCN maintenance. PMID:20920363

STAR: an integrated solution to management and visualization of sequencing data.

PubMed

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W; Ecker, Joseph R; Millar, A Harvey; Ren, Bing; Wang, Wei

2013-12-15

Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser.

Systems-on-chip approach for real-time simulation of wheel-rail contact laws

NASA Astrophysics Data System (ADS)

Mei, T. X.; Zhou, Y. J.

2013-04-01

This paper presents the development of a systems-on-chip approach to speed up the simulation of wheel-rail contact laws, which can be used to reduce the requirement for high-performance computers and enable simulation in real time for the use of hardware-in-loop for experimental studies of the latest vehicle dynamic and control technologies. The wheel-rail contact laws are implemented using a field programmable gate array (FPGA) device with a design that substantially outperforms modern general-purpose PC platforms or fixed architecture digital signal processor devices in terms of processing time, configuration flexibility and cost. In order to utilise the FPGA's parallel-processing capability, the operations in the contact laws algorithms are arranged in a parallel manner and multi-contact patches are tackled simultaneously in the design. The interface between the FPGA device and the host PC is achieved by using a high-throughput and low-latency Ethernet link. The development is based on FASTSIM algorithms, although the design can be adapted and expanded for even more computationally demanding tasks.

Emission properties of pristine and oxidatively degraded polyfluorene type polymers

NASA Astrophysics Data System (ADS)

Gamerith, Stefan; Gadermaier, Christoph; Scherf, Ullrich; List, Emil J. W.

2004-05-01

We present a detailed and comprehensive picture of the photophysics including device applications within the polyfluorene family of conjugated polymers. First, the photophysics of pristine polyfluorenes in solution and film is outlined, including a discussion of the so-called -phase, which is characterised by a more planar ground state configuration. Particular attention is also dedicated to the occurence of low energy emission bands, which often deteriorate the initially blue emission of polyfluorenes, especially in electroluminescent devices. Although the origin of these emission features has been the object of a controversial discussion, strong evidence for our current ascription to emissive on-chain fluorenone defects is given also in contrast to previous assignments to aggregates, excimers, or exciplexes. According to the current attribution fluorenone-containing polyfluorenes can be described as a guest host system. Following this picture the photoexcitation dynamics from the fs to the ms regime is outlined. Finally, polymer light emitting diodes (PLEDs) based on polyfluorene-type emitters are discussed, especially related to their degradation mechanisms and possible remedies provided by chemistry to reduce the oxidative degradation of polyfluorene-based PLEDs.

Arresting relaxation in Pickering Emulsions

NASA Astrophysics Data System (ADS)

Atherton, Tim; Burke, Chris

2015-03-01

Pickering emulsions consist of droplets of one fluid dispersed in a host fluid and stabilized by colloidal particles absorbed at the fluid-fluid interface. Everyday materials such as crude oil and food products like salad dressing are examples of these materials. Particles can stabilize non spherical droplet shapes in these emulsions through the following sequence: first, an isolated droplet is deformed, e.g. by an electric field, increasing the surface area above the equilibrium value; additional particles are then adsorbed to the interface reducing the surface tension. The droplet is then allowed to relax toward a sphere. If more particles were adsorbed than can be accommodated by the surface area of the spherical ground state, relaxation of the droplet is arrested at some non-spherical shape. Because the energetic cost of removing adsorbed colloids exceeds the interfacial driving force, these configurations can remain stable over long timescales. In this presentation, we present a computational study of the ordering present in anisotropic droplets produced through the mechanism of arrested relaxation and discuss the interplay between the geometry of the droplet, the dynamical process that produced it, and the structure of the defects observed.

Modeling Systems-Level Regulation of Host Immune Responses

PubMed Central

Thakar, Juilee; Pilione, Mylisa; Kirimanjeswara, Girish; Harvill, Eric T; Albert, Réka

2007-01-01

Many pathogens are able to manipulate the signaling pathways responsible for the generation of host immune responses. Here we examine and model a respiratory infection system in which disruption of host immune functions or of bacterial factors changes the dynamics of the infection. We synthesize the network of interactions between host immune components and two closely related bacteria in the genus Bordetellae. We incorporate existing experimental information on the timing of immune regulatory events into a discrete dynamic model, and verify the model by comparing the effects of simulated disruptions to the experimental outcome of knockout mutations. Our model indicates that the infection time course of both Bordetellae can be separated into three distinct phases based on the most active immune processes. We compare and discuss the effect of the species-specific virulence factors on disrupting the immune response during their infection of naive, antibody-treated, diseased, or convalescent hosts. Our model offers predictions regarding cytokine regulation, key immune components, and clearance of secondary infections; we experimentally validate two of these predictions. This type of modeling provides new insights into the virulence, pathogenesis, and host adaptation of disease-causing microorganisms and allows systems-level analysis that is not always possible using traditional methods. PMID:17559300

Impact of biodiversity and seasonality on Lyme-pathogen transmission.

PubMed

Lou, Yijun; Wu, Jianhong; Wu, Xiaotian

2014-11-28

Lyme disease imposes increasing global public health challenges. To better understand the joint effects of seasonal temperature variation and host community composition on the pathogen transmission, a stage-structured periodic model is proposed by integrating seasonal tick development and activity, multiple host species and complex pathogen transmission routes between ticks and reservoirs. Two thresholds, one for tick population dynamics and the other for Lyme-pathogen transmission dynamics, are identified and shown to fully classify the long-term outcomes of the tick invasion and disease persistence. Seeding with the realistic parameters, the tick reproduction threshold and Lyme disease spread threshold are estimated to illustrate the joint effects of the climate change and host community diversity on the pattern of Lyme disease risk. It is shown that climate warming can amplify the disease risk and slightly change the seasonality of disease risk. Both the "dilution effect" and "amplification effect" are observed by feeding the model with different possible alternative hosts. Therefore, the relationship between the host community biodiversity and disease risk varies, calling for more accurate measurements on the local environment, both biotic and abiotic such as the temperature and the host community composition.

Protecting Dynamic Mobile Agent against Denial of Service Attacks

NASA Astrophysics Data System (ADS)

Aggarwal, Mayank; Nipur, Pallavi

2010-11-01

Mobile Agents are softwares migrating from one node to another to fulfill the task of its owner. The introduction of mobile agents has reduced network latency, network traffic a lot but at the same time it has increased the vulnerability for attacks by malicious hosts. One such attack is `Denial of Service', once the agent is launched it is free to roam without any control of its owner, this on one hand decreases the cost of agent—owner interaction and on the other hand increases the chances of `Denial Of Service'. In Denial Of Service attack the malicious host may deny resources required by the agent and kill the agent, thus the result computed so far is lost and this may happen every time the agent visits any malicious host. In this paper we continued the work done in [10] in which the authors proposed techniques by which owner can detect the malicious host for `Denial Of Service' but they did not covered technique for dynamic routes i.e. where the host or agent initiate migrations to hosts which were not contained in the route composed by the owner. We introduced an algorithm and a model which can be useful for the above purpose.

A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins

PubMed Central

Suryawanshi, Gajendra W.; Hoffmann, Alexander

2015-01-01

Human immunodeficiency virus-1 (HIV-1) employs accessory proteins to evade innate immune responses by neutralizing the anti-viral activity of host restriction factors. Apolipoprotein B mRNA-editing enzyme 3G (APOBEC3G, A3G) and bone marrow stromal cell antigen 2 (BST2) are host resistance factors that potentially inhibit HIV-1 infection. BST2 reduces viral production by tethering budding HIV-1 particles to virus producing cells, while A3G inhibits the reverse transcription (RT) process and induces viral genome hypermutation through cytidine deamination, generating fewer replication competent progeny virus. Two HIV-1 proteins counter these cellular restriction factors: Vpu, which reduces surface BST2, and Vif, which degrades cellular A3G. The contest between these host and viral proteins influences whether HIV-1 infection is established and progresses towards AIDS. In this work, we present an age-structured multi-scale viral dynamics model of in vivo HIV-1 infection. We integrated the intracellular dynamics of anti-viral activity of the host factors and their neutralization by HIV-1 accessory proteins into the virus/cell population dynamics model. We calculate the basic reproductive ratio (Ro) as a function of host-viral protein interaction coefficients, and numerically simulated the multi-scale model to understand HIV-1 dynamics following host factor-induced perturbations. We found that reducing the influence of Vpu triggers a drop in Ro, revealing the impact of BST2 on viral infection control. Reducing Vif’s effect reveals the restrictive efficacy of A3G in blocking RT and in inducing lethal hypermutations, however, neither of these factors alone is sufficient to fully restrict HIV-1 infection. Interestingly, our model further predicts that BST2 and A3G function synergistically, and delineates their relative contribution in limiting HIV-1 infection and disease progression. We provide a robust modeling framework for devising novel combination therapies that target HIV-1 accessory proteins and boost antiviral activity of host factors. PMID:26385832

Recruitment of EB1, a Master Regulator of Microtubule Dynamics, to the Surface of the Theileria annulata Schizont

PubMed Central

Woods, Kerry L.; Theiler, Romina; Mühlemann, Marcus; Segiser, Adrian; Huber, Sandra; Ansari, Hifzur R.; Pain, Arnab; Dobbelaere, Dirk A. E.

2013-01-01

The apicomplexan parasite Theileria annulata transforms infected host cells, inducing uncontrolled proliferation and clonal expansion of the parasitized cell population. Shortly after sporozoite entry into the target cell, the surrounding host cell membrane is dissolved and an array of host cell microtubules (MTs) surrounds the parasite, which develops into the transforming schizont. The latter does not egress to invade and transform other cells. Instead, it remains tethered to host cell MTs and, during mitosis and cytokinesis, engages the cell's astral and central spindle MTs to secure its distribution between the two daughter cells. The molecular mechanism by which the schizont recruits and stabilizes host cell MTs is not known. MT minus ends are mostly anchored in the MT organizing center, while the plus ends explore the cellular space, switching constantly between phases of growth and shrinkage (called dynamic instability). Assuming the plus ends of growing MTs provide the first point of contact with the parasite, we focused on the complex protein machinery associated with these structures. We now report how the schizont recruits end-binding protein 1 (EB1), a central component of the MT plus end protein interaction network and key regulator of host cell MT dynamics. Using a range of in vitro experiments, we demonstrate that T. annulata p104, a polymorphic antigen expressed on the schizont surface, functions as a genuine EB1-binding protein and can recruit EB1 in the absence of any other parasite proteins. Binding strictly depends on a consensus SxIP motif located in a highly disordered C-terminal region of p104. We further show that parasite interaction with host cell EB1 is cell cycle regulated. This is the first description of a pathogen-encoded protein to interact with EB1 via a bona-fide SxIP motif. Our findings provide important new insight into the mode of interaction between Theileria and the host cell cytoskeleton. PMID:23675298

Molecular phylogeny of the bivalve superfamily Galeommatoidea (Heterodonta, Veneroida) reveals dynamic evolution of symbiotic lifestyle and interphylum host switching

PubMed Central

2012-01-01

Background Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, including crustaceans, holothurians, echinoids, cnidarians, sipunculans and echiurans. These symbiotic species exhibit high host specificity, commensal interactions with hosts, and extreme morphological and behavioral adaptations to symbiotic life. Host specialization to various animal groups has likely played an important role in the evolution and diversification of this bivalve group. However, the evolutionary pathway that led to their ecological diversity is not well understood, in part because of their reduced and/or highly modified morphologies that have confounded traditional taxonomy. This study elucidates the taxonomy of the Galeommatoidea and their evolutionary history of symbiotic lifestyle based on a molecular phylogenic analysis of 33 galeommatoidean and five putative galeommatoidean species belonging to 27 genera and three families using two nuclear ribosomal genes (18S and 28S ribosomal DNA) and a nuclear (histone H3) and mitochondrial (cytochrome oxidase subunit I) protein-coding genes. Results Molecular phylogeny recovered six well-supported major clades within Galeommatoidea. Symbiotic species were found in all major clades, whereas free-living species were grouped into two major clades. Species symbiotic with crustaceans, holothurians, sipunculans, and echiurans were each found in multiple major clades, suggesting that host specialization to these animal groups occurred repeatedly in Galeommatoidea. Conclusions Our results suggest that the evolutionary history of host association in Galeommatoidea has been remarkably dynamic, involving frequent host switches between different animal phyla. Such an unusual pattern of dynamic host switching is considered to have resulted from their commensalistic lifestyle, in which they maintain filter-feeding habits even in symbiotic habitats. The results of the molecular phylogenetic analysis did not correspond with the current taxonomic circumscription. Galeommatidae and Lasaeidae were polyphyletic, and Basterotia, which is traditionally assigned to Cyamioidea, formed a monophyletic clade within Galeommatoidea. PMID:22954375

Combined multireference configuration interaction/ molecular dynamics approach for calculating solvatochromic shifts: application to the n(O) --> pi* electronic transition of formaldehyde.

PubMed

Xu, ZongRong; Matsika, Spiridoula

2006-11-02

A combined quantum mechanics/molecular mechanics method is described here for considering the solvatochromic shift of excited states in solution. The quantum mechanical solute is described using high level multireference configuration interaction methods (MRCI), while molecular dynamics is used for obtaining the structure of the solvent around the solute. The electrostatic effect of the solvent is included in the quantum description of the solute in an averaged way. This method is used to study solvent effects on the n(O) --> pi* electronic transition of formaldehyde in aqueous solution. The effects of solute polarization, basis sets, and dynamical correlation on the solvatochromic shift, and on dipole moments, have been investigated.

Computational fluid dynamics - The coming revolution

NASA Technical Reports Server (NTRS)

Graves, R. A., Jr.

1982-01-01

The development of aerodynamic theory is traced from the days of Aristotle to the present, with the next stage in computational fluid dynamics dependent on superspeed computers for flow calculations. Additional attention is given to the history of numerical methods inherent in writing computer codes applicable to viscous and inviscid analyses for complex configurations. The advent of the superconducting Josephson junction is noted to place configurational demands on computer design to avoid limitations imposed by the speed of light, and a Japanese projection of a computer capable of several hundred billion operations/sec is mentioned. The NASA Numerical Aerodynamic Simulator is described, showing capabilities of a billion operations/sec with a memory of 240 million words using existing technology. Near-term advances in fluid dynamics are discussed.

Nonlinear dynamic modeling of a V-shaped metal based thermally driven MEMS actuator for RF switches

NASA Astrophysics Data System (ADS)

Bakri-Kassem, Maher; Dhaouadi, Rached; Arabi, Mohamed; Estahbanati, Shahabeddin V.; Abdel-Rahman, Eihab

2018-05-01

In this paper, we propose a new dynamic model to describe the nonlinear characteristics of a V-shaped (chevron) metallic-based thermally driven MEMS actuator. We developed two models for the thermal actuator with two configurations. The first MEMS configuration has a small tip connected to the shuttle, while the second configuration has a folded spring and a wide beam attached to the shuttle. A detailed finite element model (FEM) and a lumped element model (LEM) are proposed for each configuration to completely characterize the electro-thermal and thermo-mechanical behaviors. The nonlinear resistivity of the polysilicon layer is extracted from the measured current-voltage (I-V) characteristics of the actuator and the simulated corresponding temperatures in the FEM model, knowing the resistivity of the polysilicon at room temperature from the manufacture’s handbook. Both developed models include the nonlinear temperature-dependent material properties. Numerical simulations in comparison with experimental data using a dedicated MEMS test apparatus verify the accuracy of the proposed LEM model to represent the complex dynamics of the thermal MEMS actuator. The LEM and FEM simulation results show an accuracy ranging from a maximum of 13% error down to a minimum of 1.4% error. The actuator with the lower thermal load to air that includes a folded spring (FS), also known as high surface area actuator is compared to the actuator without FS, also known as low surface area actuator, in terms of the I-V characteristics, power consumption, and experimental static and dynamic responses of the tip displacement.

Birds Shed RNA-Viruses According to the Pareto Principle

PubMed Central

Jankowski, Mark D.; Williams, Christopher J.; Fair, Jeanne M.; Owen, Jennifer C.

2013-01-01

A major challenge in disease ecology is to understand the role of individual variation of infection load on disease transmission dynamics and how this influences the evolution of resistance or tolerance mechanisms. Such information will improve our capacity to understand, predict, and mitigate pathogen-associated disease in all organisms. In many host-pathogen systems, particularly macroparasites and sexually transmitted diseases, it has been found that approximately 20% of the population is responsible for approximately 80% of the transmission events. Although host contact rates can account for some of this pattern, pathogen transmission dynamics also depend upon host infectiousness, an area that has received relatively little attention. Therefore, we conducted a meta-analysis of pathogen shedding rates of 24 host (avian) – pathogen (RNA-virus) studies, including 17 bird species and five important zoonotic viruses. We determined that viral count data followed the Weibull distribution, the mean Gini coefficient (an index of inequality) was 0.687 (0.036 SEM), and that 22.0% (0.90 SEM) of the birds shed 80% of the virus across all studies, suggesting an adherence of viral shedding counts to the Pareto Principle. The relative position of a bird in a distribution of viral counts was affected by factors extrinsic to the host, such as exposure to corticosterone and to a lesser extent reduced food availability, but not to intrinsic host factors including age, sex, and migratory status. These data provide a quantitative view of heterogeneous virus shedding in birds that may be used to better parameterize epidemiological models and understand transmission dynamics. PMID:23991129

Gravitational collapse of dark energy field configurations and supermassive black hole formation

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

Jhalani, V.; Kharkwal, H.; Singh, A., E-mail: anupamsingh.iitk@gmail.com

Dark energy is the dominant component of the total energy density of our Universe. The primary interaction of dark energy with the rest of the Universe is gravitational. It is therefore important to understand the gravitational dynamics of dark energy. Since dark energy is a low-energy phenomenon from the perspective of particle physics and field theory, a fundamental approach based on fields in curved space should be sufficient to understand the current dynamics of dark energy. Here, we take a field theory approach to dark energy. We discuss the evolution equations for a generic dark energy field in curved space-timemore » and then discuss the gravitational collapse for dark energy field configurations. We describe the 3 + 1 BSSN formalism to study the gravitational collapse of fields for any general potential for the fields and apply this formalism to models of dark energy motivated by particle physics considerations. We solve the resulting equations for the time evolution of field configurations and the dynamics of space-time. Our results show that gravitational collapse of dark energy field configurations occurs and must be considered in any complete picture of our Universe. We also demonstrate the black hole formation as a result of the gravitational collapse of the dark energy field configurations. The black holes produced by the collapse of dark energy fields are in the supermassive black hole category with the masses of these black holes being comparable to the masses of black holes at the centers of galaxies.« less

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity

PubMed Central

Frickel, Jens; Theodosiou, Loukas

2017-01-01

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus–host and prey–predator) with a more complex three-species system (virus–host–predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host–virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host–virus coevolution in the complex system and that the virus’ effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species. PMID:28973943

Introduced brown trout alter native acanthocephalan infections in native fish.

PubMed

Paterson, Rachel A; Townsend, Colin R; Poulin, Robert; Tompkins, Daniel M

2011-09-01

1. Native parasite acquisition provides introduced species with the potential to modify native host-parasite dynamics by acting as parasite reservoirs (with the 'spillback' of infection increasing the parasite burdens of native hosts) or sinks (with the 'dilution' of infection decreasing the parasite burdens of native hosts) of infection. 2. In New Zealand, negative correlations between the presence of introduced brown trout (Salmo trutta) and native parasite burdens of the native roundhead galaxias (Galaxias anomalus) have been observed, suggesting that parasite dilution is occurring. 3. We used a multiple-scale approach combining field observations, experimental infections and dynamic population modelling to investigate whether native Acanthocephalus galaxii acquisition by brown trout alters host-parasite dynamics in native roundhead galaxias. 4. Field observations demonstrated higher infection intensity in introduced trout than in native galaxias, but only small, immature A. galaxii were present in trout. Experimental infections also demonstrated that A. galaxii does not mature in trout, although parasite establishment and initial growth were similar in the two hosts. Taken together, these results support the hypothesis that trout may serve as an infection sink for the native parasite. 5. However, dynamic population modelling predicts that A. galaxii infections in native galaxias should at most only be slightly reduced by dilution in the presence of trout. Rather, model exploration indicates parasite densities in galaxias are highly sensitive to galaxias predation on infected amphipods, and to relative abundances of galaxias and trout. Hence, trout presence may instead reduce parasite burdens in galaxias by either reducing galaxias density or by altering galaxias foraging behaviour. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

Metapopulation Dynamics of the Mistletoe and Its Host in Savanna Areas with Different Fire Occurrence

PubMed Central

Teodoro, Grazielle Sales; van den Berg, Eduardo; Arruda, Rafael

2013-01-01

Mistletoes are aerial hemiparasitic plants which occupy patches of favorable habitat (host trees) surrounded by unfavorable habitat and may be possibly modeled as a metapopulation. A metapopulation is defined as a subdivided population that persists due to the balance between colonization and extinction in discrete habitat patches. Our aim was to evaluate the dynamics of the mistletoe Psittacanthus robustus and its host Vochysia thyrsoidea in three Brazilian savanna areas using a metapopulation approach. We also evaluated how the differences in terms of fire occurrence affected the dynamic of those populations (two areas burned during the study and one was fire protected). We monitored the populations at six-month intervals. P. robustus population structure and dynamics met the expected criteria for a metapopulation: i) the suitable habitats for the mistletoe occur in discrete patches; (ii) local populations went extinct during the study and (iii) colonization of previously non-occupied patches occurred. The ratio of occupied patches decreased in all areas with time. Local mistletoe populations went extinct due to two different causes: patch extinction in area with no fire and fire killing in the burned areas. In a burned area, the largest decrease of occupied patch ratios occurred due to a fire event that killed the parasites without, however, killing the host trees. The greatest mortality of V. thyrsoidea occurred in the area without fire. In this area, all the dead trees supported mistletoe individuals and no mortality was observed for parasite-free trees. Because P. robustus is a fire sensitive species and V. thyrsoidea is fire tolerant, P. robustus seems to increase host mortality, but its effect is lessened by periodic burning that reduces the parasite loads. PMID:23776554

Host Competence: An Organismal Trait to Integrate Immunology and Epidemiology.

PubMed

Martin, Lynn B; Burgan, S C; Adelman, James S; Gervasi, Stephanie S

2016-12-01

The new fields of ecological immunology and disease ecology have begun to merge, and the classic fields of immunology and epidemiology are beginning to blend with them. This merger is occurring because the integrative study of host-parasite interactions is providing insights into disease in ways that traditional methods have not. With the advent of new tools, mathematical and technological, we could be on the verge of developing a unified theory of infectious disease, one that supersedes the barriers of jargon and tradition. Here we argue that a cornerstone of any such synthesis will be host competence, the propensity of an individual host to generate new infections in other susceptible hosts. In the last few years, the emergence of systems immunology has led to novel insight into how hosts control or eliminate pathogens. Most such efforts have stopped short of considering transmission and the requisite behaviors of infected individuals that mediate it, and few have explicitly incorporated ecological and evolutionary principles. Ultimately though, we expect that the use of a systems immunology perspective will help link suborganismal processes (i.e., health of hosts and selection on genes) to superorganismal outcomes (i.e., community-level disease dynamics and host-parasite coevolution). Recently, physiological regulatory networks (PRNs) were cast as whole-organism regulatory systems that mediate homeostasis and hence link suborganismal processes with the fitness of individuals. Here, we use the PRN construct to develop a roadmap for studying host competence, taking guidance from systems immunology and evolutionary ecology research. We argue that PRN variation underlies heterogeneity in individual host competence and hence host-parasite dynamics. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Architecture and Implementation of OpenPET Firmware and Embedded Software

PubMed Central

Abu-Nimeh, Faisal T.; Ito, Jennifer; Moses, William W.; Peng, Qiyu; Choong, Woon-Seng

2016-01-01

OpenPET is an open source, modular, extendible, and high-performance platform suitable for multi-channel data acquisition and analysis. Due to the flexibility of the hardware, firmware, and software architectures, the platform is capable of interfacing with a wide variety of detector modules not only in medical imaging but also in homeland security applications. Analog signals from radiation detectors share similar characteristics – a pulse whose area is proportional to the deposited energy and whose leading edge is used to extract a timing signal. As a result, a generic design method of the platform is adopted for the hardware, firmware, and software architectures and implementations. The analog front-end is hosted on a module called a Detector Board, where each board can filter, combine, timestamp, and process multiple channels independently. The processed data is formatted and sent through a backplane bus to a module called Support Board, where 1 Support Board can host up to eight Detector Board modules. The data in the Support Board, coming from 8 Detector Board modules, can be aggregated or correlated (if needed) depending on the algorithm implemented or runtime mode selected. It is then sent out to a computer workstation for further processing. The number of channels (detector modules), to be processed, mandates the overall OpenPET System Configuration, which is designed to handle up to 1,024 channels using 16-channel Detector Boards in the Standard System Configuration and 16,384 channels using 32-channel Detector Boards in the Large System Configuration. PMID:27110034

Configuration memory in patchwork dynamics for low-dimensional spin glasses

NASA Astrophysics Data System (ADS)

Yang, Jie; Middleton, A. Alan

2017-12-01

A patchwork method is used to study the dynamics of loss and recovery of an initial configuration in spin glass models in dimensions d =1 and d =2 . The patchwork heuristic is used to accelerate the dynamics to investigate how models might reproduce the remarkable memory effects seen in experiment. Starting from a ground-state configuration computed for one choice of nearest-neighbor spin couplings, the sample is aged up to a given scale under new random couplings, leading to the partial erasure of the original ground state. The couplings are then restored to the original choice and patchwork coarsening is again applied, in order to assess the recovery of the original state. Eventual recovery of the original ground state upon coarsening is seen in two-dimensional Ising spin glasses and one-dimensional clock models, while one-dimensional Ising spin systems neither lose nor gain overlap with the ground state during the recovery stage. The recovery for the two-dimensional Ising spin glasses suggests scaling relations that lead to a recovery length scale that grows as a power of the aging length scale.

Dynamic Spin Rig Upgraded With a Five- Axis-Controlled Three-Magnetic-Bearing Support System With Forward Excitation

NASA Technical Reports Server (NTRS)

Morrison, Carlos R.; Mehmed, Oral

2003-01-01

The NASA Glenn Research Center Dynamic Spin Rig is used for experimental evaluation of vibration analysis methods and dynamic characteristics for rotating systems. Measurements are made while rotors are spun and vibrated in a vacuum chamber. The rig has been upgraded with a new active magnetic bearing rotor support and excitation system. This design is expected to provide operational improvements over the existing rig. The rig will be able to be operated in either the old or new configuration. In the old configuration, two ball bearings support the vertical shaft of the rig, with the test article located between the bearings. Because the bearings operate in a vacuum, lubrication is limited to grease. This limits bearing life and speed. In addition, the old configuration employs two voice-coil electromagnetic shakers to apply oscillatory axial forces or transverse moments to the rotor shaft through a thrust bearing. The excitation amplitudes that can be imparted to the test article with this system are not adequate for components that are highly damped. It is expected that the new design will overcome these limitations.

An Adaptive Scheme for Robot Localization and Mapping with Dynamically Configurable Inter-Beacon Range Measurements

PubMed Central

Torres-González, Arturo; Martinez-de Dios, Jose Ramiro; Ollero, Anibal

2014-01-01

This work is motivated by robot-sensor network cooperation techniques where sensor nodes (beacons) are used as landmarks for range-only (RO) simultaneous localization and mapping (SLAM). This paper presents a RO-SLAM scheme that actuates over the measurement gathering process using mechanisms that dynamically modify the rate and variety of measurements that are integrated in the SLAM filter. It includes a measurement gathering module that can be configured to collect direct robot-beacon and inter-beacon measurements with different inter-beacon depth levels and at different rates. It also includes a supervision module that monitors the SLAM performance and dynamically selects the measurement gathering configuration balancing SLAM accuracy and resource consumption. The proposed scheme has been applied to an extended Kalman filter SLAM with auxiliary particle filters for beacon initialization (PF-EKF SLAM) and validated with experiments performed in the CONET Integrated Testbed. It achieved lower map and robot errors (34% and 14%, respectively) than traditional methods with a lower computational burden (16%) and similar beacon energy consumption. PMID:24776938

An adaptive scheme for robot localization and mapping with dynamically configurable inter-beacon range measurements.

PubMed

Torres-González, Arturo; Martinez-de Dios, Jose Ramiro; Ollero, Anibal

2014-04-25

This work is motivated by robot-sensor network cooperation techniques where sensor nodes (beacons) are used as landmarks for range-only (RO) simultaneous localization and mapping (SLAM). This paper presents a RO-SLAM scheme that actuates over the measurement gathering process using mechanisms that dynamically modify the rate and variety of measurements that are integrated in the SLAM filter. It includes a measurement gathering module that can be configured to collect direct robot-beacon and inter-beacon measurements with different inter-beacon depth levels and at different rates. It also includes a supervision module that monitors the SLAM performance and dynamically selects the measurement gathering configuration balancing SLAM accuracy and resource consumption. The proposed scheme has been applied to an extended Kalman filter SLAM with auxiliary particle filters for beacon initialization (PF-EKF SLAM) and validated with experiments performed in the CONET Integrated Testbed. It achieved lower map and robot errors (34% and 14%, respectively) than traditional methods with a lower computational burden (16%) and similar beacon energy consumption.

On-the-fly form generation and on-line metadata configuration--a clinical data management Web infrastructure in Java.

PubMed

Beck, Peter; Truskaller, Thomas; Rakovac, Ivo; Cadonna, Bruno; Pieber, Thomas R

2006-01-01

In this paper we describe the approach to build a web-based clinical data management infrastructure on top of an entity-attribute-value (EAV) database which provides for flexible definition and extension of clinical data sets as well as efficient data handling and high performance query execution. A "mixed" EAV implementation provides a flexible and configurable data repository and at the same time utilizes the performance advantages of conventional database tables for rarely changing data structures. A dynamically configurable data dictionary contains further information for data validation. The online user interface can also be assembled dynamically. A data transfer object which encapsulates data together with all required metadata is populated by the backend and directly used to dynamically render frontend forms and handle incoming data. The "mixed" EAV model enables flexible definition and modification of clinical data sets while reducing performance drawbacks of pure EAV implementations to a minimum. The system currently is in use in an electronic patient record with focus on flexibility and a quality management application (www.healthgate.at) with high performance requirements.

Detection of timescales in evolving complex systems

PubMed Central

Darst, Richard K.; Granell, Clara; Arenas, Alex; Gómez, Sergio; Saramäki, Jari; Fortunato, Santo

2016-01-01

Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system’s configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system. PMID:28004820

Preliminary report on candidates for AGARD standard aeroelastic configurations for dynamic response

NASA Technical Reports Server (NTRS)

Yates, E. Carson, Jr.

1987-01-01

At the request of the Aeroelasticity Subcommittee of the AGARD Structures and Materials Panel, a survey of member countries has been conducted to seek candidates for a prospective set of standard configurations to be used for comparison of calculated and measured dynamic aeroelastic behavior with emphasis on the transonic speed range. This set is a sequel to that established several years ago for comparisons of calculated and measured aerodynamic pressures and forces. Approximately two dozen people in the United States, and more than three dozen people in the other member countries, were contacted. This preliminary report presents the results of the survey and an analysis of those results along with recommendations for the initial set of standard configurations and for additional experimental work needed to fill significant gaps in the available information.

Development of multi-element active aerodynamics for the formula sae car

NASA Astrophysics Data System (ADS)

Merkel, James Patrick

This thesis focuses on the design, development, and implementation of an active aerodynamics system on 2013 Formula SAE car. The aerodynamics package itself consists of five element front and rear wings as well as an under body diffuser. Five element wings produce significant amounts of drag which is a compromise between the cornering ability of the car and the acceleration capability on straights. The active aerodynamics system allows for the wing angle of attack to dynamically change their configuration on track based on sensory data to optimize the wings for any given scenario. The wings are studied using computational fluid dynamics both in their maximum lift configuration as well as a minimum drag configuration. A control system is then developed using an electro mechanical actuation system to articulate the wings between these two states.

A Bewildering and Dynamic Picture of Exoplanetary Systems Identified by the Kepler Mission (Invited)

NASA Astrophysics Data System (ADS)

Jenkins, J. M.

2013-12-01

Kepler vaulted into the heavens on March 7, 2009, initiating NASA's search for Earth-size planets orbiting Sun-like stars in the habitable zone, where liquid water could exist on a rocky planetary surface. In the 4 years since, a flood of photometric data of unprecedented precision and continuity on more than 190,000 stars has provoked a watershed of 134+ confirmed or validated planets, 3200+ planetary candidates (most sub-Neptune in size and many comparable to or smaller than Earth), and a revolution in asteroseismology and astrophysics. Recent discoveries include Kepler-62 with 5 planets total, of which 2 are in the habitable zone with radii of 1.4 and 1.7 Re. Approximately 500 of the stars in the Kepler survey with planets host multiple transiting planets: 43% of planet candidates have transiting siblings. Many of these multiple transiting planet systems are dynamically packed and are unlikely, therefore, to have formed in situ. These systems experienced strong migration and evolution to arrive at the configurations we observe today, with important implications for the time-variable habitability of these planets over their histories. The half dozen circumbinary transiting planet systems discovered by Kepler to date highlight the dynamic nature of the habitable zone in systems with multiple host stars where the habitable zone may change significantly on timescales commensurate with the orbital period of the binary. While the catalog of circumbinary planets is small at this point, it already possesses at least one example of an exoplanet in the habitable zone. This implies that the majority of habitable zone planets may be circumbinary planets given the high frequency of multiple star systems and the early detection of Kepler-47b. KIC-12557548 is most likely a disintegrating sub-Mercury-sized planet. While it was probably never habitable, it represents a unique example of the dynamic nature of planetary systems. These amazing discoveries challenge our conventional notion of the habitable zone for single stars and static planetary system configurations. This talk will provide an overview of the science results from the Kepler Mission and the work ahead to derive the frequency of Earth-size planets in the habitable zone of solar-like stars from the treasure trove of Kepler data. NASA's quest for exoplanets continues with the Transiting Exoplanet Survey Satellite (TESS) mission, slated for launch in May 2017 by NASA's Explorer Program. TESS will conduct an all- sky transit survey to identify the 1000 best small exoplanets in the solar neighborhood for follow up observations and characterization. TESS's targets will include all F, G, K dwarfs from +4 to +12 magnitude and all M dwarfs known within ~200 light-years. 500,000 target stars will be observed over two years with ~500 square degrees observed continuously for a year in each hemisphere in the James Webb Space Telescopes continuously viewable zones. Since the typical TESS target star is 5 magnitudes brighter than that of Kepler and 10 times closer, TESS discoveries will afford significant opportunities to measure the masses of the exoplanets and to characterize their atmospheres with JWST, ELTs and other exoplanet explorers. TESS' discoveries will raise new questions regarding habitability that will be open to investigation through active efforts to characterize their atmospheres and search for biomarkers. Funding for this mission is provided by NASA's Science Mission Directorate.

Dynamics and Solubility of He and CO 2 in Brine

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

Ho, Tuan Anh; Tenney, Craig M.

2016-09-01

Molecular dynamics simulation was implemented using LAMMPS simulation package (1) to study the diffusivity of He 3 and CO 2 in NaCl aqueous solution. To simulate at infinite dilute gas concentration, we placed one He 3 or CO 2 molecule in an initial simulation box of 24x24x33Å 3 containing 512 water molecules and a certain number of NaCl molecules depending on the concentration. Initial configuration was set up by placing water, NaCl, and gas molecules into different regions in the simulation box. Calculating diffusion coefficient for one He or CO 2 molecule consistently yields poor results. To overcome this, formore » each simulation at specific conditions (i.e., temperature, pressure, and NaCl concentration), we conducted 50 simulations initiated from 50 different configurations. These configurations are obtained by performing the simulation starting from the initial configuration mentioned above in the NVE ensemble (i.e., constant number of particles, volume, and energy). for 100,000 time steps and collecting one configuration every 2,000 times step. The output temperature of this simulation is about 500K. The collected configurations were then equilibrated for 2ns in the NPT ensemble (i.e., constant number of particles, pressure, and temperature) followed by 9ns simulations in the NVT ensemble (i.e., constant number of particles, volume, and temperature). The time step is 1fs for all simulations.« less

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

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

Emerson, Joanne B.; Andrade, Karen; Thomas, Brian C.

The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clusteredmore » regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.« less

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

DOE PAGES

Emerson, Joanne B.; Andrade, Karen; Thomas, Brian C.; ...

2013-01-01

The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clusteredmore » regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.« less

Understanding spin configuration in the geometrically frustrated magnet TbB 4: A resonant soft X-ray scattering study

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

Huang, H.; Jang, H.; Kang, B. Y.

The frustrated magnet has been regarded as a system that could be a promising host material for the quantum spin liquid (QSL). However, it is difficult to determine the spin configuration and the corresponding mechanism in this system, because of its geometrical frustration ( i.e., crystal structure and symmetry). Herein, we systematically investigate one of the geometrically frustrated magnets, the TbB 4 compound. Using resonant soft x-ray scattering (RSXS), we explored its spin configuration, as well as Tb's quadrupole. Comprehensive evaluations of the temperature and photon energy/polarization dependences of the RSXS signals reveal the mechanism of spin reorientation upon coolingmore » down, which is the sophisticated interplay between the Tb spin and the crystal symmetry rather than its orbit (quadrupole). Here, our results and their implications would further shed a light on the search for possible realization of QSL.« less

Understanding spin configuration in the geometrically frustrated magnet TbB 4: A resonant soft X-ray scattering study

DOE PAGES

Huang, H.; Jang, H.; Kang, B. Y.; ...

2018-05-05

The frustrated magnet has been regarded as a system that could be a promising host material for the quantum spin liquid (QSL). However, it is difficult to determine the spin configuration and the corresponding mechanism in this system, because of its geometrical frustration ( i.e., crystal structure and symmetry). Herein, we systematically investigate one of the geometrically frustrated magnets, the TbB 4 compound. Using resonant soft x-ray scattering (RSXS), we explored its spin configuration, as well as Tb's quadrupole. Comprehensive evaluations of the temperature and photon energy/polarization dependences of the RSXS signals reveal the mechanism of spin reorientation upon coolingmore » down, which is the sophisticated interplay between the Tb spin and the crystal symmetry rather than its orbit (quadrupole). Here, our results and their implications would further shed a light on the search for possible realization of QSL.« less

Probing the dynamic reversibility and generation of dynamic combinatorial libraries in the presence of bacterial model oligopeptides as templating guests of tetra-carbohydrazide macrocycles using electrospray mass spectrometry.

PubMed

Nour, Hany F; Islam, Tuhidul; Fernández-Lahore, Marcelo; Kuhnert, Nikolai

2012-12-30

Over the past few decades, bacterial resistance to antibiotics has emerged as a real threat to human health. Accordingly, there is an urgent demand for the development of innovative strategies for discovering new antibiotics. We present the first use of tetra-carbohydrazide cyclophane macrocycles in dynamic combinatorial chemistry (DCC) and molecular recognition as chiral hosts binding oligopeptides, which mimic bacterial cell wall. This study introduces an innovative application of electrospray ionisation time-of-flight mass spectrometry (ESI-TOF MS) to oligopeptides recognition using DCC. A small dynamic library composed of eight functionalised macrocycles has been generated in solution and all members were characterised by ESI-TOF MS. We also probed the dynamic reversibility and mechanism of formation of tetra-carbohydrazide cyclophanes in real-time using ESI-TOF MS. Dynamic reversibility of tetra-carbohydrazide cyclophanes is favored under thermodynamic control. The mechanism of formation of tetra-carbohydrazide cyclophanes involves key dialdehyde intermediates, which have been detected and assigned according to their high-resolution m/z values. Three members of the dynamic library bind efficiently in the gas phase to a selection of oligopeptides, unique to bacteria, allowing observation of host/guest complex ions in the gas phase. We probed the mechanism of the [2+2]-cyclocondensation reaction forming library members, proved dynamic reversibility of tetra-carbohydrazide cyclophanes and showed that complex ions formed between library members and hosts can be observed in the gas phase, allowing the solution of an important problem of biological interest. Copyright © 2012 John Wiley & Sons, Ltd.

Fast Response of the Tropics to an Abrupt Loss of Arctic Sea Ice via Ocean Dynamics

NASA Astrophysics Data System (ADS)

Wang, Kun; Deser, Clara; Sun, Lantao; Tomas, Robert A.

2018-05-01

The role of ocean dynamics in the transient adjustment of the coupled climate system to an abrupt loss of Arctic sea ice is investigated using experiments with Community Climate System Model version 4 in two configurations: a thermodynamic slab mixed layer ocean and a full-depth ocean that includes both dynamics and thermodynamics. Ocean dynamics produce a distinct sea surface temperature warming maximum in the eastern equatorial Pacific, accompanied by an equatorward intensification of the Intertropical Convergence Zone and Hadley Circulation. These tropical responses are established within 25 years of ice loss and contrast markedly with the quasi-steady antisymmetric coupled response in the slab-ocean configuration. A heat budget analysis reveals the importance of anomalous vertical advection tied to a monotonic temperature increase below 200 m for the equatorial sea surface temperature warming maximum in the fully coupled model. Ocean dynamics also rapidly modify the midlatitude atmospheric response to sea ice loss.

Dynamic Stability Testing of the Genesis Sample Return Capsule

NASA Technical Reports Server (NTRS)

Cheatwood, F. McNeil; Winchenbach, Gerald L.; Hathaway, Wayne; Chapman, Gary

2000-01-01

This paper documents a series of free flight tests of a scale model of the Genesis Sample Return Capsule. These tests were conducted in the Aeroballistic Research Facility (ARF), located at Eglin AFB, FL, during April 1999 and were sponsored by NASA Langley Research Center. Because these blunt atmospheric entry shapes tend to experience small angle of attack dynamic instabilities (frequently leading to limit cycle motions), the primary purpose of the present tests was to determine the dynamic stability characteristics of the Genesis configuration. The tests were conducted over a Mach number range of 1.0 to 4.5. The results for this configuration indicate that the models were dynamically unstable at low angles of attack for all Mach numbers tested. At Mach numbers below 2.5, the models were also unstable at the higher angles of attack (above 15 deg), and motion amplitudes of up to 40 deg were experienced. Above Mach 2.5, the models were dynamically stable at the higher angles of attack.

International Space Station Model Correlation Analysis

NASA Technical Reports Server (NTRS)

Laible, Michael R.; Fitzpatrick, Kristin; Hodge, Jennifer; Grygier, Michael

2018-01-01

This paper summarizes the on-orbit structural dynamic data and the related modal analysis, model validation and correlation performed for the International Space Station (ISS) configuration ISS Stage ULF7, 2015 Dedicated Thruster Firing (DTF). The objective of this analysis is to validate and correlate the analytical models used to calculate the ISS internal dynamic loads and compare the 2015 DTF with previous tests. During the ISS configurations under consideration, on-orbit dynamic measurements were collected using the three main ISS instrumentation systems; Internal Wireless Instrumentation System (IWIS), External Wireless Instrumentation System (EWIS) and the Structural Dynamic Measurement System (SDMS). The measurements were recorded during several nominal on-orbit DTF tests on August 18, 2015. Experimental modal analyses were performed on the measured data to extract modal parameters including frequency, damping, and mode shape information. Correlation and comparisons between test and analytical frequencies and mode shapes were performed to assess the accuracy of the analytical models for the configurations under consideration. These mode shapes were also compared to earlier tests. Based on the frequency comparisons, the accuracy of the mathematical models is assessed and model refinement recommendations are given. In particular, results of the first fundamental mode will be discussed, nonlinear results will be shown, and accelerometer placement will be assessed.

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

PubMed Central

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-01-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health. PMID:26213417

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

NASA Astrophysics Data System (ADS)

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-10-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Tq Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health.

Free time minimizers for the three-body problem

NASA Astrophysics Data System (ADS)

Moeckel, Richard; Montgomery, Richard; Sánchez Morgado, Héctor

2018-03-01

Free time minimizers of the action (called "semi-static" solutions by Mañe in International congress on dynamical systems in Montevideo (a tribute to Ricardo Mañé), vol 362, pp 120-131, 1996) play a central role in the theory of weak KAM solutions to the Hamilton-Jacobi equation (Fathi in Weak KAM Theorem in Lagrangian Dynamics Preliminary Version Number 10, 2017). We prove that any solution to Newton's three-body problem which is asymptotic to Lagrange's parabolic homothetic solution is eventually a free time minimizer. Conversely, we prove that every free time minimizer tends to Lagrange's solution, provided the mass ratios lie in a certain large open set of mass ratios. We were inspired by the work of Da Luz and Maderna (Math Proc Camb Philos Soc 156:209-227, 1980) which showed that every free time minimizer for the N-body problem is parabolic and therefore must be asymptotic to the set of central configurations. We exclude being asymptotic to Euler's central configurations by a second variation argument. Central configurations correspond to rest points for the McGehee blown-up dynamics. The large open set of mass ratios are those for which the linearized dynamics at each Euler rest point has a complex eigenvalue.

Dynamic Instability Leading to Increased Interchange Reconnection Rates

NASA Astrophysics Data System (ADS)

Edmondson, J. K.; Antiochos, S. K.; Zurbuchen, T. H.

2008-12-01

Interchange reconnection is widely believed to play an important role in coronal magnetic field dynamics. In this investigation we investigate the 3D dynamics of interchange reconnection by extending the concept of a magnetic null-point to a null-volume, the so-called "acute-cusp field" configuration. The acute-cusp field geometry is characterized by high-beta plasma confined with favorable curvature, surrounded by a low-beta environment. First, we construct an initial translationally-symmetric potential field configuration. This configuration contains the required topological characteristics of four separate flux systems in the perpendicular plane. We then drive the system by a slow, incompressible, uniform flow at the boundary. The resulting evolution is calculated by solving numerically the MHD equations in full 3D Cartesian coordinates using the Adaptively Refined MHD Solver developed at the U.S. Naval Research Laboratory. Field shearing along the topological boundaries changes the shape of the acute-cusp field surface separating the high and low plasma beta regions. An extended, 2D current sheet is generated by the photospheric driving. We discuss the effect of 3D perturbations on the current sheet dynamics and on the rate of the resulting interchange reconnection. Finally, we discuss the implications of our simulations for coronal observations. This work has been supported, in part, by the NASA HTP and SR&T programs.

Switchable Chiral Selection of Aspartic Acids by Dynamic States of Brushite

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

Jiang, Wenge; Pan, Haihua; Zhang, Zhisen

Here, we show the chiral recognition and separation of aspartic acid (Asp) enantiomers by achiral brushite due to the asymmetries of their dynamical steps in its nonequilibrium states. Growing brushite has a higher adsorption affinity to d-Asp, while l-Asp is predominant on the dissolving brushite surface. Microstructural characterization reveals that chiral selection is mainly attributed to brushite [101] steps, which exhibit two different configurations during crystal growth and dissolution, respectively, with each preferring a distinct enantiomer due to this asymmetry. Because these transition step configurations have different stabilities, they subsequently result in asymmetric adsorption. Furthermore, by varying free energy barriersmore » through solution thermodynamic driving force (i.e., supersaturation), the dominant nonequilibrium intermediate states can be switched and chiral selection regulated. This finding highlights that the dynamic steps can be vital for chiral selection, which may provide a potential pathway for chirality generation through the dynamic nature.« less

Switchable Chiral Selection of Aspartic Acids by Dynamic States of Brushite

DOE PAGES

Jiang, Wenge; Pan, Haihua; Zhang, Zhisen; ...

2017-06-15

Here, we show the chiral recognition and separation of aspartic acid (Asp) enantiomers by achiral brushite due to the asymmetries of their dynamical steps in its nonequilibrium states. Growing brushite has a higher adsorption affinity to d-Asp, while l-Asp is predominant on the dissolving brushite surface. Microstructural characterization reveals that chiral selection is mainly attributed to brushite [101] steps, which exhibit two different configurations during crystal growth and dissolution, respectively, with each preferring a distinct enantiomer due to this asymmetry. Because these transition step configurations have different stabilities, they subsequently result in asymmetric adsorption. Furthermore, by varying free energy barriersmore » through solution thermodynamic driving force (i.e., supersaturation), the dominant nonequilibrium intermediate states can be switched and chiral selection regulated. This finding highlights that the dynamic steps can be vital for chiral selection, which may provide a potential pathway for chirality generation through the dynamic nature.« less

Developing, mechanizing and testing of a digital active flutter suppression system for a modified B-52 wind-tunnel model

NASA Technical Reports Server (NTRS)

Matthew, J. R.

1980-01-01

A digital flutter suppression system was developed and mechanized for a significantly modified version of the 1/30-scale B-52E aeroelastic wind tunnel model. A model configuration was identified that produced symmetric and antisymmetric flutter modes that occur at 2873N/sq m (60 psf) dynamic pressure with violent onset. The flutter suppression system, using one trailing edge control surface and the accelerometers on each wing, extended the flutter dynamic pressure of the model beyond the design limit of 4788N/sq m (100 psf). The hardware and software required to implement the flutter suppression system were designed and mechanized using digital computers in a fail-operate configuration. The model equipped with the system was tested in the Transonic Dynamics Tunnel at NASA Langley Research Center and results showed the flutter dynamic pressure of the model was extended beyond 4884N/sq m (102 psf).

A CFD study of complex missile and store configurations in relative motion

NASA Technical Reports Server (NTRS)

Baysal, Oktay

1995-01-01

An investigation was conducted from May 16, 1990 to August 31, 1994 on the development of computational fluid dynamics (CFD) methodologies for complex missiles and the store separation problem. These flowfields involved multiple-component configurations, where at least one of the objects was engaged in relative motion. The two most important issues that had to be addressed were: (1) the unsteadiness of the flowfields (time-accurate and efficient CFD algorithms for the unsteady equations), and (2) the generation of grid systems which would permit multiple and moving bodies in the computational domain (dynamic domain decomposition). The study produced two competing and promising methodologies, and their proof-of-concept cases, which have been reported in the open literature: (1) Unsteady solutions on dynamic, overlapped grids, which may also be perceived as moving, locally-structured grids, and (2) Unsteady solutions on dynamic, unstructured grids.

Stochastic Dynamics through Hierarchically Embedded Markov Chains

NASA Astrophysics Data System (ADS)

Vasconcelos, Vítor V.; Santos, Fernando P.; Santos, Francisco C.; Pacheco, Jorge M.

2017-02-01

Studying dynamical phenomena in finite populations often involves Markov processes of significant mathematical and/or computational complexity, which rapidly becomes prohibitive with increasing population size or an increasing number of individual configuration states. Here, we develop a framework that allows us to define a hierarchy of approximations to the stationary distribution of general systems that can be described as discrete Markov processes with time invariant transition probabilities and (possibly) a large number of states. This results in an efficient method for studying social and biological communities in the presence of stochastic effects—such as mutations in evolutionary dynamics and a random exploration of choices in social systems—including situations where the dynamics encompasses the existence of stable polymorphic configurations, thus overcoming the limitations of existing methods. The present formalism is shown to be general in scope, widely applicable, and of relevance to a variety of interdisciplinary problems.

Stochastic Dynamics through Hierarchically Embedded Markov Chains.

PubMed

Vasconcelos, Vítor V; Santos, Fernando P; Santos, Francisco C; Pacheco, Jorge M

2017-02-03

Studying dynamical phenomena in finite populations often involves Markov processes of significant mathematical and/or computational complexity, which rapidly becomes prohibitive with increasing population size or an increasing number of individual configuration states. Here, we develop a framework that allows us to define a hierarchy of approximations to the stationary distribution of general systems that can be described as discrete Markov processes with time invariant transition probabilities and (possibly) a large number of states. This results in an efficient method for studying social and biological communities in the presence of stochastic effects-such as mutations in evolutionary dynamics and a random exploration of choices in social systems-including situations where the dynamics encompasses the existence of stable polymorphic configurations, thus overcoming the limitations of existing methods. The present formalism is shown to be general in scope, widely applicable, and of relevance to a variety of interdisciplinary problems.

Dynamical configurations of celestial systems comprised of multiple irregular bodies

NASA Astrophysics Data System (ADS)

Jiang, Yu; Zhang, Yun; Baoyin, Hexi; Li, Junfeng

2016-09-01

This manuscript considers the main features of the nonlinear dynamics of multiple irregular celestial body systems. The gravitational potential, static electric potential, and magnetic potential are considered. Based on the three established potentials, we show that three conservative values exist for this system, including a Jacobi integral. The equilibrium conditions for the system are derived and their stability analyzed. The equilibrium conditions of a celestial system comprised of n irregular bodies are reduced to 12n - 9 equations. The dynamical results are applied to simulate the motion of multiple-asteroid systems. The simulation is useful for the study of the stability of multiple irregular celestial body systems and for the design of spacecraft orbits to triple-asteroid systems discovered in the solar system. The dynamical configurations of the five triple-asteroid systems 45 Eugenia, 87 Sylvia, 93 Minerva, 216 Kleopatra, and 136617 1994CC, and the six-body system 134340 Pluto are calculated and analyzed.

Dynamic defense and network randomization for computer systems

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

Chavez, Adrian R.; Stout, William M. S.; Hamlet, Jason R.

The various technologies presented herein relate to determining a network attack is taking place, and further to adjust one or more network parameters such that the network becomes dynamically configured. A plurality of machine learning algorithms are configured to recognize an active attack pattern. Notification of the attack can be generated, and knowledge gained from the detected attack pattern can be utilized to improve the knowledge of the algorithms to detect a subsequent attack vector(s). Further, network settings and application communications can be dynamically randomized, wherein artificial diversity converts control systems into moving targets that help mitigate the early reconnaissancemore » stages of an attack. An attack(s) based upon a known static address(es) of a critical infrastructure network device(s) can be mitigated by the dynamic randomization. Network parameters that can be randomized include IP addresses, application port numbers, paths data packets navigate through the network, application randomization, etc.« less

Bacterial Serine/Threonine Protein Kinases in Host-Pathogen Interactions*

PubMed Central

Canova, Marc J.; Molle, Virginie

2014-01-01

In bacterial pathogenesis, monitoring and adapting to the dynamically changing environment in the host and an ability to disrupt host immune responses are critical. The virulence determinants of pathogenic bacteria include the sensor/signaling proteins of the serine/threonine protein kinase (STPK) family that have a dual role of sensing the environment and subverting specific host defense processes. STPKs can sense a wide range of signals and coordinate multiple cellular processes to mount an appropriate response. Here, we review some of the well studied bacterial STPKs that are essential virulence factors and that modify global host responses during infection. PMID:24554701

Bacterial serine/threonine protein kinases in host-pathogen interactions.

PubMed

Canova, Marc J; Molle, Virginie

2014-04-04

In bacterial pathogenesis, monitoring and adapting to the dynamically changing environment in the host and an ability to disrupt host immune responses are critical. The virulence determinants of pathogenic bacteria include the sensor/signaling proteins of the serine/threonine protein kinase (STPK) family that have a dual role of sensing the environment and subverting specific host defense processes. STPKs can sense a wide range of signals and coordinate multiple cellular processes to mount an appropriate response. Here, we review some of the well studied bacterial STPKs that are essential virulence factors and that modify global host responses during infection.

A systematic investigation of SO2 removal dynamics by coal-based activated cokes: The synergic enhancement effect of hierarchical pore configuration and gas components

NASA Astrophysics Data System (ADS)

Sun, Fei; Gao, Jihui; Liu, Xin; Tang, Xiaofan; Wu, Shaohua

2015-12-01

For the aim to break through the long-term roadblock to porous carbon based SO2 removal technology, typical coal-based activated cokes differing in terms of surface area, pore configuration and surface functional properties, were employed to investigate the SO2 removal dynamics. Among the employed activated cokes, the one with a hierarchically porous structure greatly enhanced the SO2 removal dynamics under the simulated flue gas compositions. More detailedly, SO2 separate adsorption property under normal temperature and pressure evidenced that monolayer SO2 molecules anchoring on micropore surface is the main adsorption pattern. The catalytic oxidation of SO2 follows the Eley-Rideal mechanism by which SO2 was firstly oxidized by molecular oxygen into SO3 which could depart partially to release the active sites for further adsorption. For the role of hierarchical pore configuration, it was proposed that micropores serve as gas adsorption and reaction accommodation, meso-/macropores act as byproduct H2SO4 transport and buffing reservoirs, which may in turn gives rise to the recovery of active sites in micropores and guarantees the continuous proceeding of sulfur-containing species transformation in the micropores. The present results suggest that pore configuration or interconnecting pattern, but not mere surface area or pore volume, should be favourably considered for optimizing heterogeneous gas-solid adsorption and reaction.

Modeling the dynamical interaction between epidemics on overlay networks

NASA Astrophysics Data System (ADS)

Marceau, Vincent; Noël, Pierre-André; Hébert-Dufresne, Laurent; Allard, Antoine; Dubé, Louis J.

2011-08-01

Epidemics seldom occur as isolated phenomena. Typically, two or more viral agents spread within the same host population and may interact dynamically with each other. We present a general model where two viral agents interact via an immunity mechanism as they propagate simultaneously on two networks connecting the same set of nodes. By exploiting a correspondence between the propagation dynamics and a dynamical process performing progressive network generation, we develop an analytical approach that accurately captures the dynamical interaction between epidemics on overlay networks. The formalism allows for overlay networks with arbitrary joint degree distribution and overlap. To illustrate the versatility of our approach, we consider a hypothetical delayed intervention scenario in which an immunizing agent is disseminated in a host population to hinder the propagation of an undesirable agent (e.g., the spread of preventive information in the context of an emerging infectious disease).

Interaction of the branes in the presence of the background fields: The dynamical, nonintersecting, perpendicular, wrapped-fractional configuration

NASA Astrophysics Data System (ADS)

Maghsoodi, Elham; Kamani, Davoud

2017-05-01

We shall obtain the interaction of the Dp1- and Dp2-branes in the toroidal-orbifold space-time Tn × ℝ1,d-n-5 × ℂ2/ℤ 2. The configuration of the branes is nonintersecting, perpendicular, moving-rotating, wrapped-fractional with background fields. For this, we calculate the bosonic boundary state corresponding to a dynamical fractional-wrapped Dp-brane in the presence of the Kalb-Ramond field, a U1 gauge potential and an open string tachyon field. The long-range behavior of the interaction amplitude will be extracted.

Microstructural comparison of the kinematics of discrete and continuum dislocations models

NASA Astrophysics Data System (ADS)

Sandfeld, Stefan; Po, Giacomo

2015-12-01

The Continuum Dislocation Dynamics (CDD) theory and the Discrete Dislocation Dynamics (DDD) method are compared based on concise mathematical formulations of the coarse graining of discrete data. A numerical tool for converting from a discrete to a continuum representation of a given dislocation configuration is developed, which allows to directly compare both simulation approaches based on continuum quantities (e.g. scalar density, geometrically necessary densities, mean curvature). Investigating the evolution of selected dislocation configurations within analytically given velocity fields for both DDD and CDD reveals that CDD contains a surprising number of important microstructural details.

Bacterial pathogen manipulation of host membrane trafficking.

PubMed

Asrat, Seblewongel; de Jesús, Dennise A; Hempstead, Andrew D; Ramabhadran, Vinay; Isberg, Ralph R

2014-01-01

Pathogens use a vast number of strategies to alter host membrane dynamics. Targeting the host membrane machinery is important for the survival and pathogenesis of several extracellular, vacuolar, and cytosolic bacteria. Membrane manipulation promotes bacterial replication while suppressing host responses, allowing the bacterium to thrive in a hostile environment. This review provides a comprehensive summary of various strategies used by both extracellular and intracellular bacteria to hijack host membrane trafficking machinery. We start with mechanisms used by bacteria to alter the plasma membrane, delve into the hijacking of various vesicle trafficking pathways, and conclude by summarizing bacterial adaptation to host immune responses. Understanding bacterial manipulation of host membrane trafficking provides insights into bacterial pathogenesis and uncovers the molecular mechanisms behind various processes within a eukaryotic cell.

Consequences of Landscape Fragmentation on Lyme Disease Risk: A Cellular Automata Approach

PubMed Central

Li, Sen; Hartemink, Nienke; Speybroeck, Niko; Vanwambeke, Sophie O.

2012-01-01

The abundance of infected Ixodid ticks is an important component of human risk of Lyme disease, and various empirical studies have shown that this is associated, at least in part, to landscape fragmentation. In this study, we aimed at exploring how varying woodland fragmentation patterns affect the risk of Lyme disease, through infected tick abundance. A cellular automata model was developed, incorporating a heterogeneous landscape with three interactive components: an age-structured tick population, a classical disease transmission function, and hosts. A set of simplifying assumptions were adopted with respect to the study objective and field data limitations. In the model, the landscape influences both tick survival and host movement. The validation of the model was performed with an empirical study. Scenarios of various landscape configurations (focusing on woodland fragmentation) were simulated and compared. Lyme disease risk indices (density and infection prevalence of nymphs) differed considerably between scenarios: (i) the risk could be higher in highly fragmented woodlands, which is supported by a number of recently published empirical studies, and (ii) grassland could reduce the risk in adjacent woodland, which suggests landscape fragmentation studies of zoonotic diseases should not focus on the patch-level woodland patterns only, but also on landscape-level adjacent land cover patterns. Further analysis of the simulation results indicated strong correlations between Lyme disease risk indices and the density, shape and aggregation level of woodland patches. These findings highlight the strong effect of the spatial patterns of local host population and movement on the spatial dynamics of Lyme disease risks, which can be shaped by woodland fragmentation. In conclusion, using a cellular automata approach is beneficial for modelling complex zoonotic transmission systems as it can be combined with either real world landscapes for exploring direct spatial effects or artificial representations for outlining possible empirical investigations. PMID:22761842

Crystal structures and molecular dynamics studies of the inclusion compounds of β-citronellol in β-cyclodextrin, heptakis(2,6-di-O-methyl)-β-cyclodextrin and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin

NASA Astrophysics Data System (ADS)

Fourtaka, Katerina; Christoforides, Elias; Mentzafos, Dimitris; Bethanis, Kostas

2018-06-01

The crystal structures of the inclusion complexes of the β-citronellol (cl) inβ-Cyclodextrin (β-CD), heptakis(2,6-di-O-methyl)-β-Cyclodextrin (DM-β-CD) and heptakis(2,3,6-tri-O-methyl)-β-Cyclodextrin (TM-β-CD) have being investigated by X-ray crystallography. The cl/β-CD inclusion complex crystallizes in the P1space group forming dimers which are arranged along the c-axis according to the Intermediate Channel packing mode. Inside the dimeric host cavity two enantiomeric guest molecules are accommodated. The inclusion complexes of cl/DM-β-CD and cl/TM-β-CD crystallize in the P212121 space group having both 1:1 guest:host stoichiometry, the guest found always with the (-)-cl enantiomeric configuration. The guest is fully encapsulated inside the DM-β-CD host cavity whereas is partially encapsulated in the TM-β-CD which is severely puckered as in all TM-β-CD complexes and its primary side is efficiently blocked by the methoxy groups. The complex units in the case of cl/DM-β-CD pack along the crystallographic a-axis in a head-to-tail manner forming columns of herringbone mode whereas in the case of cl/TM-β-CD are arranged also head-to-tail, parallel to the b-axis, in a screw-channel mode. MD simulations based on the determined crystal structures showed that in a simulated aqueous environment the guest maintains the inclusion mode observed crystallographically in every case. MM/GBSA-calculations used for comparison of the inclusion complexes binding affinity with each other, indicated that the inclusion of β-citronellol in TM-β-CD is less favorable than in β-CD and DM-β-CD.

Floquet topological phases with symmetry in all dimensions

NASA Astrophysics Data System (ADS)

Roy, Rahul; Harper, Fenner

2017-05-01

Dynamical systems may host a number of remarkable symmetry-protected phases that are qualitatively different from their static analogs. In this work, we consider the phase space of symmetry-respecting unitary evolutions in detail and identify several distinct classes of evolution that host dynamical order. Using ideas from group cohomology, we construct a set of interacting Floquet drives that generate dynamical symmetry-protected topological order for each nontrivial cohomology class in every dimension, illustrating our construction with explicit two-dimensional examples. We also identify a set of symmetry-protected Floquet drives that lie outside of the group cohomology construction, and a further class of symmetry-respecting topological drives which host chiral edge modes. We use these special drives to define a notion of phase (stable to a class of local perturbations in the bulk) and the concepts of relative and absolute topological order, which can be applied to many different classes of unitary evolutions. These include fully many-body localized unitary evolutions and time crystals.

A limited host immune range facilitates the creation and maintenance of diversity in parasite virulence

PubMed Central

Best, Alex; Hoyle, Andy

2013-01-01

A vast theoretical literature has explored the evolutionary dynamics of parasite virulence. The classic result from this modelling work is that, assuming a saturating transmission–virulence trade-off, there is a single evolutionary optimum where the parasite optimizes the epidemiological R0. However, there are an increasing number of models that have shown how ecological and epidemiological feedbacks to evolution can instead result in the creation and maintenance of multiple parasite strains. Here, we fully explore one such example, where recovered hosts have a limited ‘immune range’ resulting in partial cross-immunity to parasite strains that they have not previously encountered. Taking an adaptive dynamics approach, we show that, provided this immune range is not too wide, high levels of diversity can evolve and be maintained through multiple branching events. We argue that our model provides a more realistic picture of disease dynamics in vertebrate host populations and may be a key explanatory factor in the high levels of parasite diversity seen in natural systems. PMID:24516712

The role of hyperparasitism in microbial pathogen ecology and evolution.

PubMed

Parratt, Steven R; Laine, Anna-Liisa

2016-08-01

Many micro-organisms employ a parasitic lifestyle and, through their antagonistic interactions with host populations, have major impacts on human, agricultural and natural ecosystems. Most pathogens are likely to host parasites of their own, that is, hyperparasites, but how nested chains of parasites impact on disease dynamics is grossly neglected in the ecological and evolutionary literature. In this minireview we argue that the diversity and dynamics of micro-hyperparasites are an important component of natural host-pathogen systems. We use the current literature from a handful of key systems to show that observed patterns of pathogen virulence and disease dynamics may well be influenced by hyperparasites. Exploring these factors will shed light on many aspects of microbial ecology and disease biology, including resistance-virulence evolution, apparent competition, epidemiology and ecosystem stability. Considering the importance of hyperparasites in natural populations will have applied consequences for the field of biological control and therapeutic science, where hyperparastism is employed as a control mechanism but not necessarily ecologically understood.

Investigating Bacterial-Animal Symbioses with Light Sheet Microscopy

PubMed Central

Taormina, Michael J.; Jemielita, Matthew; Stephens, W. Zac; Burns, Adam R.; Troll, Joshua V.; Parthasarathy, Raghuveer; Guillemin, Karen

2014-01-01

SUMMARY Microbial colonization of the digestive tract is a crucial event in vertebrate development, required for maturation of host immunity and establishment of normal digestive physiology. Advances in genomic, proteomic, and metabolomic technologies are providing a more detailed picture of the constituents of the intestinal habitat, but these approaches lack the spatial and temporal resolution needed to characterize the assembly and dynamics of microbial communities in this complex environment. We report the use of light sheet microscopy to provide high resolution imaging of bacterial colonization of the zebrafish intestine. The methodology allows us to characterize bacterial population dynamics across the entire organ and the behaviors of individual bacterial and host cells throughout the colonization process. The large four-dimensional datasets generated by these imaging approaches require new strategies for image analysis. When integrated with other “omics” datasets, information about the spatial and temporal dynamics of microbial cells within the vertebrate intestine will provide new mechanistic insights into how microbial communities assemble and function within hosts. PMID:22983029

Dragging in a Dynamic Geometry Environment through the Lens of Variation

ERIC Educational Resources Information Center

Leung, Allen

2008-01-01

What makes Dynamic Geometry Environment (DGE) a powerful mathematical knowledge acquisition microworld is its ability to visually make explicit the implicit dynamism of thinking about mathematical geometrical concepts. One of DGE's powers is to equip us with the ability to retain the background of a geometrical configuration while we can…

U1108 performance model

NASA Technical Reports Server (NTRS)

Trachta, G.

1976-01-01

A model of Univac 1108 work flow has been developed to assist in performance evaluation studies and configuration planning. Workload profiles and system configurations are parameterized for ease of experimental modification. Outputs include capacity estimates and performance evaluation functions. The U1108 system is conceptualized as a service network; classical queueing theory is used to evaluate network dynamics.

Transonic aeroelastic analysis of launch vehicle configurations. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Filgueirasdeazevedo, Joao Luiz

1988-01-01

A numerical study of the aeroelastic stability of typical launch vehicle configurations in transonic flight is performed. Recent computational fluid dynamics techniques are used to simulate the transonic aerodynamic flow fields, as opposed to relying on experimental data for the unsteady aerodynamic pressures. The flow solver is coupled to an appropriate structural representation of the vehicle. The aerodynamic formulation is based on the thin layer approximation to the Reynolds-Averaged Navier-Stokes equations, where the account for turbulent mixing is done by the two-layer Baldwin and Lomax algebraic eddy viscosity model. The structural-dynamic equations are developed considering free-free flexural vibration of an elongated beam with variable properties and are cast in modal form. Aeroelastic analyses are performed by integrating simultaneously in the two sets of equations. By tracing the growth or decay of a perturbed oscillation, the aeroelastic stability of a given constant configuration can be ascertained. The method is described in detail, and results that indicate its application are presented. Applications include some validation cases for the algorithm developed, as well as the study of configurations known to have presented flutter programs in the past.

Stability analysis of an F/A-18 E/F cable mount m odel

NASA Technical Reports Server (NTRS)

Thompson, Nancy; Farmer, Moses

1994-01-01

A full-span F/A-18 E/F cable mounted wind tunnel model is part of a flutter clearance program at the NASA Langley Transonic Dynamics Tunnel. Parametric analysis of this model using GRUMCBL software was conducted to assess stability for wind tunnel tests. Two configurations of the F/A-18 E/F were examined. The parameters examined were pulley-cable friction, mach number, dynamic pressure, cable geometry, center of gravity location, cable tension, snubbing the model, drag, and test medium. For the nominal cable geometry (Cable Geometry 1), Configuration One was unstable for cases with higher pulley-cable friction coefficients. A new cable geometry (Cable Geometry 3) was determined in which Configuration One was stable for all cases evaluated. Configuration Two with the nominal center of gravity position was found to be unstable for cases with higher pulley-cable friction coefficients; however, the model was stable when the center of gravity moved forward 1/2. The model was tested using the cable mount system during the initial wind tunnel entry and was stable as predicted.

DBMS as a Tool for Project Management

NASA Technical Reports Server (NTRS)

Linder, H.

1984-01-01

Scientific objectives of crustal dynamics are listed as well as the contents of the centralized data information system for the crustal dynamics project. The system provides for project observation schedules, gives project configuration control information and project site information.

Development of numerical methods for overset grids with applications for the integrated Space Shuttle vehicle

NASA Technical Reports Server (NTRS)

Chan, William M.

1995-01-01

Algorithms and computer code developments were performed for the overset grid approach to solving computational fluid dynamics problems. The techniques developed are applicable to compressible Navier-Stokes flow for any general complex configurations. The computer codes developed were tested on different complex configurations with the Space Shuttle launch vehicle configuration as the primary test bed. General, efficient and user-friendly codes were produced for grid generation, flow solution and force and moment computation.

CFD validation experiments at the Lockheed-Georgia Company

NASA Technical Reports Server (NTRS)

Malone, John B.; Thomas, Andrew S. W.

1987-01-01

Information is given in viewgraph form on computational fluid dynamics (CFD) validation experiments at the Lockheed-Georgia Company. Topics covered include validation experiments on a generic fighter configuration, a transport configuration, and a generic hypersonic vehicle configuration; computational procedures; surface and pressure measurements on wings; laser velocimeter measurements of a multi-element airfoil system; the flowfield around a stiffened airfoil; laser velocimeter surveys of a circulation control wing; circulation control for high lift; and high angle of attack aerodynamic evaluations.

Microbiome dynamics of human epidermis following skin barrier disruption

PubMed Central

2012-01-01

Background Recent advances in sequencing technologies have enabled metagenomic analyses of many human body sites. Several studies have catalogued the composition of bacterial communities of the surface of human skin, mostly under static conditions in healthy volunteers. Skin injury will disturb the cutaneous homeostasis of the host tissue and its commensal microbiota, but the dynamics of this process have not been studied before. Here we analyzed the microbiota of the surface layer and the deeper layers of the stratum corneum of normal skin, and we investigated the dynamics of recolonization of skin microbiota following skin barrier disruption by tape stripping as a model of superficial injury. Results We observed gender differences in microbiota composition and showed that bacteria are not uniformly distributed in the stratum corneum. Phylogenetic distance analysis was employed to follow microbiota development during recolonization of injured skin. Surprisingly, the developing neo-microbiome at day 14 was more similar to that of the deeper stratum corneum layers than to the initial surface microbiome. In addition, we also observed variation in the host response towards superficial injury as assessed by the induction of antimicrobial protein expression in epidermal keratinocytes. Conclusions We suggest that the microbiome of the deeper layers, rather than that of the superficial skin layer, may be regarded as the host indigenous microbiome. Characterization of the skin microbiome under dynamic conditions, and the ensuing response of the microbial community and host tissue, will shed further light on the complex interaction between resident bacteria and epidermis. PMID:23153041

Assured crew return vehicle post landing configuration design and test

NASA Technical Reports Server (NTRS)

1992-01-01

The 1991-1992 senior Mechanical and Aerospace Engineering Design class continued work on the post landing configurations for the Assured Crew Return Vehicle (ACRV) and the Emergency Egress Couch (EEC). The ACRV will be permanently docked to Space Station Freedom fulfilling NASA's commitment of Assured Crew Return Capability in the event of an accident or illness aboard Space Station Freedom. The EEC provides medical support and a transportation surface for an incapacitated crew member. The objective of the projects was to give the ACRV Project Office data to feed into their feasibility studies. Four design teams were given the task of developing models with dynamically and geometrically scaled characteristics. Groups one and two combined efforts to design a one-fifth scale model for the Apollo Command Module derivative, an on-board flotation system, and a lift attachment point system. This model was designed to test the feasibility of a rigid flotation and stabilization system and to determine the dynamics associated with lifting the vehicle during retrieval. However, due to priorities, it was not built. Group three designed a one-fifth scale model of the Johnson Space Center (JSC) benchmark configuration, the Station Crew Return Alternative Module (SCRAM) with a lift attachment point system. This model helped to determine the flotation and lifting characteristics of the SCRAM configuration. Group four designed a full scale EEC with changeable geometric and geometric and dynamic characteristics. This model provided data on the geometric characteristics of the EEC and on the placement of the CG and moment of inertia. It also gave the helicopter rescue personnel direct input to the feasibility study. Section 1 describes in detail the design of a one-fifth scale model of the Apollo Command Module Derivative (ACMD) ACRV. The objective of the ACMD Configuration Model Team was to use geometric and dynamic constraints to design a one-fifth scale working model of the Apollo Command Module Derivative (ACMD) configuration with a Lift Attachment Point (LAP) System. This model was required to incorporate a rigidly mounted flotation system and the egress system designed the previous academic year. The LAP system was to be used to determine the dynamic effects of locating the lifting points at different locations on the vehicle. The team was then to build and test the model; however, due to priorities, this did not occur. To better simulate the ACMD after a water landing, the nose cone section was removed and the deck area exposed. The areas researched during the design process were construction, center of gravity and moment of inertia, and lift attachment points.

Low-speed longitudinal and lateral-directional aerodynamic characteristics of the X-31 configuration

NASA Technical Reports Server (NTRS)

Banks, Daniel W.; Gatlin, Gregory M.; Paulson, John W., Jr.

1992-01-01

An experimental investigation of a 19 pct. scale model of the X-31 configuration was completed in the Langley 14 x 22 Foot Subsonic Tunnel. This study was performed to determine the static low speed aerodynamic characteristics of the basic configuration over a large range of angle of attack and sideslip and to study the effects of strakes, leading-edge extensions (wing-body strakes), nose booms, speed-brake deployment, and inlet configurations. The ultimate purpose was to optimize the configuration for high angle of attack and maneuvering-flight conditions. The model was tested at angles of attack from -5 to 67 deg and at sideslip angles from -16 to 16 deg for speeds up to 190 knots (dynamic pressure of 120 psf).

Evolutionary dynamics of nationalism and migration

NASA Astrophysics Data System (ADS)

Barreira da Silva Rocha, André

2013-08-01

I present a dynamic evolutionary game model to address the relation between nationalism against immigrants and assimilation of the latter into the host country culture. I assume a country composed of two different large polymorphic populations, one of native citizens and the other of immigrants. A native citizen may behave nationalistically or may welcome immigrants. Immigrants may have an interest in learning the host country language or not. Evolution is modeled using replicator dynamics (RD). I also account for the presence of an enclave of immigrants in the host country. In the RD, the latter represents the immigrants’ own population effect, which contribution to fitness is controlled using a parameter ρ, 0≤ρ≤1, that represents the enclave size. In line with the empirical literature on migration, the existence of an enclave of immigrants makes assimilation less likely to occur. For large values of ρ, complete assimilation may not occur even if immigrants and natives share very close cultures and norms. Government policy regarding nationalism is modeled both exogenously and endogenously. A single or multiple asymptotically stable states exist for all cases studied but one in which the dynamics is similar to that found in the predator-prey model of Lotka-Volterra for competing species.

Double level selection in a constitutional dynamic library of coordination driven supramolecular polygons.

PubMed

Rancan, Marzio; Tessarolo, Jacopo; Casarin, Maurizio; Zanonato, Pier Luigi; Quici, Silvio; Armelao, Lidia

2014-07-21

A constitutional dynamic library (CDL) of Cu(II) metallo-supramolecular polygons has been studied as a bench test to examine an interesting selection case based on molecular recognition. Sorting of the CDL polygons is achieved through a proper guest that is hosted into the triangular metallo-macrocycle constituent. Two selection mechanisms are observed, a guest induced path and a guest templated self-assembly (virtual library approach). Remarkably, the triangular host can accommodate several guests with a degree of selectivity ranging from ∼1 to ∼10(4) for all possible guest pairs. A double level selection operates: guests drive the CDL toward the triangular polygon, and, at the same time, this is able to pick a specific guest from a set of competitive molecules, according to a selectivity-affinity correlation. Association constants of the host-guest systems have been determined. Guest competition and exchange studies have been analyzed through variable temperature UV-Vis absorption spectroscopy and single crystal X-ray diffraction studies. Molecular structures and electronic properties of the triangular polygon and of the host-guest systems also have been studied by means of all electrons density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations including dispersive contributions. DFT outcomes ultimately indicate the dispersive nature of the host-guest interactions, while TDDFT results allow a thorough assignment of the host and host-guests spectral features.

A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses.

PubMed

Gulbudak, Hayriye; Weitz, Joshua S

2016-09-28

The canonical view of the interactions between viruses and their microbial hosts presumes that changes in host and virus fate requires the initiation of infection of a host by a virus. Infection may lead to the death of the host cell and release of viruses, to the elimination of the viral genome through cellular defence mechanisms or the integration of the viral genome with the host as a chromosomal or extrachromosomal element. Here, we revisit this canonical view, inspired by recent experimental findings in which the majority of target host cells can be induced into a dormant state when exposed to either active or deactivated viruses, even when viruses are present at low relative titre. We propose that both the qualitative phenomena and the quantitative timescales of dormancy induction are consistent with the hypothesis that cellular physiology can be altered by contact on the surface of host cells rather than strictly by infection In order to test this hypothesis, we develop and study a biophysical model of contact-mediated dynamics involving virus particles and target cells. We show how virus particles can catalyse cellular transformations among many cells, even if they ultimately infect only one (or none). We also find that population-scale dormancy is robust to variation in the representation of model dynamics, including cell growth, death and recovery. © 2016 The Author(s).

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.

PubMed

Cardona, Cesar; Lax, Simon; Larsen, Peter; Stephens, Brent; Hampton-Marcell, Jarrad; Edwardson, Christian F; Henry, Chris; Van Bonn, Bill; Gilbert, Jack A

2018-01-01

Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals' human handlers, the aquarium air and water, and the dolphins' food supply. Continuous microbial exposure occurred between all sites, yet each environment maintained a characteristic microbiota, suggesting that the majority of exposure events do not result in colonization. Small changes in water physicochemistry had a significant but weak correlation with change in dolphin-associated bacterial richness but had no influence on phylogenetic diversity. Food and air microbiota were the richest and had the largest conditional influence on other microbiota in the absence of probiotics, but during probiotic administration, food alone had the largest influence on the stability of the dolphin microbiota. Our results suggest that respiratory tract and gastrointestinal epithelium interactions with air- and food-associated microbes had the biggest influence on host-microbiota dynamics, while other interactions, such as skin transmission, played only a minor role. Finally, direct oral stimulation with a foreign exogenous microbial source can have a profound effect on microbial stability. IMPORTANCE These results provide valuable insights into the ecological influence of exogenous microbial exposure, as well as laying the foundation for improving aquarium management practices. By comparing data for dolphins from aquaria that use natural versus artificial seawater, we demonstrate the potential influence of aquarium water disinfection procedures on dolphin microbial dynamics.

Collective intelligence for control of distributed dynamical systems

NASA Astrophysics Data System (ADS)

Wolpert, D. H.; Wheeler, K. R.; Tumer, K.

2000-03-01

We consider the El Farol bar problem, also known as the minority game (W. B. Arthur, The American Economic Review, 84 (1994) 406; D. Challet and Y. C. Zhang, Physica A, 256 (1998) 514). We view it as an instance of the general problem of how to configure the nodal elements of a distributed dynamical system so that they do not "work at cross purposes", in that their collective dynamics avoids frustration and thereby achieves a provided global goal. We summarize a mathematical theory for such configuration applicable when (as in the bar problem) the global goal can be expressed as minimizing a global energy function and the nodes can be expressed as minimizers of local free energy functions. We show that a system designed with that theory performs nearly optimally for the bar problem.