Bat Dynamics of Female Fast Pitch Softball Batters.

ERIC Educational Resources Information Center

Messier, Stephen P.; Owen, Marjorie G.

1984-01-01

Female fast pitch softball batters served in an examination of the dynamic characteristics of the bat during the swing through the use of three-dimensional cinematographic analysis techniques. These results were compared with those from previous studies of baseball batting. Findings are listed. (Author/DF)

Some Dynamics of Authorship.

ERIC Educational Resources Information Center

Dunkin, Mick

1992-01-01

A study of the relationship between faculty publishing and career advancement at the University of Sydney (Australia) controlled for both gender and discipline. Results revealed some previously unseen dynamics of authorship, bringing into question common assumptions about solo vs. multiple authors and order of author names. Some discipline-related…

Multi-fractal characterization of bacterial swimming dynamics: a case study on real and simulated Serratia marcescens

PubMed Central

Bogdan, Paul; Wei, Guopeng; Marculescu, Radu; Zhuang, Jiang; Carlsen, Rika Wright; Sitti, Metin

2017-01-01

To add to the current state of knowledge about bacterial swimming dynamics, in this paper, we study the fractal swimming dynamics of populations of Serratia marcescens bacteria both in vitro and in silico, while accounting for realistic conditions like volume exclusion, chemical interactions, obstacles and distribution of chemoattractant in the environment. While previous research has shown that bacterial motion is non-ergodic, we demonstrate that, besides the non-ergodicity, the bacterial swimming dynamics is multi-fractal in nature. Finally, we demonstrate that the multi-fractal characteristic of bacterial dynamics is strongly affected by bacterial density and chemoattractant concentration. PMID:28804259

Molecular dynamics modeling and simulation of void growth in two dimensions

NASA Astrophysics Data System (ADS)

Chang, H.-J.; Segurado, J.; Rodríguez de la Fuente, O.; Pabón, B. M.; LLorca, J.

2013-10-01

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

HIV Model Parameter Estimates from Interruption Trial Data including Drug Efficacy and Reservoir Dynamics

PubMed Central

Luo, Rutao; Piovoso, Michael J.; Martinez-Picado, Javier; Zurakowski, Ryan

2012-01-01

Mathematical models based on ordinary differential equations (ODE) have had significant impact on understanding HIV disease dynamics and optimizing patient treatment. A model that characterizes the essential disease dynamics can be used for prediction only if the model parameters are identifiable from clinical data. Most previous parameter identification studies for HIV have used sparsely sampled data from the decay phase following the introduction of therapy. In this paper, model parameters are identified from frequently sampled viral-load data taken from ten patients enrolled in the previously published AutoVac HAART interruption study, providing between 69 and 114 viral load measurements from 3–5 phases of viral decay and rebound for each patient. This dataset is considerably larger than those used in previously published parameter estimation studies. Furthermore, the measurements come from two separate experimental conditions, which allows for the direct estimation of drug efficacy and reservoir contribution rates, two parameters that cannot be identified from decay-phase data alone. A Markov-Chain Monte-Carlo method is used to estimate the model parameter values, with initial estimates obtained using nonlinear least-squares methods. The posterior distributions of the parameter estimates are reported and compared for all patients. PMID:22815727

Dynamical mass generation in unquenched QED using the Dyson-Schwinger equations

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

Kızılersü, Ayse; Sizer, Tom; Pennington, Michael R.

We present a comprehensive numerical study of dynamical mass generation for unquenched QED in four dimensions, in the absence of four-fermion interactions, using the Dyson-Schwinger approach. We begin with an overview of previous investigations of criticality in the quenched approximation. To this we add an analysis using a new fermion-antifermion-boson interaction ansatz, the Kizilersu-Pennington (KP) vertex, developed for an unquenched treatment. After surveying criticality in previous unquenched studies, we investigate the performance of the KP vertex in dynamical mass generation using a renormalized fully unquenched system of equations. This we compare with the results for two hybrid vertices incorporating themore » Curtis-Pennington vertex in the fermion equation. We conclude that the KP vertex is as yet incomplete, and its relative gauge-variance is due to its lack of massive transverse components in its design.« less

The promotion of cooperation by the poor in dynamic chicken games

NASA Astrophysics Data System (ADS)

Ito, Hiromu; Katsumata, Yuki; Hasegawa, Eisuke; Yoshimura, Jin

2017-02-01

The evolution of cooperative behavior is one of the most important issues in game theory. Previous studies have shown that cooperation can evolve only under highly limited conditions, and various modifications have been introduced to games to explain the evolution of cooperation. Recently, a utility function basic to game theory was shown to be dependent on current wealth as a conditional (state) variable in a dynamic version of utility theory. Here, we introduce this dynamic utility function to several games. Under certain conditions, poor players exhibit cooperative behavior in two types of chicken games (the hawk-dove game and the snowdrift game) but not in the prisoner’s dilemma game and the stag hunt game. This result indicates that cooperation can be exhibited by the poor in some chicken games. Thus, the evolution of cooperation may not be as limited as has been suggested in previous studies.

Dynamical mass generation in unquenched QED using the Dyson-Schwinger equations

DOE PAGES

Kızılersü, Ayse; Sizer, Tom; Pennington, Michael R.; ...

2015-03-13

We present a comprehensive numerical study of dynamical mass generation for unquenched QED in four dimensions, in the absence of four-fermion interactions, using the Dyson-Schwinger approach. We begin with an overview of previous investigations of criticality in the quenched approximation. To this we add an analysis using a new fermion-antifermion-boson interaction ansatz, the Kizilersu-Pennington (KP) vertex, developed for an unquenched treatment. After surveying criticality in previous unquenched studies, we investigate the performance of the KP vertex in dynamical mass generation using a renormalized fully unquenched system of equations. This we compare with the results for two hybrid vertices incorporating themore » Curtis-Pennington vertex in the fermion equation. We conclude that the KP vertex is as yet incomplete, and its relative gauge-variance is due to its lack of massive transverse components in its design.« less

On the dynamic nature of response criterion in recognition memory: effects of base rate, awareness, and feedback.

PubMed

Rhodes, Matthew G; Jacoby, Larry L

2007-03-01

The authors examined whether participants can shift their criterion for recognition decisions in response to the probability that an item was previously studied. Participants in 3 experiments were given recognition tests in which the probability that an item was studied was correlated with its location during the test. Results from all 3 experiments indicated that participants' response criteria were sensitive to the probability that an item was previously studied and that shifts in criterion were robust. In addition, awareness of the bases for criterion shifts and feedback on performance were key factors contributing to the observed shifts in decision criteria. These data suggest that decision processes can operate in a dynamic fashion, shifting from item to item.

Dynamical effects of dark matter in systems of galaxies

NASA Astrophysics Data System (ADS)

Navarro, J. F.; Garcia Lambas, D.; Sersic, J. L.

1986-06-01

Several N-body experiments were performed in order to simulate the dynamical behavior of systems of galaxies gravitationally dominated by a massive dark background. Mass estimates from the dynamics of the luminous component under the influence of such a background are discussed, assuming a constant dark/luminous mass ratio and plausible physical conditions. Previous studies (Smith, 1980, 1984) about the dependence of the virial theorem mass on the relative distributions of dark and luminous matter (Limber, 1959) are extended. It is found that the observed ratio of the virial theorem mass to luminosity in systems of galaxies of different sizes could be the result of different stages of their postvirialisation evolution as previously suggested by White and Rees (1978) and Barnes (1983). This evolution is mainly the result of the dynamical friction that dark matter exerts on the luminous component. Thus the results give support to the idea that compact groups of galaxies are dynamically more evolved than large clusters, which is expected from the 'hierarchical cluster' picture for the formation of such structures.

Controllability of Free-piston Stirling Engine/linear Alternator Driving a Dynamic Load

NASA Technical Reports Server (NTRS)

Kankam, M. David; Rauch, Jeffrey S.

1994-01-01

This paper presents the dynamic behavior of a Free-Piston Stirling Engine/linear alternator (FPSE/LA) driving a single-phase fractional horse-power induction motor. The controllability and dynamic stability of the system are discussed by means of sensitivity effects of variations in system parameters, engine controller, operating conditions, and mechanical loading on the induction motor. The approach used expands on a combined mechanical and thermodynamic formulation employed in a previous paper. The application of state-space technique and frequency domain analysis enhances understanding of the dynamic interactions. Engine-alternator parametric sensitivity studies, similar to those of the previous paper, are summarized. Detailed discussions are provided for parametric variations which relate to the engine controller and system operating conditions. The results suggest that the controllability of a FPSE-based power system is enhanced by proper operating conditions and built-in controls.

The dynamics of water in hydrated white bread investigated using quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Sjöström, J.; Kargl, F.; Fernandez-Alonso, F.; Swenson, J.

2007-10-01

The dynamics of water in fresh and in rehydrated white bread is studied using quasielastic neutron scattering (QENS). A diffusion constant for water in fresh bread, without temperature gradients and with the use of a non-destructive technique, is presented here for the first time. The self-diffusion constant for fresh bread is estimated to be Ds = 3.8 × 10-10 m2 s-1 and the result agrees well with previous findings for similar systems. It is also suggested that water exhibits a faster dynamics than previously reported in the literature using equilibration of a hydration-level gradient monitored by vibrational spectroscopy. The temperature dependence of the dynamics of low hydration bread is also investigated for T = 280-350 K. The average relaxation time at constant momentum transfer (Q) shows an Arrhenius behavior in the temperature range investigated.

Vibrational wave packet dynamics in NaK: The A 1Σ+ state

NASA Astrophysics Data System (ADS)

Andersson, L. Mauritz; Karlsson, Hans O.; Goscinski, Osvaldo; Berg, Lars-Erik; Beutter, Matthias; Hansson, Tony

1999-02-01

A combined experimental and theoretical study of the vibrational wave packet dynamics for the NaK molecule in the A 1Σ+ state is presented. The experiment utilises a 790 nm one-colour femtosecond pump-probe scheme with detection of a previously not reported dissociation pathway of the 3 1Π+ state, leading to the Na(3p)+K(4s) product channel. The dissociation is suggested to proceed via either collisionally mediated processes or a molecular cascading process via the 4 1Σ+ state, which crosses several states correlating to the Na(3p)+K(4s) limit. Time-dependent quantum mechanical calculations are used for studying the dynamics in detail. Simulations are performed both for 790 nm and for 766 nm, to relate also to earlier studies. The previous interpretations of the probe processes are revised. Inclusion of vibrational and rotational temperature effects are shown to be crucial for explaining the shape of the signal and the vibrational period, and leads to excellent agreement with the experiments.

The Effect of Dynamic Assessment on Adult Learners of Arabic: A Mixed-Method Study at the Defense Language Institute Foreign Language Center

ERIC Educational Resources Information Center

Fahmy, Mohsen M.

2013-01-01

Dynamic assessment (DA) is based on Vygotsky's (1978) sociocultural theory and his Zone of Proximal Development (ZPD). ZPD is the range of abilities bordered by the learner's assisted and independent performances. Previous studies showed promising results for DA in tutoring settings. However, they did not use proficiency-based rubrics to measure…

The dynamic-stimulus advantage of visual symmetry perception.

PubMed

Niimi, Ryosuke; Watanabe, Katsumi; Yokosawa, Kazuhiko

2008-09-01

It has been speculated that visual symmetry perception from dynamic stimuli involves mechanisms different from those for static stimuli. However, previous studies found no evidence that dynamic stimuli lead to active temporal processing and improve symmetry detection. In this study, four psychophysical experiments investigated temporal processing in symmetry perception using both dynamic and static stimulus presentations of dot patterns. In Experiment 1, rapid successive presentations of symmetric patterns (e.g., 16 patterns per 853 ms) produced more accurate discrimination of orientations of symmetry axes than static stimuli (single pattern presented through 853 ms). In Experiments 2-4, we confirmed that the dynamic-stimulus advantage depended upon presentation of a large number of unique patterns within a brief period (853 ms) in the dynamic conditions. Evidently, human vision takes advantage of temporal processing for symmetry perception from dynamic stimuli.

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

Barber, M.N.; Derrida, B.

We study the phase diagram of the two-dimensional anisotropic next-nearest neighbor Ising (ANNNI) model by comparing the time evolution of two distinct spin configurations submitted to the same thermal noise. We clearly se several dynamical transitions between ferromagnetic, paramagnetic, antiphase, and floating phases. These dynamical transitions seem to occur rather close to the transition lines determined previously in the literature.

Periodic Methods for Controlling a Satellite in Formation

DTIC Science & Technology

2002-03-01

5 5. Clohessy - Wiltshire Reference Frame................................................................... 10 6...techniques to study relative position errors within a satellite cluster [19, 24]. The dynamics were based on Clohessy - Wiltshire equations with near...dynamics model by solving the time periodic, linearized system using Floquet Theory. More accurate than the Clohessy - Wiltshire solutions used in previous

Circumpolar variation in periodicity and synchrony among gypsy moth populations

Treesearch

Derek M. Johnson; Andrew M. Liebhold; Ottar N. Bjornstad; Michael L. Mcmanus; Michael L. Mcmanus

2005-01-01

Previous studies or insect dynamics have detected spatial synchrony in intraspecific population dynamics up to, but not exceeding, 1000 km. Oddly, interspecific synchrony has recently been reported at distances well over 1000 km (at continental and circumpolar scales). While the authors implicated climatic effects as the cause for the apparent largescale interspecific...

Microsecond Simulations of DNA and Ion Transport in Nanopores with Novel Ion-Ion and Ion-Nucleotides Effective Potentials

PubMed Central

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei

2014-01-01

We developed a novel scheme based on the Grand-Canonical Monte-Carlo/Brownian Dynamics (GCMC/BD) simulations and have extended it to studies of ion currents across three nanopores with the potential for ssDNA sequencing: solid-state nanopore Si3N4, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the Inverse Monte-Carlo protocol, which maps the relevant ion-nucleotide distribution functions from an all-atom MD simulations. Combined with the previously developed simulation platform for Brownian Dynamic (BD) simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations. PMID:24738152

Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies

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

Costandy, Joseph; Michalis, Vasileios K.; Economou, Ioannis G., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu

2016-03-28

We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies.

Dynamic phase transition in the prisoner's dilemma on a lattice with stochastic modifications

NASA Astrophysics Data System (ADS)

Saif, M. Ali; Gade, Prashant M.

2010-03-01

We present a detailed study of the prisoner's dilemma game with stochastic modifications on a two-dimensional lattice, in the presence of evolutionary dynamics. By very nature of the rules, the cooperators have incentives to cheat and fear being cheated. They may cheat even when this is not dictated by the evolutionary dynamics. We consider two variants here. In each case, the agents mimic the action (cooperation or defection) in the previous time step of the most successful agent in the neighborhood. But over and above this, the fraction p of cooperators spontaneously change their strategy to pure defector at every time step in the first variant. In the second variant, there are no pure cooperators. All cooperators keep defecting with probability p at every time step. In both cases, the system switches from a coexistence state to an all-defector state for higher values of p. We show that the transition between these states unambiguously belongs to the directed percolation universality class in 2 + 1 dimensions. We also study the local persistence. The persistence exponents obtained are higher than the ones obtained in previous studies, underlining their dependence on details of the dynamics.

Nitrogen feedbacks increase future terrestrial ecosystem carbon uptake in an individual-based dynamic vegetation model

NASA Astrophysics Data System (ADS)

Wårlind, D.; Smith, B.; Hickler, T.; Arneth, A.

2014-11-01

Recently a considerable amount of effort has been put into quantifying how interactions of the carbon and nitrogen cycle affect future terrestrial carbon sinks. Dynamic vegetation models, representing the nitrogen cycle with varying degree of complexity, have shown diverging constraints of nitrogen dynamics on future carbon sequestration. In this study, we use LPJ-GUESS, a dynamic vegetation model employing a detailed individual- and patch-based representation of vegetation dynamics, to evaluate how population dynamics and resource competition between plant functional types, combined with nitrogen dynamics, have influenced the terrestrial carbon storage in the past and to investigate how terrestrial carbon and nitrogen dynamics might change in the future (1850 to 2100; one representative "business-as-usual" climate scenario). Single-factor model experiments of CO2 fertilisation and climate change show generally similar directions of the responses of C-N interactions, compared to the C-only version of the model as documented in previous studies using other global models. Under an RCP 8.5 scenario, nitrogen limitation suppresses potential CO2 fertilisation, reducing the cumulative net ecosystem carbon uptake between 1850 and 2100 by 61%, and soil warming-induced increase in nitrogen mineralisation reduces terrestrial carbon loss by 31%. When environmental changes are considered conjointly, carbon sequestration is limited by nitrogen dynamics up to the present. However, during the 21st century, nitrogen dynamics induce a net increase in carbon sequestration, resulting in an overall larger carbon uptake of 17% over the full period. This contrasts with previous results with other global models that have shown an 8 to 37% decrease in carbon uptake relative to modern baseline conditions. Implications for the plausibility of earlier projections of future terrestrial C dynamics based on C-only models are discussed.

Dynamics of Water in Gemini Surfactant-Based Lyotropic Liquid Crystals

DOE PAGES

McDaniel, Jesse G.; Mantha, Sriteja; Yethiraj, Arun

2016-09-26

The dynamics of water confined to nanometer-sized domains is important in a variety of applications ranging from proton exchange membranes to crowding effects in biophysics. In this work we study the dynamics of water in gemini surfactant-based lyotropic liquid crystals (LLCs) using molecular dynamics simulations. These systems have well characterized morphologies, e.g., hexagonal, gyroid, and lamellar, and the surfaces of the confining regions can be controlled by modifying the headgroup of the surfactants. This allows one to study the effect of topology, functionalization, and interfacial curvature on the dynamics of confined water. Through analysis of the translational diffusion and rotationalmore » relaxation we conclude that the hydration level and resulting confinement lengthscale is the predominate determiner of the rates of water dynamics, and other effects, namely surface functionality and curvature, are largely secondary. In conclusion, this novel analysis of the water dynamics in these LLC systems provides an important comparison for previous studies of water dynamics in lipid bilayers and reverse micelles.« less

Colon Stem Cell and Crypt Dynamics Exposed by Cell Lineage Reconstruction

PubMed Central

Itzkovitz, Shalev; Elbaz, Judith; Maruvka, Yosef E.; Segev, Elad; Shlush, Liran I.; Dekel, Nava; Shapiro, Ehud

2011-01-01

Stem cell dynamics in vivo are often being studied by lineage tracing methods. Our laboratory has previously developed a retrospective method for reconstructing cell lineage trees from somatic mutations accumulated in microsatellites. This method was applied here to explore different aspects of stem cell dynamics in the mouse colon without the use of stem cell markers. We first demonstrated the reliability of our method for the study of stem cells by confirming previously established facts, and then we addressed open questions. Our findings confirmed that colon crypts are monoclonal and that, throughout adulthood, the process of monoclonal conversion plays a major role in the maintenance of crypts. The absence of immortal strand mechanism in crypts stem cells was validated by the age-dependent accumulation of microsatellite mutations. In addition, we confirmed the positive correlation between physical and lineage proximity of crypts, by showing that the colon is separated into small domains that share a common ancestor. We gained new data demonstrating that colon epithelium is clustered separately from hematopoietic and other cell types, indicating that the colon is constituted of few progenitors and ruling out significant renewal of colonic epithelium from hematopoietic cells during adulthood. Overall, our study demonstrates the reliability of cell lineage reconstruction for the study of stem cell dynamics, and it further addresses open questions in colon stem cells. In addition, this method can be applied to study stem cell dynamics in other systems. PMID:21829376

Effectiveness of multi tuned liquid dampers with slat screens for reducing dynamic responses of structures

NASA Astrophysics Data System (ADS)

Nguyen, T. P.; Pham, D. T.; Ngo, K. T.

2018-04-01

Reducing vibration in structures under lateral load always attracts many researchers in during pastime, hence the mainly purpose of paper analyzes effectiveness of multiple-tuned liquid dampers for reducing dynamic responses of structures under ground acceleration of earthquakes. In this study, the multi-tuned liquid damper with slat screens (M-TLDWSS) is considered in detail for analyzing dynamic response of multi-degrees of freedom structure due to earthquake, which is more different previous studies. Then, the general equation of motion of the structure and M-TLDWSS under ground acceleration of earthquake is established based on dynamic balance of principle and solved by numerical method in the time domain. The effects of characteristic parameters of M-TLDWSS on dynamic response of the structure are investigated. The results obtained in this study demonstrate that the M-TLDWSS has significantly effectiveness for reducing dynamic response of the structure.

Neural basis for dynamic updating of object representation in visual working memory.

PubMed

Takahama, Sachiko; Miyauchi, Satoru; Saiki, Jun

2010-02-15

In real world, objects have multiple features and change dynamically. Thus, object representations must satisfy dynamic updating and feature binding. Previous studies have investigated the neural activity of dynamic updating or feature binding alone, but not both simultaneously. We investigated the neural basis of feature-bound object representation in a dynamically updating situation by conducting a multiple object permanence tracking task, which required observers to simultaneously process both the maintenance and dynamic updating of feature-bound objects. Using an event-related design, we separated activities during memory maintenance and change detection. In the search for regions showing selective activation in dynamic updating of feature-bound objects, we identified a network during memory maintenance that was comprised of the inferior precentral sulcus, superior parietal lobule, and middle frontal gyrus. In the change detection period, various prefrontal regions, including the anterior prefrontal cortex, were activated. In updating object representation of dynamically moving objects, the inferior precentral sulcus closely cooperates with a so-called "frontoparietal network", and subregions of the frontoparietal network can be decomposed into those sensitive to spatial updating and feature binding. The anterior prefrontal cortex identifies changes in object representation by comparing memory and perceptual representations rather than maintaining object representations per se, as previously suggested. Copyright 2009 Elsevier Inc. All rights reserved.

Quantifying the influence of previously burned areas on suppression effectiveness and avoided exposure: A case study of the Las Conchas Fire

Treesearch

Matthew P. Thompson; Patrick Freeborn; Jon D. Rieck; Dave Calkin; Julie W. Gilbertson-Day; Mark A. Cochrane; Michael S. Hand

2016-01-01

We present a case study of the Las Conchas Fire (2011) to explore the role of previously burned areas (wildfires and prescribed fires) on suppression effectiveness and avoided exposure. Methodological innovations include characterisation of the joint dynamics of fire growth and suppression activities, development of a fire line effectiveness framework, and...

Anchoring in 4- to 6-Year-Old Children Relates to Predictors of Reading

ERIC Educational Resources Information Center

Banai, Karen; Yifat, Rachel

2012-01-01

Previous studies suggest that anchoring, a short-term dynamic and implicit process that allows individuals to benefit from contextual information embedded in stimulus sequences, might be causally related to reading acquisition. Here we report findings from two experiments in which two previously untested predictions derived from this anchoring…

Cell Surface Mechanochemistry and the Determinants of Bleb Formation, Healing, and Travel Velocity

PubMed Central

Manakova, Kathryn; Yan, Huaming; Lowengrub, John; Allard, Jun

2016-01-01

Blebs are pressure-driven cell protrusions implicated in cellular functions such as cell division, apoptosis, and cell motility, including motility of protease-inhibited cancer cells. Because of their mechanical nature, blebs inform us about general cell-surface mechanics, including membrane dynamics, pressure propagation throughout the cytoplasm, and the architecture and dynamics of the actin cortex. Mathematical models including detailed fluid dynamics have previously been used to understand bleb expansion. Here, we develop mathematical models in two and three dimensions on longer timescales that recapitulate the full bleb life cycle, including both expansion and healing by cortex reformation, in terms of experimentally accessible biophysical parameters such as myosin contractility, osmotic pressure, and turnover of actin and ezrin. The model provides conditions under which blebbing occurs, and naturally gives rise to traveling blebs. The model predicts conditions under which blebs travel or remain stationary, as well as the bleb traveling velocity, a quantity that has remained elusive in previous models. As previous studies have used blebs as reporters of membrane tension and pressure dynamics within the cell, we have used our system to investigate various pressure equilibration models and dynamic, nonuniform membrane tension to account for the shape of a traveling bleb. We also find that traveling blebs tend to expand in all directions unless otherwise constrained. One possible constraint could be provided by spatial heterogeneity in, for example, adhesion density. PMID:27074688

A review on bridge dynamic displacement monitoring using global positioning system and accelerometer

NASA Astrophysics Data System (ADS)

Yunus, Mohd Zulkifli Mohd; Ibrahim, Nuremira; Ahmad, Fatimah Shafinaz

2018-02-01

This paper reviews previous research on bridge dynamic displacement monitoring using Global Positioning System (GPS) and an accelerometer for Structural Health Monitoring (SHM) of bridge. These include the review of the advantages and disadvantages of the measurement as well as the methodology of the measurements used in the recent research study. This review could provide a preliminary decision overview for students or researchers before initiating a research related to the bridge dynamic displacement monitoring.

Memory Dynamics and Decision Making in Younger and Older Adults

ERIC Educational Resources Information Center

Lechuga, M. Teresa; Gomez-Ariza, Carlos J.; Iglesias-Parro, Sergio; Pelegrina, Santiago

2012-01-01

The main aim of this research was to study whether memory dynamics influence older people's choices to the same extent as younger's ones. To do so, we adapted the retrieval-practice paradigm to produce variations in memory accessibility of information on which decisions were made later. Based on previous results, we expected to observe…

The Impact of a Three-Year Teacher Professional Development Course on Quality of Teaching: Strengths and Limitations of the Dynamic Approach

ERIC Educational Resources Information Center

Kyriakides, L.; Christoforidou, M.; Panayiotou, A.; Creemers, B. P. M.

2017-01-01

The dynamic approach (DA) suggests that professional development should be differentiated to meet teachers' individual needs while engaging participants into systematic and guided critical reflection. Previous experimental studies demonstrated that one-year interventions based on the DA have a positive impact on teacher effectiveness. The study…

Assessing the Effect of Spaceflight on the Propensity for Astronauts to Develop Disc Herniation

NASA Technical Reports Server (NTRS)

Feiveson, A.; Mendez, C.; Somers, J.

2015-01-01

A previous study reported that the instantaneous risk of developing a Herniated Nucleus Pulposus (HNP) was higher in astronauts who had flown at least one mission, as compared with those in the corps who had not yet flown. However, the study only analyzed time to HNP after the first mission (if any) and did not account for the possible effects of multiple missions. While many HNPs occurred well into astronauts' careers or in somecases years after retirement, the higher incidence of HNPs relatively soon after completion of space missions appears to indicate that spaceflight may lead to an increased risk of HNP. In addition, when an HNP occurs after spaceflight, is it related to previous spaceflight exposure? The purpose of this study was to investigate whether multiple missions, sex, age, vehicle landing dynamics, and flight duration affect the risk of developing an HNP usinga competing risks model. The outcome of the study will inform the Human System Risk Board assessment of back pain, inform the risk of injury due to dynamic loads, and update the previous dataset, which contained events up to December 31, 2006.

Dynamic Mesh CFD Simulations of Orion Parachute Pendulum Motion During Atmospheric Entry

NASA Technical Reports Server (NTRS)

Halstrom, Logan D.; Schwing, Alan M.; Robinson, Stephen K.

2016-01-01

This paper demonstrates the usage of computational fluid dynamics to study the effects of pendulum motion dynamics of the NASAs Orion Multi-Purpose Crew Vehicle parachute system on the stability of the vehicles atmospheric entry and decent. Significant computational fluid dynamics testing has already been performed at NASAs Johnson Space Center, but this study sought to investigate the effect of bulk motion of the parachute, such as pitching, on the induced aerodynamic forces. Simulations were performed with a moving grid geometry oscillating according to the parameters observed in flight tests. As with the previous simulations, OVERFLOW computational fluid dynamics tool is used with the assumption of rigid, non-permeable geometry. Comparison to parachute wind tunnel tests is included for a preliminary validation of the dynamic mesh model. Results show qualitative differences in the flow fields of the static and dynamic simulations and quantitative differences in the induced aerodynamic forces, suggesting that dynamic mesh modeling of the parachute pendulum motion may uncover additional dynamic effects.

Vowel selection and its effects on perturbation and nonlinear dynamic measures.

PubMed

Maccallum, Julia K; Zhang, Yu; Jiang, Jack J

2011-01-01

Acoustic analysis of voice is typically conducted on recordings of sustained vowel phonation. This study applied perturbation and nonlinear dynamic analyses to the vowels /a/, /i/, and /u/ in order to determine vowel selection effects on analysis. Forty subjects (20 males and 20 females) with normal voices participated in recording. Traditional parameters of fundamental frequency, signal-to-noise ratio, percent jitter, and percent shimmer were calculated for the signals using CSpeech. Nonlinear dynamic parameters of correlation dimension and second-order entropy were also calculated. Perturbation analysis results were largely incongruous in this study and in previous research. Fundamental frequency results corroborated previous work, indicating higher fundamental frequency for /i/ and /u/ and lower fundamental frequency for /a/. Signal-to-noise ratio results showed that /i/ and /u/ have greater harmonic levels than /a/. Results of nonlinear dynamic analysis suggested that more complex activity may be evident in /a/ than in /i/ or /u/. Percent jitter and percent shimmer may not be useful for description of acoustic differences between vowels. Fundamental frequency, signal-to-noise ratio, and nonlinear dynamic parameters may be applied to characterize /a/ as having lower frequency, higher noise, and greater nonlinear components than /i/ and /u/. Copyright © 2010 S. Karger AG, Basel.

Shiga Toxin-Producing Escherichia coli O157 Shedding Dynamics in an Australian Beef Herd

PubMed Central

Ahlstrom, Christina; Muellner, Petra; Lammers, Geraldine; Jones, Meghan; Octavia, Sophie; Lan, Ruiting; Heller, Jane

2017-01-01

Shiga toxin-producing Escherichia coli (STEC) O157 is an important foodborne pathogen that can be transmitted to humans both directly and indirectly from the feces of beef cattle, its primary reservoir. Numerous studies have investigated the shedding dynamics of E. coli O157 by beef cattle; however, the spatiotemporal trends of shedding are still not well understood. Molecular tools can increase the resolution through the use of strain typing to explore transmission dynamics within and between herds and identify strain-specific characteristics that may influence pathogenicity and spread. Previously, the shedding dynamics and molecular diversity, through the use of multilocus variable number of tandem repeat analysis (MLVA) of STEC O157, were separately investigated in an Australian beef herd over a 9-month study period. Variation in shedding was observed over time, and 33 MLVA types were identified. The study presented here combines the two datasets previously published with an aim to clarify the relationship between epidemiological variables and strain types. Three major genetic clusters (GCs) were identified that were significantly associated with the location of the cattle in different paddocks. No significant association between GCs and individual cow was observed. Results from this molecular epidemiological study provide evidence for herd-level clonal replacement over time that may have been triggered by movement to a new paddock. In conclusion, this study has provided further insight into STEC O157 shedding dynamics and pathogen transmission. Knowledge gaps remain regarding the relationship of strain types and the shedding dynamics of STEC O157 by beef cattle that could be further clarified through the use of whole-genome sequencing. PMID:29230401

Coupling fast fluid dynamics and multizone airflow models in Modelica Buildings library to simulate the dynamics of HVAC systems

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

Tian, Wei; Sevilla, Thomas Alonso; Zuo, Wangda

Historically, multizone models are widely used in building airflow and energy performance simulations due to their fast computing speed. However, multizone models assume that the air in a room is well mixed, consequently limiting their application. In specific rooms where this assumption fails, the use of computational fluid dynamics (CFD) models may be an alternative option. Previous research has mainly focused on coupling CFD models and multizone models to study airflow in large spaces. While significant, most of these analyses did not consider the coupled simulation of the building airflow with the building's Heating, Ventilation, and Air-Conditioning (HVAC) systems. Thismore » paper tries to fill the gap by integrating the models for HVAC systems with coupled multizone and CFD simulations for airflows, using the Modelica simul ation platform. To improve the computational efficiency, we incorporated a simplified CFD model named fast fluid dynamics (FFD). We first introduce the data synchronization strategy and implementation in Modelica. Then, we verify the implementation using two case studies involving an isothermal and a non-isothermal flow by comparing model simulations to experiment data. Afterward, we study another three cases that are deemed more realistic. This is done by attaching a variable air volume (VAV) terminal box and a VAV system to previous flows to assess the capability of the models in studying the dynamic control of HVAC systems. Finally, we discuss further research needs on the coupled simulation using the models.« less

Sequence learning in Parkinson's disease: Focusing on action dynamics and the role of dopaminergic medication.

PubMed

Ruitenberg, Marit F L; Duthoo, Wout; Santens, Patrick; Seidler, Rachael D; Notebaert, Wim; Abrahamse, Elger L

2016-12-01

Previous studies on movement sequence learning in Parkinson's disease (PD) have produced mixed results. A possible explanation for the inconsistent findings is that some studies have taken dopaminergic medication into account while others have not. Additionally, in previous studies the response modalities did not allow for an investigation of the action dynamics of sequential movements as they unfold over time. In the current study we investigated sequence learning in PD by specifically considering the role of medication status in a sequence learning task where mouse movements were performed. The focus on mouse movements allowed us to examine the action dynamics of sequential movement in terms of initiation time, movement time, movement accuracy, and velocity. PD patients performed the sequence learning task once on their regular medication, and once after overnight withdrawal from their medication. Results showed that sequence learning as reflected in initiation times was impaired when PD patients performed the task ON medication compared to OFF medication. In contrast, sequence learning as reflected in the accuracy of movement trajectories was enhanced when performing the task ON compared to OFF medication. Our findings suggest that while medication enhances execution processes of movement sequence learning, it may at the same time impair planning processes that precede actual execution. Overall, the current study extends earlier findings on movement sequence learning in PD by differentiating between various components of performance, and further refines previous dopamine overdose effects in sequence learning. Copyright © 2016 Elsevier Ltd. All rights reserved.

Medial surface dynamics of an in vivo canine vocal fold during phonation

NASA Astrophysics Data System (ADS)

Döllinger, Michael; Berry, David A.; Berke, Gerald S.

2005-05-01

Quantitative measurement of the medial surface dynamics of the vocal folds is important for understanding how sound is generated within the larynx. Building upon previous excised hemilarynx studies, the present study extended the hemilarynx methodology to the in vivo canine larynx. Through use of an in vivo model, the medial surface dynamics of the vocal fold were examined as a function of active thyroarytenoid muscle contraction. Data were collected using high-speed digital imaging at a sampling frequency of 2000 Hz, and a spatial resolution of 1024×1024 pixels. Chest-like and fry-like vibrations were observed, but could not be distinguished based on the input stimulation current to the recurrent laryngeal nerve. The subglottal pressure did distinguish the registers, as did an estimate of the thyroarytenoid muscle activity. Upon quantification of the three-dimensional motion, the method of Empirical Eigenfunctions was used to extract the underlying modes of vibration, and to investigate mechanisms of sustained oscillation. Results were compared with previous findings from excised larynx experiments and theoretical models. .

A high-speed photography study of cavitation in a dynamically loaded journal bearing

NASA Technical Reports Server (NTRS)

Sun, D. C.; Brewe, D. E.

1990-01-01

The earlier study made by Jacobson and Hamrock on the cavitation of liquid lubricant films in a dynamically loaded journal bearing was repeated with a quartz sleeve, which was more rigid than the Polymethylmethacrylate (PMMA) sleeve used previously. Various improvements of the test rig were made concomitantly so that the experimental errors could be better controlled and assessed. The updated speed photography experiment and its results are described.

A high speed photography study of cavitation in a dynamically loaded journal bearing

NASA Technical Reports Server (NTRS)

Sun, D. C.; Brewe, D. E.

1991-01-01

The earlier study made by Jacobson and Hamrock on the cavitation of liquid lubricant films in a dynamically loaded journal bearing was repeated with a quartz sleeve, which was more rigid than the Polymethylmethacrylate (PMMA) sleeve used previously. Various improvements of the test rig were made concomitantly so that the experimental errors could be better controlled and assessed. The updated speed photography experiment and its results are described.

Differences in the Nature of Body Image Disturbances between Female Obese Individuals with versus without a Comorbid Binge Eating Disorder: An Exploratory Study Including Static and Dynamic Aspects of Body Image

ERIC Educational Resources Information Center

Legenbauer, Tanja; Vocks, Silja; Betz, Sabrina; Puigcerver, Maria Jose Baguena; Benecke, Andrea; Troje, Nikolaus F.; Ruddel, Heinz

2011-01-01

Various components of body image were measured to assess body image disturbances in patients with obesity. To overcome limitations of previous studies, a photo distortion technique and a biological motion distortion device were included to assess static and dynamic aspects of body image. Questionnaires assessed cognitive-affective aspects, bodily…

Emergency Airway Response Team Simulation Training: A Nursing Perspective.

PubMed

Crimlisk, Janet T; Krisciunas, Gintas P; Grillone, Gregory A; Gonzalez, R Mauricio; Winter, Michael R; Griever, Susan C; Fernandes, Eduarda; Medzon, Ron; Blansfield, Joseph S; Blumenthal, Adam

Simulation-based education is an important tool in the training of professionals in the medical field, especially for low-frequency, high-risk events. An interprofessional simulation-based training program was developed to enhance Emergency Airway Response Team (EART) knowledge, team dynamics, and personnel confidence. This quality improvement study evaluated the EART simulation training results of nurse participants. Twenty-four simulation-based classes of 4-hour sessions were conducted during a 12-week period. Sixty-three nurses from the emergency department (ED) and the intensive care units (ICUs) completed the simulation. Participants were evaluated before and after the simulation program with a knowledge-based test and a team dynamics and confidence questionnaire. Additional comparisons were made between ED and ICU nurses and between nurses with previous EART experience and those without previous EART experience. Comparison of presimulation (presim) and postsimulation (postsim) results indicated a statistically significant gain in both team dynamics and confidence and Knowledge Test scores (P < .01). There were no differences in scores between ED and ICU groups in presim or postsim scores; nurses with previous EART experience demonstrated significantly higher presim scores than nurses without EART experience, but there were no differences between these nurse groups at postsim. This project supports the use of simulation training to increase nurses' knowledge, confidence, and team dynamics in an EART response. Importantly, nurses with no previous experience achieved outcome scores similar to nurses who had experience, suggesting that emergency airway simulation is an effective way to train both new and experienced nurses.

How quantizable matter gravitates: A practitioner's guide

NASA Astrophysics Data System (ADS)

Schuller, Frederic P.; Witte, Christof

2014-05-01

We present the practical step-by-step procedure for constructing canonical gravitational dynamics and kinematics directly from any previously specified quantizable classical matter dynamics, and then illustrate the application of this recipe by way of two completely worked case studies. Following the same procedure, any phenomenological proposal for fundamental matter dynamics must be supplemented with a suitable gravity theory providing the coefficients and kinematical interpretation of the matter theory, before any of the two theories can be meaningfully compared to experimental data.

Infraslow Electroencephalographic and Dynamic Resting State Network Activity.

PubMed

Grooms, Joshua K; Thompson, Garth J; Pan, Wen-Ju; Billings, Jacob; Schumacher, Eric H; Epstein, Charles M; Keilholz, Shella D

2017-06-01

A number of studies have linked the blood oxygenation level dependent (BOLD) signal to electroencephalographic (EEG) signals in traditional frequency bands (δ, θ, α, β, and γ), but the relationship between BOLD and its direct frequency correlates in the infraslow band (<1 Hz) has been little studied. Previously, work in rodents showed that infraslow local field potentials play a role in functional connectivity, particularly in the dynamic organization of large-scale networks. To examine the relationship between infraslow activity and network dynamics in humans, direct current (DC) EEG and resting state magnetic resonance imaging data were acquired simultaneously. The DC EEG signals were correlated with the BOLD signal in patterns that resembled resting state networks. Subsequent dynamic analysis showed that the correlation between DC EEG and the BOLD signal varied substantially over time, even within individual subjects. The variation in DC EEG appears to reflect the time-varying contribution of different resting state networks. Furthermore, some of the patterns of DC EEG and BOLD correlation are consistent with previous work demonstrating quasiperiodic spatiotemporal patterns of large-scale network activity in resting state. These findings demonstrate that infraslow electrical activity is linked to BOLD fluctuations in humans and that it may provide a basis for large-scale organization comparable to that observed in animal studies.

Infraslow Electroencephalographic and Dynamic Resting State Network Activity

PubMed Central

Grooms, Joshua K.; Thompson, Garth J.; Pan, Wen-Ju; Billings, Jacob; Schumacher, Eric H.; Epstein, Charles M.

2017-01-01

Abstract A number of studies have linked the blood oxygenation level dependent (BOLD) signal to electroencephalographic (EEG) signals in traditional frequency bands (δ, θ, α, β, and γ), but the relationship between BOLD and its direct frequency correlates in the infraslow band (<1 Hz) has been little studied. Previously, work in rodents showed that infraslow local field potentials play a role in functional connectivity, particularly in the dynamic organization of large-scale networks. To examine the relationship between infraslow activity and network dynamics in humans, direct current (DC) EEG and resting state magnetic resonance imaging data were acquired simultaneously. The DC EEG signals were correlated with the BOLD signal in patterns that resembled resting state networks. Subsequent dynamic analysis showed that the correlation between DC EEG and the BOLD signal varied substantially over time, even within individual subjects. The variation in DC EEG appears to reflect the time-varying contribution of different resting state networks. Furthermore, some of the patterns of DC EEG and BOLD correlation are consistent with previous work demonstrating quasiperiodic spatiotemporal patterns of large-scale network activity in resting state. These findings demonstrate that infraslow electrical activity is linked to BOLD fluctuations in humans and that it may provide a basis for large-scale organization comparable to that observed in animal studies. PMID:28462586

Variation in External Representations as Part of the Classroom Lecture: An Investigation of Virtual Cell Animations in Introductory Photosynthesis Instruction

ERIC Educational Resources Information Center

Goff, Eric E.; Reindl, Katie M.; Johnson, Christina; McClean, Phillip; Offerdahl, Erika G.; Schroeder, Noah L.; White, Alan R.

2017-01-01

The use of external representations (ERs) to introduce concepts in undergraduate biology has become increasingly common. Two of the most prevalent are static images and dynamic animations. While previous studies comparing static images and dynamic animations have resulted in somewhat conflicting findings in regards to learning outcomes, the…

Equivalence of Brownian dynamics and dynamic Monte Carlo simulations in multicomponent colloidal suspensions.

PubMed

Cuetos, Alejandro; Patti, Alessandro

2015-08-01

We propose a simple but powerful theoretical framework to quantitatively compare Brownian dynamics (BD) and dynamic Monte Carlo (DMC) simulations of multicomponent colloidal suspensions. By extending our previous study focusing on monodisperse systems of rodlike colloids, here we generalize the formalism described there to multicomponent colloidal mixtures and validate it by investigating the dynamics in isotropic and liquid crystalline phases containing spherical and rodlike particles. In order to investigate the dynamics of multicomponent colloidal systems by DMC simulations, it is key to determine the elementary time step of each species and establish a unique timescale. This is crucial to consistently study the dynamics of colloidal particles with different geometry. By analyzing the mean-square displacement, the orientation autocorrelation functions, and the self part of the van Hove correlation functions, we show that DMC simulation is a very convenient and reliable technique to describe the stochastic dynamics of any multicomponent colloidal system. Our theoretical formalism can be easily extended to any colloidal system containing size and/or shape polydisperse particles.

Comparative recruitment dynamics of Alewife and Bloater in Lakes Michigan and Huron

USGS Publications Warehouse

Collingsworth, Paris D.; Bunnell, David B.; Madenjian, Charles P.; Riley, Stephen C.

2014-01-01

The predictive power of recruitment models often relies on the identification and quantification of external variables, in addition to stock size. In theory, the identification of climatic, biotic, or demographic influences on reproductive success assists fisheries management by identifying factors that have a direct and reproducible influence on the population dynamics of a target species. More often, models are constructed as one-time studies of a single population whose results are not revisited when further data become available. Here, we present results from stock recruitment models for Alewife Alosa pseudoharengus and Bloater Coregonus hoyi in Lakes Michigan and Huron. The factors that explain variation in Bloater recruitment were remarkably consistent across populations and with previous studies that found Bloater recruitment to be linked to population demographic patterns in Lake Michigan. Conversely, our models were poor predictors of Alewife recruitment in Lake Huron but did show some agreement with previously published models from Lake Michigan. Overall, our results suggest that external predictors of fish recruitment are difficult to discern using traditional fisheries models, and reproducing the results from previous studies may be difficult particularly at low population sizes.

Mathematical multi-scale model of the cardiovascular system including mitral valve dynamics. Application to ischemic mitral insufficiency

PubMed Central

2011-01-01

Background Valve dysfunction is a common cardiovascular pathology. Despite significant clinical research, there is little formal study of how valve dysfunction affects overall circulatory dynamics. Validated models would offer the ability to better understand these dynamics and thus optimize diagnosis, as well as surgical and other interventions. Methods A cardiovascular and circulatory system (CVS) model has already been validated in silico, and in several animal model studies. It accounts for valve dynamics using Heaviside functions to simulate a physiologically accurate "open on pressure, close on flow" law. However, it does not consider real-time valve opening dynamics and therefore does not fully capture valve dysfunction, particularly where the dysfunction involves partial closure. This research describes an updated version of this previous closed-loop CVS model that includes the progressive opening of the mitral valve, and is defined over the full cardiac cycle. Results Simulations of the cardiovascular system with healthy mitral valve are performed, and, the global hemodynamic behaviour is studied compared with previously validated results. The error between resulting pressure-volume (PV) loops of already validated CVS model and the new CVS model that includes the progressive opening of the mitral valve is assessed and remains within typical measurement error and variability. Simulations of ischemic mitral insufficiency are also performed. Pressure-Volume loops, transmitral flow evolution and mitral valve aperture area evolution follow reported measurements in shape, amplitude and trends. Conclusions The resulting cardiovascular system model including mitral valve dynamics provides a foundation for clinical validation and the study of valvular dysfunction in vivo. The overall models and results could readily be generalised to other cardiac valves. PMID:21942971

Comparing the dynamics of skyrmions and superconducting vortices

NASA Astrophysics Data System (ADS)

Olson Reichhardt, C. J.; Lin, S. Z.; Ray, D.; Reichhardt, C.

2014-08-01

Vortices in type-II superconductors have attracted enormous attention as ideal systems in which to study nonequilibrium collective phenomena, since the self-ordering of the vortices competes with quenched disorder and thermal effects. Dynamic effects found in vortex systems include depinning, nonequilibrium phase transitions, creep, structural order-disorder transitions, and melting. Understanding vortex dynamics is also important for applications of superconductors which require the vortices either to remain pinned or to move in a controlled fashion. Recently, topological defects called skyrmions have been realized experimentally in chiral magnets. Here we highlight similarities and differences between skyrmion dynamics and vortex dynamics. Many of the previous ideas and experimental setups that have been applied to superconducting vortices can also be used to study skyrmions. We also discuss some of the differences between the two systems, such as the potentially large contribution of the Magnus force in the skyrmion system that can dramatically alter the dynamics and transport properties.

Macroscopic neural mass model constructed from a current-based network model of spiking neurons.

PubMed

Umehara, Hiroaki; Okada, Masato; Teramae, Jun-Nosuke; Naruse, Yasushi

2017-02-01

Neural mass models (NMMs) are efficient frameworks for describing macroscopic cortical dynamics including electroencephalogram and magnetoencephalogram signals. Originally, these models were formulated on an empirical basis of synaptic dynamics with relatively long time constants. By clarifying the relations between NMMs and the dynamics of microscopic structures such as neurons and synapses, we can better understand cortical and neural mechanisms from a multi-scale perspective. In a previous study, the NMMs were analytically derived by averaging the equations of synaptic dynamics over the neurons in the population and further averaging the equations of the membrane-potential dynamics. However, the averaging of synaptic current assumes that the neuron membrane potentials are nearly time invariant and that they remain at sub-threshold levels to retain the conductance-based model. This approximation limits the NMM to the non-firing state. In the present study, we newly propose a derivation of a NMM by alternatively approximating the synaptic current which is assumed to be independent of the membrane potential, thus adopting a current-based model. Our proposed model releases the constraint of the nearly constant membrane potential. We confirm that the obtained model is reducible to the previous model in the non-firing situation and that it reproduces the temporal mean values and relative power spectrum densities of the average membrane potentials for the spiking neurons. It is further ensured that the existing NMM properly models the averaged dynamics over individual neurons even if they are spiking in the populations.

Dropping vs. Restarting: A Dynamic Analysis of Two Newspaper Subscribing Behaviors.

ERIC Educational Resources Information Center

Zhu, Jian-Hua

In an effort to help describe and explain why people do not read and subscribe to newspapers, a study built on previous research by adding two new contributions: (1) reliance on a four-wave panel data-set rather than on a one-shot survey; and (2) use of a dynamic modeling procedure rather than cross-sectional analysis. The problem with previous…

Parametric model of servo-hydraulic actuator coupled with a nonlinear system: Experimental validation

NASA Astrophysics Data System (ADS)

Maghareh, Amin; Silva, Christian E.; Dyke, Shirley J.

2018-05-01

Hydraulic actuators play a key role in experimental structural dynamics. In a previous study, a physics-based model for a servo-hydraulic actuator coupled with a nonlinear physical system was developed. Later, this dynamical model was transformed into controllable canonical form for position tracking control purposes. For this study, a nonlinear device is designed and fabricated to exhibit various nonlinear force-displacement profiles depending on the initial condition and the type of materials used as replaceable coupons. Using this nonlinear system, the controllable canonical dynamical model is experimentally validated for a servo-hydraulic actuator coupled with a nonlinear physical system.

Investigating the Dynamics of Suicidal Ideation.

PubMed

Hallensleben, Nina; Spangenberg, Lena; Forkmann, Thomas; Rath, Dajana; Hegerl, Ulrich; Kersting, Anette; Kallert, Thomas W; Glaesmer, Heide

2018-01-01

Although the fluctuating nature of suicidal ideation (SI) has been described previously, longitudinal studies investigating the dynamics of SI are scarce. To demonstrate the fluctuation of SI across 6 days and up to 60 measurement points using smartphone-based ecological momentary assessments (EMA). Twenty inpatients with unipolar depression and current and/or lifetime suicidal ideation rated their momentary SI 10 times per day over a 6-day period. Mean squared successive difference (MSSD) was calculated as a measure of variability. Correlations of MSSD with severity of depression, number of previous depressive episodes, and history of suicidal behavior were examined. Individual trajectories of SI are shown to illustrate fluctuation. MSSD values ranged from 0.2 to 21.7. No significant correlations of MSSD with several clinical parameters were found, but there are hints of associations between fluctuation of SI and severity of depression and suicidality. Main limitation of this study is the small sample size leading to low power and probably missing potential effects. Further research with larger samples is necessary to shed light on the dynamics of SI. The results illustrate the dynamic nature and the diversity of trajectories of SI across 6 days in psychiatric inpatients with unipolar depression. Prediction of the fluctuation of SI might be of high clinical relevance. Further research using EMA and sophisticated analyses with larger samples is necessary to shed light on the dynamics of SI.

Pseudo-simple heteroclinic cycles in R4

NASA Astrophysics Data System (ADS)

Chossat, Pascal; Lohse, Alexander; Podvigina, Olga

2018-06-01

We study pseudo-simple heteroclinic cycles for a Γ-equivariant system in R4 with finite Γ ⊂ O(4) , and their nearby dynamics. In particular, in a first step towards a full classification - analogous to that which exists already for the class of simple cycles - we identify all finite subgroups of O(4) admitting pseudo-simple cycles. To this end we introduce a constructive method to build equivariant dynamical systems possessing a robust heteroclinic cycle. Extending a previous study we also investigate the existence of periodic orbits close to a pseudo-simple cycle, which depends on the symmetry groups of equilibria in the cycle. Moreover, we identify subgroups Γ ⊂ O(4) , Γ ⊄ SO(4) , admitting fragmentarily asymptotically stable pseudo-simple heteroclinic cycles. (It has been previously shown that for Γ ⊂ SO(4) pseudo-simple cycles generically are completely unstable.) Finally, we study a generalized heteroclinic cycle, which involves a pseudo-simple cycle as a subset.

Frequency-response identification of XV-15 tilt-rotor aircraft dynamics

NASA Technical Reports Server (NTRS)

Tischler, Mark B.

1987-01-01

The timely design and development of the next generation of tilt-rotor aircraft (JVX) depend heavily on the in-depth understanding of existing XV-15 dynamics and the availability of fully validated simulation models. Previous studies have considered aircraft and simulation trim characteristics, but analyses of basic flight vehicle dynamics were limited to qualitative pilot evaluation. The present study has the following objectives: documentation and evaluation of XV-15 bare-airframe dynamics; comparison of aircraft and simulation responses; and development of a validated transfer-function description of the XV-15 needed for future studies. A nonparametric frequency-response approach is used which does not depend on assumed model order or structure. Transfer-function representations are subsequently derived which fit the frequency responses in the bandwidth of greatest concern for piloted handling-qualities and control-system applications.

On the Interplay between Order Parameter Dynamics and System Parameter Dynamics in Human Perceptual-Cognitive-Behavioral Systems.

PubMed

Frank, T D

2015-04-01

Previous research has demonstrated that perceiving, thinking, and acting are human activities that correspond to self-organized patterns. The emergence of such patterns can be completely described in terms of the dynamics of the pattern amplitudes, which are referred to as order parameters. The patterns emerge at bifurcations points when certain system parameters internal and external to a human agent exceed critical values. At issue is how one might study the order parameter dynamics for sequences of consecutive, emergent perceptual, cognitive, or behavioral activities. In particular, these activities may in turn impact the system parameters that have led to the emergence of the activities in the first place. This interplay between order parameter dynamics and system parameter dynamics is discussed in general and formulated in mathematical terms. Previous work that has made use of this two-tiered framework of order parameter and system parameter dynamics are briefly addressed. As an application, a model for perception under functional fixedness is presented. Finally, it is argued that the phenomena that emerge in this framework and can be observed when human agents perceive, think, and act are just as likely to occur in pattern formation systems of the inanimate world. Consequently, these phenomena do not necessarily have a neurophysiological basis but should instead be understood from the perspective of the theory of self-organization.

Assessing Complex Emergency Management with Clinical Case-Vignettes: A Validation Study

PubMed Central

2015-01-01

Objective To evaluate whether responses to dynamic case-vignettes accurately reflect actual practices in complex emergency situations. We hypothesized that when obstetricians were faced with vignette of emergency situation identical to one they previously managed, they would report the management strategy they actually used. On the other hand, there is no reason to suppose that their response to a vignette based on a source case managed by another obstetrician would be the same as the actual management. Methods A multicenter vignette-based study was used in 7 French maternity units. We chose the example of severe postpartum hemorrhage (PPH) to study the use of case-vignettes for assessing the management of complex situations. We developed dynamic case-vignettes describing incidents of PPH in several steps, using documentation in patient files. Vignettes described the postpartum course and included multiple-choice questions detailing proposed clinical care. Each participating obstetrician was asked to evaluate 4 case-vignettes: 2 directly derived from cases they previously managed and 2 derived from other obstetricians’ cases. We compared the final treatment decision in vignette responses to those documented in the source-case by the overall agreement and the Kappa coefficient, both for the cases the obstetricians previously managed and the cases of others. Results Thirty obstetricians participated. Overall agreement between final treatment decisions in case-vignettes and documented care for cases obstetricians previously managed was 82% (Kappa coefficient: 0.75, 95% CI [0.62–0.88]). Overall agreement between final treatment decisions in case-vignettes and documented care in vignettes derived from other obstetricians’ cases was only 48% (Kappa coefficient: 0.30, 95% CI [0.12–0.48]). Final agreement with documented care was significantly better for cases based on their own previous cases than for others (p<0.001). Conclusions Dynamic case-vignettes accurately reflect actual practices in complex emergency situations. Therefore, they can be used to assess the quality of management in these situations. PMID:26383261

Generating functionals and Gaussian approximations for interruptible delay reactions

NASA Astrophysics Data System (ADS)

Brett, Tobias; Galla, Tobias

2015-10-01

We develop a generating functional description of the dynamics of non-Markovian individual-based systems in which delay reactions can be terminated before completion. This generalizes previous work in which a path-integral approach was applied to dynamics in which delay reactions complete with certainty. We construct a more widely applicable theory, and from it we derive Gaussian approximations of the dynamics, valid in the limit of large, but finite, population sizes. As an application of our theory we study predator-prey models with delay dynamics due to gestation or lag periods to reach the reproductive age. In particular, we focus on the effects of delay on noise-induced cycles.

Manifestations of Dynamical Localization in the Disordered XXZ Spin Chain

NASA Astrophysics Data System (ADS)

Elgart, Alexander; Klein, Abel; Stolz, Günter

2018-04-01

We study disordered XXZ spin chains in the Ising phase exhibiting droplet localization, a single cluster localization property we previously proved for random XXZ spin chains. It holds in an energy interval I near the bottom of the spectrum, known as the droplet spectrum. We establish dynamical manifestations of localization in the energy window I, including non-spreading of information, zero-velocity Lieb-Robinson bounds, and general dynamical clustering. Our results do not rely on knowledge of the dynamical characteristics of the model outside the droplet spectrum. A byproduct of our analysis is that for random XXZ spin chains this droplet localization can happen only inside the droplet spectrum.

Elucidating mineralisation-immobilisation dynamics in a grassland soil using triple 15N labelling in the field combined with a 15N tracing laboratory approach

NASA Astrophysics Data System (ADS)

Kleineidam, Kristina; Müller, Christoph

2017-04-01

Mineralisation is a key N transformation process supplying reactive nitrogen (N) to terrestrial ecosystems. The various soil organic matter fractions contribute to the total mineralisation according to their turnover characteristic. However, the exact mechanism and the gross dynamics of the various processes are not well understood. In this study we investigated the mineralisation-immobilisation dynamics in a grassland soil by a combined field-laboratory study. Eighteen microplots were established at a field site receiving 50 kg N ha-1 as ammonium nitrate. In nine (3 x 3) respective plots the ammonium, or the nitrate, or both moieties were 15N labelled at 60 atom%. Previous studies with this soil showed that rapid turnover occurred and available N would partly be immobilised by the microbial biomass increasing the 15N label of the soil organic nitrogen pool in the field. After one year, soil samples were taken from the 15N treated and the so far non-labelled plots and examined in a laboratory study (for details of the setup see: Müller et al., 2004). While the previously differentially 15N labelled field soils were now supplied with unlabelled ammonium nitrate, the previously unlabelled soils were now treated with either 15N labelled ammonium nitrate similar to the 15N treatments established in the field, resulting in six different 15N treatments in total. The incubation study was carried out over a two week period and data were analysed with the Ntrace model to quantify the simultaneously occurring gross N transformations while optimizing a single parameter set for all six treatments. Thus, the appearance of 15N from the previously labelled soils and the dilution of the 15N in the recently labelled treatments were assumed to be driven by the same processes and activities and were used to constrain the 15N tracing model. This approach allowed us to estimate the individual gross N transformation rates with a much higher accuracy than if only a common triple labelling approach had been used. Here we present detailed gross N turnover dynamics and an improved conceptual model for the mineralisation-immobilisation dynamics in grassland soil. Literature cited Müller, C., Stevens, R.J., Laughlin, R.J., 2004. A 15N tracing model to analyse N transformations in old grassland soil. Soil Biology & Biochemistry 36, 619-632.

Toward the Multivariate Modeling of Achievement, Aptitude, and Personality.

ERIC Educational Resources Information Center

Foshay, Wellesley R.; Misanchuk, Earl R.

1981-01-01

A multivariate investigation of the dynamics of cumulative achievement studied the influence of course grades, personality traits, environmental variables, and previous performance. The latter was the best single predictor of performance. (CJ)

Dynamic balance performance and noncontact lower extremity injury in college football players: an initial study.

PubMed

Butler, Robert J; Lehr, Michael E; Fink, Michael L; Kiesel, Kyle B; Plisky, Phillip J

2013-09-01

Field expedient screening tools that can identify individuals at an elevated risk for injury are needed to minimize time loss in American football players. Previous research has suggested that poor dynamic balance may be associated with an elevated risk for injury in athletes; however, this has yet to be examined in college football players. To determine if dynamic balance deficits are associated with an elevated risk of injury in collegiate football players. It was hypothesized that football players with lower performance and increased asymmetry in dynamic balance would be at an elevated risk for sustaining a noncontact lower extremity injury. Prospective cohort study. Fifty-nine collegiate American football players volunteered for this study. Demographic information, injury history, and dynamic balance testing performance were collected, and noncontact lower extremity injuries were recorded over the course of the season. Receiver operator characteristic curves were calculated based on performance on the Star Excursion Balance Test (SEBT), including composite score and asymmetry, to determine the population-specific risk cut-off point. Relative risk was then calculated based on these variables, as well as previous injury. A cut-off point of 89.6% composite score on the SEBT optimized the sensitivity (100%) and specificity (71.7%). A college football player who scored below 89.6% was 3.5 times more likely to get injured. Poor performance on the SEBT may be related to an increased risk for sustaining a noncontact lower extremity injury over the course of a competitive American football season. College football players should be screened preseason using the SEBT to identify those at an elevated risk for injury based upon dynamic balance performance to implement injury mitigation strategies to this specific subgroup of athletes.

Memory Dynamics in Cross-linked Actin Networks

NASA Astrophysics Data System (ADS)

Scheff, Danielle; Majumdar, Sayantan; Gardel, Margaret

Cells demonstrate the remarkable ability to adapt to mechanical stimuli through rearrangement of the actin cytoskeleton, a cross-linked network of actin filaments. In addition to its importance in cell biology, understanding this mechanical response provides strategies for creation of novel materials. A recent study has demonstrated that applied stress can encode mechanical memory in these networks through changes in network geometry, which gives rise to anisotropic shear response. Under later shear, the network is stiffer in the direction of the previously applied stress. However, the dynamics behind the encoding of this memory are unknown. To address this question, we explore the effect of varying either the rigidity of the cross-linkers or the length of actin filament on the time scales required for both memory encoding and over which it later decays. While previous experiments saw only a long-lived memory, initial results suggest another mechanism where memories relax relatively quickly. Overall, our study is crucial for understanding the process by which an external stress can impact network arrangement and thus the dynamics of memory formation.

Exploiting molecular dynamics in Nested Sampling simulations of small peptides

NASA Astrophysics Data System (ADS)

Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

2016-04-01

Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2.

PubMed

Spellmon, Nicholas; Sun, Xiaonan; Sirinupong, Nualpun; Edwards, Brian; Li, Chunying; Yang, Zhe

2015-01-01

SMYD proteins are an exciting field of study as they are linked to many types of cancer-related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open-closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative correlated inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to by a twisting motion of the C-lobe with respect to the N-lobe and a clamshell-like motion between the lobes. Dynamical network analysis defines possible allosteric paths for the correlated dynamics. There are nine communities in the dynamical network with six in the N-lobe and three in the C-lobe, and the communication between the lobes is mediated by a lobe-bridging β hairpin. This study provides insight into the dynamical nature of SMYD2 and could facilitate better understanding of SMYD2 substrate specificity.

Science: Database Programs and the Study of Seashells.

ERIC Educational Resources Information Center

McCurry, Niki; McCurry, Alan

1992-01-01

Discusses the dynamics and outcomes of an unplanned classroom activity that developed from the integration of the use of spreadsheets with the study of the characteristics of previously collected seashells, specifically their color, size, shape, texture, and any other obvious differences. (JJK)

Estimating Power System Dynamic States Using Extended Kalman Filter

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

Huang, Zhenyu; Schneider, Kevin P.; Nieplocha, Jaroslaw

2014-10-31

Abstract—The state estimation tools which are currently deployed in power system control rooms are based on a steady state assumption. As a result, the suite of operational tools that rely on state estimation results as inputs do not have dynamic information available and their accuracy is compromised. This paper investigates the application of Extended Kalman Filtering techniques for estimating dynamic states in the state estimation process. The new formulated “dynamic state estimation” includes true system dynamics reflected in differential equations, not like previously proposed “dynamic state estimation” which only considers the time-variant snapshots based on steady state modeling. This newmore » dynamic state estimation using Extended Kalman Filter has been successfully tested on a multi-machine system. Sensitivity studies with respect to noise levels, sampling rates, model errors, and parameter errors are presented as well to illustrate the robust performance of the developed dynamic state estimation process.« less

Dynamics of a thermo-responsive microgel colloid near to the glass transition

NASA Astrophysics Data System (ADS)

Di, Xiaojun; Peng, Xiaoguang; McKenna, Gregory B.

2014-02-01

In a previous study, we used diffusing wave spectroscopy (DWS) to investigate the aging signatures of a thermo-sensitive colloidal glass and compared them with those of molecular glasses from the perspective of the Kovacs temperature-jump, volume recovery experiments [X. Di, K. Z. Win, G. B. McKenna, T. Narita, F. Lequeux, S. R. Pullela, and Z. Cheng, Phys. Rev. Lett. 106, 095701 (2011)]. In order to further look into the glassy behavior of colloidal systems, we have synthesized a new core/shell particle with lower temperature sensitivity and studied the aging signatures of concentrated systems, again following Kovacs' protocol. Similar signatures of aging to those observed previously were seen in this new system. Moreover, a systematic study of the temperature dependence of the dynamics of the new system for different weight concentrations was performed and the dynamic fragility index m was determined. We have also explored the use of the properties determined from the DWS measurements to obtain macroscopic rheological parameters - storage modulus G'(ω) and loss modulus G″(ω) - using a generalized Stokes-Einstein approach. The micro-rheological and macro-rheological values are in reasonable agreement.

A multilayer approach for price dynamics in financial markets

NASA Astrophysics Data System (ADS)

Biondo, Alessio Emanuele; Pluchino, Alessandro; Rapisarda, Andrea

2017-02-01

We introduce a new Self-Organized Criticality (SOC) model for simulating price evolution in an artificial financial market, based on a multilayer network of traders. The model also implements, in a quite realistic way with respect to previous studies, the order book dynamics, by considering two assets with variable fundamental prices. Fat tails in the probability distributions of normalized returns are observed, together with other features of real financial markets.

Argumentation Text Construction by Japanese as a Foreign Language Writers: A Dynamic View of Transfer

ERIC Educational Resources Information Center

Rinnert, Carol; Kobauashi, Hiroe; Katayama, Akemi

2015-01-01

This study takes a dynamic view of transfer as reusing and reshaping previous knowledge in new writing contexts to investigate how novice Japanese as a foreign language (JFL) writers draw on knowledge across languages to construct L1 and L2 texts. We analyzed L1 English and L2 Japanese argumentation essays by the same JFL writers (N = 19) and L1…

Development of interatomic potential of Ge(1- x - y )Si x Sn y ternary alloy semiconductors for classical lattice dynamics simulation

NASA Astrophysics Data System (ADS)

Tomita, Motohiro; Ogasawara, Masataka; Terada, Takuya; Watanabe, Takanobu

2018-04-01

We provide the parameters of Stillinger-Weber potentials for GeSiSn ternary mixed systems. These parameters can be used in molecular dynamics (MD) simulations to reproduce phonon properties and thermal conductivities. The phonon dispersion relation is derived from the dynamical structure factor, which is calculated by the space-time Fourier transform of atomic trajectories in an MD simulation. The phonon properties and thermal conductivities of GeSiSn ternary crystals calculated using these parameters mostly reproduced both the findings of previous experiments and earlier calculations made using MD simulations. The atomic composition dependence of these properties in GeSiSn ternary crystals obtained by previous studies (both experimental and theoretical) and the calculated data were almost exactly reproduced by our proposed parameters. Moreover, the results of the MD simulation agree with the previous calculations made using a time-independent phonon Boltzmann transport equation with complicated scattering mechanisms. These scattering mechanisms are very important in complicated nanostructures, as they allow the heat-transfer properties to be more accurately calculated by MD simulations. This work enables us to predict the phonon- and heat-related properties of bulk group IV alloys, especially ternary alloys.

Dynamic adjustments of cognitive control: oscillatory correlates of the conflict adaptation effect.

PubMed

Pastötter, Bernhard; Dreisbach, Gesine; Bäuml, Karl-Heinz T

2013-12-01

It is a prominent idea that cognitive control mediates conflict adaptation, in that response conflict in a previous trial triggers control adjustments that reduce conflict in a current trial. In the present EEG study, we investigated the dynamics of cognitive control in a response-priming task by examining the effects of previous trial conflict on intertrial and current trial oscillatory brain activities, both on the electrode and the source level. Behavioral results showed conflict adaptation effects for RTs and response accuracy. Physiological results showed sustained intertrial effects in left parietal theta power, originating in the left inferior parietal cortex, and midcentral beta power, originating in the left and right (pre)motor cortex. Moreover, physiological analysis revealed a current trial conflict adaptation effect in midfrontal theta power, originating in the ACC. Correlational analyses showed that intertrial effects predicted conflict-induced midfrontal theta power in currently incongruent trials. In addition, conflict adaptation effects in midfrontal theta power and RTs were positively related. Together, these findings point to a dynamic cognitive control system that, as a function of previous trial type, up- and down-regulates attention and preparatory motor activities in anticipation of the next trial.

Autonomous dynamic obstacle avoidance for bacteria-powered microrobots (BPMs) with modified vector field histogram

PubMed Central

Kim, Hoyeon; Cheang, U. Kei

2017-01-01

In order to broaden the use of microrobots in practical fields, autonomous control algorithms such as obstacle avoidance must be further developed. However, most previous studies of microrobots used manual motion control to navigate past tight spaces and obstacles while very few studies demonstrated the use of autonomous motion. In this paper, we demonstrated a dynamic obstacle avoidance algorithm for bacteria-powered microrobots (BPMs) using electric field in fluidic environments. A BPM consists of an artificial body, which is made of SU-8, and a high dense layer of harnessed bacteria. BPMs can be controlled using externally applied electric fields due to the electrokinetic property of bacteria. For developing dynamic obstacle avoidance for BPMs, a kinematic model of BPMs was utilized to prevent collision and a finite element model was used to characteristic the deformation of an electric field near the obstacle walls. In order to avoid fast moving obstacles, we modified our previously static obstacle avoidance approach using a modified vector field histogram (VFH) method. To validate the advanced algorithm in experiments, magnetically controlled moving obstacles were used to intercept the BPMs as the BPMs move from the initial position to final position. The algorithm was able to successfully guide the BPMs to reach their respective goal positions while avoiding the dynamic obstacles. PMID:29020016

A concentrated parameter model for the human cardiovascular system including heart valve dynamics and atrioventricular interaction.

PubMed

Korakianitis, Theodosios; Shi, Yubing

2006-09-01

Numerical modeling of the human cardiovascular system has always been an active research direction since the 19th century. In the past, various simulation models of different complexities were proposed for different research purposes. In this paper, an improved numerical model to study the dynamic function of the human circulation system is proposed. In the development of the mathematical model, the heart chambers are described with a variable elastance model. The systemic and pulmonary loops are described based on the resistance-compliance-inertia concept by considering local effects of flow friction, elasticity of blood vessels and inertia of blood in different segments of the blood vessels. As an advancement from previous models, heart valve dynamics and atrioventricular interaction, including atrial contraction and motion of the annulus fibrosus, are specifically modeled. With these improvements the developed model can predict several important features that were missing in previous numerical models, including regurgitant flow on heart valve closure, the value of E/A velocity ratio in mitral flow, the motion of the annulus fibrosus (called the KG diaphragm pumping action), etc. These features have important clinical meaning and their changes are often related to cardiovascular diseases. Successful simulation of these features enhances the accuracy of simulations of cardiovascular dynamics, and helps in clinical studies of cardiac function.

Dynamic flux balancing elucidates NAD(P)H production as limiting response to furfural inhibition in Saccharomyces cerevisiae.

PubMed

Pornkamol, Unrean; Franzen, Carl J

2015-08-01

Achieving efficient and economical lignocellulose-based bioprocess requires a robust organism tolerant to furfural, a major inhibitory compound present in lignocellulosic hydrolysate. The aim of this study was to develop a model that could generate quantitative descriptions of cell metabolism for elucidating the cell's adaptive response to furfural. Such a modelling tool could provide strategies for the design of more robust cells. A dynamic flux balance (dFBA) model of Saccharomyces cerevisiae was created by coupling a kinetic fermentation model with a previously published genome-scale stoichiometric model. The dFBA model was used for studying intracellular and extracellular flux responses to furfural perturbations under steady state and dynamic conditions. The predicted effects of furfural on dynamic flux profiles agreed well with previously published experimental results. The model showed that the yeast cell adjusts its metabolism in response to furfural challenge by increasing fluxes through the pentose phosphate pathway, TCA cycle, and proline and serine biosynthesis in order to meet the high demand of NAD(P)H cofactors. The model described here can be used to aid in systematic optimization of the yeast, as well as of the fermentation process, for efficient lignocellulosic ethanol production. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Autonomous dynamic obstacle avoidance for bacteria-powered microrobots (BPMs) with modified vector field histogram.

PubMed

Kim, Hoyeon; Cheang, U Kei; Kim, Min Jun

2017-01-01

In order to broaden the use of microrobots in practical fields, autonomous control algorithms such as obstacle avoidance must be further developed. However, most previous studies of microrobots used manual motion control to navigate past tight spaces and obstacles while very few studies demonstrated the use of autonomous motion. In this paper, we demonstrated a dynamic obstacle avoidance algorithm for bacteria-powered microrobots (BPMs) using electric field in fluidic environments. A BPM consists of an artificial body, which is made of SU-8, and a high dense layer of harnessed bacteria. BPMs can be controlled using externally applied electric fields due to the electrokinetic property of bacteria. For developing dynamic obstacle avoidance for BPMs, a kinematic model of BPMs was utilized to prevent collision and a finite element model was used to characteristic the deformation of an electric field near the obstacle walls. In order to avoid fast moving obstacles, we modified our previously static obstacle avoidance approach using a modified vector field histogram (VFH) method. To validate the advanced algorithm in experiments, magnetically controlled moving obstacles were used to intercept the BPMs as the BPMs move from the initial position to final position. The algorithm was able to successfully guide the BPMs to reach their respective goal positions while avoiding the dynamic obstacles.

Factors influencing crime rates: an econometric analysis approach

NASA Astrophysics Data System (ADS)

Bothos, John M. A.; Thomopoulos, Stelios C. A.

2016-05-01

The scope of the present study is to research the dynamics that determine the commission of crimes in the US society. Our study is part of a model we are developing to understand urban crime dynamics and to enhance citizens' "perception of security" in large urban environments. The main targets of our research are to highlight dependence of crime rates on certain social and economic factors and basic elements of state anticrime policies. In conducting our research, we use as guides previous relevant studies on crime dependence, that have been performed with similar quantitative analyses in mind, regarding the dependence of crime on certain social and economic factors using statistics and econometric modelling. Our first approach consists of conceptual state space dynamic cross-sectional econometric models that incorporate a feedback loop that describes crime as a feedback process. In order to define dynamically the model variables, we use statistical analysis on crime records and on records about social and economic conditions and policing characteristics (like police force and policing results - crime arrests), to determine their influence as independent variables on crime, as the dependent variable of our model. The econometric models we apply in this first approach are an exponential log linear model and a logit model. In a second approach, we try to study the evolvement of violent crime through time in the US, independently as an autonomous social phenomenon, using autoregressive and moving average time-series econometric models. Our findings show that there are certain social and economic characteristics that affect the formation of crime rates in the US, either positively or negatively. Furthermore, the results of our time-series econometric modelling show that violent crime, viewed solely and independently as a social phenomenon, correlates with previous years crime rates and depends on the social and economic environment's conditions during previous years.

The study on the parallel processing based time series correlation analysis of RBC membrane flickering in quantitative phase imaging

NASA Astrophysics Data System (ADS)

Lee, Minsuk; Won, Youngjae; Park, Byungjun; Lee, Seungrag

2017-02-01

Not only static characteristics but also dynamic characteristics of the red blood cell (RBC) contains useful information for the blood diagnosis. Quantitative phase imaging (QPI) can capture sample images with subnanometer scale depth resolution and millisecond scale temporal resolution. Various researches have been used QPI for the RBC diagnosis, and recently many researches has been developed to decrease the process time of RBC information extraction using QPI by the parallel computing algorithm, however previous studies are interested in the static parameters such as morphology of the cells or simple dynamic parameters such as root mean square (RMS) of the membrane fluctuations. Previously, we presented a practical blood test method using the time series correlation analysis of RBC membrane flickering with QPI. However, this method has shown that there is a limit to the clinical application because of the long computation time. In this study, we present an accelerated time series correlation analysis of RBC membrane flickering using the parallel computing algorithm. This method showed consistent fractal scaling exponent results of the surrounding medium and the normal RBC with our previous research.

Dynamic signatures of the transition from stacking disordered to hexagonal ice: Dielectric and nuclear magnetic resonance studies

NASA Astrophysics Data System (ADS)

Gainaru, C.; Vynokur, E.; Köster, K. W.; Fuentes-Landete, V.; Spettel, N.; Zollner, J.; Loerting, T.; Böhmer, R.

2018-04-01

Using various temperature-cycling protocols, the dynamics of ice I were studied via dielectric spectroscopy and nuclear magnetic resonance relaxometry on protonated and deuterated samples obtained by heating high-density amorphous ices as well as crystalline ice XII. Previous structural studies of ice I established that at temperatures of about 230 K, the stacking disorder of the cubic/hexagonal oxygen lattice vanishes. The present dielectric and nuclear magnetic resonance investigations of spectral changes disclose that the memory of the existence of a precursor phase is preserved in the hydrogen matrix up to 270 K. This finding of hydrogen mobility lower than that of the undoped hexagonal ice near the melting point highlights the importance of dynamical investigations of the transitions between various ice phases and sheds new light on the dynamics in ice I in general.

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

Characteristics of axillary lymph nodes apparent on dynamic contrast-enhanced breast MRI in healthy women.

PubMed

Krammer, Julia; Engel, Dorothee; Nissen, Johanna; Schnitzer, Andreas; Suetterlin, Marc; Schoenberg, Stefan O; Wasser, Klaus

2012-01-01

The study was initiated to characterize and better understand the natural characteristics of axillary lymph nodes (LNs) apparent on dynamic breast magnetic resonance imaging (MRI). The most important finding in 71 subjects that included healthy women was that 41% showed strong enhanced axillary LNs. The dynamic curves of these LNs revealed an initial mean signal increase of 197% (±58%), all of them with a following plateau (34%) or washout (66%). Our study points out that the previous understanding of contrast enhancement in breast lesions should be taken with care when assessing axillary LNs. This has to be considered especially in preoperative breast MRI. Copyright © 2012 Elsevier Inc. All rights reserved.

Videos and Animations for Vocabulary Learning: A Study on Difficult Words

ERIC Educational Resources Information Center

Lin, Chih-cheng; Tseng, Yi-fang

2012-01-01

Studies on using still images and dynamic videos in multimedia annotations produced inconclusive results. A further examination, however, showed that the principle of using videos to explain complex concepts was not observed in the previous studies. This study was intended to investigate whether videos, compared with pictures, better assist…

Use of dynamic occupancy models to assess the response of Darters (Teleostei: Percidae) to varying hydrothermal conditions in a southeastern United States tailwater

USGS Publications Warehouse

Shea, C.P.; Bettoli, Phillip William; Potoka, K. M.; Saylor, C. F.; Shute, P. W.

2015-01-01

During the past 100 years, most large rivers in North America have been altered for flood control, hydropower, navigation or water supply development. Although these activities clearly provide important human services, their associated environmental disturbances can profoundly affect stream-dwelling organisms. We used dynamic multi-species occupancy models combined with a trait-based approach to estimate the influence of site-level and species-level characteristics on patch dynamic rates for 15 darter species native to the Elk River, a large, flow-regulated Tennessee River tributary in Tennessee and Alabama. Dynamic occupancy modelling results indicated that for every 2.5 °C increase in stream temperature, darters were 3.94 times more likely to colonize previously unoccupied stream reaches. Additionally, large-bodied darter species were 3.72 times more likely to colonize stream reaches compared with small-bodied species, but crevice-spawning darter species were 5.24 times less likely to colonize previously unoccupied stream reaches. In contrast, darters were 2.21 times less likely to become locally extinct for every 2.5 °C increase in stream temperature, but high stream discharge conditions elevated the risk of local extinction. Lastly, the presence of populations in neighbouring upstream study reaches contributed to a lower risk of extinction, whereas the presence of populations in neighbouring downstream study reaches contributed to higher rates of colonization. Our study demonstrates the application of a trait-based approach combined with a metapopulation framework to assess the patch dynamics of darters in a regulated river. Results from our study will provide a baseline for evaluating the ecological consequences of alternative dam operations.

Muscular outputs during dynamic bench press under stable versus unstable conditions.

PubMed

Koshida, Sentaro; Urabe, Yukio; Miyashita, Koji; Iwai, Kanzunori; Kagimori, Aya

2008-09-01

Previous studies have suggested that resistance training exercise under unstable conditions decreases the isometric force output, yet little is known about its influence on muscular outputs during dynamic movement. The objective of this study was to investigate the effect of an unstable condition on power, force, and velocity outputs during the bench press. Twenty male collegiate athletes (mean age, 21.3 +/- 1.5 years; mean height, 167.7 +/- 7.7 cm; mean weight, 75.9 +/- 17.5 kg) participated in this study. Each subject attempted 3 sets of single bench presses with 50% of 1 repetition maximum (1RM) under a stable condition with a flat bench and an unstable condition with a Swiss ball. Acceleration data were obtained with an accelerometer attached to the center of a barbell shaft, and peak outputs of power, force, and velocity were computed. Although significant loss of the peak outputs was found under the unstable condition (p < 0.017), their reduction rates remained relatively low, approximately 6% for force and 10% for power and velocity outputs, compared with previous findings. Such small reduction rates of muscular outputs may not compromise the training effect. Prospective studies are necessary to confirm whether the resistance training under an unstable condition permits the improvement of dynamic performance and trunk stability.

The Development of a Dual-Warhead Impact System for Dynamic Linearity Measurement of a High-g Micro-Electro-Mechanical-Systems (MEMS) Accelerometer

PubMed Central

Shi, Yunbo; Yang, Zhicai; Ma, Zongmin; Cao, Huiliang; Kou, Zhiwei; Zhi, Dan; Chen, Yanxiang; Feng, Hengzhen; Liu, Jun

2016-01-01

Despite its extreme significance, dynamic linearity measurement for high-g accelerometers has not been discussed experimentally in previous research. In this study, we developed a novel method using a dual-warhead Hopkinson bar to measure the dynamic linearity of a high-g acceleration sensor with a laser interference impact experiment. First, we theoretically determined that dynamic linearity is a performance indicator that can be used to assess the quality merits of high-g accelerometers and is the basis of the frequency response. We also found that the dynamic linearity of the dual-warhead Hopkinson bar without an accelerometer is 2.5% experimentally. Further, we verify that dynamic linearity of the accelerometer is 3.88% after calibrating the Hopkinson bar with the accelerometer. The results confirm the reliability and feasibility of measuring dynamic linearity for high-g accelerometers using this method. PMID:27338383

Dynamic in-vivo assessment of navicular drop while running in barefoot, minimalist, and motion control footwear conditions.

PubMed

Hoffman, Scott E; Peltz, Cathryn D; Haladik, Jeffrey A; Divine, George; Nurse, Matthew A; Bey, Michael J

2015-03-01

Running-related injuries are common and previous research has suggested that the magnitude and/or rate of pronation may contribute to the development of these injuries. Accurately and directly measuring pronation can be challenging, and therefore previous research has often relied on navicular drop (under both static and dynamic conditions) as an indirect assessment of pronation. The objectives of this study were to use dynamic, biplane X-ray imaging to assess the effects of three footwear conditions (barefoot, minimalist shoes, motion control shoes) on the magnitude and rate of navicular drop during running, and to determine the association between static and dynamic measures of navicular drop. Twelve healthy distance runners participated in this study. The magnitude and rate of navicular drop were determined by tracking the 3D position of the navicular from biplane radiographic images acquired at 60Hz during the stance phase of overground running. Static assessments of navicular drop and foot posture were also recorded in each subject. Footwear condition was not found to have a significant effect on the magnitude of navicular drop (p=0.22), but motion control shoes had a slower navicular drop rate than running barefoot (p=0.05) or in minimalist shoes (p=0.05). In an exploratory analysis, static assessments of navicular drop and foot posture were found to be poor predictors of dynamic navicular drop in all footwear conditions (p>0.18). Copyright © 2015 Elsevier B.V. All rights reserved.

The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion.

PubMed

Mogo, César; Brandão, João

2014-06-30

READY (REActive DYnamics) is a program for studying reactive dynamic systems using a global potential energy surface (PES) built from previously existing PESs corresponding to each of the most important elementary reactions present in the system. We present an application to the combustion dynamics of a mixture of hydrogen and oxygen using accurate PESs for all the systems involving up to four oxygen and hydrogen atoms. Results at the temperature of 4000 K and pressure of 2 atm are presented and compared with model based on rate constants. Drawbacks and advantages of this approach are discussed and future directions of research are pointed out. Copyright © 2014 Wiley Periodicals, Inc.

Dynamic Skin Patterns in Cephalopods

PubMed Central

How, Martin J.; Norman, Mark D.; Finn, Julian; Chung, Wen-Sung; Marshall, N. Justin

2017-01-01

Cephalopods are unrivaled in the natural world in their ability to alter their visual appearance. These mollusks have evolved a complex system of dermal units under neural, hormonal, and muscular control to produce an astonishing variety of body patterns. With parallels to the pixels on a television screen, cephalopod chromatophores can be coordinated to produce dramatic, dynamic, and rhythmic displays, defined collectively here as “dynamic patterns.” This study examines the nature, context, and potential functions of dynamic patterns across diverse cephalopod taxa. Examples are presented for 21 species, including 11 previously unreported in the scientific literature. These range from simple flashing or flickering patterns, to highly complex passing wave patterns involving multiple skin fields. PMID:28674500

Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations.

PubMed

Kessler, Jan; Elgabarty, Hossam; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

2015-08-06

The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab initio molecular dynamics simulations in conjunction with an instantaneous surface definition [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

The effects of spatial dynamics on a wormhole throat

NASA Astrophysics Data System (ADS)

Alias, Anuar; Wan Abdullah, Wan Ahmad Tajuddin

2018-02-01

Previous studies on dynamic wormholes were focused on the dynamics of the wormhole itself, be it either rotating or evolutionary in character and also in various frameworks from classical to braneworld cosmological models. In this work, we modeled a dynamic factor that represents the spatial dynamics in terms of spacetime expansion and contraction surrounding the wormhole itself. Using an RS2-based braneworld cosmological model, we modified the spacetime metric of Wong and subsequently employed the method of Bronnikov, where it is observed that a traversable wormhole is easier to exist in an expanding brane universe, however it is difficult to exist in a contracting brane universe due to stress-energy tensors requirement. This model of spatial dynamic factor affecting the wormhole throat can also be applied on the cyclic or the bounce universe model.

Training Maneuver Evaluation for Reduced Order Modeling of Stability & Control Properties Using Computational Fluid Dynamics

DTIC Science & Technology

2013-03-01

reduced order model is created. Finally, previous research in this area of study will be examined, and its application to this research will be...TRAINING MANEUVER EVALUATION FOR REDUCED ORDER MODELING OF STABILITY & CONTROL PROPERTIES USING COMPUTATIONAL FLUID DYNAMICS THESIS Craig Curtis...Government and is not subject to copyright protection in the United States. AFIT-ENY-13-M-28 TRAINING MANEUVER EVALUATION FOR REDUCED ORDER MODELING OF

Estimating the Wind Resource in Uttarakhand: Comparison of Dynamic Downscaling with Doppler Lidar Wind Measurements

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

Lundquist, J. K.; Pukayastha, A.; Martin, C.

Previous estimates of the wind resources in Uttarakhand, India, suggest minimal wind resources in this region. To explore whether or not the complex terrain in fact provides localized regions of wind resource, the authors of this study employed a dynamic down scaling method with the Weather Research and Forecasting model, providing detailed estimates of winds at approximately 1 km resolution in the finest nested simulation.

Identifying Challenges in Supervising School Psychologists

ERIC Educational Resources Information Center

Harvey, Virginia Smith; Pearrow, Melissa

2010-01-01

Previous studies suggest that the majority of school psychologists do not believe they receive sufficient supervision, despite a growing body of research providing empirical support for supervision to maintain and improve skills. This study explores the dynamics underlying the challenges of providing adequate supervision to school psychologists.…

Dynamic Relationships: Identifying Moderators That Maximize Benefits Associated with Diversity

ERIC Educational Resources Information Center

Denson, Nida; Chang, Mitchell J.

2015-01-01

This study examined factors that can moderate the relationship between cross-racial interaction and undergraduate students' development. While previous studies have shown that students benefit from interacting across racial differences, they have not examined whether those educational benefits are moderated by other factors. The moderators…

Molecular dynamics studies of pathways of water movement in cyanobacterial photosystem II

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

Gabdulkhakov, A. G., E-mail: azat@vega.protres.ru; Kljashtorny, V. G.; Dontsova, M. V.

2015-01-15

Photosystem II (PSII) catalyzes the light-induced generation of oxygen from water. The oxygen-evolving complex is buried deep in the protein on the lumenal side of PSII, and water molecules need to pass through protein subunits to reach the active site—the manganese cluster. Previous studies on the elucidation of water channels in PSII were based on an analysis of the cavities in the static PSII structure determined by X-ray diffraction. In the present study, we perform molecular dynamics simulations of the water movement in the transport system of PSII.

Two-dimensional solitary waves and periodic waves on coupled nonlinear electrical transmission lines

NASA Astrophysics Data System (ADS)

Wang, Heng; Zheng, Shuhua

2017-06-01

By using the dynamical system approach, the exact travelling wave solutions for a system of coupled nonlinear electrical transmission lines are studied. Based on this method, the bifurcations of phase portraits of a dynamical system are given. The two-dimensional solitary wave solutions and periodic wave solutions on coupled nonlinear transmission lines are obtained. With the aid of Maple, the numerical simulations are conducted for solitary wave solutions and periodic wave solutions to the model equation. The results presented in this paper improve upon previous studies.

Chaotic itinerancy in the oscillator neural network without Lyapunov functions.

PubMed

Uchiyama, Satoki; Fujisaka, Hirokazu

2004-09-01

Chaotic itinerancy (CI), which is defined as an incessant spontaneous switching phenomenon among attractor ruins in deterministic dynamical systems without Lyapunov functions, is numerically studied in the case of an oscillator neural network model. The model is the pseudoinverse-matrix version of the previous model [S. Uchiyama and H. Fujisaka, Phys. Rev. E 65, 061912 (2002)] that was studied theoretically with the aid of statistical neurodynamics. It is found that CI in neural nets can be understood as the intermittent dynamics of weakly destabilized chaotic retrieval solutions. Copyright 2004 American Institute of Physics

Dynamic testing in schizophrenia: does training change the construct validity of a test?

PubMed

Wiedl, Karl H; Schöttke, Henning; Green, Michael F; Nuechterlein, Keith H

2004-01-01

Dynamic testing typically involves specific interventions for a test to assess the extent to which test performance can be modified, beyond level of baseline (static) performance. This study used a dynamic version of the Wisconsin Card Sorting Test (WCST) that is based on cognitive remediation techniques within a test-training-test procedure. From results of previous studies with schizophrenia patients, we concluded that the dynamic and static versions of the WCST should have different construct validity. This hypothesis was tested by examining the patterns of correlations with measures of executive functioning, secondary verbal memory, and verbal intelligence. Results demonstrated a specific construct validity of WCST dynamic (i.e., posttest) scores as an index of problem solving (Tower of Hanoi) and secondary verbal memory and learning (Auditory Verbal Learning Test), whereas the impact of general verbal capacity and selective attention (Verbal IQ, Stroop Test) was reduced. It is concluded that the construct validity of the test changes with dynamic administration and that this difference helps to explain why the dynamic version of the WCST predicts functional outcome better than the static version.

Aurally aided visual search performance in a dynamic environment

NASA Astrophysics Data System (ADS)

McIntire, John P.; Havig, Paul R.; Watamaniuk, Scott N. J.; Gilkey, Robert H.

2008-04-01

Previous research has repeatedly shown that people can find a visual target significantly faster if spatial (3D) auditory displays direct attention to the corresponding spatial location. However, previous research has only examined searches for static (non-moving) targets in static visual environments. Since motion has been shown to affect visual acuity, auditory acuity, and visual search performance, it is important to characterize aurally-aided search performance in environments that contain dynamic (moving) stimuli. In the present study, visual search performance in both static and dynamic environments is investigated with and without 3D auditory cues. Eight participants searched for a single visual target hidden among 15 distracting stimuli. In the baseline audio condition, no auditory cues were provided. In the 3D audio condition, a virtual 3D sound cue originated from the same spatial location as the target. In the static search condition, the target and distractors did not move. In the dynamic search condition, all stimuli moved on various trajectories at 10 deg/s. The results showed a clear benefit of 3D audio that was present in both static and dynamic environments, suggesting that spatial auditory displays continue to be an attractive option for a variety of aircraft, motor vehicle, and command & control applications.

Temporal and spectral characteristics of dynamic functional connectivity between resting-state networks reveal information beyond static connectivity

PubMed Central

Yeh, Hsiang J.; Guindani, Michele; Vannucci, Marina; Haneef, Zulfi; Stern, John M.

2018-01-01

Estimation of functional connectivity (FC) has become an increasingly powerful tool for investigating healthy and abnormal brain function. Static connectivity, in particular, has played a large part in guiding conclusions from the majority of resting-state functional MRI studies. However, accumulating evidence points to the presence of temporal fluctuations in FC, leading to increasing interest in estimating FC as a dynamic quantity. One central issue that has arisen in this new view of connectivity is the dramatic increase in complexity caused by dynamic functional connectivity (dFC) estimation. To computationally handle this increased complexity, a limited set of dFC properties, primarily the mean and variance, have generally been considered. Additionally, it remains unclear how to integrate the increased information from dFC into pattern recognition techniques for subject-level prediction. In this study, we propose an approach to address these two issues based on a large number of previously unexplored temporal and spectral features of dynamic functional connectivity. A Generalized Autoregressive Conditional Heteroskedasticity (GARCH) model is used to estimate time-varying patterns of functional connectivity between resting-state networks. Time-frequency analysis is then performed on dFC estimates, and a large number of previously unexplored temporal and spectral features drawn from signal processing literature are extracted for dFC estimates. We apply the investigated features to two neurologic populations of interest, healthy controls and patients with temporal lobe epilepsy, and show that the proposed approach leads to substantial increases in predictive performance compared to both traditional estimates of static connectivity as well as current approaches to dFC. Variable importance is assessed and shows that there are several quantities that can be extracted from dFC signal which are more informative than the traditional mean or variance of dFC. This work illuminates many previously unexplored facets of the dynamic properties of functional connectivity between resting-state networks, and provides a platform for dynamic functional connectivity analysis that facilitates its usage as an investigative measure for healthy as well as abnormal brain function. PMID:29320526

Nonlinear Dynamic Modeling of a Supersonic Commercial Transport Turbo-Machinery Propulsion System for Aero-Propulso-Servo-Elasticity Research

NASA Technical Reports Server (NTRS)

Connolly, Joseph W.; Kopasakis, George; Carlson, Jan-Renee; Woolwine, Kyle

2015-01-01

This paper covers the development of an integrated nonlinear dynamic model for a variable cycle turbofan engine, supersonic inlet, and convergent-divergent nozzle that can be integrated with an aeroelastic vehicle model to create an overall Aero-Propulso-Servo-Elastic (APSE) modeling tool. The primary focus of this study is to provide a means to capture relevant thrust dynamics of a full supersonic propulsion system by using relatively simple quasi-one dimensional computational fluid dynamics (CFD) methods that will allow for accurate control algorithm development and capture the key aspects of the thrust to feed into an APSE model. Previously, propulsion system component models have been developed and are used for this study of the fully integrated propulsion system. An overview of the methodology is presented for the modeling of each propulsion component, with a focus on its associated coupling for the overall model. To conduct APSE studies the de- scribed dynamic propulsion system model is integrated into a high fidelity CFD model of the full vehicle capable of conducting aero-elastic studies. Dynamic thrust analysis for the quasi-one dimensional dynamic propulsion system model is presented along with an initial three dimensional flow field model of the engine integrated into a supersonic commercial transport.

Nonlinear Dynamic Modeling of a Supersonic Commercial Transport Turbo-Machinery Propulsion System for Aero-Propulso-Servo-Elasticity Research

NASA Technical Reports Server (NTRS)

Connolly, Joe; Carlson, Jan-Renee; Kopasakis, George; Woolwine, Kyle

2015-01-01

This paper covers the development of an integrated nonlinear dynamic model for a variable cycle turbofan engine, supersonic inlet, and convergent-divergent nozzle that can be integrated with an aeroelastic vehicle model to create an overall Aero-Propulso-Servo-Elastic (APSE) modeling tool. The primary focus of this study is to provide a means to capture relevant thrust dynamics of a full supersonic propulsion system by using relatively simple quasi-one dimensional computational fluid dynamics (CFD) methods that will allow for accurate control algorithm development and capture the key aspects of the thrust to feed into an APSE model. Previously, propulsion system component models have been developed and are used for this study of the fully integrated propulsion system. An overview of the methodology is presented for the modeling of each propulsion component, with a focus on its associated coupling for the overall model. To conduct APSE studies the described dynamic propulsion system model is integrated into a high fidelity CFD model of the full vehicle capable of conducting aero-elastic studies. Dynamic thrust analysis for the quasi-one dimensional dynamic propulsion system model is presented along with an initial three dimensional flow field model of the engine integrated into a supersonic commercial transport.

Single-Molecule Spectroscopy and Imaging Studies of Protein Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter

2012-04-01

Enzymatic reactions and protein-protein interactions are traditionally studied at the ensemble level, despite significant static and dynamic inhomogeneities. Subtle conformational changes play a crucial role in protein functions, and these protein conformations are highly dynamic rather than being static. We applied AFM-enhanced single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of T4 lysozyme and HPPK enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation. Our new approach is applicable to a wide range of single-molecule FRET measurements for protein conformational changes under enzymatic reactions.

Project-Based Learning and Student Knowledge Construction during Asynchronous Online Discussion

ERIC Educational Resources Information Center

Koh, Joyce Hwee Ling; Herring, Susan C.; Hew, Khe Foon

2010-01-01

Project-based learning engages students in problem solving through artefact design. However, previous studies of online project-based learning have focused primarily on the dynamics of online collaboration; students' knowledge construction throughout this process has not been examined thoroughly. This case study analyzed the relationship between…

Considerations of solar wind dynamics in mapping of Jupiter's auroral features to magnetospheric sources

NASA Astrophysics Data System (ADS)

Gyalay, S.; Vogt, M.; Withers, P.

2015-12-01

Previous studies have mapped locations from the magnetic equator to the ionosphere in order to understand how auroral features relate to magnetospheric sources. Vogt et al. (2011) in particular mapped equatorial regions to the ionosphere by using a method of flux equivalence—requiring that the magnetic flux in a specified region at the equator is equal to the magnetic flux in the region to which it maps in the ionosphere. This is preferred to methods relying on tracing field lines from global Jovian magnetic field models, which are inaccurate beyond 30 Jupiter radii from the planet. That previous study produced a two-dimensional model—accounting for changes with radial distance and local time—of the normal component of the magnetic field in the equatorial region. However, this two-dimensional fit—which aggregated all equatorial data from Pioneer 10, Pioneer 11, Voyager 1, Voyager 2, Ulysses, and Galileo—did not account for temporal variability resulting from changing solar wind conditions. Building off of that project, this study aims to map the Jovian aurora to the magnetosphere for two separate cases: with a nominal magnetosphere, and with a magnetosphere compressed by high solar wind dynamic pressure. Using the Michigan Solar Wind Model (mSWiM) to predict the solar wind conditions upstream of Jupiter, intervals of high solar wind dynamic pressure were separated from intervals of low solar wind dynamic pressure—thus creating two datasets of magnetometer measurements to be used for two separate 2D fits, and two separate mappings.

Temporal Dynamic Controllability Revisited

NASA Technical Reports Server (NTRS)

Morris, Paul H.; Muscettola, Nicola

2005-01-01

An important issue for temporal planners is the ability to handle temporal uncertainty. We revisit the question of how to determine whether a given set of temporal requirements are feasible in the light of uncertain durations of some processes. In particular, we consider how best to determine whether a network is Dynamically Controllable, i.e., whether a dynamic strategy exists for executing the network that is guaranteed to satisfy the requirements. Previous work has shown the existence of a pseudo-polynomial algorithm for testing Dynamic Controllability. Here, we greatly simplify the previous framework, and present a true polynomial algorithm with a cutoff based only on the number of nodes.

The impact of multiple information on coupled awareness-epidemic dynamics in multiplex networks

NASA Astrophysics Data System (ADS)

Pan, Yaohui; Yan, Zhijun

2018-02-01

Growing interest has emerged in the study of the interplay between awareness and epidemics in multiplex networks. However, previous studies on this issue usually assume that all aware individuals take the same level of precautions, ignoring individual heterogeneity. In this paper, we investigate the coupled awareness-epidemic dynamics in multiplex networks considering individual heterogeneity. Here, the precaution levels are heterogeneous and depend on three types of information: contact information and local and global prevalence information. The results show that contact-based precautions can decrease the epidemic prevalence and augment the epidemic threshold, but prevalence-based precautions, regardless of local or global information, can only decrease the epidemic prevalence. Moreover, unlike previous studies in single-layer networks, we do not find a greater impact of local prevalence information on the epidemic prevalence compared to global prevalence information. In addition, we find that the altruistic behaviors of infected individuals can effectively suppress epidemic spreading, especially when the level of contact-based precaution is high.

Normal modes of synchronous rotation

NASA Astrophysics Data System (ADS)

Varadi, Ferenc; Musotto, Susanna; Moore, William; Schubert, Gerald

2005-07-01

The dynamics of synchronous rotation and physical librations are revisited in order to establish a conceptually simple and general theoretical framework applicable to a variety of problems. Our motivation comes from disagreements between the results of numerical simulations and those of previous theoretical studies, and also because different theoretical studies disagree on basic features of the dynamics. We approach the problem by decomposing the orientation matrix of the body into perfectly synchronous rotation and deviation from the equilibrium state. The normal modes of the linearized equations are computed in the case of a circular satellite orbit, yielding both the periods and the eigenspaces of three librations. Libration in longitude decouples from the other two, vertical modes. There is a fast vertical mode with a period very close to the average rotational period. It corresponds to tilting the body around a horizontal axis while retaining nearly principal-axis rotation. In the inertial frame, this mode appears as nutation and free precession. The other vertical mode, a slow one, is the free wobble. The effects of the nodal precession of the orbit are investigated from the point of view of Cassini states. We test our theory using numerical simulations of the full equations of the dynamics and discuss the disagreements among our study and previous ones. The numerical simulations also reveal that in the case of eccentric orbits large departures from principal-axis rotation are possible due to a resonance between free precession and wobble. We also revisit the history of the Moon's rotational state and show that it switched from one Cassini state to another when it was at 46.2 Earth radii. This number disagrees with the value 34.2 derived in a previous study.

Preferred gait and walk-run transition speeds in ostriches measured using GPS-IMU sensors.

PubMed

Daley, Monica A; Channon, Anthony J; Nolan, Grant S; Hall, Jade

2016-10-15

The ostrich (Struthio camelus) is widely appreciated as a fast and agile bipedal athlete, and is a useful comparative bipedal model for human locomotion. Here, we used GPS-IMU sensors to measure naturally selected gait dynamics of ostriches roaming freely over a wide range of speeds in an open field and developed a quantitative method for distinguishing walking and running using accelerometry. We compared freely selected gait-speed distributions with previous laboratory measures of gait dynamics and energetics. We also measured the walk-run and run-walk transition speeds and compared them with those reported for humans. We found that ostriches prefer to walk remarkably slowly, with a narrow walking speed distribution consistent with minimizing cost of transport (CoT) according to a rigid-legged walking model. The dimensionless speeds of the walk-run and run-walk transitions are slower than those observed in humans. Unlike humans, ostriches transition to a run well below the mechanical limit necessitating an aerial phase, as predicted by a compass-gait walking model. When running, ostriches use a broad speed distribution, consistent with previous observations that ostriches are relatively economical runners and have a flat curve for CoT against speed. In contrast, horses exhibit U-shaped curves for CoT against speed, with a narrow speed range within each gait for minimizing CoT. Overall, the gait dynamics of ostriches moving freely over natural terrain are consistent with previous lab-based measures of locomotion. Nonetheless, ostriches, like humans, exhibit a gait-transition hysteresis that is not explained by steady-state locomotor dynamics and energetics. Further study is required to understand the dynamics of gait transitions. © 2016. Published by The Company of Biologists Ltd.

Quasispecies dynamics on a network of interacting genotypes and idiotypes: formulation of the model

NASA Astrophysics Data System (ADS)

Barbosa, Valmir C.; Donangelo, Raul; Souza, Sergio R.

2015-01-01

A quasispecies is the stationary state of a set of interrelated genotypes that evolve according to the usual principles of selection and mutation. Quasispecies studies have for the most part concentrated on the possibility of errors during genotype replication and their role in promoting either the survival or the demise of the quasispecies. In a previous work, we introduced a network model of quasispecies dynamics, based on a single probability parameter (p) and capable of addressing several plausibility issues of previous models. Here we extend that model by pairing its network with another one aimed at modeling the dynamics of the immune system when confronted with the quasispecies. The new network is based on the idiotypic-network model of immunity and, together with the previous one, constitutes a network model of interacting genotypes and idiotypes. The resulting model requires further parameters and as a consequence leads to a vast phase space. We have focused on a particular niche in which it is possible to observe the trade-offs involved in the quasispecies' survival or destruction. Within this niche, we give simulation results that highlight some key preconditions for quasispecies survival. These include a minimum initial abundance of genotypes relative to that of the idiotypes and a minimum value of p. The latter, in particular, is to be contrasted with the stand-alone quasispecies network of our previous work, in which arbitrarily low values of p constitute a guarantee of quasispecies survival.

Boldness by habituation and social interactions: a model.

PubMed

Oosten, Johanneke E; Magnhagen, Carin; Hemelrijk, Charlotte K

2010-04-01

Most studies of animal personality attribute personality to genetic traits. But a recent study by Magnhagen and Staffan (Behav Ecol Sociobiol 57:295-303, 2005) on young perch in small groups showed that boldness, a central personality trait, is also shaped by social interactions and by previous experience. The authors measured boldness by recording the duration that an individual spent near a predator and the speed with which it fed there. They found that duration near the predator increased over time and was higher the higher the average boldness of other group members. In addition, the feeding rate of shy individuals was reduced if other members of the same group were bold. The authors supposed that these behavioral dynamics were caused by genetic differences, social interactions, and habituation to the predator. However, they did not quantify exactly how this could happen. In the present study, we therefore use an agent-based model to investigate whether these three factors may explain the empirical findings. We choose an agent-based model because this type of model is especially suited to study the relation between behavior at an individual level and behavioral dynamics at a group level. In our model, individuals were either hiding in vegetation or feeding near a predator, whereby their behavior was affected by habituation and by two social mechanisms: social facilitation to approach the predator and competition over food. We show that even if we start the model with identical individuals, these three mechanisms were sufficient to reproduce the behavioral dynamics of the empirical study, including the consistent differences among individuals. Moreover, if we start the model with individuals that already differ in boldness, the behavioral dynamics produced remained the same. Our results indicate the importance of previous experience and social interactions when studying animal personality empirically.

Effect of Interpersonal Interaction on Festinating Gait Rehabilitation in Patients with Parkinson’s Disease

PubMed Central

Uchitomi, Hirotaka; Ogawa, Ken-ichiro; Orimo, Satoshi; Wada, Yoshiaki; Miyake, Yoshihiro

2016-01-01

Although human walking gait rhythms are generated by native individual gait dynamics, these gait dynamics change during interactions between humans. A typical phenomenon is synchronization of gait rhythms during cooperative walking. Our previous research revealed that fluctuation characteristics in stride interval of subjects with Parkinson’s disease changed from random to 1/f fluctuation as fractal characteristics during cooperative walking with the gait assist system Walk-Mate, which emulates a human interaction using interactive rhythmic cues. Moreover, gait dynamics were relearned through Walk-Mate gait training. However, the system’s clinical efficacy was unclear because the previous studies did not focus on specific gait rhythm disorder symptoms. Therefore, this study aimed to evaluate the effect of Walk-Mate on festinating gait among subjects with Parkinson’s disease. Three within-subject experimental conditions were used: (1) preinteraction condition, (2) interaction condition, and (3) postinteraction condition. The only difference between conditions was the interactive rhythmic cues generated by Walk-Mate. Because subjects with festinating gait gradually and involuntarily decreased their stride interval, the regression slope of stride interval as an index of severity of preinteraction festinating gait was elevated. The regression slope in the interaction condition was more gradual than during the preinteraction condition, indicating that the interactive rhythmic cues contributed to relieving festinating gait and stabilizing gait dynamics. Moreover, the gradual regression slope was carried over to the postinteraction condition, indicating that subjects with festinating gait have the potential to relearn stable gait dynamics. These results suggest that disordered gait dynamics are clinically restored through interactive rhythmic cues and that Walk-Mate may have the potential to assist therapists in more effective rehabilitation. Trial Registration: UMIN Clinical Trials Registry UMIN000012591 PMID:27253376

Effect of Interpersonal Interaction on Festinating Gait Rehabilitation in Patients with Parkinson's Disease.

PubMed

Uchitomi, Hirotaka; Ogawa, Ken-Ichiro; Orimo, Satoshi; Wada, Yoshiaki; Miyake, Yoshihiro

2016-01-01

Although human walking gait rhythms are generated by native individual gait dynamics, these gait dynamics change during interactions between humans. A typical phenomenon is synchronization of gait rhythms during cooperative walking. Our previous research revealed that fluctuation characteristics in stride interval of subjects with Parkinson's disease changed from random to 1/f fluctuation as fractal characteristics during cooperative walking with the gait assist system Walk-Mate, which emulates a human interaction using interactive rhythmic cues. Moreover, gait dynamics were relearned through Walk-Mate gait training. However, the system's clinical efficacy was unclear because the previous studies did not focus on specific gait rhythm disorder symptoms. Therefore, this study aimed to evaluate the effect of Walk-Mate on festinating gait among subjects with Parkinson's disease. Three within-subject experimental conditions were used: (1) preinteraction condition, (2) interaction condition, and (3) postinteraction condition. The only difference between conditions was the interactive rhythmic cues generated by Walk-Mate. Because subjects with festinating gait gradually and involuntarily decreased their stride interval, the regression slope of stride interval as an index of severity of preinteraction festinating gait was elevated. The regression slope in the interaction condition was more gradual than during the preinteraction condition, indicating that the interactive rhythmic cues contributed to relieving festinating gait and stabilizing gait dynamics. Moreover, the gradual regression slope was carried over to the postinteraction condition, indicating that subjects with festinating gait have the potential to relearn stable gait dynamics. These results suggest that disordered gait dynamics are clinically restored through interactive rhythmic cues and that Walk-Mate may have the potential to assist therapists in more effective rehabilitation. UMIN Clinical Trials Registry UMIN000012591.

Perceiving while producing: Modeling the dynamics of phonological planning

PubMed Central

Roon, Kevin D.; Gafos, Adamantios I.

2016-01-01

We offer a dynamical model of phonological planning that provides a formal instantiation of how the speech production and perception systems interact during online processing. The model is developed on the basis of evidence from an experimental task that requires concurrent use of both systems, the so-called response-distractor task in which speakers hear distractor syllables while they are preparing to produce required responses. The model formalizes how ongoing response planning is affected by perception and accounts for a range of results reported across previous studies. It does so by explicitly addressing the setting of parameter values in representations. The key unit of the model is that of the dynamic field, a distribution of activation over the range of values associated with each representational parameter. The setting of parameter values takes place by the attainment of a stable distribution of activation over the entire field, stable in the sense that it persists even after the response cue in the above experiments has been removed. This and other properties of representations that have been taken as axiomatic in previous work are derived by the dynamics of the proposed model. PMID:27440947

Effect of aging on dynamic postural stability and variability during a multi-directional lean and reach object transportation task.

PubMed

Huntley, Andrew H; Zettel, John L; Vallis, Lori Ann

2016-01-01

A "reach and transport object" task that represents common activities of daily living may provide improved insight into dynamic postural stability and movement variability deficits in older adults compared to previous lean to reach and functional reach tests. Healthy young and older, community dwelling adults performed three same elevation object transport tasks and two multiple elevation object transport tasks under two self-selected speeds, self-paced and fast-paced. Dynamic postural stability and movement variability was quantified by whole-body center of mass motion. Older adults demonstrated significant decrements in frontal plane stability during the multiple elevation tasks while exhibiting the same movement variability as their younger counterparts, regardless of task speed. Interestingly, older adults did not exhibit a tradeoff in maneuverability in favour of maintaining stability throughout the tasks, as has previously been reported. In conclusion, the multi-planar, ecologically relevant tasks employed in the current study were specific enough to elucidate decrements in dynamic stability, and thus may be useful for assessing fall risk in older adults with suspected postural instability. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Dynamics of molecules in extreme rotational states

PubMed Central

Yuan, Liwei; Teitelbaum, Samuel W.; Robinson, Allison; Mullin, Amy S.

2011-01-01

We have constructed an optical centrifuge with a pulse energy that is more than 2 orders of magnitude larger than previously reported instruments. This high pulse energy enables us to create large enough number densities of molecules in extreme rotational states to perform high-resolution state-resolved transient IR absorption measurements. Here we report the first studies of energy transfer dynamics involving molecules in extreme rotational states. In these studies, the optical centrifuge drives CO2 molecules into states with J ∼ 220 and we use transient IR probing to monitor the subsequent rotational, translational, and vibrational energy flow dynamics. The results reported here provide the first molecular insights into the relaxation of molecules with rotational energy that is comparable to that of a chemical bond.

Collisional model for granular impact dynamics.

PubMed

Clark, Abram H; Petersen, Alec J; Behringer, Robert P

2014-01-01

When an intruder strikes a granular material from above, the grains exert a stopping force which decelerates and stops the intruder. Many previous studies have used a macroscopic force law, including a drag force which is quadratic in velocity, to characterize the decelerating force on the intruder. However, the microscopic origins of the force-law terms are still a subject of debate. Here, drawing from previous experiments with photoelastic particles, we present a model which describes the velocity-squared force in terms of repeated collisions with clusters of grains. From our high speed photoelastic data, we infer that "clusters" correspond to segments of the strong force network that are excited by the advancing intruder. The model predicts a scaling relation for the velocity-squared drag force that accounts for the intruder shape. Additionally, we show that the collisional model predicts an instability to rotations, which depends on the intruder shape. To test this model, we perform a comprehensive experimental study of the dynamics of two-dimensional granular impacts on beds of photoelastic disks, with different profiles for the leading edge of the intruder. We particularly focus on a simple and useful case for testing shape effects by using triangular-nosed intruders. We show that the collisional model effectively captures the dynamics of intruder deceleration and rotation; i.e., these two dynamical effects can be described as two different manifestations of the same grain-scale physical processes.

Femtosecond Polarization Phase Selective (PPS) High Magnetic Field Studies of Electron-Spin-Hole (ESH) Dynamics: New Tools for Ultrafast Imaging Fe-centered ESH Transfer Mechanisms Steps

NASA Astrophysics Data System (ADS)

Rupnik, Kresimir; Cooper, Benjamin; Dunne, Taylor; Gerosa, Katherine; Mercer, Kaitlyn; McGill, Stephen

In previous work, new Nanoparticle-enzyme Based Hybrids (NEBH) synthesis methods were investigated for nanoparticles of different shapes and electron energies. These hybrids can provide electromagnetic-field-driven ESH separations and transfers to desired molecular locations. Of paramount biomedical interest are the activity centers (including Fe-clusters) in proteins that perform their intended function and help synthesize other molecules. In this work we discuss results of our recent in situ ESH dynamics measurements: we use <15fs (Vitara) PPS broad band pulses and ultrahigh, 25T, magnetic fields from Split-helix magnet at NHMFL. Work included multi-spectral domain PPS harmonic generations and PPS sum frequency generations. Model compounds, including cytochromes, were used for testing and calibrations and previously studied Fe-S enzymes were prepared for measurements. While PPS opto-magnetic methods are known for their insight into electronic structure, our femtosecond measurements can provide ultrafast dynamic imaging of ESH mechanisms decision making steps. UF-PPS Project, performed in part at NHMFL, supported by NSF CA No. DMR-1157490, and 0654118 and U.S. DOE.

Elastic constants and dynamics in nematic liquid crystals

NASA Astrophysics Data System (ADS)

Humpert, Anja; Allen, Michael P.

2015-09-01

In this paper, we present molecular dynamics calculations of the Frank elastic constants, and associated time correlation functions, in nematic liquid crystals. We study two variants of the Gay-Berne potential, and use system sizes of half a million molecules, significantly larger than in previous studies of elastic behaviour. Equilibrium orientational fluctuations in reciprocal (k-) space were calculated, to determine the elastic constants by fitting at low |k|; our results indicate that small system size may be a source of inaccuracy in previous work. Furthermore, the dynamics of the Gay-Berne nematic were studied by calculating time correlation functions of components of the order tensor, together with associated components of the velocity field, for a set of wave vectors k. Confirming our earlier work, we found exponential decay for splay and twist correlations, and oscillatory exponential decay for the bend correlation. In this work, we confirm similar behaviour for the corresponding velocity components. In all cases, the decay rates, and oscillation frequencies, were found to be accurately proportional to k2 for small k, as predicted by the equations of nematodynamics. However, the observation of oscillatory bend fluctuations, and corresponding oscillatory shear flow decay, is in contradiction to the usual assumptions appearing in the literature, and in standard texts. We discuss the advantages and drawbacks of using large systems in these calculations.

Model-based functional neuroimaging using dynamic neural fields: An integrative cognitive neuroscience approach

PubMed Central

Wijeakumar, Sobanawartiny; Ambrose, Joseph P.; Spencer, John P.; Curtu, Rodica

2017-01-01

A fundamental challenge in cognitive neuroscience is to develop theoretical frameworks that effectively span the gap between brain and behavior, between neuroscience and psychology. Here, we attempt to bridge this divide by formalizing an integrative cognitive neuroscience approach using dynamic field theory (DFT). We begin by providing an overview of how DFT seeks to understand the neural population dynamics that underlie cognitive processes through previous applications and comparisons to other modeling approaches. We then use previously published behavioral and neural data from a response selection Go/Nogo task as a case study for model simulations. Results from this study served as the ‘standard’ for comparisons with a model-based fMRI approach using dynamic neural fields (DNF). The tutorial explains the rationale and hypotheses involved in the process of creating the DNF architecture and fitting model parameters. Two DNF models, with similar structure and parameter sets, are then compared. Both models effectively simulated reaction times from the task as we varied the number of stimulus-response mappings and the proportion of Go trials. Next, we directly simulated hemodynamic predictions from the neural activation patterns from each model. These predictions were tested using general linear models (GLMs). Results showed that the DNF model that was created by tuning parameters to capture simultaneously trends in neural activation and behavioral data quantitatively outperformed a Standard GLM analysis of the same dataset. Further, by using the GLM results to assign functional roles to particular clusters in the brain, we illustrate how DNF models shed new light on the neural populations’ dynamics within particular brain regions. Thus, the present study illustrates how an interactive cognitive neuroscience model can be used in practice to bridge the gap between brain and behavior. PMID:29118459

Direct dynamics simulations of the unimolecular dissociation of dioxetane: Probing the non-RRKM dynamics

NASA Astrophysics Data System (ADS)

Malpathak, Shreyas; Ma, Xinyou; Hase, William L.

2018-04-01

In a previous UB3LYP/6-31G* direct dynamics simulation, non-Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular dynamics was found for vibrationally excited 1,2-dioxetane (DO); [R. Sun et al., J. Chem. Phys. 137, 044305 (2012)]. In the work reported here, these dynamics are studied in more detail using the same direct dynamics method. Vibrational modes of DO were divided into 4 groups, based on their characteristic motions, and each group excited with the same energy. To compare with the dynamics of these groups, an additional group of trajectories comprising a microcanonical ensemble was also simulated. The results of these simulations are consistent with the previous study. The dissociation probability, N(t)/N(0), for these excitation groups were all different. Groups A, B, and C, without initial excitation in the O-O stretch reaction coordinate, had a time lag to of 0.25-1.0 ps for the first dissociation to occur. Somewhat surprisingly, the C-H stretch Group A and out-of-plane motion Group C excitations had exponential dissociation probabilities after to, with a rate constant ˜2 times smaller than the anharmonic RRKM value. Groups B and D, with excitation of the H-C-H bend and wag, and ring bend and stretch modes, respectively, had bi-exponential dissociation probabilities. For Group D, with excitation localized in the reaction coordinate, the initial rate constant is ˜7 times larger than the anharmonic RRKM value, substantial apparent non-RRKM dynamics. N(t)/N(0) for the random excitation trajectories was non-exponential, indicating intrinsic non-RRKM dynamics. For the trajectory integration time of 13.5 ps, 9% of these trajectories did not dissociate in comparison to the RRKM prediction of 0.3%. Classical power spectra for these trajectories indicate they have regular intramolecular dynamics. The N(t)/N(0) for the excitation groups are well described by a two-state coupled phase space model. From the intercept of N(t)/N(0) with random excitation, the anharmonic correction to the RRKM rate constant is approximately a factor of 1.5.

A novel simplified model for torsional vibration analysis of a series-parallel hybrid electric vehicle

NASA Astrophysics Data System (ADS)

Tang, Xiaolin; Yang, Wei; Hu, Xiaosong; Zhang, Dejiu

2017-02-01

In this study, based on our previous work, a novel simplified torsional vibration dynamic model is established to study the torsional vibration characteristics of a compound planetary hybrid propulsion system. The main frequencies of the hybrid driveline are determined. In contrast to vibration characteristics of the previous 16-degree of freedom model, the simplified model can be used to accurately describe the low-frequency vibration property of this hybrid powertrain. This study provides a basis for further vibration control of the hybrid powertrain during the process of engine start/stop.

Quasisaddles as relevant points of the potential energy surface in the dynamics of supercooled liquids

NASA Astrophysics Data System (ADS)

Angelani, L.; Di Leonardo, R.; Ruocco, G.; Scala, A.; Sciortino, F.

2002-06-01

The supercooled dynamics of a Lennard-Jones model liquid is numerically investigated studying relevant points of the potential energy surface, i.e., the minima of the square gradient of total potential energy V. The main findings are (i) the number of negative curvatures n of these sampled points appears to extrapolate to zero at the mode coupling critical temperature Tc; (ii) the temperature behavior of n(T) has a close relationship with the temperature behavior of the diffusivity; (iii) the potential energy landscape shows a high regularity in the distances among the relevant points and in their energy location. Finally we discuss a model of the landscape, previously introduced by Madan and Keyes [J. Chem. Phys. 98, 3342 (1993)], able to reproduce the previous findings.

Correlation lengths in hydrodynamic models of active nematics.

PubMed

Hemingway, Ewan J; Mishra, Prashant; Marchetti, M Cristina; Fielding, Suzanne M

2016-09-28

We examine the scaling with activity of the emergent length scales that control the nonequilibrium dynamics of an active nematic liquid crystal, using two popular hydrodynamic models that have been employed in previous studies. In both models we find that the chaotic spatio-temporal dynamics in the regime of fully developed active turbulence is controlled by a single active scale determined by the balance of active and elastic stresses, regardless of whether the active stress is extensile or contractile in nature. The observed scaling of the kinetic energy and enstrophy with activity is consistent with our single-length scale argument and simple dimensional analysis. Our results provide a unified understanding of apparent discrepancies in the previous literature and demonstrate that the essential physics is robust to the choice of model.

The dynamical crossover phenomenon in bulk water, confined water and protein hydration water.

PubMed

Mallamace, Francesco; Corsaro, Carmelo; Baglioni, Piero; Fratini, Emiliano; Chen, Sow-Hsin

2012-02-15

We discuss a phenomenon regarding water that was until recently a subject of scientific controversy, i.e. the dynamical crossover from fragile-to-strong glass-forming material, for both bulk and protein hydration water. Such a crossover is characterized by a temperature T(L) at which significant dynamical changes occur, such as violation of the Stokes-Einstein relation and changes of behaviour of homologous transport parameters such as the density relaxation time and the viscosity. In this respect we will consider carefully the dynamic properties of water-protein systems. More precisely, we will study proteins and their hydration water as far as bulk and confined water. In order to clarify the controversy we will discuss in a comparative way many previous and new experimental data that have emerged using different techniques and molecular dynamic simulation (MD). We point out the reasons for the different dynamical findings from the use of different experimental techniques.

Controlling Hydrogel Mechanics via Bio-Inspired Polymer-Nanoparticle Bond Dynamics.

PubMed

Li, Qiaochu; Barrett, Devin G; Messersmith, Phillip B; Holten-Andersen, Niels

2016-01-26

Interactions between polymer molecules and inorganic nanoparticles can play a dominant role in nanocomposite material mechanics, yet control of such interfacial interaction dynamics remains a significant challenge particularly in water. This study presents insights on how to engineer hydrogel material mechanics via nanoparticle interface-controlled cross-link dynamics. Inspired by the adhesive chemistry in mussel threads, we have incorporated iron oxide nanoparticles (Fe3O4 NPs) into a catechol-modified polymer network to obtain hydrogels cross-linked via reversible metal-coordination bonds at Fe3O4 NP surfaces. Unique material mechanics result from the supra-molecular cross-link structure dynamics in the gels; in contrast to the previously reported fluid-like dynamics of transient catechol-Fe(3+) cross-links, the catechol-Fe3O4 NP structures provide solid-like yet reversible hydrogel mechanics. The structurally controlled hierarchical mechanics presented here suggest how to develop hydrogels with remote-controlled self-healing dynamics.

Communication: Polymer entanglement dynamics: Role of attractive interactions

DOE PAGES

Grest, Gary S.

2016-10-10

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes to the late time diffusive regime, highly coarse grained models with purely repulsive interactions between monomers are widely used since they are computationally the most efficient. In this paper, using large scale molecular dynamics simulations, the effect of including the attractive interaction between monomers on the dynamics of entangled polymer melts is explored for the first time over a wide temperature range. Attractive interactions have little effect onmore » the local packing for all temperatures T and on the chain mobility for T higher than about twice the glass transition T g. Finally, these results, across a broad range of molecular weight, show that to study the dynamics of entangled polymer melts, the interactions can be treated as pure repulsive, confirming a posteriori the validity of previous studies and opening the way to new large scale numerical simulations.« less

Live dynamic analysis of the developing cardiovascular system in mice

NASA Astrophysics Data System (ADS)

Lopez, Andrew L.; Wang, Shang; Larin, Kirill V.; Larina, Irina V.

2017-02-01

The study of the developing cardiovascular system in mice is important for understanding human cardiogenesis and congenital heart defects. Our research focuses on imaging early development in the mouse embryo to specifically understand cardiovascular development under the regulation of dynamic factors like contractile force and blood flow using optical coherence tomography (OCT). We have previously developed an OCT based approach that combines static embryo culture and advanced image processing with computational modeling to live-image mouse embryos and obtain 4D (3D+time) cardiodynamic datasets. Here we present live 4D dynamic blood flow imaging of the early embryonic mouse heart in correlation with heart wall movement. We are using this approach to understand how specific mutations impact heart wall dynamics, and how this influences flow patterns and cardiogenesis. We perform studies in mutant embryos with cardiac phenotypes such as myosin regulatory light chain 2, atrial isoform (Mlc2a). This work is brings us closer to understanding the connections between dynamic mechanical factors and gene programs responsible for early cardiovascular development.

Clearing out a maze: A model of chemotactic motion in porous media

NASA Astrophysics Data System (ADS)

Schilling, Tanja; Voigtmann, Thomas

2017-12-01

We study the anomalous dynamics of a biased "hungry" (or "greedy") random walk on a percolating cluster. The model mimics chemotaxis in a porous medium: In close resemblance to the 1980s arcade game PAC-MA N ®, the hungry random walker consumes food, which is initially distributed in the maze, and biases its movement towards food-filled sites. We observe that the mean-squared displacement of the process follows a power law with an exponent that is different from previously known exponents describing passive or active microswimmer dynamics. The change in dynamics is well described by a dynamical exponent that depends continuously on the propensity to move towards food. It results in slower differential growth when compared to the unbiased random walk.

Simulation of hydrodynamically interacting particles near a no-slip boundary

NASA Astrophysics Data System (ADS)

Swan, James W.; Brady, John F.

2007-11-01

The dynamics of spherical particles near a single plane wall are computed using an extension of the Stokesian dynamics method that includes long-range many-body and pairwise lubrication interactions between the spheres and the wall in Stokes flow. Extra care is taken to ensure that the mobility and resistance tensors are symmetric, positive, and definite—something which is ineluctable for particles in low-Reynolds-number flows. We discuss why two previous simulation methods for particles near a plane wall, one using multipole expansions and the other using the Rotne-Prager tensor, fail to produce symmetric resistance and mobility tensors. Additionally, we offer some insight on how the Stokesian dynamics paradigm might be extended to study the dynamics of particles in any confining geometry.

Simulated sudden increase in geomagnetic activity and its effect on heart rate variability: Experimental verification of correlation studies.

PubMed

Caswell, Joseph M; Singh, Manraj; Persinger, Michael A

2016-08-01

Previous research investigating the potential influence of geomagnetic factors on human cardiovascular state has tended to converge upon similar inferences although the results remain relatively controversial. Furthermore, previous findings have remained essentially correlational without accompanying experimental verification. An exception to this was noted for human brain activity in a previous study employing experimental simulation of sudden geomagnetic impulses in order to assess correlational results that had demonstrated a relationship between geomagnetic perturbations and neuroelectrical parameters. The present study employed the same equipment in a similar procedure in order to validate previous findings of a geomagnetic-cardiovascular dynamic with electrocardiography and heart rate variability measures. Results indicated that potential magnetic field effects on frequency components of heart rate variability tended to overlap with previous correlational studies where low frequency power and the ratio between low and high frequency components of heart rate variability appeared affected. In the present study, a significant increase in these particular parameters was noted during geomagnetic simulation compared to baseline recordings. Copyright © 2016 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

The Direct Effect of Flexible Walls on Fontan Connection Fluid Dynamics

NASA Astrophysics Data System (ADS)

Tree, Mike; Fagan, Kiley; Yoganathan, Ajit

2014-11-01

The current standard treatment for sufferers of congenital heart defects is the palliative Fontan procedure. The Fontan procedure results in an anastomosis of major veins directly to the branched pulmonary arteries bypassing the dysfunctional ventricle. This total cavopulmonary connection (TCPC) extends life past birth, but Fontan patients still suffer long-term complications like decreased exercise capacity, protein-losing enteropathy, and pulmonary arteriovenous malformations (PAVM). These complications have direct ties to fluid dynamics within the connection. Previous experimental and computation studies of Fontan connection fluid dynamics employed rigid vessel models. More recent studies utilize flexible models, but a direct comparison of the fundamental fluid dynamics between rigid and flexible vessels only exists for a computational model, without a direct experimental validation. Thus, this study was a direct comparison of fluid dynamics within a rigid and two compliant idealized TCPCs. 2D particle image velocimetry measurements were collected at the connection center plane. Results include power loss, hepatic flow distribution, fluid shear stress, and flow structure recognition. The effect of flexible walls on these values and clinical impact will be discussed.

Functional dynamics of cell surface membrane proteins

NASA Astrophysics Data System (ADS)

Nishida, Noritaka; Osawa, Masanori; Takeuchi, Koh; Imai, Shunsuke; Stampoulis, Pavlos; Kofuku, Yutaka; Ueda, Takumi; Shimada, Ichio

2014-04-01

Cell surface receptors are integral membrane proteins that receive external stimuli, and transmit signals across plasma membranes. In the conventional view of receptor activation, ligand binding to the extracellular side of the receptor induces conformational changes, which convert the structure of the receptor into an active conformation. However, recent NMR studies of cell surface membrane proteins have revealed that their structures are more dynamic than previously envisioned, and they fluctuate between multiple conformations in an equilibrium on various timescales. In addition, NMR analyses, along with biochemical and cell biological experiments indicated that such dynamical properties are critical for the proper functions of the receptors. In this review, we will describe several NMR studies that revealed direct linkage between the structural dynamics and the functions of the cell surface membrane proteins, such as G-protein coupled receptors (GPCRs), ion channels, membrane transporters, and cell adhesion molecules.

Functional dynamics of cell surface membrane proteins.

PubMed

Nishida, Noritaka; Osawa, Masanori; Takeuchi, Koh; Imai, Shunsuke; Stampoulis, Pavlos; Kofuku, Yutaka; Ueda, Takumi; Shimada, Ichio

2014-04-01

Cell surface receptors are integral membrane proteins that receive external stimuli, and transmit signals across plasma membranes. In the conventional view of receptor activation, ligand binding to the extracellular side of the receptor induces conformational changes, which convert the structure of the receptor into an active conformation. However, recent NMR studies of cell surface membrane proteins have revealed that their structures are more dynamic than previously envisioned, and they fluctuate between multiple conformations in an equilibrium on various timescales. In addition, NMR analyses, along with biochemical and cell biological experiments indicated that such dynamical properties are critical for the proper functions of the receptors. In this review, we will describe several NMR studies that revealed direct linkage between the structural dynamics and the functions of the cell surface membrane proteins, such as G-protein coupled receptors (GPCRs), ion channels, membrane transporters, and cell adhesion molecules. Copyright © 2013 Elsevier Inc. All rights reserved.

Extensional channel flow revisited: a dynamical systems perspective

PubMed Central

Meseguer, Alvaro; Mellibovsky, Fernando; Weidman, Patrick D.

2017-01-01

Extensional self-similar flows in a channel are explored numerically for arbitrary stretching–shrinking rates of the confining parallel walls. The present analysis embraces time integrations, and continuations of steady and periodic solutions unfolded in the parameter space. Previous studies focused on the analysis of branches of steady solutions for particular stretching–shrinking rates, although recent studies focused also on the dynamical aspects of the problems. We have adopted a dynamical systems perspective, analysing the instabilities and bifurcations the base state undergoes when increasing the Reynolds number. It has been found that the base state becomes unstable for small Reynolds numbers, and a transitional region including complex dynamics takes place at intermediate Reynolds numbers, depending on the wall acceleration values. The base flow instabilities are constitutive parts of different codimension-two bifurcations that control the dynamics in parameter space. For large Reynolds numbers, the restriction to self-similarity results in simple flows with no realistic behaviour, but the flows obtained in the transition region can be a valuable tool for the understanding of the dynamics of realistic Navier–Stokes solutions. PMID:28690413

Modelling opinion formation driven communities in social networks

NASA Astrophysics Data System (ADS)

Iñiguez, Gerardo; Barrio, Rafael A.; Kertész, János; Kaski, Kimmo K.

2011-09-01

In a previous paper we proposed a model to study the dynamics of opinion formation in human societies by a co-evolution process involving two distinct time scales of fast transaction and slower network evolution dynamics. In the transaction dynamics we take into account short range interactions as discussions between individuals and long range interactions to describe the attitude to the overall mood of society. The latter is handled by a uniformly distributed parameter α, assigned randomly to each individual, as quenched personal bias. The network evolution dynamics is realised by rewiring the societal network due to state variable changes as a result of transaction dynamics. The main consequence of this complex dynamics is that communities emerge in the social network for a range of values in the ratio between time scales. In this paper we focus our attention on the attitude parameter α and its influence on the conformation of opinion and the size of the resulting communities. We present numerical studies and extract interesting features of the model that can be interpreted in terms of social behaviour.

Dynamic stabilization of Rayleigh-Taylor instability: Experiments with Newtonian fluids as surrogates for ablation fronts

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

Rodriguez Prieto, G.; Piriz, A. R.; Lopez Cela, J. J.

2013-01-15

A previous theory on dynamic stabilization of Rayleigh-Taylor instability at interfaces between Newtonian fluids is reformulated in order to make evident the analogy of this problem with the related one on dynamic stabilization of ablation fronts in the framework of inertial confinement fusion. Explicit analytical expressions are obtained for the boundaries of the dynamically stable region which turns out to be completely analogue to the stability charts obtained for the case of ablation fronts. These results allow proposing experiments with Newtonian fluids as surrogates for studying the case of ablation fronts. Experiments with Newtonian fluids are presented which demonstrate themore » validity of the theoretical approach and encourage to pursue experimental research on ablation fronts to settle the feasibility of dynamic stabilization in the inertial confinement fusion scenario.« less

Viability of Cross-Flow Fan with Helical Blades for Vertical Take-off and Landing Aircraft

DTIC Science & Technology

2012-09-01

fluid dynamics (CFD) software, ANSYS - CFX , a three-dimensional (3-D) straight-bladed model was validated against previous study’s experimental results...computational fluid dynamics software (CFD), ANSYS - CFX , a three-dimensional (3-D) straight-bladed model was validated against previous study’s experimental...37 B. SIZING PARAMETERS AND ILLUSTRATION ................................. 37 APPENDIX B. ANSYS CFX PARAMETERS

Spontaneous Facial Mimicry in Response to Dynamic Facial Expressions

ERIC Educational Resources Information Center

Sato, Wataru; Yoshikawa, Sakiko

2007-01-01

Based on previous neuroscientific evidence indicating activation of the mirror neuron system in response to dynamic facial actions, we hypothesized that facial mimicry would occur while subjects viewed dynamic facial expressions. To test this hypothesis, dynamic/static facial expressions of anger/happiness were presented using computer-morphing…

Observability of nonlinear dynamics: normalized results and a time-series approach.

PubMed

Aguirre, Luis A; Bastos, Saulo B; Alves, Marcela A; Letellier, Christophe

2008-03-01

This paper investigates the observability of nonlinear dynamical systems. Two difficulties associated with previous studies are dealt with. First, a normalized degree observability is defined. This permits the comparison of different systems, which was not generally possible before. Second, a time-series approach is proposed based on omnidirectional nonlinear correlation functions to rank a set of time series of a system in terms of their potential use to reconstruct the original dynamics without requiring the knowledge of the system equations. The two approaches proposed in this paper and a former method were applied to five benchmark systems and an overall agreement of over 92% was found.

Quantum dynamical simulation of photoinduced electron transfer processes in dye-semiconductor systems: theory and application to coumarin 343 at TiO₂.

PubMed

Li, Jingrui; Kondov, Ivan; Wang, Haobin; Thoss, Michael

2015-04-10

A recently developed methodology to simulate photoinduced electron transfer processes at dye-semiconductor interfaces is outlined. The methodology employs a first-principles-based model Hamiltonian and accurate quantum dynamics simulations using the multilayer multiconfiguration time-dependent Hartree approach. This method is applied to study electron injection in the dye-semiconductor system coumarin 343-TiO2. Specifically, the influence of electronic-vibrational coupling is analyzed. Extending previous work, we consider the influence of Dushinsky rotation of the normal modes as well as anharmonicities of the potential energy surfaces on the electron transfer dynamics.

Are fixed grain size ratios useful proxies for loess sedimentation dynamics? Experiences from Remizovka, Kazakhstan

NASA Astrophysics Data System (ADS)

Schulte, Philipp; Sprafke, Tobias; Rodrigues, Leonor; Fitzsimmons, Kathryn E.

2018-04-01

Loess-paleosol sequences (LPS) are sensitive terrestrial archives of past aeolian dynamics and paleoclimatic changes within the Quaternary. Grain size (GS) analysis is commonly used to interpret aeolian dynamics and climate influences on LPS, based on granulometric parameters such as specific GS classes, ratios of GS classes and statistical manipulation of GS data. However, the GS distribution of a loess sample is not solely a function of aeolian dynamics; rather complex polygenetic depositional and post-depositional processes must be taken into account. This study assesses the reliability of fixed GS ratios as proxies for past sedimentation dynamics using the case study of Remizovka in southeast Kazakhstan. Continuous sampling of the upper 8 m of the profile, which shows extremely weak pedogenic alteration and is therefore dominated by primary aeolian activity, indicates that fixed GS ratios do not adequately serve as proxies for loess sedimentation dynamics. We find through the calculation of single value parameters, that "true" variations within sensitive GS classes are masked by relative changes of the more frequent classes. Heatmap signatures provide the visualization of GS variability within LPS without significant data loss within the measured classes of a sample, or across all measured samples. We also examine the effect of two different commonly used laser diffraction devices on GS ratio calculation by duplicate measurements, the Beckman Coulter (LS13320) and a Malvern Mastersizer Hydro (MM2000), as well as the applicability and significance of the so-called "twin peak ratio" previously developed on samples from the same section. The LS13320 provides higher resolution results than the MM2000, nevertheless the GS ratios related to variations in the silt-sized fraction were comparable. However, we could not detect a twin peak within the coarse silt as detected in the original study using the same device. Our GS measurements differ from previous works at Remizovka in several instances, calling into question the interpretation of paleoclimatic implications using GS data alone.

Fluorescence quenching studies of potential-dependent DNA reorientation dynamics at glassy carbon electrode surfaces.

PubMed

Li, Qin; Cui, Chenchen; Higgins, Daniel A; Li, Jun

2012-09-05

The potential-dependent reorientation dynamics of double-stranded DNA (ds-DNA) attached to planar glassy carbon electrode (GCE) surfaces were investigated. The orientation state of surface-bound ds-DNA was followed by monitoring the fluorescence from a 6-carboxyfluorescein (FAM6) fluorophore covalently linked to the distal end of the DNA. Positive potentials (i.e., +0.2 V vs open circuit potential, OCP) caused the ds-DNA to align parallel to the electrode surface, resulting in strong dipole-electrode quenching of FAM6 fluorescence. Switching of the GCE potential to negative values (i.e., -0.2 V vs OCP) caused the ds-DNA to reorient perpendicular to the electrode surface, with a concomitant increase in FAM6 fluorescence. In addition to the very fast (submilliseconds) dynamics of the initial reorientation process, slow (0.1-0.9 s) relaxation of FAM6 fluorescence to intermediate levels was also observed after potential switching. These dynamics have not been previously described in the literature. They are too slow to be explained by double layer charging, and chronoamperometry data showed no evidence of such effects. Both the amplitude and rate of the dynamics were found to depend upon buffer concentration, and ds-DNA length, demonstrating a dependence on the double layer field. The dynamics are concluded to arise from previously undetected complexities in the mechanism of potential-dependent ds-DNA reorientation. The possible origins of these dynamics are discussed. A better understanding of these dynamics will lead to improved models for potential-dependent ds-DNA reorientation at electrode surfaces and will facilitate the development of advanced electrochemical devices for detection of target DNAs.

Short Animation Movies as Advance Organizers in Physics Teaching: A Preliminary Study

ERIC Educational Resources Information Center

Koscianski, Andre; Ribeiro, Rafael Joao; da Silva, Sani Carvalho Rutz

2012-01-01

Background: Advance organizers are instructional materials that help students use previous knowledge to make links with new information. Short animation movies are a possible format and are well suited for physics, as they can portray dynamic phenomena and represent abstract concepts. Purpose: The study aimed to determine guidelines for the…

Understanding Educational Policy Formation: The Case of School Violence Policies in Israel

ERIC Educational Resources Information Center

Fast, Idit

2016-01-01

This study explores mechanisms underlying processes of educational policy formation. Previous studies have given much attention to processes of diffusion when accounting for educational policy formation. Less account has been given to the day-to-day institutional dynamics through which educational policies develop and change. Building on extensive…

Comparison of Methods for Determining Boundary Layer Edge Conditions for Transition Correlations

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Berry, Scott A.; Hollis, Brian R.; Horvath, Thomas J.

2003-01-01

Data previously obtained for the X-33 in the NASA Langley Research Center 20-Inch Mach 6 Air Tunnel have been reanalyzed to compare methods for determining boundary layer edge conditions for use in transition correlations. The experimental results were previously obtained utilizing the phosphor thermography technique to monitor the status of the boundary layer downstream of discrete roughness elements via global heat transfer images of the X-33 windward surface. A boundary layer transition correlation was previously developed for this data set using boundary layer edge conditions calculated using an inviscid/integral boundary layer approach. An algorithm was written in the present study to extract boundary layer edge quantities from higher fidelity viscous computational fluid dynamic solutions to develop transition correlations that account for viscous effects on vehicles of arbitrary complexity. The boundary layer transition correlation developed for the X-33 from the viscous solutions are compared to the previous boundary layer transition correlations. It is shown that the boundary layer edge conditions calculated using an inviscid/integral boundary layer approach are significantly different than those extracted from viscous computational fluid dynamic solutions. The present results demonstrate the differences obtained in correlating transition data using different computational methods.

Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

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

Dahlen, Oda, E-mail: oda.dahlen@ntnu.no; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no

Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimentalmore » data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.« less

Dynamics and Instabilities of the Shastry-Sutherland Model

NASA Astrophysics Data System (ADS)

Wang, Zhentao; Batista, Cristian D.

2018-06-01

We study the excitation spectrum in the dimer phase of the Shastry-Sutherland model by using an unbiased variational method that works in the thermodynamic limit. The method outputs dynamical correlation functions in all possible channels. This output is exploited to identify the order parameters with the highest susceptibility (single or multitriplon condensation in a specific channel) upon approaching a quantum phase transition in the magnetic field versus the J'/J phase diagram. We find four different instabilities: antiferro spin nematic, plaquette spin nematic, stripe magnetic order, and plaquette order, two of which have been reported in previous studies.

Dynamic analysis of gas-core reactor system

NASA Technical Reports Server (NTRS)

Turner, K. H., Jr.

1973-01-01

A heat transfer analysis was incorporated into a previously developed model CODYN to obtain a model of open-cycle gaseous core reactor dynamics which can predict the heat flux at the cavity wall. The resulting model was used to study the sensitivity of the model to the value of the reactivity coefficients and to determine the system response for twenty specified perturbations. In addition, the model was used to study the effectiveness of several control systems in controlling the reactor. It was concluded that control drums located in the moderator region capable of inserting reactivity quickly provided the best control.

Analysis of regional-scale vegetation dynamics of Mexico using stratified AVHRR NDVI data. [Normalized Difference Vegetaion Index

NASA Technical Reports Server (NTRS)

Turcotte, Kevin M.; Kramber, William J.; Venugopal, Gopalan; Lulla, Kamlesh

1989-01-01

Previous studies have shown that a good relationship exists between AVHRR Normalized Difference Vegetation Index (NDVI) measurements, and both regional-scale patterns of vegetation seasonality and productivity. Most of these studies used known samples of vegetation types. An alternative approach, and the objective was to examine the above relationships by analyzing one year of AVHRR NDVI data that was stratified using a small-scale vegetation map of Mexico. The results show that there is a good relationship between AVHRR NDVI measurements and regional-scale vegetation dynamics of Mexico.

Computational Fluid Dynamics at ICMA (Institute for Computational Mathematics and Applications)

DTIC Science & Technology

1988-10-18

PERSONAL. AUTHOR(S) Charles A. Hall and Thomas A. Porsching 13a. TYPE OF REPORT 13b. TIME COVERED 114. DATE OF REPORT (YearMOth, De ) 1. PAGE COUNT...of ten ICtA (Institute for Computational Mathe- matics and Applications) personnel, relating to the general area of computational fluid mechanics...questions raised in the previous subsection. Our previous work in this area concentrated on a study of the differential geometric aspects of the prob- lem

Dynamic stabilization of classical Rayleigh-Taylor instability

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

Piriz, A. R.; Piriz, S. A.; Tahir, N. A.

2011-09-15

Dynamic stabilization of classical Rayleigh-Taylor instability is studied by modeling the interface vibration with the simplest possible wave form, namely, a sequence of Dirac deltas. As expected, stabilization results to be impossible. However, in contradiction to previously reported results obtained with a sinusoidal driving, it is found that in general the perturbation amplitude is larger than in the classical case. Therefore, no beneficial effect can be obtained from the vertical vibration of a Rayleigh-Taylor unstable interface between two ideal fluids.

Detection and Analysis of Complex Patterns of Ice Dynamics in Antarctica from ICESat Laser Altimetry

NASA Astrophysics Data System (ADS)

Babonis, Gregory Scott

There remains much uncertainty in estimating the amount of Antarctic ice mass change, its dynamic component, and its spatial and temporal patterns. This work remedies the limitations of previous studies by generating the first detailed reconstruction of total and dynamic ice thickness and mass changes across Antarctica, from ICESat satellite altimetry observations in 2003-2009 using the Surface Elevation Reconstruction and Change Detection (SERAC) method. Ice sheet thickness changes are calculated with quantified error estimates for each time when ICESat flew over a ground-track crossover region, at approximately 110,000 locations across the Antarctic Ice Sheet. The time series are partitioned into changes due to surficial processes and ice dynamics. The new results markedly improve the spatial and temporal resolution of surface elevation, volume, and mass change rates for the AIS, and can be sampled at annual temporal resolutions. The results indicate a complex spatiotemporal pattern of dynamic mass loss in Antarctica, especially along individual outlet glaciers, and allow for the quantification of the annual contribution of Antarctic ice loss to sea level rise. Over 5000 individual locations exhibit either strong dynamic ice thickness change patterns, accounting for approximately 500 unique spatial clusters that identify regions likely influenced by subglacial hydrology. The spatial distribution and temporal behavior of these regions reveal the complexity and short-time scale variability in the subglacial hydrological system. From the 500 unique spatial clusters, over 370 represent newly identified, and not previously published, potential subglacial water bodies indicating an active subglacial hydrological system over a much larger region than previously observed. These numerous new observations of dynamic changes provide more than simply a larger set of data. Examination of both regional and local scale dynamic change patterns across Antarctica shows newly discovered connections between the geology and ice sheet dynamics of Antarctica, particularly along the boundary between East and West Antarctica in the Pagano Shear Zone. Additionally, increased dynamic activity is shown to concentrate in regions of Antarctica most likely to experience catastrophic failure and collapse in the future. Further quantification of mass and volume changes demonstrates that the methods described within allow for a true reconciliation between different satellite methods of measuring ice sheet mass and volume balance, and show that Antarctica is losing enough mass between 2003 and 2009 to raise global sea levels 0.1 mm/yr during that time. Additionally, analysis of local patterns of dynamic ice thickness changes shows that there is continued or increased ice loss, since before the ICESat mission period, in many of the coastal sectors of Antarctica.

Effects of Solid Fraction on Droplet Wetting and Vapor Condensation: A Molecular Dynamic Simulation Study.

PubMed

Gao, Shan; Liao, Quanwen; Liu, Wei; Liu, Zhichun

2017-10-31

Recently, numerous studies focused on the wetting process of droplets on various surfaces at a microscale level. However, there are a limited number of studies about the mechanism of condensation on patterned surfaces. The present study performed the dynamic wetting behavior of water droplets and condensation process of water molecules on substrates with different pillar structure parameters, through molecular dynamic simulation. The dynamic wetting results indicated that droplets exhibit Cassie state, PW state, and Wenzel state successively on textured surfaces with decreasing solid fraction. The droplets possess a higher static contact angle and a smaller spreading exponent on textured surfaces than those on smooth surfaces. The condensation processes, including the formation, growth, and coalescence of a nanodroplet, are simulated and quantitatively recorded, which are difficult to be observed by experiments. In addition, a wetting transition and a dewetting transition were observed and analyzed in condensation on textured surfaces. Combining these simulation results with previous theoretical and experimental studies will guide us to understand the hypostasis and mechanism of the condensation more clearly.

The Met Office HadGEM3-ES chemistry-climate model: evaluation of stratospheric dynamics and its impact on ozone

NASA Astrophysics Data System (ADS)

Hardiman, Steven C.; Butchart, Neal; O'Connor, Fiona M.; Rumbold, Steven T.

2017-03-01

Free-running and nudged versions of a Met Office chemistry-climate model are evaluated and used to investigate the impact of dynamics versus transport and chemistry within the model on the simulated evolution of stratospheric ozone. Metrics of the dynamical processes relevant for simulating stratospheric ozone are calculated, and the free-running model is found to outperform the previous model version in 10 of the 14 metrics. In particular, large biases in stratospheric transport and tropical tropopause temperature, which existed in the previous model version, are substantially reduced, making the current model more suitable for the simulation of stratospheric ozone. The spatial structure of the ozone hole, the area of polar stratospheric clouds, and the increased ozone concentrations in the Northern Hemisphere winter stratosphere following sudden stratospheric warmings, were all found to be sensitive to the accuracy of the dynamics and were better simulated in the nudged model than in the free-running model. Whilst nudging can, in general, provide a useful tool for removing the influence of dynamical biases from the evolution of chemical fields, this study shows that issues can remain in the climatology of nudged models. Significant biases in stratospheric vertical velocities, age of air, water vapour, and total column ozone still exist in the Met Office nudged model. Further, these can lead to biases in the downward flux of ozone into the troposphere.

Vehicle dynamic analysis using neuronal network algorithms

NASA Astrophysics Data System (ADS)

Oloeriu, Florin; Mocian, Oana

2014-06-01

Theoretical developments of certain engineering areas, the emergence of new investigation tools, which are better and more precise and their implementation on-board the everyday vehicles, all these represent main influence factors that impact the theoretical and experimental study of vehicle's dynamic behavior. Once the implementation of these new technologies onto the vehicle's construction had been achieved, it had led to more and more complex systems. Some of the most important, such as the electronic control of engine, transmission, suspension, steering, braking and traction had a positive impact onto the vehicle's dynamic behavior. The existence of CPU on-board vehicles allows data acquisition and storage and it leads to a more accurate and better experimental and theoretical study of vehicle dynamics. It uses the information offered directly by the already on-board built-in elements of electronic control systems. The technical literature that studies vehicle dynamics is entirely focused onto parametric analysis. This kind of approach adopts two simplifying assumptions. Functional parameters obey certain distribution laws, which are known in classical statistics theory. The second assumption states that the mathematical models are previously known and have coefficients that are not time-dependent. Both the mentioned assumptions are not confirmed in real situations: the functional parameters do not follow any known statistical repartition laws and the mathematical laws aren't previously known and contain families of parameters and are mostly time-dependent. The purpose of the paper is to present a more accurate analysis methodology that can be applied when studying vehicle's dynamic behavior. A method that provides the setting of non-parametrical mathematical models for vehicle's dynamic behavior is relying on neuronal networks. This method contains coefficients that are time-dependent. Neuronal networks are mostly used in various types' system controls, thus being a non-linear process identification algorithm. The common use of neuronal networks for non-linear processes is justified by the fact that both have the ability to organize by themselves. That is why the neuronal networks best define intelligent systems, thus the word `neuronal' is sending one's mind to the biological neuron cell. The paper presents how to better interpret data fed from the on-board computer and a new way of processing that data to better model the real life dynamic behavior of the vehicle.

Neural correlates of the perception of dynamic versus static facial expressions of emotion.

PubMed

Kessler, Henrik; Doyen-Waldecker, Cornelia; Hofer, Christian; Hoffmann, Holger; Traue, Harald C; Abler, Birgit

2011-04-20

This study investigated brain areas involved in the perception of dynamic facial expressions of emotion. A group of 30 healthy subjects was measured with fMRI when passively viewing prototypical facial expressions of fear, disgust, sadness and happiness. Using morphing techniques, all faces were displayed as still images and also dynamically as a film clip with the expressions evolving from neutral to emotional. Irrespective of a specific emotion, dynamic stimuli selectively activated bilateral superior temporal sulcus, visual area V5, fusiform gyrus, thalamus and other frontal and parietal areas. Interaction effects of emotion and mode of presentation (static/dynamic) were only found for the expression of happiness, where static faces evoked greater activity in the medial prefrontal cortex. Our results confirm previous findings on neural correlates of the perception of dynamic facial expressions and are in line with studies showing the importance of the superior temporal sulcus and V5 in the perception of biological motion. Differential activation in the fusiform gyrus for dynamic stimuli stands in contrast to classical models of face perception but is coherent with new findings arguing for a more general role of the fusiform gyrus in the processing of socially relevant stimuli.

On the hydrogen-bond network and the non-Arrhenius transport properties of water

NASA Astrophysics Data System (ADS)

Galamba, N.

2017-01-01

We study the structural and dynamic transformations of SPC/E water with temperature, through molecular dynamics (MD), and discuss the non-Arrhenius behavior of the transport properties and orientational dynamics, and the magnitude of the breakdown of the Stokes-Einstein (SE) and the Stokes-Einstein-Debye (SED) relations, in the light of these transformations. Our results show that deviations from Arrhenius behavior of the self-diffusion at low temperatures cannot be exclusively explained by the reduction of water defects (interstitial waters) and the increase of the local tetrahedrality, thus, suggesting the importance of the slowdown of collective rearrangements. Interestingly we find that at high temperatures (T  ⩾  340 K) water defects lead to a slight increase of the tetrahedrality and a decrease of the self-diffusion, opposite to water at low temperatures. The relative magnitude of the breakdown of the SE and the SED relations is found to be in accord with recent experiments (Dehaoui et al 2015 Proc. Natl Acad. Sci. USA 112 12020) resolving the discrepancy with previous MD results. Further, we show that SPC/E hydrogen-bond (HB) lifetimes deviate from Arrhenious behaviour at low temperatures in contrast with some previous MD studies. This deviation is nevertheless much smaller than that observed for the orientational dynamics and the transport properties of water, consistent with the relaxation times measured by several experimental methods. The HB acceptor exchange dynamics defined here by the acceptor switch and reform (librational dynamics) frequencies exhibit similar Arrhenius deviations, thus explaining to some extent the non-Arrhenius behavior of the transport properties and of the orientational dynamics of water. Our results also show that the fraction of HB switches through a bifurcated pathway follow a power law with the temperature decrease. Thus, at low temperatures HB acceptor switches are less frequent but occur on a faster time scale consistent with the temperature dependence of the ratio of the rotational relaxation times for the different Legendre polynomial ranks.

On the hydrogen-bond network and the non-Arrhenius transport properties of water.

PubMed

Galamba, N

2017-01-11

We study the structural and dynamic transformations of SPC/E water with temperature, through molecular dynamics (MD), and discuss the non-Arrhenius behavior of the transport properties and orientational dynamics, and the magnitude of the breakdown of the Stokes-Einstein (SE) and the Stokes-Einstein-Debye (SED) relations, in the light of these transformations. Our results show that deviations from Arrhenius behavior of the self-diffusion at low temperatures cannot be exclusively explained by the reduction of water defects (interstitial waters) and the increase of the local tetrahedrality, thus, suggesting the importance of the slowdown of collective rearrangements. Interestingly we find that at high temperatures (T  ⩾  340 K) water defects lead to a slight increase of the tetrahedrality and a decrease of the self-diffusion, opposite to water at low temperatures. The relative magnitude of the breakdown of the SE and the SED relations is found to be in accord with recent experiments (Dehaoui et al 2015 Proc. Natl Acad. Sci. USA 112 12020) resolving the discrepancy with previous MD results. Further, we show that SPC/E hydrogen-bond (HB) lifetimes deviate from Arrhenious behaviour at low temperatures in contrast with some previous MD studies. This deviation is nevertheless much smaller than that observed for the orientational dynamics and the transport properties of water, consistent with the relaxation times measured by several experimental methods. The HB acceptor exchange dynamics defined here by the acceptor switch and reform (librational dynamics) frequencies exhibit similar Arrhenius deviations, thus explaining to some extent the non-Arrhenius behavior of the transport properties and of the orientational dynamics of water. Our results also show that the fraction of HB switches through a bifurcated pathway follow a power law with the temperature decrease. Thus, at low temperatures HB acceptor switches are less frequent but occur on a faster time scale consistent with the temperature dependence of the ratio of the rotational relaxation times for the different Legendre polynomial ranks.

Spatial and temporal dynamics of root exudation: how important is heterogeneity in allelopathic interactions?

PubMed

Weidenhamer, Jeffrey D; Mohney, Brian K; Shihada, Nader; Rupasinghe, Maduka

2014-08-01

Understanding allelopathy has been hindered by the lack of methods available to monitor the dynamics of allelochemicals in the soil. Previous work has demonstrated the feasibility of using polydimethylsiloxane (PDMS) microtubing (silicone tubing microextraction, or STME) to construct sampling devices to monitor the release of lipophilic allelochemicals from plant roots. The objective of this study was to use such sampling devices to intensively monitor thiophene fluxes beneath marigolds over several weeks to gain insight into the magnitude of temporal and spatial heterogeneity in these fluxes. Marigolds were grown in rhizoboxes (20.5 x 20.5 x 3.0 cm) with 16 individual STME samplers per box. Thiophene sampling and HPLC analysis began 45 days after planting. At the end of the study, roots around each sampler were analyzed by HPLC. Results confirmed the tremendous spatial and temporal heterogeneity in thiophene production seen in our previous studies. STME probes show that thiophene concentrations generally increase over time; however, these effects were sampling-port specific. When sampling ports were monitored at 12 h intervals, fluxes at each port ranged from 0 to 2,510 ng day(-1). Fluxes measured over daylight hr averaged 29 % higher than those measured overnight. Fluxes were less than 1 % on average of the total thiophene content of surrounding roots. While the importance of such heterogeneity, or "patchiness", in the root zone has been recognized for soil nutrients, the potential importance in allelopathic interactions has seldom been considered. The reasons for this variability are unclear, but are being investigated. Our results demonstrate that STME can be used as a tool to provide a more finely-resolved picture of allelochemical dynamics in the root zone than has previously been available.

Computer simulation on the collision-sticking dynamics of two colloidal particles in an optical trap.

PubMed

Xu, Shenghua; Sun, Zhiwei

2007-04-14

Collisions of a particle pair induced by optical tweezers have been employed to study colloidal stability. In order to deepen insights regarding the collision-sticking dynamics of a particle pair in the optical trap that were observed in experimental approaches at the particle level, the authors carry out a Brownian dynamics simulation. In the simulation, various contributing factors, including the Derjaguin-Landau-Verwey-Overbeek interaction of particles, hydrodynamic interactions, optical trapping forces on the two particles, and the Brownian motion, were all taken into account. The simulation reproduces the tendencies of the accumulated sticking probability during the trapping duration for the trapped particle pair described in our previous study and provides an explanation for why the two entangled particles in the trap experience two different statuses.

A dynamical systems model for nuclear power plant risk

NASA Astrophysics Data System (ADS)

Hess, Stephen Michael

The recent transition to an open access generation marketplace has forced nuclear plant operators to become much more cost conscious and focused on plant performance. Coincidentally, the regulatory perspective also is in a state of transition from a command and control framework to one that is risk-informed and performance-based. Due to these structural changes in the economics and regulatory system associated with commercial nuclear power plant operation, there is an increased need for plant management to explicitly manage nuclear safety risk. Application of probabilistic risk assessment techniques to model plant hardware has provided a significant contribution to understanding the potential initiating events and equipment failures that can lead to core damage accidents. Application of the lessons learned from these analyses has supported improved plant operation and safety over the previous decade. However, this analytical approach has not been nearly as successful in addressing the impact of plant processes and management effectiveness on the risks of plant operation. Thus, the research described in this dissertation presents a different approach to address this issue. Here we propose a dynamical model that describes the interaction of important plant processes among themselves and their overall impact on nuclear safety risk. We first provide a review of the techniques that are applied in a conventional probabilistic risk assessment of commercially operating nuclear power plants and summarize the typical results obtained. The limitations of the conventional approach and the status of research previously performed to address these limitations also are presented. Next, we present the case for the application of an alternative approach using dynamical systems theory. This includes a discussion of previous applications of dynamical models to study other important socio-economic issues. Next, we review the analytical techniques that are applicable to analysis of these models. Details of the development of the mathematical risk model are presented. This includes discussion of the processes included in the model and the identification of significant interprocess interactions. This is followed by analysis of the model that demonstrates that its dynamical evolution displays characteristics that have been observed at commercially operating plants. The model is analyzed using the previously described techniques from dynamical systems theory. From this analysis, several significant insights are obtained with respect to the effective control of nuclear safety risk. Finally, we present conclusions and recommendations for further research.

The thermochemical, two-phase dynamics of subduction zones: results from new, fully coupled models

NASA Astrophysics Data System (ADS)

Rees Jones, D. W.; Katz, R. F.; May, D.; Tian, M.; Rudge, J. F.

2017-12-01

Subduction zones are responsible for most of Earth's subaerial volcanism. However, previous geodynamic modelling of subduction zones has largely neglected magmatism. We previously showed that magmatism has a significant thermal impact, by advecting sensible heat into the lithosphere beneath arc volcanos [1]. Inclusion of this effect helps reconcile subduction zone models with petrological and heat flow observations. Many important questions remain, including how magma-mantle dynamics of subduction zones affects the position of arc volcanos and the character of their lavas. In this presentation, we employ a fully coupled, thermochemical, two-phase flow theory to investigate the dynamics of subduction zones. We present the first results from our new software (SubFUSc), which solves the coupled equations governing conservation of mass, momentum, energy and chemical species. The presence and migration of partial melts affect permeability and mantle viscosity (both directly and through their thermal impact); these, in turn, feed back on the magma-mantle flow. Thus our fully coupled modelling improves upon previous two-phase models that decoupled the governing equations and fixed the thermal structure [2]. To capture phase change, we use a novel, simplified model of the mantle melting in the presence of volatile species. As in the natural system, volatiles are associated with low-degree melting at temperatures beneath the anhydrous solidus; dehydration reactions in the slab supply volatiles into the wedge, triggering silicic melting. We simulate the migration of melts under buoyancy forces and dynamic pressure gradients. We thereby demonstrate the dynamical controls on the pattern of subduction-zone volcanism (particularly its location, magnitude, and chemical composition). We build on our previous study of the thermal consequences of magma genesis and segregation. We address the question of what controls the location of arc volcanoes themselves [3]. [1] Rees Jones, D. W., Katz, R. F., Tian, M and Rudge, J. F. (2017). Thermal impact of magmatism in subduction zones. arxiv.org/abs/1701.02550 [2] Wilson, C. R., Spiegelman, M., van Keken, P. E., & Hacker, B. R. (2014). EPSL, doi:10.1016/j.epsl.2014.05.052 [3] England, P. C., Katz, Richard F. (2010). Nature, doi:10.1038/nature09417

Coseismic Damage Generation in Fault Zones by Successive High Strain Rate Loading Experiments

NASA Astrophysics Data System (ADS)

Aben, F. M.; Doan, M. L.; Renard, F.; Toussaint, R.; Reuschlé, T.; Gratier, J. P.

2014-12-01

Damage zones of active faults control both resistance to rupture and transport properties of the fault. Hence, knowing the rock damage's origin is important to constrain its properties. Here we study experimentally the damage generated by a succession of dynamic loadings, a process mimicking the stress history of a rock sample located next to an active fault. A propagating rupture generates high frequency stress perturbations next to its tip. This dynamic loading creates pervasive damage (pulverization), as multiple fractures initiate and grow simultaneously. Previous single loading experiments have shown a strain rate threshold for pulverization. Here, we focus on conditions below this threshold and the dynamic peak stress to constrain: 1) if there is dynamic fracturing at these conditions and 2) if successive loadings (cumulative seismic events) result in pervasive fracturing, effectively reducing the pulverization threshold to milder conditions. Monzonite samples were dynamically loaded (strain rate > 50 s-1) several times below the dynamic peak strength, using a Split Hopkinson Pressure Bar apparatus. Several quasi-static experiments were conducted as well (strain rate < 10-5-s). Samples loaded up to stresses above the quasi-static uniaxial compressive strength (qsUCS) systematically fragmented or pulverized after four successive loadings. We measured several damage proxies (P-wave velocity, porosity), that show a systematic increase in damage with each load. In addition, micro-computed tomography acquisition on several damage samples revealed the growth of a pervasive fracture network between ensuing loadings. Samples loaded dynamically below the qsUCS failed along one fracture after a variable amount of loadings and damage proxies do not show any a systematic trend. Our conclusions is that milder dynamic loading conditions, below the dynamic peak strength, result in pervasive dynamic fracturing. Also, successive loadings effectively lower the pulverization threshold of the rock. However, the peak loading stress must exceed the qsUCS of the rock, otherwise quasi-static fracturing occurs. Pulverized rocks found in the field are therefore witnesses of previous large earthquakes.

Excited state non-adiabatic dynamics of pyrrole: A time-resolved photoelectron spectroscopy and quantum dynamics study

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

Wu, Guorong; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023; Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026

The dynamics of pyrrole excited at wavelengths in the range 242-217 nm are studied using a combination of time-resolved photoelectron spectroscopy and wavepacket propagations performed using the multi-configurational time-dependent Hartree method. Excitation close to the origin of pyrrole’s electronic spectrum, at 242 and 236 nm, is found to result in an ultrafast decay of the system from the ionization window on a single timescale of less than 20 fs. This behaviour is explained fully by assuming the system to be excited to the A{sub 2}(πσ{sup ∗}) state, in accord with previous experimental and theoretical studies. Excitation at shorter wavelengths hasmore » previously been assumed to result predominantly in population of the bright A{sub 1}(ππ{sup ∗}) and B{sub 2}(ππ{sup ∗}) states. We here present time-resolved photoelectron spectra at a pump wavelength of 217 nm alongside detailed quantum dynamics calculations that, together with a recent reinterpretation of pyrrole’s electronic spectrum [S. P. Neville and G. A. Worth, J. Chem. Phys. 140, 034317 (2014)], suggest that population of the B{sub 1}(πσ{sup ∗}) state (hitherto assumed to be optically dark) may occur directly when pyrrole is excited at energies in the near UV part of its electronic spectrum. The B{sub 1}(πσ{sup ∗}) state is found to decay on a timescale of less than 20 fs by both N-H dissociation and internal conversion to the A{sub 2}(πσ{sup ∗}) state.« less

Intersection of neighborhood dynamics and socioeconomic status in small-area walkability: the Heart Healthy Hoods project.

PubMed

Gullón, Pedro; Bilal, Usama; Cebrecos, Alba; Badland, Hannah M; Galán, Iñaki; Franco, Manuel

2017-06-06

Previous studies found a complex relationship between area-level socioeconomic status (SES) and walkability. These studies did not include neighborhood dynamics. Our aim was to study the association between area-level SES and walkability in the city of Madrid (Spain) evaluating the potential effect modification of neighborhood dynamics. All census sections of the city of Madrid (n = 2415) were included. Area-level SES was measured using a composite index of 7 indicators in 4 domains (education, wealth, occupation and living conditions). Two neighborhood dynamics factors were computed: gentrification, proxied by change in education levels in the previous 10 years, and neighborhood age, proxied by median year of construction of housing units in the area. Walkability was measured using a composite index of 4 indicators (Residential Density, Population Density, Retail Destinations and Street Connectivity). We modeled the association using linear mixed models with random intercepts. Area-level SES and walkability were inversely and significantly associated. Areas with lower SES showed the highest walkability. This pattern did not hold for areas with an increase in education level, where the association was flat (no decrease in walkability with higher SES). Moreover, the association was attenuated in newly built areas: the association was stronger in areas built before 1975, weaker in areas built between 1975 and 1990 and flat in areas built from 1990 on. Areas with higher neighborhood socioeconomic status had lower walkability in Madrid. This disadvantage in walkability was not present in recently built or gentrified areas.

A gyrokinetic one-dimensional scrape-off layer model of an edge-localized mode heat pulse

DOE PAGES

Shi, E. L.; Hakim, A. H.; Hammett, G. W.

2015-02-03

An electrostatic gyrokinetic-based model is applied to simulate parallel plasma transport in the scrape-off layer to a divertor plate. We focus on a test problem that has been studied previously, using parameters chosen to model a heat pulse driven by an edge-localized mode in JET. Previous work has used direct particle-in-cellequations with full dynamics, or Vlasov or fluid equations with only parallel dynamics. With the use of the gyrokinetic quasineutrality equation and logical sheathboundary conditions, spatial and temporal resolution requirements are no longer set by the electron Debye length and plasma frequency, respectively. Finally, this test problem also helps illustratemore » some of the physics contained in the Hamiltonian form of the gyrokineticequations and some of the numerical challenges in developing an edge gyrokinetic code.« less

Tsallis q-triplet, intermittent turbulence and Portevin-Le Chatelier effect

NASA Astrophysics Data System (ADS)

Iliopoulos, A. C.; Aifantis, E. C.

2018-05-01

In this paper, we extend a previous study concerning Portevin-LeChatelier (PLC) effect and Tsallis statistics (Iliopoulos et al., 2015). In particular, we estimate Tsallis' q-triplet, namely {qstat, qsens, qrel} for two sets of stress serration time series concerning the deformation of Cu-15%Al alloy corresponding to different deformation temperatures and thus types (A and B) of PLC bands. The results concerning the stress serrations analysis reveal that Tsallis q- triplet attains values different from unity ({qstat, qsens, qrel} ≠ {1,1,1}). In particular, PLC type A bands' serrations were found to follow Tsallis super-q-Gaussian, non-extensive, sub-additive, multifractal statistics indicating that the underlying dynamics are at the edge of chaos, characterized by global long range correlations and power law scaling. For PLC type B bands' serrations, the results revealed a Tsallis sub-q-Gaussian, non-extensive, super-additive, multifractal statistical profile. In addition, our results reveal also significant differences in statistical and dynamical features, indicating important variations of the stress field dynamics in terms of rate of entropy production, relaxation dynamics and non-equilibrium meta-stable stationary states. We also estimate parameters commonly used for characterizing fully developed turbulence, such as structure functions and flatness coefficient (F), in order to provide further information about jerky flow underlying dynamics. Finally, we use two multifractal models developed to describe turbulence, namely Arimitsu and Arimitsu (A&A) [2000, 2001] theoretical model which is based on Tsallis statistics and p-model to estimate theoretical multifractal spectrums f(a). Furthermore, we estimate flatness coefficient (F) using a theoretical formula based on Tsallis statistics. The theoretical results are compared with the experimental ones showing a remarkable agreement between modeling and experiment. Finally, the results of this study verify, as well as, extend previous studies which stated that type B and type A PLC bands underlying dynamics are connected with distinct dynamical behavior, namely chaotic behavior for the first and self-organized critical (SOC) behavior for the latter, while they shed new light concerning the turbulent character of the PLC jerky flow.

Betwixt and Between: Academic Developers in the Margins

ERIC Educational Resources Information Center

Little, Deandra; Green, David A.

2012-01-01

Previously, the authors developed a theoretical framework drawing on an early sociological study of migration to explore how marginality--being between cultures--might account for academic developers' "hybrid" academic identities and help them navigate institutional power dynamics. Based on data from semi-structured interviews, this…

Preferential sites for InAsP/InP quantum wire nucleation using molecular dynamics

NASA Astrophysics Data System (ADS)

Nuñez-Moraleda, Bernardo; Pizarro, Joaquin; Guerrero, Elisa; Guerrero-Lebrero, Maria P.; Yáñez, Andres; Molina, Sergio Ignacio; Galindo, Pedro Luis

2014-11-01

In this paper, stress fields at the surface of the capping layer of self-assembled InAsP quantum wires grown on an InP (001) substrate have been determined from atomistic models using molecular dynamics and Stillinger-Weber potentials. To carry out these calculations, the quantum wire compositional distribution was extracted from previous works, where the As and P distributions were determined by electron energy loss spectroscopy and high-resolution aberration-corrected Z-contrast imaging. Preferential sites for the nucleation of wires on the surface of the capping layer were studied and compared with (i) previous simulations using finite element analysis to solve anisotropic elastic theory equations and (ii) experimentally measured locations of stacked wires. Preferential nucleation sites of stacked wires were determined by the maximum stress location at the MD model surface in good agreement with experimental results and those derived from finite element analysis. This indicates that MD simulations based on empirical potentials provide a suitable and flexible tool to study strain dependent atom processes.

Transient Mobility on Submonolayer Island Growth: An Exploration of Asymptotic Effects in Modeling

NASA Astrophysics Data System (ADS)

Morales-Cifuentes, Josue; Einstein, Theodore L.; Pimpinelli, Alberto

In studies of epitaxial growth, modeling of the smallest stable cluster (i+1 monomers, with i the critical nucleus size), is paramount in understanding growth dynamics. Our previous work has tackled submonolayer growth by modeling the effect of ballistic monomers, hot-precursors, on diffusive dynamics. Different scaling regimes and energies were predicted, with initial confirmation by applying to para-hexaphenyl submonolayer studies. Lingering questions about the applicability and behavior of the model are addressed. First, we show how an asymptotic approximation based on the growth exponent, α (N Fα) allows for robustness of modeling to experimental data; second, we answer questions about non-monotonicity by exploring the behavior of the growth exponent across realizable parameter spaces; third, we revisit our previous para-hexaphenyl work and examine relevant physical parameters, namely the speed of the hot-monomers. We conclude with an exploration of how the new asymptotic approximation can be used to strengthen the application of our model to other physical systems.

Cu nuclear magnetic resonance study of charge and spin stripe order in La 1.875 Ba 0.125 CuO 4

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

Pelc, D.; Grafe, H. -J.; Gu, G. D.

In this paper, we present a Cu nuclear magnetic/quadrupole resonance study of the charge stripe ordered phase of LBCO, with detection of previously unobserved (“wiped-out”) signal. We show that spin-spin and spin-lattice relaxation rates are strongly enhanced in the charge ordered phase, explaining the apparent signal decrease in earlier investigations. The enhancement is caused by magnetic, rather than charge fluctuations, conclusively confirming the long-suspected assumption that spin fluctuations are responsible for the wipeout effect. Observation of the full Cu signal enables insight into the spin and charge dynamics of the stripe-ordered phase, and measurements in external magnetic fields provide informationmore » on the nature and suppression of spin fluctuations associated with charge order. Lastly, we find glassy spin dynamics, in agreement with previous work, and incommensurate static charge order with charge modulation amplitude similar to other cuprate compounds, suggesting that the amplitude of charge stripes is universal in the cuprates.« less

Cu nuclear magnetic resonance study of charge and spin stripe order in La 1.875 Ba 0.125 CuO 4

DOE PAGES

Pelc, D.; Grafe, H. -J.; Gu, G. D.; ...

2017-02-15

In this paper, we present a Cu nuclear magnetic/quadrupole resonance study of the charge stripe ordered phase of LBCO, with detection of previously unobserved (“wiped-out”) signal. We show that spin-spin and spin-lattice relaxation rates are strongly enhanced in the charge ordered phase, explaining the apparent signal decrease in earlier investigations. The enhancement is caused by magnetic, rather than charge fluctuations, conclusively confirming the long-suspected assumption that spin fluctuations are responsible for the wipeout effect. Observation of the full Cu signal enables insight into the spin and charge dynamics of the stripe-ordered phase, and measurements in external magnetic fields provide informationmore » on the nature and suppression of spin fluctuations associated with charge order. Lastly, we find glassy spin dynamics, in agreement with previous work, and incommensurate static charge order with charge modulation amplitude similar to other cuprate compounds, suggesting that the amplitude of charge stripes is universal in the cuprates.« less

Coupling between amino acid and water dynamics by broadband dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Saiz, Luciana; Cerveny, Silvina

2014-05-01

The dynamics of proline aqueous solution was investigated for water concentrations from 40 to 60 wt% by dielectric spectroscopy (106 - 109 Hz) in the temperature range from 230 to 300 K, where the solutions remain amorphous. We found two relaxation processes, related with the reorientation of proline and water as previously observed in a higher frequency range at room temperature [1]. We found that both dynamics are strongly coupled, as previously observed in hydrated proteins powders, in spite of the fact that a single amino acid is a molecule much simpler than a protein.

Studies of vorticity imbalance and stability, moisture budget, atmospheric energetics, and gradients of meteorological parameters during AVE 3

NASA Technical Reports Server (NTRS)

Scoggins, J. R. (Editor)

1978-01-01

Four diagnostic studies of AVE 3. are presented. AVE 3 represents a high wind speed wintertime situation, while most AVE's analyzed previously represented springtime conditions with rather low wind speeds. The general areas of analysis include the examination of budgets of vorticity, moisture, kinetic energy, and potential energy and a synoptic and statistical study of the horizontal gradients of meteorological parameters. Conclusions are integrated with and compared to those obtained in previously analyzed experiments (mostly springtime weather situations) so as to establish a more definitive understanding of the structure and dynamics of the atmosphere under a wide range of synoptic conditions.

Troponin structure: its modulation by Ca(2+) and phosphorylation studied by molecular dynamics simulations.

PubMed

Zamora, Juan Eiros; Papadaki, Maria; Messer, Andrew E; Marston, Steven B; Gould, Ian R

2016-07-27

The only available crystal structure of the human cardiac troponin molecule (cTn) in the Ca(2+) activated state does not include crucial segments, including the N-terminus of the cTn inhibitory subunit (cTnI). We have applied all-atom molecular dynamics (MD) simulations to study the structure and dynamics of cTn, both in the unphosphorylated and bis-phosphorylated states at Ser23/Ser24 of cTnI. We performed multiple microsecond MD simulations of wild type (WT) cTn (6, 5 μs) and bisphosphorylated (SP23/SP24) cTn (9 μs) on a 419 amino acid cTn model containing human sequence cTnC (1-161), cTnI (1-171) and cTnT (212-298), including residues not present in the crystal structure. We have compared our results to previous computational studies, and proven that longer simulations and a water box of at least 25 Å are needed to sample the interesting conformational shifts both in the native and bis-phosphorylated states. As a consequence of the introduction into the model of the C-terminus of cTnT that was missing in previous studies, cTnC-cTnI interactions that are responsible for the cTn dynamics are altered. We have also shown that phosphorylation does not increase cTn fluctuations, and its effects on the protein-protein interaction profiles cannot be assessed in a significant way. Finally, we propose that phosphorylation could provoke a loss of Ca(2+) by stabilizing out-of-coordination distances of the cTnC's EF hand II residues, and in particular Ser 69.

Quadrupedal rodent gait compensations in a low dose monoiodoacetate model of osteoarthritis.

PubMed

Lakes, Emily H; Allen, Kyle D

2018-06-01

Rodent gait analysis provides robust, quantitative results for preclinical musculoskeletal and neurological models. In prior work, surgical models of osteoarthritis have been found to result in a hind limb shuffle-stepping gait compensation, while a high dose monoiodoacetate (MIA, 3 mg) model resulted in a hind limb antalgic gait. However, it is unknown whether the antalgic gait caused by MIA is associated with severity of degeneration from the high dosage or the whole-joint degeneration associated with glycolysis inhibition. This study evaluates rodent gait changes resulting from a low dose, 1 mg unilateral intra-articular injection of MIA compared to saline injected and naïve rats. Spatiotemporal and dynamic gait parameters were collected from a total of 42 male Lewis rats spread across 3 time points: 1, 2, and 4 weeks post-injection. To provide a detailed analysis of this low dose MIA model, gait analysis was used to uniquely quantify both fore and hind limb gait parameters. Our data indicate that 1 mg of MIA caused relatively minor degeneration and a shuffle-step gait compensation, similar to the compensation observed in prior surgical models. These data from a 1 mg MIA model show a different gait compensation compared to a previously studied 3 mg model. This 1 mg MIA model resulted in gait compensations more similar to a previously studied surgical model of osteoarthritis. Additionally, this study provides detailed 4 limb analysis of rodent gait that includes spatiotemporal and dynamic data from the same gait trial. These data highlight the importance of measuring dynamic data in combination with spatiotemporal data, since compensatory gait patterns may not be captured by spatial, temporal, or dynamic characterizations alone. Copyright © 2018 Elsevier B.V. All rights reserved.

Dynamic Analysis of Spur Gear Transmissions (DANST). PC Version 3.00 User Manual

NASA Technical Reports Server (NTRS)

Oswald, Fred B.; Lin, Hsiang Hsi; Delgado, Irebert R.

1996-01-01

DANST is a FORTRAN computer program for static and dynamic analysis of spur gear systems. The program can be used for parametric studies to predict the static transmission error, dynamic load, tooth bending stress and other properties of spur gears as they are influenced by operating speed, torque, stiffness, damping, inertia, and tooth profile. DANST performs geometric modeling and dynamic analysis for low- or high-contact-ratio spur gears. DANST can simulate gear systems with contact ratios ranging from one to three. It was designed to be easy to use and it is extensively documented in several previous reports and by comments in the source code. This report describes installing and using a new PC version of DANST, covers input data requirements and presents examples.

Ultrafast photodissociation dynamics of 1,4-diiodobenzene

NASA Astrophysics Data System (ADS)

Stankus, Brian; Zotev, Nikola; Rogers, David M.; Gao, Yan; Odate, Asami; Kirrander, Adam; Weber, Peter M.

2018-05-01

The photodissociation dynamics of 1,4-diiodobenzene is investigated using ultrafast time-resolved photoelectron spectroscopy. Following excitation by laser pulses at 271 nm, the excited-state dynamics is probed by resonance-enhanced multiphoton ionization with 405 nm probe pulses. A progression of Rydberg states, which come into resonance sequentially, provide a fingerprint of the dissociation dynamics of the molecule. The initial excitation decays with a lifetime of 33 ± 4 fs, in good agreement with a previous study. The spectrum is interpreted by reference to ab initio calculations at the CASPT2(18,14) level, including spin-orbit coupling. We propose that both the 5B1 and 6B1 states are excited initially, and based on the calculations, we identify diabatic spin-orbit coupled states corresponding to the main dissociation pathways.

Influence of light-induced conical intersection on the photodissociation dynamics of D2(+) starting from individual vibrational levels.

PubMed

Halász, Gábor J; Csehi, András; Vibók, Ágnes; Cederbaum, Lorenz S

2014-12-26

Previous works have shown that dressing of diatomic molecules by standing or by running laser waves gives rise to the appearance of so-called light-induced conical intersections (LICIs). Because of the strong nonadiabatic couplings, the existence of such LICIs may significantly change the dynamical properties of a molecular system. In our former paper (J. Phys. Chem. A 2013, 117, 8528), the photodissociation dynamics of the D(2)(+) molecule were studied in the LICI framework starting the initial vibrational nuclear wave packet from the superposition of all the vibrational states initially produced by ionizing D(2). The present work complements our previous investigation by letting the initial nuclear wave packets start from different individual vibrational levels of D(2)(+), in particular, above the energy of the LICI. The kinetic energy release spectra, the total dissociation probabilities, and the angular distributions of the photofragments are calculated and discussed. An interesting phenomenon has been found in the spectra of the photofragments. Applying the light-induced adiabatic picture supported by LICI, explanations are given for the unexpected structure of the spectra.

Dynamic model based on voltage transfer curve for pattern formation in dielectric barrier glow discharge

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

Li, Ben; He, Feng; Ouyang, Jiting, E-mail: jtouyang@bit.edu.cn

2015-12-15

Simulation work is very important for understanding the formation of self-organized discharge patterns. Previous works have witnessed different models derived from other systems for simulation of discharge pattern, but most of these models are complicated and time-consuming. In this paper, we introduce a convenient phenomenological dynamic model based on the basic dynamic process of glow discharge and the voltage transfer curve (VTC) to study the dielectric barrier glow discharge (DBGD) pattern. VTC is an important characteristic of DBGD, which plots the change of wall voltage after a discharge as a function of the initial total gap voltage. In the modeling,more » the combined effect of the discharge conditions is included in VTC, and the activation-inhibition effect is expressed by a spatial interaction term. Besides, the model reduces the dimensionality of the system by just considering the integration effect of current flow. All these greatly facilitate the construction of this model. Numerical simulations turn out to be in good accordance with our previous fluid modeling and experimental result.« less

Vortex dynamics in ruptured and unruptured intracranial aneurysms

NASA Astrophysics Data System (ADS)

Trylesinski, Gabriel; Varble, Nicole; Xiang, Jianping; Meng, Hui

2013-11-01

Intracranial aneurysms (IAs) are potentially devastating pathological dilations of arterial walls that affect 2-5% of the population. In our previous CFD study of 119 IAs, we found that ruptured aneurysms were correlated with complex flow pattern and statistically predictable by low wall shear stress and high oscillatory shear index. To understand flow mechanisms that drive the pathophysiology of aneurysm wall leading to either stabilization or growth and rupture, we aim at exploring vortex dynamics of aneurysmal flow and provide insight into the correlation between the previous predictive morphological parameters and wall hemodynamic metrics. We adopt the Q-criterion definition of coherent structures (CS) and analyze the CS dynamics in aneurysmal flows for both ruptured and unruptured IA cases. For the first time, we draw relevant biological conclusions concerning aneurysm flow mechanisms and pathophysiological outcome. In pulsatile simulations, the coherent structures are analyzed in these 119 patient-specific geometries obtained using 3D angiograms. The images were reconstructed and CFD were performed. Upon conclusion of this work, better understanding of flow patterns of unstable aneurysms may lead to improved clinical outcome.

Polymer physics experiments with single DNA molecules

NASA Astrophysics Data System (ADS)

Smith, Douglas E.

1999-11-01

Bacteriophage DNA molecules were taken as a model flexible polymer chain for the experimental study of polymer dynamics at the single molecule level. Video fluorescence microscopy was used to directly observe the conformational dynamics of fluorescently labeled molecules, optical tweezers were used to manipulate individual molecules, and micro-fabricated flow cells were used to apply controlled hydrodynamic strain to molecules. These techniques constitute a powerful new experimental approach in the study of basic polymer physics questions. I have used these techniques to study the diffusion and relaxation of isolated and entangled polymer molecules and the hydrodynamic deformation of polymers in elongational and shear flows. These studies revealed a rich, and previously unobserved, ``molecular individualism'' in the dynamical behavior of single molecules. Individual measurements on ensembles of identical molecules allowed the average conformation to be determined as well as the underlying probability distributions for molecular conformation. Scaling laws, that predict the dependence of properties on chain length and concentration, were also tested. The basic assumptions of the reptation model were directly confirmed by visualizing the dynamics of entangled chains.

Exploratory Study of RNA Polymerase II Using Dynamic Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Rhodin, Thor; Umemura, Kazuo; Gad, Mohammed; Jarvis, Suzanne; Ishikawa, Mitsuru; Fu, Jianhua

2002-03-01

An exploratory study of the microtopological dimensions and shape features of yeast RNA polymerase II (y-poly II) on freshly cleaved mica was made in phosphate aqueous buffer solution at room temperature following previous work by Hansma and others. The molecules were imaged by stabilization on freshly cleaved mica at a limiting resolution of 10 Å and scanned using dynamical atomic force microscopy with a 10 nm multi-wall carbon nanotube in the resonance frequency modulation mode. They indicated microtopological shape and dimensional features similar to those predicted by electron density plots derived from the X-ray crystallographic model. It is concluded that this is considered primarily a feasibility study with definitive conclusions subject to more detailed systematic measurements of the 3D microtopology. These measurements appear to establish validity of the noncontact atomic force microscopy (nc-AFM) approach into defining the primary microtopology and biochemical functionality of RNA polymerase II. Further nc-AFM studies at higher resolution using dynamical nc-AFM will be required to clearly define the detailed 3D microtopology of RNA polymerase II in anaerobic aqueous environments for both static and dynamic conditions.

General methods for sensitivity analysis of equilibrium dynamics in patch occupancy models

USGS Publications Warehouse

Miller, David A.W.

2012-01-01

Sensitivity analysis is a useful tool for the study of ecological models that has many potential applications for patch occupancy modeling. Drawing from the rich foundation of existing methods for Markov chain models, I demonstrate new methods for sensitivity analysis of the equilibrium state dynamics of occupancy models. Estimates from three previous studies are used to illustrate the utility of the sensitivity calculations: a joint occupancy model for a prey species, its predators, and habitat used by both; occurrence dynamics from a well-known metapopulation study of three butterfly species; and Golden Eagle occupancy and reproductive dynamics. I show how to deal efficiently with multistate models and how to calculate sensitivities involving derived state variables and lower-level parameters. In addition, I extend methods to incorporate environmental variation by allowing for spatial and temporal variability in transition probabilities. The approach used here is concise and general and can fully account for environmental variability in transition parameters. The methods can be used to improve inferences in occupancy studies by quantifying the effects of underlying parameters, aiding prediction of future system states, and identifying priorities for sampling effort.

Adaptive two-regime method: Application to front propagation

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

Robinson, Martin, E-mail: martin.robinson@maths.ox.ac.uk; Erban, Radek, E-mail: erban@maths.ox.ac.uk; Flegg, Mark, E-mail: mark.flegg@monash.edu

2014-03-28

The Adaptive Two-Regime Method (ATRM) is developed for hybrid (multiscale) stochastic simulation of reaction-diffusion problems. It efficiently couples detailed Brownian dynamics simulations with coarser lattice-based models. The ATRM is a generalization of the previously developed Two-Regime Method [Flegg et al., J. R. Soc., Interface 9, 859 (2012)] to multiscale problems which require a dynamic selection of regions where detailed Brownian dynamics simulation is used. Typical applications include a front propagation or spatio-temporal oscillations. In this paper, the ATRM is used for an in-depth study of front propagation in a stochastic reaction-diffusion system which has its mean-field model given in termsmore » of the Fisher equation [R. Fisher, Ann. Eugen. 7, 355 (1937)]. It exhibits a travelling reaction front which is sensitive to stochastic fluctuations at the leading edge of the wavefront. Previous studies into stochastic effects on the Fisher wave propagation speed have focused on lattice-based models, but there has been limited progress using off-lattice (Brownian dynamics) models, which suffer due to their high computational cost, particularly at the high molecular numbers that are necessary to approach the Fisher mean-field model. By modelling only the wavefront itself with the off-lattice model, it is shown that the ATRM leads to the same Fisher wave results as purely off-lattice models, but at a fraction of the computational cost. The error analysis of the ATRM is also presented for a morphogen gradient model.« less

Clinical Feasibility of Free-Breathing Dynamic T1-Weighted Imaging With Gadoxetic Acid-Enhanced Liver Magnetic Resonance Imaging Using a Combination of Variable Density Sampling and Compressed Sensing.

PubMed

Yoon, Jeong Hee; Yu, Mi Hye; Chang, Won; Park, Jin-Young; Nickel, Marcel Dominik; Son, Yohan; Kiefer, Berthold; Lee, Jeong Min

2017-10-01

The purpose of the study was to investigate the clinical feasibility of free-breathing dynamic T1-weighted imaging (T1WI) using Cartesian sampling, compressed sensing, and iterative reconstruction in gadoxetic acid-enhanced liver magnetic resonance imaging (MRI). This retrospective study was approved by our institutional review board, and the requirement for informed consent was waived. A total of 51 patients at high risk of breath-holding failure underwent dynamic T1WI in a free-breathing manner using volumetric interpolated breath-hold (BH) examination with compressed sensing reconstruction (CS-VIBE) and hard gating. Timing, motion artifacts, and image quality were evaluated by 4 radiologists on a 4-point scale. For patients with low image quality scores (<3) on the late arterial phase, respiratory motion-resolved (extradimension [XD]) reconstruction was additionally performed and reviewed in the same manner. In addition, in 68.6% (35/51) patients who had previously undergone liver MRI, image quality and motion artifacts on dynamic phases using CS-VIBE were compared with previous BH-T1WIs. In all patients, adequate arterial-phase timing was obtained at least once. Overall image quality of free-breathing T1WI was 3.30 ± 0.59 on precontrast and 2.68 ± 0.70, 2.93 ± 0.65, and 3.30 ± 0.49 on early arterial, late arterial, and portal venous phases, respectively. In 13 patients with lower than average image quality (<3) on the late arterial phase, motion-resolved reconstructed T1WI (XD-reconstructed CS-VIBE) significantly reduced motion artifacts (P < 0.002-0.021) and improved image quality (P < 0.0001-0.002). In comparison with previous BH-T1WI, CS-VIBE with hard gating or XD reconstruction showed less motion artifacts and better image quality on precontrast, arterial, and portal venous phases (P < 0.0001-0.013). Volumetric interpolated breath-hold examination with compressed sensing has the potential to provide consistent, motion-corrected free-breathing dynamic T1WI for liver MRI in patients at high risk of breath-holding failure.

The cultural implications of growth: Modeling nonlinear interaction of trait selection and population dynamics

NASA Astrophysics Data System (ADS)

Antoci, Angelo; Galeotti, Marcello; Russu, Paolo; Luigi Sacco, Pier

2018-05-01

In this paper, we study a nonlinear model of the interaction between trait selection and population dynamics, building on previous work of Ghirlanda et al. [Theor. Popul. Biol. 77, 181-188 (2010)] and Antoci et al. [Commun. Nonlinear Sci. Numer. Simul. 58, 92-106 (2018)]. We establish some basic properties of the model dynamics and present some simulations of the fine-grained structure of alternative dynamic regimes for chosen combinations of parameters. The role of the parameters that govern the reinforcement/corruption of maladaptive vs. adaptive traits is of special importance in determining the model's dynamic evolution. The main implication of this result is the need to pay special attention to the structural forces that may favor the emergence and consolidation of maladaptive traits in contemporary socio-economies, as it is the case, for example, for the stimulation of dysfunctional consumption habits and lifestyles in the pursuit of short-term profits.

The cultural implications of growth: Modeling nonlinear interaction of trait selection and population dynamics.

PubMed

Antoci, Angelo; Galeotti, Marcello; Russu, Paolo; Luigi Sacco, Pier

2018-05-01

In this paper, we study a nonlinear model of the interaction between trait selection and population dynamics, building on previous work of Ghirlanda et al. [Theor. Popul. Biol. 77, 181-188 (2010)] and Antoci et al. [Commun. Nonlinear Sci. Numer. Simul. 58, 92-106 (2018)]. We establish some basic properties of the model dynamics and present some simulations of the fine-grained structure of alternative dynamic regimes for chosen combinations of parameters. The role of the parameters that govern the reinforcement/corruption of maladaptive vs. adaptive traits is of special importance in determining the model's dynamic evolution. The main implication of this result is the need to pay special attention to the structural forces that may favor the emergence and consolidation of maladaptive traits in contemporary socio-economies, as it is the case, for example, for the stimulation of dysfunctional consumption habits and lifestyles in the pursuit of short-term profits.

Melt-growth dynamics in CdTe crystals

DOE PAGES

Zhou, X. W.; Ward, D. K.; Wong, B. M.; ...

2012-06-01

We use a new, quantum-mechanics-based bond-order potential (BOP) to reveal melt growth dynamics and fine scale defect formation mechanisms in CdTe crystals. Previous molecular dynamics simulations of semiconductors have shown qualitatively incorrect behavior due to the lack of an interatomic potential capable of predicting both crystalline growth and property trends of many transitional structures encountered during the melt → crystal transformation. Here, we demonstrate successful molecular dynamics simulations of melt growth in CdTe using a BOP that significantly improves over other potentials on property trends of different phases. Our simulations result in a detailed understanding of defect formation during themore » melt growth process. Equally important, we show that the new BOP enables defect formation mechanisms to be studied at a scale level comparable to empirical molecular dynamics simulation methods with a fidelity level approaching quantum-mechanical methods.« less

Dynamical mechanism of atrial fibrillation: A topological approach

NASA Astrophysics Data System (ADS)

Marcotte, Christopher D.; Grigoriev, Roman O.

2017-09-01

While spiral wave breakup has been implicated in the emergence of atrial fibrillation, its role in maintaining this complex type of cardiac arrhythmia is less clear. We used the Karma model of cardiac excitation to investigate the dynamical mechanisms that sustain atrial fibrillation once it has been established. The results of our numerical study show that spatiotemporally chaotic dynamics in this regime can be described as a dynamical equilibrium between topologically distinct types of transitions that increase or decrease the number of wavelets, in general agreement with the multiple wavelets' hypothesis. Surprisingly, we found that the process of continuous excitation waves breaking up into discontinuous pieces plays no role whatsoever in maintaining spatiotemporal complexity. Instead, this complexity is maintained as a dynamical balance between wave coalescence—a unique, previously unidentified, topological process that increases the number of wavelets—and wave collapse—a different topological process that decreases their number.

Improved Temperature Dynamic Model of Turbine Subcomponents for Facilitation of Generalized Tip Clearance Control

NASA Technical Reports Server (NTRS)

Kypuros, Javier A.; Colson, Rodrigo; Munoz, Afredo

2004-01-01

This paper describes efforts conducted to improve dynamic temperature estimations of a turbine tip clearance system to facilitate design of a generalized tip clearance controller. This work builds upon research previously conducted and presented in and focuses primarily on improving dynamic temperature estimations of the primary components affecting tip clearance (i.e. the rotor, blades, and casing/shroud). The temperature profiles estimated by the previous model iteration, specifically for the rotor and blades, were found to be inaccurate and, more importantly, insufficient to facilitate controller design. Some assumptions made to facilitate the previous results were not valid, and thus improvements are presented here to better match the physical reality. As will be shown, the improved temperature sub- models, match a commercially validated model and are sufficiently simplified to aid in controller design.

Electronic Health Records: Overcoming Obstacles to Improve Acceptance and Utilization for Mental Health Clinicians

ERIC Educational Resources Information Center

Odom, Stephen A.

2017-01-01

The dynamics and progress of the integration of the electronic health record (EHR) into health-care disciplines have been described and examined using theories related to technology adoption. Previous studies have examined health-care clinician resistance to the EHR in primary care, hospital, and urgent care medical settings, but few studies have…

The Poor Little Rich District: The Effects of Suburbanization on a Rural School and Community

ERIC Educational Resources Information Center

Howley, Aimee; Carnes, Marilyn; Eldridge, Anita; Huber, Donna; Lado, Longun Moses; Kotler, Ruth; Turner, Maryalice

2005-01-01

Contextualized in relationship to other case studies about rural districts that have experienced population growth and decline as well as in relationship to the small sociological literature on "boom towns," this study considered the dynamics that seem to be interfering with one previously rural and now suburbanizing district's ability to address…

Oman Drilling Project GT3 site survey: dynamics at the roof of an oceanic magma chamber

NASA Astrophysics Data System (ADS)

France, L.; Nicollet, C.; Debret, B.; Lombard, M.; Berthod, C.; Ildefonse, B.; Koepke, J.

2017-12-01

Oman Drilling Project (OmanDP) aims at bringing new constraints on oceanic crust accretion and evolution by drilling Holes in the whole ophiolite section (mantle and crust). Among those, operations at GT3 in the Sumail massif drilled 400 m to sample the dike - gabbro transition that corresponds to the top (gabbros) and roof (dikes) of the axial magma chamber, an interface where hydrothermal and magmatic system interacts. Previous studies based on oceanic crust formed at present day fast-spreading ridges and preserved in ophiolites have highlighted that this interface is a dynamic horizon where the axial melt lens that top the main magma chamber can intrude, reheat, and partially assimilate previously hydrothermally altered roof rocks. Here we present the preliminary results obtained in GT3 area that have allowed the community to choose the drilling site. We provide a geological and structural map of the area, together with new petrographic and chemical constraints on the dynamics of the dike - gabbro transition. Our new results allow us to quantify the dynamic processes, and to propose that 1/ the intrusive contact of the varitextured gabbro within the dikes highlights the intrusion of the melt lens top in the dike rooting zone, 2/ both dikes and previously crystallized gabbros are reheated, and recrystallized by underlying melt lens dynamics (up to 1050°C, largely above the hydrous solidus temperature of altered dikes and gabbros), 3/ the reheating range can be > 200°C, 4/ the melt lens depth variations for a given ridge position is > 200m, 5/ the reheating stage and associated recrystallization within the dikes occurred under hydrous conditions, 6/ the reheating stage is recorded at the root zone of the sheeted dike complex by one of the highest stable conductive thermal gradient ever recorded on Earth ( 3°C/m), 7/ local chemical variations in recrystallized dikes and gabbros are highlighted and used to quantify crystallization and anatectic processes, and the presence of trapped melt, 8/ melt lens cannibalism is attested by numerous assimilation figures close its roof. Besides providing a general context for future studies at OmanDP GT3 site, those new results allow us to quantify the dynamic processes that govern the layer 2 - layer 3 transition in ocean lithosphere.

Dynamic Bioreactor Culture of High Volume Engineered Bone Tissue

PubMed Central

Nguyen, Bao-Ngoc B.; Ko, Henry; Moriarty, Rebecca A.; Etheridge, Julie M.

2016-01-01

Within the field of tissue engineering and regenerative medicine, the fabrication of tissue grafts of any significant size—much less a whole organ or tissue—remains a major challenge. Currently, tissue-engineered constructs cultured in vitro have been restrained in size primarily due to the diffusion limit of oxygen and nutrients to the center of these grafts. Previously, we developed a novel tubular perfusion system (TPS) bioreactor, which allows the dynamic culture of bead-encapsulated cells and increases the supply of nutrients to the entire cell population. More interestingly, the versatility of TPS bioreactor allows a large range of engineered tissue volumes to be cultured, including large bone grafts. In this study, we utilized alginate-encapsulated human mesenchymal stem cells for the culture of a tissue-engineered bone construct in the size and shape of the superior half of an adult human femur (∼200 cm3), a 20-fold increase over previously reported volumes of in vitro engineered bone grafts. Dynamic culture in TPS bioreactor not only resulted in high cell viability throughout the femur graft, but also showed early signs of stem cell differentiation through increased expression of osteogenic genes and proteins, consistent with our previous models of smaller bone constructs. This first foray into full-scale bone engineering provides the foundation for future clinical applications of bioengineered bone grafts. PMID:26653703

Dynamic optical imaging of vascular and metabolic reactivity in rheumatoid joints.

PubMed

Lasker, Joseph M; Fong, Christopher J; Ginat, Daniel T; Dwyer, Edward; Hielscher, Andreas H

2007-01-01

Dynamic optical imaging is increasingly applied to clinically relevant areas such as brain and cancer imaging. In this approach, some external stimulus is applied and changes in relevant physiological parameters (e.g., oxy- or deoxyhemoglobin concentrations) are determined. The advantage of this approach is that the prestimulus state can be used as a reference or baseline against which the changes can be calibrated. Here we present the first application of this method to the problem of characterizing joint diseases, especially effects of rheumatoid arthritis (RA) in the proximal interphalangeal finger joints. Using a dual-wavelength tomographic imaging system together with previously implemented model-based iterative image reconstruction schemes, we have performed initial dynamic imaging case studies on a limited number of healthy volunteers and patients diagnosed with RA. Focusing on three cases studies, we illustrated our major finds. These studies support our hypothesis that differences in the vascular reactivity exist between affected and unaffected joints.

Study on the Vehicle Dynamic Load Considering the Vehicle-Pavement Coupled Effect

NASA Astrophysics Data System (ADS)

Xu, H. L.; He, L.; An, D.

2017-11-01

The vibration of vehicle-pavement interaction system is sophisticated random vibration process and the vehicle-pavement coupled effect was not considered in the previous study. A new linear elastic model of the vehicle-pavement coupled system was established in the paper. The new model was verified with field measurement which could reflect the real vibration between vehicle and pavement. Using the new model, the study on the vehicle dynamic load considering the vehicle-pavement coupled effect showed that random forces (centralization) between vehicle and pavement were influenced largely by vehicle-pavement coupled effect. Numerical calculation indicated that the maximum of random forces in coupled model was 2.4 times than that in uncoupled model. Inquiring the reason, it was found that the main vibration frequency of the vehicle non-suspension system was similar with that of the vehicle suspension system in the coupled model and the resonance vibration lead to vehicle dynamic load increase significantly.

The implications of linking the dynamic performance and turnover literatures.

PubMed

Sturman, M C; Trevor, C O

2001-08-01

This article examines how the literatures of dynamic performance and the performance-turnover relationship inform each other. The nonrandom performance turnover relationship suggests that dynamic performance studies may be biased by their elimination of participants who do not remain for the entire study period. The authors demonstrated that the performance slopes of those who leave an organization differ from the performance slopes of those who remain. This finding suggests that studies of the performance-turnover relationship need to consider employee performance trends when predicting turnover. Replicating and extending the research of D. A. Harrison, M. Virick, and S. William (1996), the authors found that performance changes from the previous month and performance trends measured over a longer time period explained variance in voluntary turnover beyond current performance. Finally, the authors showed that performance trends interacted with current performance in the prediction of voluntary turnover.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

PubMed

Wall, Michael E; Van Benschoten, Andrew H; Sauter, Nicholas K; Adams, Paul D; Fraser, James S; Terwilliger, Thomas C

2014-12-16

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

Cortico-striatal language pathways dynamically adjust for syntactic complexity: A computational study.

PubMed

Szalisznyó, Krisztina; Silverstein, David; Teichmann, Marc; Duffau, Hugues; Smits, Anja

2017-01-01

A growing body of literature supports a key role of fronto-striatal circuits in language perception. It is now known that the striatum plays a role in engaging attentional resources and linguistic rule computation while also serving phonological short-term memory capabilities. The ventral semantic and the dorsal phonological stream dichotomy assumed for spoken language processing also seems to play a role in cortico-striatal perception. Based on recent studies that correlate deep Broca-striatal pathways with complex syntax performance, we used a previously developed computational model of frontal-striatal syntax circuits and hypothesized that different parallel language pathways may contribute to canonical and non-canonical sentence comprehension separately. We modified and further analyzed a thematic role assignment task and corresponding reservoir computing model of language circuits, as previously developed by Dominey and coworkers. We examined the models performance under various parameter regimes, by influencing how fast the presented language input decays and altering the temporal dynamics of activated word representations. This enabled us to quantify canonical and non-canonical sentence comprehension abilities. The modeling results suggest that separate cortico-cortical and cortico-striatal circuits may be recruited differently for processing syntactically more difficult and less complicated sentences. Alternatively, a single circuit would need to dynamically and adaptively adjust to syntactic complexity. Copyright © 2016. Published by Elsevier Inc.

Structure and Dynamics of Polymers in Cylindrical Nanoconfinement: A Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

Pressly, James; Riggleman, Robert; Winey, Karen

The structure and dynamics of polymers under nanoconfinement is critical for understanding how polymers behave in applications from hydraulic fracking to fabricating integrated circuits. We previously used simulations to explore the effect of the diameter of cylindrical pores (d = 10-40 σ, where σ is the unit length in reduced units) on polymer end-to-end distance (Ree,perp, Ree,par) , entanglement density, melt diffusion coefficient (D), and local relaxation time (τperp, τpar) at fixed polymer chain length (N = 350). These studies found D, Ree,par, and τperp increased with increasing confinement while entanglement density, Ree,perp, and τpar decreased. Experiments also found that D increased but to a lesser extent. Here, we examine the molecular weight dependence of these properties using N = 25, 50, 100, 200, 350, and 500 confined to pores of diameter 14 σ to examine a range of confinements. Our preliminary results show that as N increases D and Ree,par, increase as well, relative to the unconfined state, while entanglement density and Ree,perp decrease, consistent with our previous work. Interestingly, τ is shown to be independent of chain length indicating the impact of confinement imposed by reducing pore diameter is distinct from that imposed by increasing chain length.

Dynamic loop gain increases upon adopting the supine body position during sleep in patients with obstructive sleep apnoea.

PubMed

Joosten, Simon A; Landry, Shane A; Sands, Scott A; Terrill, Philip I; Mann, Dwayne; Andara, Christopher; Skuza, Elizabeth; Turton, Anthony; Berger, Philip; Hamilton, Garun S; Edwards, Bradley A

2017-11-01

Obstructive sleep apnoea (OSA) is typically worse in the supine versus lateral sleeping position. One potential factor driving this observation is a decrease in lung volume in the supine position which is expected by theory to increase a key OSA pathogenic factor: dynamic ventilatory control instability (i.e. loop gain). We aimed to quantify dynamic loop gain in OSA patients in the lateral and supine positions, and to explore the relationship between change in dynamic loop gain and change in lung volume with position. Data from 20 patients enrolled in previous studies on the effect of body position on OSA pathogenesis were retrospectively analysed. Dynamic loop gain was calculated from routinely collected polysomnographic signals using a previously validated mathematical model. Lung volumes were measured in the awake state with a nitrogen washout technique. Dynamic loop gain was significantly higher in the supine than in the lateral position (0.77 ± 0.15 vs 0.68 ± 0.14, P = 0.012). Supine functional residual capacity (FRC) was significantly lower than lateral FRC (81.0 ± 15.4% vs 87.3 ± 18.4% of the seated FRC, P = 0.021). The reduced FRC we observed on moving to the supine position was predicted by theory to increase loop gain by 10.2 (0.6, 17.1)%, a value similar to the observed increase of 8.4 (-1.5, 31.0)%. Dynamic loop gain increased by a small but statistically significant amount when moving from the lateral to supine position and this may, in part, contribute to the worsening of OSA in the supine sleeping position. © 2017 Asian Pacific Society of Respirology.

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.

Atmospheric Transport and Mixing linked to Rossby Wave Breaking in GFDL Dynamical Core

NASA Astrophysics Data System (ADS)

Liu, C.; Barnes, E. A.

2015-12-01

Atmospheric transport and mixing plays an important role in the global energy balance and the distribution of health-related chemical constituents. Previous studies suggest a close linkage between large-scale transport and Rossby wave breaking (RWB). In this work, we use the GFDL spectral dynamical core to investigate this relationship and study the response of RWB-related transport in different climate scenarios. In a standard control run, we quantify the contribution of RWB to the total transport and mixing of an idealized tracer. In addition, we divide the contribution further into the two types of RWB - anticyclonic wave breaking (AWB) and cyclonic wave breaking (CWB) -- and contrast their efficiency at transport and mixing. Our results are compared to a previous study in which the transport ability of the two types of RWB is studied for individual baroclinic wave life-cycles. In a series of sensitivity runs, we study the response of RWB-related transport and mixing to various states of the jet streams. The responses of the mean strength, frequency, and the efficiency of RWB-related transport are documented and the implications for the transport and mixing in a warmer climate are discussed.

Dielectric Study of Alcohols Using Broadband Terahertz Time Domain Spectroscopy (THz-TDS).

NASA Astrophysics Data System (ADS)

Sarkar, Sohini; Saha, Debasis; Banerjee, Sneha; Mukherjee, Arnab; Mandal, Pankaj

2016-06-01

Broadband Terahertz-Time Domain Spectroscopy (THz-TDS) (1-10 THz) has been utilized to study the complex dielectric properties of methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, and 1-octanol. Previous reports on dielectric study of alcohols were limited to 5 THz. At THz (1 THz = 33.33 wn = 4 meV) frequency range (0.1 to 15 THz), the molecular reorientation and several intermolecular vibrations (local oscillation of dipoles) may coexist and contribute to the overall liquid dynamics. We find that the Debye type relaxations barely contribute beyond 1 THz, rather three harmonic oscillators dominate the entire spectral range. To get insights on the modes responsible for the observed absorption in THz frequency range, we performed all atom molecular dynamics (MD) using OPLS force field and ab initio quantum calculations. Combined experimental and theoretical study reveal that the complex dielectric functions of alcohols have contribution from a) alkyl group oscillation within H-bonded network ( 1 THz), b) intermolecular H-bond stretching ( 5 THz) , and c) librational motions in alcohols. The present work, therefore, complements all previous studies on alcohols at lower frequencies and provides a clear picture on them in a broad spectral range from microwave to 10 THz.

Global dynamic optimization approach to predict activation in metabolic pathways.

PubMed

de Hijas-Liste, Gundián M; Klipp, Edda; Balsa-Canto, Eva; Banga, Julio R

2014-01-06

During the last decade, a number of authors have shown that the genetic regulation of metabolic networks may follow optimality principles. Optimal control theory has been successfully used to compute optimal enzyme profiles considering simple metabolic pathways. However, applying this optimal control framework to more general networks (e.g. branched networks, or networks incorporating enzyme production dynamics) yields problems that are analytically intractable and/or numerically very challenging. Further, these previous studies have only considered a single-objective framework. In this work we consider a more general multi-objective formulation and we present solutions based on recent developments in global dynamic optimization techniques. We illustrate the performance and capabilities of these techniques considering two sets of problems. First, we consider a set of single-objective examples of increasing complexity taken from the recent literature. We analyze the multimodal character of the associated non linear optimization problems, and we also evaluate different global optimization approaches in terms of numerical robustness, efficiency and scalability. Second, we consider generalized multi-objective formulations for several examples, and we show how this framework results in more biologically meaningful results. The proposed strategy was used to solve a set of single-objective case studies related to unbranched and branched metabolic networks of different levels of complexity. All problems were successfully solved in reasonable computation times with our global dynamic optimization approach, reaching solutions which were comparable or better than those reported in previous literature. Further, we considered, for the first time, multi-objective formulations, illustrating how activation in metabolic pathways can be explained in terms of the best trade-offs between conflicting objectives. This new methodology can be applied to metabolic networks with arbitrary topologies, non-linear dynamics and constraints.

An experimental study of nonlinear dynamic system identification

NASA Technical Reports Server (NTRS)

Stry, Greselda I.; Mook, D. Joseph

1990-01-01

A technique for robust identification of nonlinear dynamic systems is developed and illustrated using both simulations and analog experiments. The technique is based on the Minimum Model Error optimal estimation approach. A detailed literature review is included in which fundamental differences between the current approach and previous work is described. The most significant feature of the current work is the ability to identify nonlinear dynamic systems without prior assumptions regarding the form of the nonlinearities, in constrast to existing nonlinear identification approaches which usually require detailed assumptions of the nonlinearities. The example illustrations indicate that the method is robust with respect to prior ignorance of the model, and with respect to measurement noise, measurement frequency, and measurement record length.

Coastal oceanography sets the pace of rocky intertidal community dynamics.

PubMed

Menge, B A; Lubchenco, J; Bracken, M E S; Chan, F; Foley, M M; Freidenburg, T L; Gaines, S D; Hudson, G; Krenz, C; Leslie, H; Menge, D N L; Russell, R; Webster, M S

2003-10-14

The structure of ecological communities reflects a tension among forces that alter populations. Marine ecologists previously emphasized control by locally operating forces (predation, competition, and disturbance), but newer studies suggest that inputs from large-scale oceanographically modulated subsidies (nutrients, particulates, and propagules) can strongly influence community structure and dynamics. On New Zealand rocky shores, the magnitude of such subsidies differs profoundly between contrasting oceanographic regimes. Community structure, and particularly the pace of community dynamics, differ dramatically between intermittent upwelling regimes compared with relatively persistent down-welling regimes. We suggest that subsidy rates are a key determinant of the intensity of species interactions, and thus of structure in marine systems, and perhaps also nonmarine communities.

Anxiogenic Patterns in Mother-Child Interactions

ERIC Educational Resources Information Center

Harvison, Kyle W.; Chapman, L. Kevin; Ballash, Natalie G.; Woodruff-Borden, Janet

2008-01-01

The current study examined psychosocial variables associated with the development of anxiety in children. While previous literature has established parental affectionless control as an important contributor to the development of anxiety in children, few have examined this construct within the dynamic context of parent-child interaction. In the…

Changes to soil organic N dynamics with leguminous woody plant encroachment into grasslands

USDA-ARS?s Scientific Manuscript database

The encroachment of nitrogen-fixing trees and shrubs into grasslands and savannas occurs worldwide. In the Rio Grande Plains region of southern Texas, previous studies have shown that woody encroachment by leguminous Prosopis glandulosa (mesquite) trees increases soil and microbial biomass nitrogen ...

Experimental study of complex mixed-mode oscillations generated in a Bonhoeffer-van der Pol oscillator under weak periodic perturbation

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

Shimizu, Kuniyasu, E-mail: kuniyasu.shimizu@it-chiba.ac.jp; Sekikawa, Munehisa; Inaba, Naohiko

2015-02-15

Bifurcations of complex mixed-mode oscillations denoted as mixed-mode oscillation-incrementing bifurcations (MMOIBs) have frequently been observed in chemical experiments. In a previous study [K. Shimizu et al., Physica D 241, 1518 (2012)], we discovered an extremely simple dynamical circuit that exhibits MMOIBs. Our model was represented by a slow/fast Bonhoeffer-van der Pol circuit under weak periodic perturbation near a subcritical Andronov-Hopf bifurcation point. In this study, we experimentally and numerically verify that our dynamical circuit captures the essence of the underlying mechanism causing MMOIBs, and we observe MMOIBs and chaos with distinctive waveforms in real circuit experiments.

A possible structural signature of the onset of cooperativity in metallic liquids

NASA Astrophysics Data System (ADS)

Dai, R.; Ashcraft, R.; Kelton, K. F.

2018-05-01

It is widely, although not universally, believed that there must be a connection between liquid dynamics and the structure. Previous supporting studies, for example, have demonstrated a link between the structural evolution in the liquid and kinetic fragility. Here, new results are presented that strengthen the evidence for a connection. By combining the results from high-energy synchrotron X-ray scattering studies of containerlessly processed supercooled liquids with viscosity measurements, an accelerated rate of structural ordering beyond the nearest neighbors in the liquid is demonstrated to correlate with the temperature at which the viscosity transitions from Arrhenius to super-Arrhenius behavior. This is the first confirmation of predictions from several recent molecular dynamics studies.

Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics

PubMed Central

Lythgoe, Katrina A.; Blanquart, François

2016-01-01

The viral population of HIV-1, like many pathogens that cause systemic infection, is structured and differentiated within the body. The dynamics of cellular immune trafficking through the blood and within compartments of the body has also received wide attention. Despite these advances, mathematical models, which are widely used to interpret and predict viral and immune dynamics in infection, typically treat the infected host as a well-mixed homogeneous environment. Here, we present mathematical, analytical, and computational results that demonstrate that consideration of the spatial structure of the viral population within the host radically alters predictions of previous models. We study the dynamics of virus replication and cytotoxic T lymphocytes (CTLs) within a metapopulation of spatially segregated patches, representing T cell areas connected by circulating blood and lymph. The dynamics of the system depend critically on the interaction between CTLs and infected cells at the within-patch level. We show that for a wide range of parameters, the system admits an unexpected outcome called the shifting-mosaic steady state. In this state, the whole body’s viral population is stable over time, but the equilibrium results from an underlying, highly dynamic process of local infection and clearance within T-cell centers. Notably, and in contrast to previous models, this new model can explain the large differences in set-point viral load (SPVL) observed between patients and their distribution, as well as the relatively low proportion of cells infected at any one time, and alters the predicted determinants of viral load variation. PMID:27706164

Regulation of Cortical Dynamic Range by Background Synaptic Noise and Feedforward Inhibition

PubMed Central

Khubieh, Ayah; Ratté, Stéphanie; Lankarany, Milad; Prescott, Steven A.

2016-01-01

The cortex encodes a broad range of inputs. This breadth of operation requires sensitivity to weak inputs yet non-saturating responses to strong inputs. If individual pyramidal neurons were to have a narrow dynamic range, as previously claimed, then staggered all-or-none recruitment of those neurons would be necessary for the population to achieve a broad dynamic range. Contrary to this explanation, we show here through dynamic clamp experiments in vitro and computer simulations that pyramidal neurons have a broad dynamic range under the noisy conditions that exist in the intact brain due to background synaptic input. Feedforward inhibition capitalizes on those noise effects to control neuronal gain and thereby regulates the population dynamic range. Importantly, noise allows neurons to be recruited gradually and occludes the staggered recruitment previously attributed to heterogeneous excitation. Feedforward inhibition protects spike timing against the disruptive effects of noise, meaning noise can enable the gain control required for rate coding without compromising the precise spike timing required for temporal coding. PMID:26209846

NASTRAN analysis of the 1/8-scale space shuttle dynamic model

NASA Technical Reports Server (NTRS)

Bernstein, M.; Mason, P. W.; Zalesak, J.; Gregory, D. J.; Levy, A.

1973-01-01

The space shuttle configuration has more complex structural dynamic characteristics than previous launch vehicles primarily because of the high model density at low frequencies and the high degree of coupling between the lateral and longitudinal motions. An accurate analytical representation of these characteristics is a primary means for treating structural dynamics problems during the design phase of the shuttle program. The 1/8-scale model program was developed to explore the adequacy of available analytical modeling technology and to provide the means for investigating problems which are more readily treated experimentally. The basic objectives of the 1/8-scale model program are: (1) to provide early verification of analytical modeling procedures on a shuttle-like structure, (2) to demonstrate important vehicle dynamic characteristics of a typical shuttle design, (3) to disclose any previously unanticipated structural dynamic characteristics, and (4) to provide for development and demonstration of cost effective prototype testing procedures.

Performance recovery of a class of uncertain non-affine systems with unmodelled dynamics: an indirect dynamic inversion method

NASA Astrophysics Data System (ADS)

Yi, Bowen; Lin, Shuyi; Yang, Bo; Zhang, Weidong

2018-02-01

This paper presents an output feedback indirect dynamic inversion (IDI) approach for a class of uncertain nonaffine systems with input unmodelled dynamics. Compared with previous approaches to achieve performance recovery, the proposed method aims at dealing with a broader class of nonaffine-in-control systems with triangular structure. An IDI state feedback law is designed first, in which less knowledge of the model plant is needed compared to earlier approximate dynamic inversion methods, thus yielding more robust performance. After that, an extended high-gain observer is designed to accomplish the task with output feedback. Finally, we prove that the designed IDI controller is equivalent to an adaptive proportional-integral (PI) controller, with respect to both time response equivalence and robustness equivalence. The conclusion implies that for the studied strict-feedback non-affine systems with unmodelled dynamics, there always exits a PI controller to stabilise the systems. The effectiveness and benefits of the designed approach are verified by three examples.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

From powder to solution: hydration dependence of human hemoglobin dynamics correlated to body temperature.

PubMed

Stadler, A M; Digel, I; Embs, J P; Unruh, T; Tehei, M; Zaccai, G; Büldt, G; Artmann, G M

2009-06-17

A transition in hemoglobin (Hb), involving partial unfolding and aggregation, has been shown previously by various biophysical methods. The correlation between the transition temperature and body temperature for Hb from different species, suggested that it might be significant for biological function. To focus on such biologically relevant human Hb dynamics, we studied the protein internal picosecond motions as a response to hydration, by elastic and quasielastic neutron scattering. Rates of fast diffusive motions were found to be significantly enhanced with increasing hydration from fully hydrated powder to concentrated Hb solution. In concentrated protein solution, the data showed that amino acid side chains can explore larger volumes above body temperature than expected from normal temperature dependence. The body temperature transition in protein dynamics was absent in fully hydrated powder, indicating that picosecond protein dynamics responsible for the transition is activated only at a sufficient level of hydration. A collateral result from the study is that fully hydrated protein powder samples do not accurately describe all aspects of protein picosecond dynamics that might be necessary for biological function.

Differentiation Driven Changes in the Dynamic Organization of Basal Transcription Initiation

PubMed Central

Giglia-Mari, Giuseppina; Mourgues, Sophie; Nonnekens, Julie; Andrieux, Lise O.; de Wit, Jan; Miquel, Catherine; Wijgers, Nils; Maas, Alex; Fousteri, Maria; Hoeijmakers, Jan H. J.; Vermeulen, Wim

2009-01-01

Studies based on cell-free systems and on in vitro–cultured living cells support the concept that many cellular processes, such as transcription initiation, are highly dynamic: individual proteins stochastically bind to their substrates and disassemble after reaction completion. This dynamic nature allows quick adaptation of transcription to changing conditions. However, it is unknown to what extent this dynamic transcription organization holds for postmitotic cells embedded in mammalian tissue. To allow analysis of transcription initiation dynamics directly into living mammalian tissues, we created a knock-in mouse model expressing fluorescently tagged TFIIH. Surprisingly and in contrast to what has been observed in cultured and proliferating cells, postmitotic murine cells embedded in their tissue exhibit a strong and long-lasting transcription-dependent immobilization of TFIIH. This immobilization is both differentiation driven and development dependent. Furthermore, although very statically bound, TFIIH can be remobilized to respond to new transcriptional needs. This divergent spatiotemporal transcriptional organization in different cells of the soma revisits the generally accepted highly dynamic concept of the kinetic framework of transcription and shows how basic processes, such as transcription, can be organized in a fundamentally different fashion in intact organisms as previously deduced from in vitro studies. PMID:19841728

Kv1 channels control spike threshold dynamics and spike timing in cortical pyramidal neurones

PubMed Central

Higgs, Matthew H; Spain, William J

2011-01-01

Abstract Previous studies showed that cortical pyramidal neurones (PNs) have a dynamic spike threshold that functions as a high-pass filter, enhancing spike timing in response to high-frequency input. While it is commonly assumed that Na+ channel inactivation is the primary mechanism of threshold accommodation, the possible role of K+ channel activation in fast threshold changes has not been well characterized. The present study tested the hypothesis that low-voltage activated Kv1 channels affect threshold dynamics in layer 2–3 PNs, using α-dendrotoxin (DTX) or 4-aminopyridine (4-AP) to block these conductances. We found that Kv1 blockade reduced the dynamic changes of spike threshold in response to a variety of stimuli, including stimulus-evoked synaptic input, current steps and ramps of varied duration, and noise. Analysis of the responses to noise showed that Kv1 channels increased the coherence of spike output with high-frequency components of the stimulus. A simple model demonstrates that a dynamic spike threshold can account for this effect. Our results show that the Kv1 conductance is a major mechanism that contributes to the dynamic spike threshold and precise spike timing of cortical PNs. PMID:21911608

Income distribution patterns from a complete social security database

NASA Astrophysics Data System (ADS)

Derzsy, N.; Néda, Z.; Santos, M. A.

2012-11-01

We analyze the income distribution of employees for 9 consecutive years (2001-2009) using a complete social security database for an economically important district of Romania. The database contains detailed information on more than half million taxpayers, including their monthly salaries from all employers where they worked. Besides studying the characteristic distribution functions in the high and low/medium income limits, the database allows us a detailed dynamical study by following the time-evolution of the taxpayers income. To our knowledge, this is the first extensive study of this kind (a previous Japanese taxpayers survey was limited to two years). In the high income limit we prove once again the validity of Pareto’s law, obtaining a perfect scaling on four orders of magnitude in the rank for all the studied years. The obtained Pareto exponents are quite stable with values around α≈2.5, in spite of the fact that during this period the economy developed rapidly and also a financial-economic crisis hit Romania in 2007-2008. For the low and medium income category we confirmed the exponential-type income distribution. Following the income of employees in time, we have found that the top limit of the income distribution is a highly dynamical region with strong fluctuations in the rank. In this region, the observed dynamics is consistent with a multiplicative random growth hypothesis. Contrarily with previous results obtained for the Japanese employees, we find that the logarithmic growth-rate is not independent of the income.

A point of application study to determine the accuracy, precision and reliability of a low-cost balance plate for center of pressure measurement.

PubMed

Goble, Daniel J; Khan, Ehran; Baweja, Harsimran S; O'Connor, Shawn M

2018-04-11

Changes in postural sway measured via force plate center of pressure have been associated with many aspects of human motor ability. A previous study validated the accuracy and precision of a relatively new, low-cost and portable force plate called the Balance Tracking System (BTrackS). This work compared a laboratory-grade force plate versus BTrackS during human-like dynamic sway conditions generated by an inverted pendulum device. The present study sought to extend previous validation attempts for BTrackS using a more traditional point of application (POA) approach. Computer numerical control (CNC) guided application of ∼155 N of force was applied five times to each of 21 points on five different BTrackS Balance Plate (BBP) devices with a hex-nose plunger. Results showed excellent agreement (ICC > 0.999) between the POAs and measured COP by the BBP devices, as well as high accuracy (<1% average percent error) and precision (<0.1 cm average standard deviation of residuals). The ICC between BBP devices was exceptionally high (ICC > 0.999) providing evidence of almost perfect inter-device reliability. Taken together, these results provide an important, static corollary to the previously obtained dynamic COP results from inverted pendulum testing of the BBP. Copyright © 2018 Elsevier Ltd. All rights reserved.

Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations.

PubMed

Yuhara, Daisuke; Brumby, Paul E; Wu, David T; Sum, Amadeu K; Yasuoka, Kenji

2018-05-14

To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Yuhara, Daisuke; Brumby, Paul E.; Wu, David T.; Sum, Amadeu K.; Yasuoka, Kenji

2018-05-01

To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

A molecular dynamics study of the atomic structure of (CaO)x(SiO2)1-x glasses.

PubMed

Mead, Robert N; Mountjoy, Gavin

2006-07-27

The local atomic environment of Ca in (CaO)x(SiO2)1-x glasses is of interest because of the role of Ca in soda-lime glass, the application of calcium silicate glasses as biomaterials, and the previous experimental measurement of the Ca-Ca correlation in CaSiO(3) glass. Molecular dynamics has been used to obtain models of (CaO)x(SiO2)1-x glasses with x = 0, 0.1, 0.2, 0.3, 0.4, and 0.5, and with approximately 1000 atoms and size approximately 25 A. As expected, the models contain a tetrahedral silica network, the connectivity of which decreases as x increases. In the glass-forming region, i.e., x = 0.4 and 0.5, Ca has a mixture of 6- and 7-fold coordination. Bridging oxygen makes an important contribution to the coordination of Ca, with most bridging oxygens coordinated to 2 Si plus 1 Ca. The x = 0.5 model is in reasonable agreement with previous experimental studies, and does not substantiate the previous theory of cation ordering, which predicted Ca arranged in sheets. In the phase-separated region, i.e., x = 0.1 and 0.2, there is marked clustering of Ca.

Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal.

PubMed

Shibuta, Yasushi; Sakane, Shinji; Miyoshi, Eisuke; Okita, Shin; Takaki, Tomohiro; Ohno, Munekazu

2017-04-05

Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue. Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi-graphics processing unit parallel computation combined with the rapid progress in high-performance computational environments.Nucleation is a fundamental physical process, however it is a long-standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion-atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.

Using molecular dynamics simulations and finite element method to study the mechanical properties of nanotube reinforced polyethylene and polyketone

NASA Astrophysics Data System (ADS)

Rouhi, S.; Alizadeh, Y.; Ansari, R.; Aryayi, M.

2015-09-01

Molecular dynamics simulations are used to study the mechanical behavior of single-walled carbon nanotube reinforced composites. Polyethylene and polyketone are selected as the polymer matrices. The effects of nanotube atomic structure and diameter on the mechanical properties of polymer matrix nanocomposites are investigated. It is shown that although adding nanotube to the polymer matrix raises the longitudinal elastic modulus significantly, the transverse tensile and shear moduli do not experience important change. As the previous finite element models could not be used for polymer matrices with the atom types other than carbon, molecular dynamics simulations are used to propose a finite element model which can be used for any polymer matrices. It is shown that this model can predict Young’s modulus with an acceptable accuracy.

Cellular automata approach for the dynamics of HIV infection under antiretroviral therapies: The role of the virus diffusion

NASA Astrophysics Data System (ADS)

González, Ramón E. R.; de Figueirêdo, Pedro Hugo; Coutinho, Sérgio

2013-10-01

We study a cellular automata model to test the timing of antiretroviral therapy strategies for the dynamics of infection with human immunodeficiency virus (HIV). We focus on the role of virus diffusion when its population is included in previous cellular automata model that describes the dynamics of the lymphocytes cells population during infection. This inclusion allows us to consider the spread of infection by the virus-cell interaction, beyond that which occurs by cell-cell contagion. The results show an acceleration of the infectious process in the absence of treatment, but show better efficiency in reducing the risk of the onset of AIDS when combined antiretroviral therapies are used even with drugs of low effectiveness. Comparison of results with clinical data supports the conclusions of this study.

The dynamic response of visual accommodation over a seven-day period

NASA Technical Reports Server (NTRS)

Randle, R. J.; Murphy, M. R.

1974-01-01

Four college students, ranging in age from 18 to 21 years, were tested on their dynamic, monocular accommodation responses to a square wave stimulus and sine waves of two frequencies. The tests were conducted over a period of seven days in a controlled environment, each subject being tested once every three hours. Latency, magnitude, velocity, gain and phase lag of the responses were measured, and means and standard deviations were computed. The latency of response was stable throughout and agreed fairly well with previous studies. The response magnitude was relatively stable. Three of the subjects had higher velocities on receding targets; one was faster on approaching targets. The group mean velocity increased over the seven days of the study. In keeping with the trend to faster dynamics over the seven days, both gain and phase lag improved.

Identification of drivers of (dis)liking based on dynamic sensory profiles: Comparison of Temporal Dominance of Sensations and Temporal Check-all-that-apply.

PubMed

Ares, Gastón; Alcaire, Florencia; Antúnez, Lucía; Vidal, Leticia; Giménez, Ana; Castura, John C

2017-02-01

Temporal Dominance of Sensations (TDS) and Temporal Check-all-that-apply (TCATA) are two multi-attribute methods for dynamic sensory characterization. Previous research has shown that both methodologies provide complementary information. However, it remains an open question which of the two approaches better explains consumers' hedonic perception of products. In this context, the aim of the present work was to compare TDS and TCATA in terms of their ability to identify the influence of the dynamic sensory profile of food products on consumer overall liking scores. Two consumer studies were conducted using two different product categories (French bread and vanilla milk desserts). In each study, a between-subjects design was used to obtain dynamic sensory profiles using TDS and TCATA. After the dynamic sensory characterization tasks consumers rated their liking using a 9-point hedonic scale. Across the two studies, both methodologies provided similar information on the main drivers of liking and disliking, particularly when samples showed clear differences in liking. However, in one of the studies attribute applicability from TCATA provided additional insights on the influence of the dynamics of the sensory characteristics of products on consumers' liking. Results of the present work stress the complementarity between TCATA and TDS and highlight the potentiality of TCATA to provide a more detailed description of the dynamics of sensory perception during consumption. Copyright © 2016 Elsevier Ltd. All rights reserved.

Residue solvent accessibilities in the unfolded polypeptide chain.

PubMed Central

Zielenkiewicz, P; Saenger, W

1992-01-01

The difference of solvent accessibilities in the native and unfolded states of the protein is used as a measure of the hydrophobic contribution to the free energy of folding. We present a new approximation of amino acids solvent accessibilities in the unfolded state based on the 1-ns molecular dynamics simulation of Ala-X-Ala tripeptides at a temperature of 368 K. The standard accessibility values averaged from the molecular dynamics study are significantly lower from those previously obtained by considering only selected conformations of Ala-X-Ala tripeptides. PMID:1489908

Ab initio molecular dynamics simulations of the initial stages of solid-electrolyte interphase formation on lithium ion battery graphitic anodes.

PubMed

Leung, Kevin; Budzien, Joanne L

2010-07-07

The decomposition of ethylene carbonate (EC) during the initial growth of solid-electrolyte interphase (SEI) films at the solvent-graphitic anode interface is critical to lithium ion battery operations. Ab initio molecular dynamics simulations of explicit liquid EC/graphite interfaces are conducted to study these electrochemical reactions. We show that carbon edge terminations are crucial at this stage, and that achievable experimental conditions can lead to surprisingly fast EC breakdown mechanisms, yielding decomposition products seen in experiments but not previously predicted.

A comparative analysis of dynamic grids vs. virtual grids using the A3pviGrid framework.

PubMed

Shankaranarayanan, Avinas; Amaldas, Christine

2010-11-01

With the proliferation of Quad/Multi-core micro-processors in mainstream platforms such as desktops and workstations; a large number of unused CPU cycles can be utilized for running virtual machines (VMs) as dynamic nodes in distributed environments. Grid services and its service oriented business broker now termed cloud computing could deploy image based virtualization platforms enabling agent based resource management and dynamic fault management. In this paper we present an efficient way of utilizing heterogeneous virtual machines on idle desktops as an environment for consumption of high performance grid services. Spurious and exponential increases in the size of the datasets are constant concerns in medical and pharmaceutical industries due to the constant discovery and publication of large sequence databases. Traditional algorithms are not modeled at handing large data sizes under sudden and dynamic changes in the execution environment as previously discussed. This research was undertaken to compare our previous results with running the same test dataset with that of a virtual Grid platform using virtual machines (Virtualization). The implemented architecture, A3pviGrid utilizes game theoretic optimization and agent based team formation (Coalition) algorithms to improve upon scalability with respect to team formation. Due to the dynamic nature of distributed systems (as discussed in our previous work) all interactions were made local within a team transparently. This paper is a proof of concept of an experimental mini-Grid test-bed compared to running the platform on local virtual machines on a local test cluster. This was done to give every agent its own execution platform enabling anonymity and better control of the dynamic environmental parameters. We also analyze performance and scalability of Blast in a multiple virtual node setup and present our findings. This paper is an extension of our previous research on improving the BLAST application framework using dynamic Grids on virtualization platforms such as the virtual box.

Translational and rotational dynamics of monosaccharide solutions.

PubMed

Lelong, Gérald; Howells, W Spencer; Brady, John W; Talón, César; Price, David L; Saboungi, Marie-Louise

2009-10-01

Molecular dynamics computer simulations have been carried out on aqueous solutions of glucose at concentrations bracketing those previously measured with quasi-elastic neutron scattering (QENS), in order to investigate the motions and interactions of the sugar and water molecules. In addition, QENS measurements have been carried out on fructose solutions to determine whether the effects previously observed for glucose apply to monosaccharide solutions. The simulations indicate a dynamical analogy between higher solute concentration and lower temperature that could provide a key explanation of the bioprotective phenomena observed in many living organisms. The experimental results on fructose solutions show qualitatively similar behavior to the glucose solutions. The dynamics of the water molecules are essentially the same, while the translational diffusion of the sugar molecules is slightly faster in the fructose solutions.

Dynamic transcriptional signatures and network responses for clinical symptoms in influenza-infected human subjects using systems biology approaches.

PubMed

Linel, Patrice; Wu, Shuang; Deng, Nan; Wu, Hulin

2014-10-01

Recent studies demonstrate that human blood transcriptional signatures may be used to support diagnosis and clinical decisions for acute respiratory viral infections such as influenza. In this article, we propose to use a newly developed systems biology approach for time course gene expression data to identify significant dynamically response genes and dynamic gene network responses to viral infection. We illustrate the methodological pipeline by reanalyzing the time course gene expression data from a study with healthy human subjects challenged by live influenza virus. We observed clear differences in the number of significant dynamic response genes (DRGs) between the symptomatic and asymptomatic subjects and also identified DRG signatures for symptomatic subjects with influenza infection. The 505 common DRGs shared by the symptomatic subjects have high consistency with the signature genes for predicting viral infection identified in previous works. The temporal response patterns and network response features were carefully analyzed and investigated.

Spin dynamics in helical molecules with nonlinear interactions

NASA Astrophysics Data System (ADS)

Díaz, E.; Albares, P.; Estévez, P. G.; Cerveró, J. M.; Gaul, C.; Diez, E.; Domínguez-Adame, F.

2018-04-01

It is widely admitted that the helical conformation of certain chiral molecules may induce a sizable spin selectivity observed in experiments. Spin selectivity arises as a result of the interplay between a helicity-induced spin–orbit coupling (SOC) and electric dipole fields in the molecule. From the theoretical point of view, different phenomena might affect the spin dynamics in helical molecules, such as quantum dephasing, dissipation and the role of metallic contacts. With a few exceptions, previous studies usually neglect the local deformation of the molecule about the carrier, but this assumption seems unrealistic to describe charge transport in molecular systems. We introduce an effective model describing the electron spin dynamics in a deformable helical molecule with weak SOC. We find that the electron–lattice interaction allows the formation of stable solitons such as bright solitons with well defined spin projection onto the molecule axis. We present a thorough study of these bright solitons and analyze their possible impact on the spin dynamics in deformable helical molecules.

Electrogenic properties of the Na+/K+ ATPase control transitions between normal and pathological brain states

PubMed Central

Krishnan, Giri P.; Filatov, Gregory; Shilnikov, Andrey

2015-01-01

Ionic concentrations fluctuate significantly during epileptic seizures. In this study, using a combination of in vitro electrophysiology, computer modeling, and dynamical systems analysis, we demonstrate that changes in the potassium and sodium intra- and extracellular ion concentrations ([K+] and [Na+], respectively) during seizure affect the neuron dynamics by modulating the outward Na+/K+ pump current. First, we show that an increase of the outward Na+/K+ pump current mediates termination of seizures when there is a progressive increase in the intracellular [Na+]. Second, we show that the Na+/K+ pump current is crucial in maintaining the stability of the physiological network state; a reduction of this current leads to the onset of seizures via a positive-feedback loop. We then present a novel dynamical mechanism for bursting in neurons with a reduced Na+/K+ pump. Overall, our study demonstrates the profound role of the current mediated by Na+/K+ ATPase on the stability of neuronal dynamics that was previously unknown. PMID:25589588

Modeling behavior dynamics using computational psychometrics within virtual worlds.

PubMed

Cipresso, Pietro

2015-01-01

In case of fire in a building, how will people behave in the crowd? The behavior of each individual affects the behavior of others and, conversely, each one behaves considering the crowd as a whole and the individual others. In this article, I propose a three-step method to explore a brand new way to study behavior dynamics. The first step relies on the creation of specific situations with standard techniques (such as mental imagery, text, video, and audio) and an advanced technique [Virtual Reality (VR)] to manipulate experimental settings. The second step concerns the measurement of behavior in one, two, or many individuals focusing on parameters extractions to provide information about the behavior dynamics. Finally, the third step, which uses the parameters collected and measured in the previous two steps in order to simulate possible scenarios to forecast through computational models, understand, and explain behavior dynamics at the social level. An experimental study was also included to demonstrate the three-step method and a possible scenario.

A dynamical systems analysis of the kinematics of time-periodic vortex shedding past a circular cylinder

NASA Technical Reports Server (NTRS)

Ottino, Julio M.

1991-01-01

Computer flow simulation aided by dynamical systems analysis is used to investigate the kinematics of time-periodic vortex shedding past a two-dimensional circular cylinder in the context of the following general questions: (1) Is a dynamical systems viewpoint useful in the understanding of this and similar problems involving time-periodic shedding behind bluff bodies; and (2) Is it indeed possible, by adopting such a point of view, to complement previous analyses or to understand kinematical aspects of the vortex shedding process that somehow remained hidden in previous approaches. We argue that the answers to these questions are positive. Results are described.

Ethnic Stigma, Academic Anxiety, and Intrinsic Motivation in Middle Childhood

ERIC Educational Resources Information Center

Gillen-O'Neel, Cari; Ruble, Diane N.; Fuligni, Andrew J.

2011-01-01

Previous research addressing the dynamics of stigma and academics has focused on African American adolescents and adults. The present study examined stigma awareness, academic anxiety, and intrinsic motivation among 451 young (ages 6-11) and diverse (African American, Chinese, Dominican, Russian, and European American) students. Results indicated…

Students' Abstraction in Recognizing, Building with and Constructing a Quadrilateral

ERIC Educational Resources Information Center

Budiarto, Mega Teguh; Rahaju, Endah Budi; Hartono, Sugi

2017-01-01

This study aims to implement empirically students' abstraction with socio-cultural background of Indonesia. Abstraction is an activity that involves a vertical reorganization of previously constructed mathematics into a new mathematical structure. The principal components of the model are three dynamic nested epistemic actions: recognizing,…

Using measures of information content and complexity of time series as hydrologic metrics

USDA-ARS?s Scientific Manuscript database

The information theory has been previously used to develop metrics that allowed to characterize temporal patterns in soil moisture dynamics, and to evaluate and to compare performance of soil water flow models. The objective of this study was to apply information and complexity measures to characte...

Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment.

PubMed

Besmer, Michael D; Epting, Jannis; Page, Rebecca M; Sigrist, Jürg A; Huggenberger, Peter; Hammes, Frederik

2016-12-07

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality - particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL -1 . The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems.

Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment

PubMed Central

Besmer, Michael D.; Epting, Jannis; Page, Rebecca M.; Sigrist, Jürg A.; Huggenberger, Peter; Hammes, Frederik

2016-01-01

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality – particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL−1. The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems. PMID:27924920

Dynamics of Charged Species in Ionic-Neutral Block Copolymer and Surfactant Complexes [Structural Relaxation and Dynamics of Ionic-Neutral Block Copolymer Surfactant Complexes

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

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.

Structure–property relationships of ionic block copolymer (BCP) surfactant complexes are critical toward the progress of favorable engineering design of efficient charge-transport materials. In this paper, molecular dynamics simulations are used to understand the dynamics of charged-neutral BCP and surfactant complexes. The dynamics are examined for two different systems: charged-neutral double-hydrophilic and hydrophobic–hydrophilic block copolymers with oppositely charged surfactant moieties. The dynamics of the surfactant head, tails, and charges are studied for five different BCP volume fractions. We observe that the dynamics of the different species solely depend on the balance between electrostatic and entropic interactions between the charged species andmore » the neutral monomers. The favorable hydrophobic–hydrophobic interactions and the unfavorable hydrophobic–hydrophilic interactions determine the mobilities of the monomers. The dynamical properties of the charge species influence complex formation. Structural relaxations exhibit length-scale dependent behavior, with slower relaxation at the radius of gyration length-scale and faster relaxation at the segmental length-scale, consistent with previous results. The dynamical analysis correlates ion-exchange kinetics to the self-assembly behavior of the complexes.« less

Dynamics of Charged Species in Ionic-Neutral Block Copolymer and Surfactant Complexes [Structural Relaxation and Dynamics of Ionic-Neutral Block Copolymer Surfactant Complexes

DOE PAGES

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.; ...

2017-06-21

Structure–property relationships of ionic block copolymer (BCP) surfactant complexes are critical toward the progress of favorable engineering design of efficient charge-transport materials. In this paper, molecular dynamics simulations are used to understand the dynamics of charged-neutral BCP and surfactant complexes. The dynamics are examined for two different systems: charged-neutral double-hydrophilic and hydrophobic–hydrophilic block copolymers with oppositely charged surfactant moieties. The dynamics of the surfactant head, tails, and charges are studied for five different BCP volume fractions. We observe that the dynamics of the different species solely depend on the balance between electrostatic and entropic interactions between the charged species andmore » the neutral monomers. The favorable hydrophobic–hydrophobic interactions and the unfavorable hydrophobic–hydrophilic interactions determine the mobilities of the monomers. The dynamical properties of the charge species influence complex formation. Structural relaxations exhibit length-scale dependent behavior, with slower relaxation at the radius of gyration length-scale and faster relaxation at the segmental length-scale, consistent with previous results. The dynamical analysis correlates ion-exchange kinetics to the self-assembly behavior of the complexes.« less

Dynamic visual noise reduces confidence in short-term memory for visual information.

PubMed

Kemps, Eva; Andrade, Jackie

2012-05-01

Previous research has shown effects of the visual interference technique, dynamic visual noise (DVN), on visual imagery, but not on visual short-term memory, unless retention of precise visual detail is required. This study tested the prediction that DVN does also affect retention of gross visual information, specifically by reducing confidence. Participants performed a matrix pattern memory task with three retention interval interference conditions (DVN, static visual noise and no interference control) that varied from trial to trial. At recall, participants indicated whether or not they were sure of their responses. As in previous research, DVN did not impair recall accuracy or latency on the task, but it did reduce recall confidence relative to static visual noise and no interference. We conclude that DVN does distort visual representations in short-term memory, but standard coarse-grained recall measures are insensitive to these distortions.

Quantum molecular dynamics of warm dense iron and a five-phase equation of state

NASA Astrophysics Data System (ADS)

Sjostrom, Travis; Crockett, Scott

2018-05-01

Through quantum molecular dynamics (QMD), utilizing both Kohn-Sham (orbital-based) and orbital-free density functional theory, we calculate the equation of state of warm dense iron in the density range 7 -30 g/cm 3 and temperatures from 1 to 100 eV. A critical examination of the iron pseudopotential is made, from which we find a significant improvement at high pressure to the previous QMD calculations of Wang et al. [Phys. Rev. E 89, 023101 (2014), 10.1103/PhysRevE.89.023101]. Our results also significantly extend the ranges of density and temperature that were attempted in that prior work. We calculate the shock Hugoniot and find very good agreement with experimental results to pressures over 20 TPa. These results are then incorporated with previous studies to generate a five-phase equation of state for iron.

Antibiotic-induced population fluctuations and stochastic clearance of bacteria

PubMed Central

Le, Dai; Şimşek, Emrah; Chaudhry, Waqas

2018-01-01

Effective antibiotic use that minimizes treatment failures remains a challenge. A better understanding of how bacterial populations respond to antibiotics is necessary. Previous studies of large bacterial populations established the deterministic framework of pharmacodynamics. Here, characterizing the dynamics of population extinction, we demonstrated the stochastic nature of eradicating bacteria with antibiotics. Antibiotics known to kill bacteria (bactericidal) induced population fluctuations. Thus, at high antibiotic concentrations, the dynamics of bacterial clearance were heterogeneous. At low concentrations, clearance still occurred with a non-zero probability. These striking outcomes of population fluctuations were well captured by our probabilistic model. Our model further suggested a strategy to facilitate eradication by increasing extinction probability. We experimentally tested this prediction for antibiotic-susceptible and clinically-isolated resistant bacteria. This new knowledge exposes fundamental limits in our ability to predict bacterial eradication. Additionally, it demonstrates the potential of using antibiotic concentrations that were previously deemed inefficacious to eradicate bacteria. PMID:29508699

The unusual dynamics of parasite actin result from isodesmic polymerization

PubMed Central

Skillman, Kristen M.; Ma, Christopher I.; Fremont, Daved H.; Diraviyam, Karthikeyan; Cooper, John A.; Sept, David; Sibley, L. David

2013-01-01

Previous reports have indicated that parasite actins are short and inherently unstable, despite being required for motility. Here, we re-examine the polymerization properties of actin in Toxoplasma gondii (TgACTI), unexpectedly finding that it exhibits isodesmic polymerization in contrast to the conventional nucleation-elongation process of all previously studied actins from both eukaryotes and bacteria. TgACTI polymerization kinetics lacks both a lag phase and critical concentration, normally characteristic of actins. Unique among actins, the kinetics of assembly can be fit with a single set of rate constants for all subunit interactions, without need for separate nucleation and elongation rates. This isodesmic model accurately predicts the assembly, disassembly, and the size distribution of TgACTI filaments in vitro, providing a mechanistic explanation for actin dynamics in vivo. Our findings expand the repertoire of mechanisms by which actin polymerization is governed and offer clues about the evolution of self-assembling, stabilized protein polymers. PMID:23921463

Effect of Forcing Function on Nonlinear Acoustic Standing Waves

NASA Technical Reports Server (NTRS)

Finkheiner, Joshua R.; Li, Xiao-Fan; Raman, Ganesh; Daniels, Chris; Steinetz, Bruce

2003-01-01

Nonlinear acoustic standing waves of high amplitude have been demonstrated by utilizing the effects of resonator shape to prevent the pressure waves from entering saturation. Experimentally, nonlinear acoustic standing waves have been generated by shaking an entire resonating cavity. While this promotes more efficient energy transfer than a piston-driven resonator, it also introduces complicated structural dynamics into the system. Experiments have shown that these dynamics result in resonator forcing functions comprised of a sum of several Fourier modes. However, previous numerical studies of the acoustics generated within the resonator assumed simple sinusoidal waves as the driving force. Using a previously developed numerical code, this paper demonstrates the effects of using a forcing function constructed with a series of harmonic sinusoidal waves on resonating cavities. From these results, a method will be demonstrated which allows the direct numerical analysis of experimentally generated nonlinear acoustic waves in resonators driven by harmonic forcing functions.

Turbulent convection in an anelastic rotating sphere: A model for the circulation on the giant planets

NASA Astrophysics Data System (ADS)

Kaspi, Yohai

This thesis studies the dynamics of a rotating compressible gas sphere, driven by internal convection, as a model for the dynamics on the giant planets. We develop a new general circulation model for the Jovian atmosphere, based on the MITgcm dynamical core augmenting the nonhydrostatic model. The grid extends deep into the planet's interior allowing the model to compute the dynamics of a whole sphere of gas rather than a spherical shell (including the strong variations in gravity and the equation of state). Different from most previous 3D convection models, this model is anelastic rather than Boussinesq and thereby incorporates the full density variation of the planet. We show that the density gradients caused by convection drive the system away from an isentropic and therefore barotropic state as previously assumed, leading to significant baroclinic shear. This shear is concentrated mainly in the upper levels and associated with baroclinic compressibility effects. The interior flow organizes in large cyclonically rotating columnar eddies parallel to the rotation axis, which drive upgradient angular momentum eddy fluxes, generating the observed equatorial superrotation. Heat fluxes align with the axis of rotation, contributing to the observed flat meridional emission. We show the transition from weak convection cases with symmetric spiraling columnar modes similar to those found in previous analytic linear theory, to more turbulent cases which exhibit similar, though less regular and solely cyclonic, convection columns which manifest on the surface in the form of waves embedded within the superrotation. We develop a mechanical understanding of this system and scaling laws by studying simpler configurations and the dependence on physical properties such as the rotation period, bottom boundary location and forcing structure. These columnar cyclonic structures propagate eastward, driven by dynamics similar to that of a Rossby wave except that the restoring planetary vorticity gradient is in the opposite direction, due to the spherical geometry in the interior. We further study these interior dynamics using a simplified barotropic annulus model, which shows that the planetary vorticity radial variation causes the eddy angular momentum flux divergence, which drives the superrotating equatorial flow. In addition we study the interaction of the interior dynamics with a stable exterior weather layer, using a quasigeostrophic two layer channel model on a beta plane, where the columnar interior is therefore represented by a negative beta effect. We find that baroclinic instability of even a weak shear can drive strong, stable multiple zonal jets. For this model we find an analytic nonlinear solution, truncated to one growing mode, that exhibits a multiple jet meridional structure, driven by the nonlinear interaction between the eddies. Finally, given the density field from our 3D convection model we derive the high order gravitational spectra of Jupiter, which is a measurable quantity for the upcoming JUNO mission to Jupiter. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

Stability of the bcc phase of 4He close to the melting curve: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Belonoshko, A. B.; Koči, L.; Rosengren, A.

2012-01-01

We have investigated whether the Aziz [J. Chem. Phys.JCPSA60021-960610.1063/1.438007 70, 4330 (1979)] model for 4He renders the body-centered cubic phase more stable than the face-centered cubic phase in the proximity of the melting curve. Using molecular dynamics, we have simulated these solid phases in equilibrium with the liquid at a number of densities. In contrast to previous free energy molecular dynamics calculations, the model stabilizes the body-centered cubic phase. The stability field is just 5∘ wide below the melting curve at pressures around 140 Kbar and about 70∘ wide at pressures around 750 Kbar. Considering that the body-centered cubic phase is dynamically unstable at low temperature, this result bears striking similarities to transition metal phase diagrams.

Dynamic functional connectivity: Promise, issues, and interpretations

PubMed Central

Hutchison, R. Matthew; Womelsdorf, Thilo; Allen, Elena A.; Bandettini, Peter A.; Calhoun, Vince D.; Corbetta, Maurizio; Penna, Stefania Della; Duyn, Jeff H.; Glover, Gary H.; Gonzalez-Castillo, Javier; Handwerker, Daniel A.; Keilholz, Shella; Kiviniemi, Vesa; Leopold, David A.; de Pasquale, Francesco; Sporns, Olaf; Walter, Martin; Chang, Catie

2013-01-01

The brain must dynamically integrate, coordinate, and respond to internal and external stimuli across multiple time scales. Non-invasive measurements of brain activity with fMRI have greatly advanced our understanding of the large-scale functional organization supporting these fundamental features of brain function. Conclusions from previous resting-state fMRI investigations were based upon static descriptions of functional connectivity (FC), and only recently studies have begun to capitalize on the wealth of information contained within the temporal features of spontaneous BOLD FC. Emerging evidence suggests that dynamic FC metrics may index changes in macroscopic neural activity patterns underlying critical aspects of cognition and behavior, though limitations with regard to analysis and interpretation remain. Here, we review recent findings, methodological considerations, neural and behavioral correlates, and future directions in the emerging field of dynamic FC investigations. PMID:23707587

Temperature Measurements in Dynamically-loaded Systems Using Neutron Resonance Spectroscopy (NRS) at LANSCE

NASA Astrophysics Data System (ADS)

Yuan, V. W.

2002-12-01

In previous attempts to determine the internal temperature in systems subjected to dynamic loading, experimenters have usually relied on surface-based optical techniques that are often hampered by insufficient information regarding the emissivity of the surfaces under study. Neutron Resonance Spectroscopy (NRS) is a technique that uses Doppler-broadened neutron resonances to measure internal temperatures in dynamically-loaded samples. NRS has developed its own target-moderator assembly to provide single pulses with an order of magnitude higher brightness than the Lujan production target. The resonance line shapes from which temperature information is extracted are also influenced by non-temperature-dependent broadening from the moderator and detector phosphorescence. Dynamic NRS experiments have been performed to measure the temperature in a silver sheet jet and behind the passage of a shock wave in molybdenum.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Dynamics of regional brain activity in epilepsy: a cross-disciplinary study on both intracranial and scalp-recorded epileptic seizures.

PubMed

Minadakis, George; Ventouras, Errikos; Gatzonis, Stylianos D; Siatouni, Anna; Tsekou, Hara; Kalatzis, Ioannis; Sakas, Damianos E; Stonham, John

2014-04-01

Recent cross-disciplinary literature suggests a dynamical analogy between earthquakes and epileptic seizures. This study extends the focus of inquiry for the applicability of models for earthquake dynamics to examine both scalp-recorded and intracranial electroencephalogram recordings related to epileptic seizures. First, we provide an updated definition of the electric event in terms of magnitude and we focus on the applicability of (i) a model for earthquake dynamics, rooted in a nonextensive Tsallis framework, (ii) the traditional Gutenberg and Richter law and (iii) an alternative method for the magnitude-frequency relation for earthquakes. Second, we apply spatiotemporal analysis in terms of nonextensive statistical physics and we further examine the behavior of the parameters included in the nonextensive formula for both types of electroencephalogram recordings under study. We confirm the previously observed power-law distribution, showing that the nonextensive formula can adequately describe the sequences of electric events included in both types of electroencephalogram recordings. We also show the intermittent behavior of the epileptic seizure cycle which is analogous to the earthquake cycles and we provide evidence of self-affinity of the regional electroencephalogram epileptic seizure activity. This study may provide a framework for the analysis and interpretation of epileptic brain activity and other biological phenomena with similar underlying dynamical mechanisms.

Insights into mid-latitude storm track dynamics from simulations with an idealized dry GCM

NASA Astrophysics Data System (ADS)

Mbengue, C. O.; Schneider, T.

2012-12-01

The mid-latitude storm tracks play an important role in balancing the earth's heat and momentum budget. They have a significant human impact through precipitation and adverse weather conditions; thus, the storm track response to changing climatic conditions is of great interest. In this study, we investigate the climatological response of the mid-latitude storm tracks to varying mean global temperature and convective static stability, using an idealized dry GCM. We demonstrate storm track migration in response to changes in global-mean surface temperatures without modifying the surface pole-equator temperature contrast or including moisture-related effects. The results help interpret the findings of previous global warming studies in which the mid-latitude storm tracks migrate poleward with increasing mean global temperatures. In our study, the storm track position is found to be particularly sensitive to changes in tropical static stability and tropopause height and their effect on the Hadley circulation. The mechanisms driving the dynamics of the mid-latitude storm tracks have been elusive. However, making use of the simplified framework employed in this study, which lends itself to dynamical decompositions, we have been able to improve upon some existing theories on storm track dynamics in dry atmospheres, as well as make additional observations. Previous studies into dry atmospheric dynamics have shown a linear scaling between eddy kinetic energy, a robust measure of the level of storminess, and the mean available potential energy (MAPE). This scaling is utilized in a decomposition that shows that the dominant quantity in storm track dynamics is the meridional gradient of the potential temperature—a measure of baroclinicity. This observation leads us to look for dynamical mechanisms that, on average, dictate the location of regions of elevated baroclinicity. Some credible explanations include the effects on mid-latitude isentropic slopes through a raising or lowering of the tropical tropopause, and effects of a migrating terminus of the Hadley cell. In a simulation where we only vary the convective lapse rate, the decomposition reinforces the meridional temperature gradient as the major determinant of the location of the maximum of MAPE and, by extension, the location of the storm tracks. This is surprising considering that static stability constitutes one of the components of the decomposition. This revelation suggests that static stability plays an indirect role in storm track dynamics through temperature gradients, which is plausible since static stability can affect temperature gradients through its interaction with isentropic slopes. Furthermore, upper tropospheric temperature gradients can be modified by the convective lapse rate through its effect on the depth of the troposphere. The results contained herein can be used to supplement ongoing storm track work in moist atmospheres, using more comprehensive GCMs to understand storm track dynamics in an earth-like environment.

Morphological characteristics of motile plants for dynamic motion

NASA Astrophysics Data System (ADS)

Song, Kahye; Yeom, Eunseop; Kim, Kiwoong; Lee, Sang Joon

2014-11-01

Most plants have been considered as non-motile organisms. However, plants move in response to environmental changes for survival. In addition, some species drive dynamic motions in a short period of time. Mimosa pudica is a plant that rapidly shrinks its body in response to external stimuli. It has specialized organs that are omnidirectionally activated due to morphological features. In addition, scales of pinecone open or close up depending on humidity for efficient seed release. A number of previous studies on the dynamic motion of plants have been investigated in a biochemical point of view. In this study, the morphological characteristics of those motile organs were investigated by using X-ray CT and micro-imaging techniques. The results show that the dynamic motions of motile plants are supported by structural features related with water transport. These studies would provide new insight for better understanding the moving mechanism of motile plant in morphological point of view. This research was financially supported by the Creative Research Initiative of the Ministry of Science, ICT and Future Planning (MSIP) and the National Research Foundation (NRF) of Korea (Grant Number: 2008-0061991).

Hsc70 chaperone activity is required for the cytosolic slow axonal transport of synapsin

PubMed Central

Ganguly, Archan; Han, Xuemei; Das, Utpal; Caillol, Ghislaine

2017-01-01

Soluble cytosolic proteins vital to axonal and presynaptic function are synthesized in the neuronal soma and conveyed via slow axonal transport. Our previous studies suggest that the overall slow transport of synapsin is mediated by dynamic assembly/disassembly of cargo complexes followed by short-range vectorial transit (the “dynamic recruitment” model). However, neither the composition of these complexes nor the mechanistic basis for the dynamic behavior is understood. In this study, we first examined putative cargo complexes associated with synapsin using coimmunoprecipitation and multidimensional protein identification technology mass spectrometry (MS). MS data indicate that synapsin is part of a multiprotein complex enriched in chaperones/cochaperones including Hsc70. Axonal synapsin–Hsc70 coclusters are also visualized by two-color superresolution microscopy. Inhibition of Hsc70 ATPase activity blocked the slow transport of synapsin, disrupted axonal synapsin organization, and attenuated Hsc70–synapsin associations, advocating a model where Hsc70 activity dynamically clusters cytosolic proteins into cargo complexes, allowing transport. Collectively, our study offers insight into the molecular organization of cytosolic transport complexes and identifies a novel regulator of slow transport. PMID:28559423

Gloss discrimination and eye movements

NASA Astrophysics Data System (ADS)

Phillips, Jonathan B.; Ferwerda, James A.; Nunziata, Ann

2010-02-01

Human observers are able to make fine discriminations of surface gloss. What cues are they using to perform this task? In previous studies, we identified two reflection-related cues-the contrast of the reflected image (c, contrast gloss) and the sharpness of reflected image (d, distinctness-of-image gloss)--but these were for objects rendered in standard dynamic range (SDR) images with compressed highlights. In ongoing work, we are studying the effects of image dynamic range on perceived gloss, comparing high dynamic range (HDR) images with accurate reflections and SDR images with compressed reflections. In this paper, we first present the basic findings of this gloss discrimination study then present an analysis of eye movement recordings that show where observers were looking during the gloss discrimination task. The results indicate that: 1) image dynamic range has significant influence on perceived gloss, with surfaces presented in HDR images being seen as glossier and more discriminable than their SDR counterparts; 2) observers look at both light source highlights and environmental interreflections when judging gloss; and 3) both of these results are modulated by surface geometry and scene illumination.

Dynamics of Cooperation in a Task Completion Social Dilemma

PubMed Central

Passino, Kevin M.

2017-01-01

We study the situation where the members of a community have the choice to participate in the completion of a common task. The process of completing the task involves only costs and no benefits to the individuals that participate in this process. However, completing the task results in changes that significantly benefit the community and that exceed the participation efforts. A task completion social dilemma arises when the short-term participation costs dissipate any interest in the community members to contribute to the task completion process and therefore to obtain the benefits that result from completing the task. In this work, we model the task completion problem using a dynamical system that characterizes the participation dynamics in the community and the task completion process. We show how this model naturally allows for the incorporation of several mechanisms that facilitate the emergence of cooperation and that have been studied in previous research on social dilemmas, including communication across a network, and indirect reciprocity through relative reputation. We provide mathematical analyses and computer simulations to study the qualitative properties of the participation dynamics in the community for different scenarios. PMID:28125721

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

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.

Structure–property relationships of ionic block copolymer (BCP) surfactant complexes are critical toward the progress of favorable engineering design of efficient charge-transport materials. In this paper, molecular dynamics simulations are used to understand the dynamics of charged-neutral BCP and surfactant complexes. The dynamics are examined for two different systems: charged-neutral double-hydrophilic and hydrophobic–hydrophilic block copolymers with oppositely charged surfactant moieties. The dynamics of the surfactant head, tails, and charges are studied for five different BCP volume fractions. We observe that the dynamics of the different species solely depend on the balance between electrostatic and entropic interactions between the charged species andmore » the neutral monomers. The favorable hydrophobic–hydrophobic interactions and the unfavorable hydrophobic–hydrophilic interactions determine the mobilities of the monomers. The dynamical properties of the charge species influence complex formation. Structural relaxations exhibit length-scale dependent behavior, with slower relaxation at the radius of gyration length-scale and faster relaxation at the segmental length-scale, consistent with previous results. The dynamical analysis correlates ion-exchange kinetics to the self-assembly behavior of the complexes.« less

Using Social Network Graphs as Visualization Tools to Influence Peer Selection Decision-Making Strategies to Access Information about Complex Socioscientific Issues

ERIC Educational Resources Information Center

Yoon, Susan A.

2011-01-01

This study extends previous research that explores how visualization affordances that computational tools provide and social network analyses that account for individual- and group-level dynamic processes can work in conjunction to improve learning outcomes. The study's main hypothesis is that when social network graphs are used in instruction,…

Improving Cybersecurity Incident Response Team (CSIRT) Skills, Dynamics and Effectiveness

DTIC Science & Technology

2017-03-01

recommendations for optimal CSIRT performance. 15. SUBJECT TERMS Cyber Incident Response, Response Teams, Cognitive Task Analysis 16. SECURITY...conducted a study of the cognitive , social, personality, and motivational requirements involved in cybersecurity incident response and then validated...corporate CSIRTs, and academic institution CSIRTs. • Survey of Non-Technical KSAOs. Previous known studies of CSIRTs did not examine cognitive , social, and

The Impact of Procedural and Epistemological Knowledge on Conceptual Understanding: The Case of Density and Floating-Sinking Phenomena

ERIC Educational Resources Information Center

Zoupidis, Anastasios; Pnevmatikos, Dimitrios; Spyrtou, Anna; Kariotoglou, Petros

2016-01-01

The aim of the present study was twofold. First, we aimed to replicate the findings of previous studies which had showed a substantial improvement on procedural and epistemological knowledge after direct instruction and their maintenance in time. Second, we aimed to examine the dynamic relationships of the procedural (control of variables…

On the Dynamic Nature of Response Criterion in Recognition Memory: Effects of Base Rate, Awareness, and Feedback

ERIC Educational Resources Information Center

Rhodes, Matthew G.; Jacoby, Larry L.

2007-01-01

The authors examined whether participants can shift their criterion for recognition decisions in response to the probability that an item was previously studied. Participants in 3 experiments were given recognition tests in which the probability that an item was studied was correlated with its location during the test. Results from all 3…

Molecular-dynamics simulations of alkaline-earth metal cations in water by atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Li, Xin

2005-09-01

Intermolecular potential for alkaline-earth metal (Be(2+), Mg(2+), and Ca(2+)) cations in water has been derived using the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), and it is consistent with what was previously applied to the hydration study of the monovalent cations. Parameters for the effective interaction between a cation and a water molecule were determined, reproducing the ab initio results. The static, dynamic, and thermodynamic properties of Be(2+)(aq), Mg(2+)(aq), and Ca(2+)(aq) were studied using these potential parameters. Be(2+) requires a more complicated form of the potential function than Mg(2+) and Ca(2+) in order to obtain better fits. Strong influences of the twofold charged cations on the structures of the hydration shells and some other properties of aqueous ionic solutions are discussed and compared with the results of a previous study of monovalent cations in water. At the same time, comparative study of the hydration properties of each cation is also discussed. This work demonstrates that ABEEM/MM provides a useful tool in the exploration of the hydration of double-charged cations in water.

Binocular rivalry in children on the autism spectrum

PubMed Central

Lunghi, Claudia; Neil, Louise; Burr, David; Pellicano, Elizabeth

2017-01-01

When different images are presented to the eyes, the brain is faced with ambiguity, causing perceptual bistability: visual perception continuously alternates between the monocular images, a phenomenon called binocular rivalry. Many models of rivalry suggest that its temporal dynamics depend on mutual inhibition among neurons representing competing images. These models predict that rivalry should be different in autism, which has been proposed to present an atypical ratio of excitation and inhibition [the E/I imbalance hypothesis; Rubenstein & Merzenich, 2003]. In line with this prediction, some recent studies have provided evidence for atypical binocular rivalry dynamics in autistic adults. In this study, we examined if these findings generalize to autistic children. We developed a child‐friendly binocular rivalry paradigm, which included two types of stimuli, low‐ and high‐complexity, and compared rivalry dynamics in groups of autistic and age‐ and intellectual ability‐matched typical children. Unexpectedly, the two groups of children presented the same number of perceptual transitions and the same mean phase durations (times perceiving one of the two stimuli). Yet autistic children reported mixed percepts for a shorter proportion of time (a difference which was in the opposite direction to previous adult studies), while elevated autistic symptomatology was associated with shorter mixed perception periods. Rivalry in the two groups was affected similarly by stimulus type, and consistent with previous findings. Our results suggest that rivalry dynamics are differentially affected in adults and developing autistic children and could be accounted for by hierarchical models of binocular rivalry, including both inhibition and top‐down influences. Autism Res 2017. ©2017 The Authors Autism Research published by Wiley Periodicals, Inc. on behalf of International Society for Autism Research Autism Res 2017, 10: 1096–1106. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. PMID:28301094

Multijoint kinetic chain analysis of knee extension during the soccer instep kick.

PubMed

Naito, Kozo; Fukui, Yosuke; Maruyama, Takeo

2010-04-01

Although previous studies have shown that motion-dependent interactions between adjacent segments play an important role in producing knee extension during the soccer instep kick, detailed knowledge about the mechanisms underlying those interactions is lacking. The present study aimed to develop a 3-D dynamical model for the multijoint kinetic chain of the instep kick in order to quantify the contributions of the causal dynamical factors to the production of maximum angular velocity during knee extension. Nine collegiate soccer players volunteered to participate in the experiment and performed instep kicking movements while 3-D positional data and the ground reaction force were measured. A dynamical model was developed in the form of a linked system containing 8 segments and 18 joint rotations, and the knee extension/flexion motion was decomposed into causal factors related to muscular moment, gyroscopic moment, centrifugal force, Coriolis force, gravity, proximal endpoint linear acceleration, and external force-dependent terms. The rapid knee extension during instep kicking was found to result almost entirely from kicking leg centrifugal force, trunk rotation muscular moment, kicking leg Coriolis force, and trunk rotation gyroscopic-dependent components. Based on the finding that rapid knee extension during instep kicking stems from multiple dynamical factors, it is suggested that the multijoint kinetic chain analysis used in the present study is more useful for achieving a detailed understanding of the cause of rapid kicking leg movement than the previously used 2-D, two-segment kinetic chain model. The present results also indicated that the centrifugal effect due to the kicking hip flexion angular velocity contributed substantially to the generation of a rapid knee extension, suggesting that the adjustment between the kicking hip flexion angular velocity and the leg configuration (knee flexion angle) is more important for effective instep kicking than other joint kinematics.

Dust environment and dynamical history of a sample of short-period comets . II. 81P/Wild 2 and 103P/Hartley 2

NASA Astrophysics Data System (ADS)

Pozuelos, F. J.; Moreno, F.; Aceituno, F.; Casanova, V.; Sota, A.; López-Moreno, J. J.; Castellano, J.; Reina, E.; Climent, A.; Fernández, A.; San Segundo, A.; Häusler, B.; González, C.; Rodriguez, D.; Bryssinck, E.; Cortés, E.; Rodriguez, F. A.; Baldris, F.; García, F.; Gómez, F.; Limón, F.; Tifner, F.; Muler, G.; Almendros, I.; de los Reyes, J. A.; Henríquez, J. A.; Moreno, J. A.; Báez, J.; Bel, J.; Camarasa, J.; Curto, J.; Hernández, J. F.; González, J. J.; Martín, J. J.; Salto, J. L.; Lopesino, J.; Bosch, J. M.; Ruiz, J. M.; Vidal, J. R.; Ruiz, J.; Sánchez, J.; Temprano, J.; Aymamí, J. M.; Lahuerta, L.; Montoro, L.; Campas, M.; García, M. A.; Canales, O.; Benavides, R.; Dymock, R.; García, R.; Ligustri, R.; Naves, R.; Lahuerta, S.; Pastor, S.

2014-11-01

Aims: This paper is a continuation of the first paper in this series, where we presented an extended study of the dust environment of a sample of short-period comets and their dynamical history. On this occasion, we focus on comets 81P/Wild 2 and 103P/Hartley 2, which are of special interest as targets of the spacecraft missions Stardust and EPOXI. Methods: As in the previous study, we used two sets of observational data: a set of images, acquired at Sierra Nevada and Lulin observatories, and the Afρ data as a function of the heliocentric distance provided by the amateur astronomical association Cometas-Obs. The dust environment of comets (dust loss rate, ejection velocities, and size distribution of the particles) was derived from our Monte Carlo dust tail code. To determine their dynamical history we used the numerical integrator Mercury 6.2 to ascertain the time spent by these objects in the Jupiter family Comet region. Results: From the dust analysis, we conclude that both 81P/Wild 2 and 103P/Hartley 2 are dusty comets, with an annual dust production rate of 2.8 × 109 kg yr-1 and (0.4-1.5) × 109 kg yr-1, respectively. From the dynamical analysis, we determined their time spent in the Jupiter family Comet region as ~40 yr in the case of 81P/Wild 2 and ~1000 yr for comet 103P/Hartley 2. These results imply that 81P/Wild 2 is the youngest and the most active comet of the eleven short-period comets studied so far, which tends to favor the correlation between the time spent in JFCs region and the comet activity previously discussed.

Generalization of Dynamics Learning Across Changes in Movement Amplitude

PubMed Central

Mattar, Andrew A. G.

2010-01-01

Studies on generalization show the nature of how learning is encoded in the brain. Previous studies have shown rather limited generalization of dynamics learning across changes in movement direction, a finding that is consistent with the idea that learning is primarily local. In contrast, studies show a broader pattern of generalization across changes in movement amplitude, suggesting a more general form of learning. To understand this difference, we performed an experiment in which subjects held a robotic manipulandum and made movements to targets along the body midline. Subjects were trained in a velocity-dependent force field while moving to a 15 cm target. After training, subjects were tested for generalization using movements to a 30 cm target. We used force channels in conjunction with movements to the 30 cm target to assess the extent of generalization. Force channels restricted lateral movements and allowed us to measure force production during generalization. We compared actual lateral forces to the forces expected if dynamics learning generalized fully. We found that, during the test for generalization, subjects produced reliably less force than expected. Force production was appropriate for the portion of the transfer movement in which velocities corresponded to those experienced with the 15 cm target. Subjects failed to produce the expected forces when velocities exceeded those experienced in the training task. This suggests that dynamics learning generalizes little beyond the range of one's experience. Consistent with this result, subjects who trained on the 30 cm target showed full generalization to the 15 cm target. We performed two additional experiments that show that interleaved trials to the 30 cm target during training on the 15 cm target can resolve the difference between the current results and those reported previously. PMID:20463200

Dynamic Courseware Generation on the WWW.

ERIC Educational Resources Information Center

Vassileva, Julita; Deters, Ralph

1998-01-01

The Dynamic Courseware Generator (DCG), which runs on a Web server, was developed for the authoring of adaptive computer-assisted learning courses. It generates an individual course according to the learner's goals and previous knowledge, and dynamically adapts the course according to the learner's success in knowledge acquisition. The tool may be…

Dynamics in Higher Education Politics: A Theoretical Model

ERIC Educational Resources Information Center

Kauko, Jaakko

2013-01-01

This article presents a model for analysing dynamics in higher education politics (DHEP). Theoretically the model draws on the conceptual history of political contingency, agenda-setting theories and previous research on higher education dynamics. According to the model, socio-historical complexity can best be analysed along two dimensions: the…

The V-band Empirical Mass-luminosity Relation for Main Sequence Stars

NASA Astrophysics Data System (ADS)

Xia, Fang; Fu, Yan-Ning

2010-07-01

Stellar mass is an indispensable parameter in the studies of stellar physics and stellar dynamics. On the one hand, the most reliable way to determine the stellar dynamical mass is via orbital determinations of binaries. On the other hand, however, most stellar masses have to be estimated by using the mass luminosity relation (MLR). Therefore, it is important to obtain the empirical MLR through fitting the data of stellar dynamical mass and luminosity. The effect of metallicity can make this relation disperse in the V-band, but studies show that this is mainly limited to the case when the stellar mass is less than 0.6M⊙ Recently, many relevant data have been accumulated for main sequence stars with larger masses, which make it possible to significantly improve the corresponding MLR. Using a fitting method which can reasonably assign weights to the observational data including two quantities with different dimensions, we obtain a V-band MLR based on the dynamical masses and luminosities of 203 main sequence stars. In comparison with the previous work, the improved MLR is statistically significant, and the relative error of mass estimation reaches about 5%. Therefore, our MLR is useful not only in the studies of statistical nature, but also in the studies of concrete stellar systems, such as the long-term dynamical study and the short-term positioning study of a specific multiple star system.

The V Band Empirical Mass-Luminosity Relation for Main Sequence Stars

NASA Astrophysics Data System (ADS)

Xia, F.; Fu, Y. N.

2010-01-01

Stellar mass is an indispensable parameter in the studies of stellar physics and stellar dynamics. On the one hand, the most reliable way to determine the stellar dynamical mass is via orbital determination of binaries. On the other hand, however, most stellar masses have to be estimated by using the mass-luminosity relation (MLR). Therefore, it is important to obtain the empirical MLR through fitting the data of stellar dynamical mass and luminosity. The effect of metallicity can make this relation disperse in the V-band, but studies show that this is mainly limited to the case when the stellar mass is less than 0.6M⊙. Recently, many relevant data have been accumulated for main sequence stars with larger mass, which make it possible to significantly improve the corresponding MLR. Using a fitting method which can reasonably assign weight to the observational data including two quantities with different dimensions, we obtain a V-band MLR based on the dynamical masses and luminosities of 203 main sequence stars. Compared with the previous work, the improved MLR is statistically significant, and the relative error of mass estimation reaches about 5%. Therefore, our MLR is useful not only in studies of statistical nature, but also in studies of concrete stellar systems, such as the long-term dynamical study and the short-term positioning study of a specific multiple star system.

Effects of temperature on consumer-resource interactions.

PubMed

Amarasekare, Priyanga

2015-05-01

Understanding how temperature variation influences the negative (e.g. self-limitation) and positive (e.g. saturating functional responses) feedback processes that characterize consumer-resource interactions is an important research priority. Previous work on this topic has yielded conflicting outcomes with some studies predicting that warming should increase consumer-resource oscillations and others predicting that warming should decrease consumer-resource oscillations. Here, I develop a consumer-resource model that both synthesizes previous findings in a common framework and yields novel insights about temperature effects on consumer-resource dynamics. I report three key findings. First, when the resource species' birth rate exhibits a unimodal temperature response, as demonstrated by a large number of empirical studies, the temperature range over which the consumer-resource interaction can persist is determined by the lower and upper temperature limits to the resource species' reproduction. This contrasts with the predictions of previous studies, which assume that the birth rate exhibits a monotonic temperature response, that consumer extinction is determined by temperature effects on consumer species' traits, rather than the resource species' traits. Secondly, the comparative analysis I have conducted shows that whether warming leads to an increase or decrease in consumer-resource oscillations depends on the manner in which temperature affects intraspecific competition. When the strength of self-limitation increases monotonically with temperature, warming causes a decrease in consumer-resource oscillations. However, if self-limitation is strongest at temperatures physiologically optimal for reproduction, a scenario previously unanalysed by theory but amply substantiated by empirical data, warming can cause an increase in consumer-resource oscillations. Thirdly, the model yields testable comparative predictions about consumer-resource dynamics under alternative hypotheses for how temperature affects competitive and resource acquisition traits. Importantly, it does so through empirically quantifiable metrics for predicting temperature effects on consumer viability and consumer-resource oscillations, which obviates the need for parameterizing complex dynamical models. Tests of these metrics with empirical data on a host-parasitoid interaction yield realistic estimates of temperature limits for consumer persistence and the propensity for consumer-resource oscillations, highlighting their utility in predicting temperature effects, particularly warming, on consumer-resource interactions in both natural and agricultural settings. © 2014 The Author. Journal of Animal Ecology © 2014 British Ecological Society.

Effects of Peanut-Tobacco Rotations on Population Dynamics of Meloidogyne arenaria in Mixed Race Populations.

PubMed

Hirunsalee, A; Barker, K R; Beute, M K

1995-06-01

A 3-year microplot study was initiated to characterize the population dynamics, reproduction potential, and survivorship of single or mixed populations of Meloidogyne arenaria race 1 (Ma1) and race 2 (Ma2), as affected by crop rotations of peanut 'Florigiant' and M. incognita races 1 and 3-resistant 'McNair 373' and susceptible 'Coker 371-Gold' tobacco. Infection, reproduction, and root damage by Ma2 on peanut and by Ma1 on resistant tobacco were limited in the first year. Infection, reproduction, and root-damage potentials on susceptible tobacco were similar for Ma1 and Ma2. In the mixed (1:1) population, Ma1 was dominant on peanut and Ma2 was dominant on both tobacco cultivars. Crop rotation affected the population dynamics of different nematode races. For years 2 and 3, the low numbers of Ma1 and Ma2 from a previous-year poor host increased rapidly on suitable hosts. Ma1 had greater reproduction factors ([RF] = population density at harvest/population density at preplandng) than did Ma2 and Ma1 + Ma2 in second-year peanut plots following first-year resistant tobacco, and in third-year peanut plots following second-year tobacco. In mixed infestations, Ma1 predominated over Ma2 in previous-year peanut plots, whereas Ma2 predominated over Ma1 in previous-year tobacco plots. Moderate damage on resistant tobacco was induced by Ma1 in the second year. In the third year, moderate damage on peanut was associated with 'Ma2' from previous-year peanut plots. The resistant tobacco supported sufficient reproduction of Ma1 over 2 years to effect moderate damage and yield suppression to peanut in year 3.

Effects of Peanut-Tobacco Rotations on Population Dynamics of Meloidogyne arenaria in Mixed Race Populations

PubMed Central

Hirunsalee, Anan; Barker, K. R.; Beute, M. K.

1995-01-01

A 3-year microplot study was initiated to characterize the population dynamics, reproduction potential, and survivorship of single or mixed populations of Meloidogyne arenaria race 1 (Ma1) and race 2 (Ma2), as affected by crop rotations of peanut 'Florigiant' and M. incognita races 1 and 3-resistant 'McNair 373' and susceptible 'Coker 371-Gold' tobacco. Infection, reproduction, and root damage by Ma2 on peanut and by Ma1 on resistant tobacco were limited in the first year. Infection, reproduction, and root-damage potentials on susceptible tobacco were similar for Ma1 and Ma2. In the mixed (1:1) population, Ma1 was dominant on peanut and Ma2 was dominant on both tobacco cultivars. Crop rotation affected the population dynamics of different nematode races. For years 2 and 3, the low numbers of Ma1 and Ma2 from a previous-year poor host increased rapidly on suitable hosts. Ma1 had greater reproduction factors ([RF] = population density at harvest/population density at preplandng) than did Ma2 and Ma1 + Ma2 in second-year peanut plots following first-year resistant tobacco, and in third-year peanut plots following second-year tobacco. In mixed infestations, Ma1 predominated over Ma2 in previous-year peanut plots, whereas Ma2 predominated over Ma1 in previous-year tobacco plots. Moderate damage on resistant tobacco was induced by Ma1 in the second year. In the third year, moderate damage on peanut was associated with 'Ma2' from previous-year peanut plots. The resistant tobacco supported sufficient reproduction of Ma1 over 2 years to effect moderate damage and yield suppression to peanut in year 3. PMID:19277278

Oscillations and Multiple Equilibria in Microvascular Blood Flow.

PubMed

Karst, Nathaniel J; Storey, Brian D; Geddes, John B

2015-07-01

We investigate the existence of oscillatory dynamics and multiple steady-state flow rates in a network with a simple topology and in vivo microvascular blood flow constitutive laws. Unlike many previous analytic studies, we employ the most biologically relevant models of the physical properties of whole blood. Through a combination of analytic and numeric techniques, we predict in a series of two-parameter bifurcation diagrams a range of dynamical behaviors, including multiple equilibria flow configurations, simple oscillations in volumetric flow rate, and multiple coexistent limit cycles at physically realizable parameters. We show that complexity in network topology is not necessary for complex behaviors to arise and that nonlinear rheology, in particular the plasma skimming effect, is sufficient to support oscillatory dynamics similar to those observed in vivo.

Pattern dynamics of the reaction-diffusion immune system.

PubMed

Zheng, Qianqian; Shen, Jianwei; Wang, Zhijie

2018-01-01

In this paper, we will investigate the effect of diffusion, which is ubiquitous in nature, on the immune system using a reaction-diffusion model in order to understand the dynamical behavior of complex patterns and control the dynamics of different patterns. Through control theory and linear stability analysis of local equilibrium, we obtain the optimal condition under which the system loses stability and a Turing pattern occurs. By combining mathematical analysis and numerical simulation, we show the possible patterns and how these patterns evolve. In addition, we establish a bridge between the complex patterns and the biological mechanism using the results from a previous study in Nature Cell Biology. The results in this paper can help us better understand the biological significance of the immune system.

Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

NASA Astrophysics Data System (ADS)

Palczynski, Karol; Wilke, Andreas; Paeschke, Manfred; Dzubiella, Joachim

2017-09-01

Linking the experimentally accessible macroscopic properties of thermoplastic polymers to their microscopic static and dynamic properties is a key requirement for targeted material design. Classical molecular dynamics simulations enable us to study the structural and dynamic behavior of molecules on microscopic scales, and statistical physics provides a framework for relating these properties to the macroscopic properties. We take a first step toward creating an automated workflow for the theoretical prediction of thermoplastic material properties by developing an expeditious method for parameterizing a simple yet surprisingly powerful coarse-grained bisphenol-A polycarbonate model which goes beyond previous coarse-grained models and successfully reproduces the thermal expansion behavior, the glass transition temperature as a function of the molecular weight, and several elastic properties.

Critical short-time dynamics in a system with interacting static and diffusive populations

NASA Astrophysics Data System (ADS)

Argolo, C.; Quintino, Yan; Gleria, Iram; Lyra, M. L.

2012-01-01

We study the critical short-time dynamical behavior of a one-dimensional model where diffusive individuals can infect a static population upon contact. The model presents an absorbing phase transition from an active to an inactive state. Previous calculations of the critical exponents based on quasistationary quantities have indicated an unusual crossover from the directed percolation to the diffusive contact process universality classes. Here we show that the critical exponents governing the slow short-time dynamic evolution of several relevant quantities, including the order parameter, its relative fluctuations, and correlation function, reinforce the lack of universality in this model. Accurate estimates show that the critical exponents are distinct in the regimes of low and high recovery rates.

Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos.

PubMed

Zhao, Ziqing W; White, Melanie D; Bissiere, Stephanie; Levi, Valeria; Plachta, Nicolas

2016-12-23

Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.

Communication: Energy transfer and reaction dynamics for DCl scattering on Au(111): An ab initio molecular dynamics study.

PubMed

Kolb, Brian; Guo, Hua

2016-07-07

Scattering and dissociative chemisorption of DCl on Au(111) are investigated using ab initio molecular dynamics with a slab model, in which the top two layers of Au are mobile. Substantial kinetic energy loss in the scattered DCl is found, but the amount of energy transfer is notably smaller than that observed in the experiment. On the other hand, the dissociative chemisorption probability reproduces the experimental trend with respect to the initial kinetic energy, but is about one order of magnitude larger than the reported initial sticking probability. While the theory-experiment agreement is significantly improved from the previous rigid surface model, the remaining discrepancies are still substantial, calling for further scrutiny in both theory and experiment.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Further evidences for sleep instability and impaired spindle-delta dynamics in schizophrenia: a whole-night polysomnography study with neuroloop-gain and sleep-cycle analysis.

PubMed

Sasidharan, Arun; Kumar, Sunil; Nair, Ajay Kumar; Lukose, Ammu; Marigowda, Vrinda; John, John P; Kutty, Bindu M

2017-10-01

Sleep offers a unique window into the brain dysfunctions in schizophrenia. Many past sleep studies have reported abnormalities in both macro-sleep architecture (like increased awakenings) as well as micro-sleep-architecture (like spindle deficits) in patients with schizophrenia (PSZ). The present study attempts to replicate previous reports of macro- and micro-sleep-architectural abnormalities in schizophrenia. In addition, the study also examined sleep-stage changes and spindle-delta dynamics across sleep-cycles to provide further evidence in support of the dysfunctional thalamocortical mechanisms causing sleep instability and poor sleep maintenance associated with schizophrenia pathophysiology. Whole-night polysomnography was carried out among 45 PSZ and 39 age- and gender-matched healthy control subjects. Sleep-stage dynamics were assessed across sleep-cycles using a customized software algorithm. Spindle-delta dynamics across sleep-cycles were determined using neuroloop-gain analysis. PSZ showed macro-sleep architecture abnormalities such as prolonged sleeplessness, increased intermittent-awakenings, long sleep-onset latency, reduced non-rapid eye movement (NREM) stage 2 sleep, increased stage transitions, and poor sleep efficiency. They also showed reduced spindle density (sigma neuroloop-gain) but comparable slow wave density (delta neuroloop-gain) throughout the sleep. Sleep-cycle-wise analysis revealed transient features of sleep instability due to significantly increased intermittent awakenings especially in the first and third sleep-cycles, and unstable and recurrent stage transitions in both NREM (first sleep-cycle) and rapid eye movement (REM) sleep-periods (second sleep-cycle). Spindle deficits were persistent across the first three cycles and were positively correlated with sleep disruption during the subsequent REM sleep. In addition to replicating previously reported sleep deficits in PSZ, the current study showed subtle deficits in NREM-REM alterations across whole-night polysomnography. These results point towards a possible maladaptive interplay between unstable thalamocortical networks, resulting in sleep-cycle-specific instability patterns associated with schizophrenia pathophysiology. Copyright © 2017 Elsevier B.V. All rights reserved.

Methodology for dynamic biaxial tension testing of pregnant uterine tissue.

PubMed

Manoogian, Sarah; Mcnally, Craig; Calloway, Britt; Duma, Stefan

2007-01-01

Placental abruption accounts for 50% to 70% of fetal losses in motor vehicle crashes. Since automobile crashes are the leading cause of traumatic fetal injury mortality in the United States, research of this injury mechanism is important. Before research can adequately evaluate current and future restraint designs, a detailed model of the pregnant uterine tissues is necessary. The purpose of this study is to develop a methodology for testing the pregnant uterus in biaxial tension at a rate normally seen in a motor vehicle crash. Since the majority of previous biaxial work has established methods for quasi-static testing, this paper combines previous research and new methods to develop a custom designed system to strain the tissue at a dynamic rate. Load cells and optical markers are used for calculating stress strain curves of the perpendicular loading axes. Results for this methodology show images of a tissue specimen loaded and a finite verification of the optical strain measurement. The biaxial test system dynamically pulls the tissue to failure with synchronous motion of four tissue grips that are rigidly coupled to the tissue specimen. The test device models in situ loading conditions of the pregnant uterus and overcomes previous limitations of biaxial testing. A non-contact method of measuring strains combined with data reduction to resolve the stresses in two directions provides the information necessary to develop a three dimensional constitutive model of the material. Moreover, future research can apply this method to other soft tissues with similar in situ loading conditions.

Investigating multiphoton phenomena using nonlinear dynamics

NASA Astrophysics Data System (ADS)

Huang, Shu

Many seemingly simple systems can display extraordinarily complex dynamics which has been studied and uncovered through nonlinear dynamical theory. The leitmotif of this thesis is changing phase-space structures and their (linear or non-linear) stabilities by adding control functions (which act on the system as external perturbations) to the relevant Hamiltonians. These phase-space structures may be periodic orbits, invariant tori or their stable and unstable manifolds. One-electron systems and diatomic molecules are fundamental and important staging ground for new discoveries in nonlinear dynamics. In past years, increasing emphasis and effort has been put on the control or manipulation of these systems. Recent developments of nonlinear dynamical tools can provide efficient ways of doing so. In the first subtopic of the thesis, we are adding a control function to restore tori at prescribed locations in phase space. In the remainder of the thesis, a control function with parameters is used to change the linear stability of the periodic orbits which govern the processes in question. In this thesis, we report our theoretical analyses on multiphoton ionization of Rydberg atoms exposed to strong microwave fields and the dissociation of diatomic molecules exposed to bichromatic lasers using nonlinear dynamical tools. This thesis is composed of three subtopics. In the first subtopic, we employ local control theory to reduce the stochastic ionization of hydrogen atom in a strong microwave field by adding a relatively small control term to the original Hamiltonian. In the second subtopic, we perform periodic orbit analysis to investigate multiphoton ionization driven by a bichromatic microwave field. Our results show quantitative and qualitative agreement with previous studies, and hence identify the mechanism through which short periodic orbits organize the dynamics in multiphoton ionization. In addition, we achieve substantial time savings with this approach. In the third subtopic we extend our periodic orbit analysis to the dissociation of diatomic molecules driven by a bichromatic laser. In this problem, our results based on periodic orbit analysis again show good agreement with previous work, and hence promise more potential applications of this approach in molecular physics.

Linear perturbations in spherically symmetric dust cosmologies including a cosmological constant

NASA Astrophysics Data System (ADS)

Meyer, Sven; Bartelmann, Matthias

2017-12-01

We study the dynamical behaviour of gauge-invariant linear perturbations in spherically symmetric dust cosmologies including a cosmological constant. In contrast to spatially homogeneous FLRW models, the reduced degree of spatial symmetry causes a non-trivial dynamical coupling of gauge-invariant quantities already at first order perturbation theory and the strength and influence of this coupling on the spacetime evolution is investigated here. We present results on the underlying dynamical equations augmented by a cosmological constant and integrate them numerically. We also present a method to derive cosmologically relevant initial variables for this setup. Estimates of angular power spectra for each metric variable are computed and evaluated on the central observer's past null cone. By comparing the full evolution to the freely evolved initial profiles, the coupling strength will be determined for a best fit radially inhomogeneous patch obtained in previous works (see [1]). We find that coupling effects are not noticeable within the cosmic variance limit and can therefore safely be neglected for a relevant cosmological scenario. On the contrary, we find very strong coupling effects in a best fit spherical void model matching the distance redshift relation of SNe which is in accordance with previous findings using parametric void models.

Regulation of Cortical Dynamic Range by Background Synaptic Noise and Feedforward Inhibition.

PubMed

Khubieh, Ayah; Ratté, Stéphanie; Lankarany, Milad; Prescott, Steven A

2016-08-01

The cortex encodes a broad range of inputs. This breadth of operation requires sensitivity to weak inputs yet non-saturating responses to strong inputs. If individual pyramidal neurons were to have a narrow dynamic range, as previously claimed, then staggered all-or-none recruitment of those neurons would be necessary for the population to achieve a broad dynamic range. Contrary to this explanation, we show here through dynamic clamp experiments in vitro and computer simulations that pyramidal neurons have a broad dynamic range under the noisy conditions that exist in the intact brain due to background synaptic input. Feedforward inhibition capitalizes on those noise effects to control neuronal gain and thereby regulates the population dynamic range. Importantly, noise allows neurons to be recruited gradually and occludes the staggered recruitment previously attributed to heterogeneous excitation. Feedforward inhibition protects spike timing against the disruptive effects of noise, meaning noise can enable the gain control required for rate coding without compromising the precise spike timing required for temporal coding. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Depictive Gestures as Evidence for Dynamic Mental Imagery in Four Types of Student Reasoning

NASA Astrophysics Data System (ADS)

Stephens, A. Lynn; Clement, John J.

2007-01-01

We discuss evidence for the use of runnable imagery (imagistic simulation) in four types of student reasoning. In an in-depth case study of a high school physics class, we identified multiple instances of students running mental models, using analogies, using extreme cases, and using Gedanken experiments. Previous case studies of expert scientists have indicated that these processes can be central during scientific model construction; here we discuss their spontaneous use by students. We also discuss their association with spontaneous, depictive gestures, which we interpret as an indicator of the use of dynamic and kinesthetic imagery. Of the numerous instances of these forms of reasoning observed in the class, most were associated with depictive gestures and over half with gestures that depicted motion or force. This evidence suggests that runnable, dynamic mental imagery can be very important in student reasoning.

Ferroelastic domain switching dynamics under electrical and mechanical excitations.

PubMed

Gao, Peng; Britson, Jason; Nelson, Christopher T; Jokisaari, Jacob R; Duan, Chen; Trassin, Morgan; Baek, Seung-Hyub; Guo, Hua; Li, Linze; Wang, Yiran; Chu, Ying-Hao; Minor, Andrew M; Eom, Chang-Beom; Ramesh, Ramamoorthy; Chen, Long-Qing; Pan, Xiaoqing

2014-05-02

In thin film ferroelectric devices, switching of ferroelastic domains can significantly enhance electromechanical response. Previous studies have shown disagreement regarding the mobility or immobility of ferroelastic domain walls, indicating that switching behaviour strongly depends on specific microstructures in ferroelectric systems. Here we study the switching dynamics of individual ferroelastic domains in thin Pb(Zr0.2,Ti0.8)O3 films under electrical and mechanical excitations by using in situ transmission electron microscopy and phase-field modelling. We find that ferroelastic domains can be effectively and permanently stabilized by dislocations at the substrate interface while similar domains at free surfaces without pinning dislocations can be removed by either electric or stress fields. For both electrical and mechanical switching, ferroelastic switching is found to occur most readily at the highly active needle points in ferroelastic domains. Our results provide new insights into the understanding of polarization switching dynamics as well as the engineering of ferroelectric devices.

Ferroelastic domain switching dynamics under electrical and mechanical excitations

NASA Astrophysics Data System (ADS)

Gao, Peng; Britson, Jason; Nelson, Christopher T.; Jokisaari, Jacob R.; Duan, Chen; Trassin, Morgan; Baek, Seung-Hyub; Guo, Hua; Li, Linze; Wang, Yiran; Chu, Ying-Hao; Minor, Andrew M.; Eom, Chang-Beom; Ramesh, Ramamoorthy; Chen, Long-Qing; Pan, Xiaoqing

2014-05-01

In thin film ferroelectric devices, switching of ferroelastic domains can significantly enhance electromechanical response. Previous studies have shown disagreement regarding the mobility or immobility of ferroelastic domain walls, indicating that switching behaviour strongly depends on specific microstructures in ferroelectric systems. Here we study the switching dynamics of individual ferroelastic domains in thin Pb(Zr0.2,Ti0.8)O3 films under electrical and mechanical excitations by using in situ transmission electron microscopy and phase-field modelling. We find that ferroelastic domains can be effectively and permanently stabilized by dislocations at the substrate interface while similar domains at free surfaces without pinning dislocations can be removed by either electric or stress fields. For both electrical and mechanical switching, ferroelastic switching is found to occur most readily at the highly active needle points in ferroelastic domains. Our results provide new insights into the understanding of polarization switching dynamics as well as the engineering of ferroelectric devices.

Ab initio treatment of ion-induced charge transfer dynamics of isolated 2-deoxy-D-ribose.

PubMed

Bacchus-Montabonel, Marie-Christine

2014-08-21

Modeling-induced radiation damage in biological systems, in particular, in DNA building blocks, is of major concern in cancer therapy studies. Ion-induced charge-transfer dynamics may indeed be involved in proton and hadrontherapy treatments. We have thus performed a theoretical approach of the charge-transfer dynamics in collision of C(4+) ions and protons with isolated 2-deoxy-D-ribose in a wide collision energy range by means of ab initio quantum chemistry molecular methods. The comparison of both projectile ions has been performed with regard to previous theoretical and experimental results. The charge transfer appears markedly less efficient with the 2-deoxy-D-ribose target than that with pyrimidine nucleobases, which would induce an enhancement of the fragmentation process in agreement with experimental measurements. The mechanism has been analyzed with regard to inner orbital excitations, and qualitative tendencies have been pointed out for studies on DNA buiding block damage.

Dendritic spine dynamics leading to spine elimination after repeated inductions of LTD

PubMed Central

Hasegawa, Sho; Sakuragi, Shigeo; Tominaga-Yoshino, Keiko; Ogura, Akihiko

2015-01-01

Memory is fixed solidly by repetition. However, the cellular mechanism underlying this repetition-dependent memory consolidation/reconsolidation remains unclear. In our previous study using stable slice cultures of the rodent hippocampus, we found long-lasting synaptic enhancement/suppression coupled with synapse formation/elimination after repeated inductions of chemical LTP/LTD, respectively. We proposed these phenomena as useful model systems for analyzing repetition-dependent memory consolidation. Recently, we analyzed the dynamics of dendritic spines during development of the enhancement, and found that the spines increased in number following characteristic stochastic processes. The current study investigates spine dynamics during the development of the suppression. We found that the rate of spine retraction increased immediately leaving that of spine generation unaltered. Spine elimination occurred independent of the pre-existing spine density on the dendritic segment. In terms of elimination, mushroom-type spines were not necessarily more stable than stubby-type and thin-type spines. PMID:25573377

Dynamical phase transitions at finite temperature from fidelity and interferometric Loschmidt echo induced metrics

NASA Astrophysics Data System (ADS)

Mera, Bruno; Vlachou, Chrysoula; Paunković, Nikola; Vieira, Vítor R.; Viyuela, Oscar

2018-03-01

We study finite-temperature dynamical quantum phase transitions (DQPTs) by means of the fidelity and the interferometric Loschmidt echo (LE) induced metrics. We analyze the associated dynamical susceptibilities (Riemannian metrics), and derive analytic expressions for the case of two-band Hamiltonians. At zero temperature, the two quantities are identical, nevertheless, at finite temperatures they behave very differently. Using the fidelity LE, the zero-temperature DQPTs are gradually washed away with temperature, while the interferometric counterpart exhibits finite-temperature phase transitions. We analyze the physical differences between the two finite-temperature LE generalizations, and argue that, while the interferometric one is more sensitive and can therefore provide more information when applied to genuine quantum (microscopic) systems, when analyzing many-body macroscopic systems, the fidelity-based counterpart is a more suitable quantity to study. Finally, we apply the previous results to two representative models of topological insulators in one and two dimensions.

Four-time 7Li stimulated-echo spectroscopy for the study of dynamic heterogeneities: Application to lithium borate glass.

PubMed

Storek, M; Tilly, J F; Jeffrey, K R; Böhmer, R

2017-09-01

To study the nature of the nonexponential ionic hopping in solids a pulse sequence was developed that yields four-time stimulated-echo functions of previously inaccessible spin-3/2-nuclei such as 7 Li. It exploits combined Zeeman and octupolar order as longitudinal carrier state. Higher-order correlation functions were successfully generated for natural-abundance and isotopically-enriched lithium diborate glasses. Four-time 7 Li measurements are presented and compared with two-time correlation functions. The results are discussed with reference to approaches devised to quantify the degree of nonexponentiality in glass forming systems and evidence for the occurrence of dynamic heterogeneities and dynamic exchange were found. Additional experiments using the 6 Li species illustrate the challenge posed by subensemble selection when the dipolar interactions are not very much smaller than the quadrupolar ones. Copyright © 2017 Elsevier Inc. All rights reserved.

A biphasic parameter estimation method for quantitative analysis of dynamic renal scintigraphic data

NASA Astrophysics Data System (ADS)

Koh, T. S.; Zhang, Jeff L.; Ong, C. K.; Shuter, B.

2006-06-01

Dynamic renal scintigraphy is an established method in nuclear medicine, commonly used for the assessment of renal function. In this paper, a biphasic model fitting method is proposed for simultaneous estimation of both vascular and parenchymal parameters from renal scintigraphic data. These parameters include the renal plasma flow, vascular and parenchymal mean transit times, and the glomerular extraction rate. Monte Carlo simulation was used to evaluate the stability and confidence of the parameter estimates obtained by the proposed biphasic method, before applying the method on actual patient study cases to compare with the conventional fitting approach and other established renal indices. The various parameter estimates obtained using the proposed method were found to be consistent with the respective pathologies of the study cases. The renal plasma flow and extraction rate estimated by the proposed method were in good agreement with those previously obtained using dynamic computed tomography and magnetic resonance imaging.

Seasonal variation in the free-running period in two Talitrus saltator populations from Italian beaches differing in morphodynamics and human disturbance

NASA Astrophysics Data System (ADS)

Nardi, M.; Morgan, E.; Scapini, F.

2003-10-01

The sandhopper Talitrus saltator Montagu (Amphipoda) is a widespread species adapted to different changing environmental conditions and which typically shows a clear circadian rhythm of locomotor activity. The populations from two beaches on the western Italian coast differing in coastline dynamics (eroded versus dynamically stable) and human disturbance (inside a natural park versus freely used and cleaned for leisure) were studied to highlight intrapopulation variation in the endogenous locomotor rhythm. The activity of adult sandhoppers was studied under constant laboratory conditions within individual recording chambers. Variation of the free-running period was analysed at individual level within each population. Greater variability was found than previously reported for the circadian rhythm period of T. saltator, and seasonal variation was shown for the first time. Differences in the level of variation were correlated with coastline dynamics.

Theoretical studies on a carbonaceous molecular bearing: association thermodynamics and dual-mode rolling dynamics† †Electronic supplementary information (ESI) available: Supplementary figures, tables and atomic coordinates of representative geometries. See DOI: 10.1039/c5sc00335k

PubMed Central

Nakamura, Kosuke; Hitosugi, Shunpei; Sato, Sota; Tokoyama, Hiroaki; Yamakado, Hideo; Ohno, Koichi

2015-01-01

The thermodynamics and dynamics of a carbonaceous molecular bearing comprising a belt-persistent tubular molecule and a fullerene molecule have been investigated using density functional theory (DFT). Among ten representative methods, two DFT methods afforded an association energy that reasonably reproduced the experimental enthalpy of –12.5 kcal mol–1 at the unique curved π-interface. The dynamics of the molecular bearing, which was assembled solely with van der Waals interactions, exhibited small energy barriers with maximum values of 2–3 kcal mol–1 for the rolling motions. The dynamic motions responded sensitively to the steric environment and resulted in two distinct motions, precession and spin, which explained the unique NMR observations that were not clarified in previous experimental studies. PMID:29142679

Computational Fluid Dynamics Modeling of a Supersonic Nozzle and Integration into a Variable Cycle Engine Model

NASA Technical Reports Server (NTRS)

Connolly, Joseph W.; Friedlander, David; Kopasakis, George

2015-01-01

This paper covers the development of an integrated nonlinear dynamic simulation for a variable cycle turbofan engine and nozzle that can be integrated with an overall vehicle Aero-Propulso-Servo-Elastic (APSE) model. A previously developed variable cycle turbofan engine model is used for this study and is enhanced here to include variable guide vanes allowing for operation across the supersonic flight regime. The primary focus of this study is to improve the fidelity of the model's thrust response by replacing the simple choked flow equation convergent-divergent nozzle model with a MacCormack method based quasi-1D model. The dynamic response of the nozzle model using the MacCormack method is verified by comparing it against a model of the nozzle using the conservation element/solution element method. A methodology is also presented for the integration of the MacCormack nozzle model with the variable cycle engine.

Computational Fluid Dynamics Modeling of a Supersonic Nozzle and Integration into a Variable Cycle Engine Model

NASA Technical Reports Server (NTRS)

Connolly, Joseph W.; Friedlander, David; Kopasakis, George

2014-01-01

This paper covers the development of an integrated nonlinear dynamic simulation for a variable cycle turbofan engine and nozzle that can be integrated with an overall vehicle Aero-Propulso-Servo-Elastic (APSE) model. A previously developed variable cycle turbofan engine model is used for this study and is enhanced here to include variable guide vanes allowing for operation across the supersonic flight regime. The primary focus of this study is to improve the fidelity of the model's thrust response by replacing the simple choked flow equation convergent-divergent nozzle model with a MacCormack method based quasi-1D model. The dynamic response of the nozzle model using the MacCormack method is verified by comparing it against a model of the nozzle using the conservation element/solution element method. A methodology is also presented for the integration of the MacCormack nozzle model with the variable cycle engine.

Random walks on activity-driven networks with attractiveness

NASA Astrophysics Data System (ADS)

Alessandretti, Laura; Sun, Kaiyuan; Baronchelli, Andrea; Perra, Nicola

2017-05-01

Virtually all real-world networks are dynamical entities. In social networks, the propensity of nodes to engage in social interactions (activity) and their chances to be selected by active nodes (attractiveness) are heterogeneously distributed. Here, we present a time-varying network model where each node and the dynamical formation of ties are characterized by these two features. We study how these properties affect random-walk processes unfolding on the network when the time scales describing the process and the network evolution are comparable. We derive analytical solutions for the stationary state and the mean first-passage time of the process, and we study cases informed by empirical observations of social networks. Our work shows that previously disregarded properties of real social systems, such as heterogeneous distributions of activity and attractiveness as well as the correlations between them, substantially affect the dynamical process unfolding on the network.

The Moderating Effects of Cluster B Personality Traits on Violence Reduction Training: A Mixed-Model Analysis

ERIC Educational Resources Information Center

Gerhart, James I.; Ronan, George F.; Russ, Eric; Seymour, Bailey

2013-01-01

Cognitive behavioral therapies have positive effects on anger and aggression; however, individuals differ in their response to treatment. The authors previously found that dynamic factors, such as increases in readiness to change, are associated with enhanced outcomes for violence reduction training. This study investigated how less dynamic…

Impaired Overt Facial Mimicry in Response to Dynamic Facial Expressions in High-Functioning Autism Spectrum Disorders

ERIC Educational Resources Information Center

Yoshimura, Sayaka; Sato, Wataru; Uono, Shota; Toichi, Motomi

2015-01-01

Previous electromyographic studies have reported that individuals with autism spectrum disorders (ASD) exhibited atypical patterns of facial muscle activity in response to facial expression stimuli. However, whether such activity is expressed in visible facial mimicry remains unknown. To investigate this issue, we videotaped facial responses in…

Molecular and cellular characterization of the tomato pollen profilin, LePro1

USDA-ARS?s Scientific Manuscript database

Profilin is an actin-binding protein involved in the dynamic turnover and restructuring of the actin cytoskeleton in all eukaryotic cells. We previously cloned a profilin gene, designated as LePro1 from tomato pollen. To investigate its biological role, in the present study, We investigated the tem...

Temperature and earthworm effects on C and N dynamics in oak stands along an urban-rural land use gradient

Treesearch

R. V. Pouyat; P. M. Groffman; M. M. Carreiro; P. Bohlen; R. W. Parmelee

1996-01-01

In previous studies of an urban-rural land use gradient in the New York City metropolitan area, urban forest soils had higher heavy metal concentrations, soil temperatures, and abundances of earthworms than rural soils, while rural soils had higher abundances of fungi.

Aligning Sales Curriculum Content and Pedagogy with Practitioners' Needs

ERIC Educational Resources Information Center

Newberry, Robert; Collins, Marianne K.

2015-01-01

Meeting the instructional needs of both students and sales practitioners is a common challenge for sales educators. The dynamic and ever evolving nature of the sales landscape, in conjunction with the need to align sales curriculum with relevant business practices is the focus of this article. Building on previous research, this study investigates…

Dynamic flashing yellow arrow (FYA): a study on variable left-turn mode operational and safety impacts phase II - model expansion and testing.

DOT National Transportation Integrated Search

2016-06-01

The flashing yellow arrow (FYA) signal display creates an opportunity to enhance the left-turn phase with a : variable mode that can be changed on demand. The previously developed decision support system (DSS) in : phase I facilitated the selection o...

Academic Writing in Korea: Its Dynamic Landscape and Implications for Intercultural Rhetoric

ERIC Educational Resources Information Center

Kim, Eun-Young Julia

2017-01-01

Previous studies on intercultural rhetoric have frequently drawn from examples from Asian writers, especially those of Chinese and Japanese origin, but relatively little information has surfaced in scholarly literature regarding L2 writers from Korea. To fill this gap, this article provides an overview of how academic writing is conceived and…

The study of human venous system dynamics using hybrid computer modeling

NASA Technical Reports Server (NTRS)

Snyder, M. F.; Rideout, V. C.

1972-01-01

A computer-based model of the cardiovascular system was created emphasizing effects on the systemic venous system. Certain physiological aspects were emphasized: effects of heart rate, tilting, changes in respiration, and leg muscular contractions. The results from the model showed close correlation with findings previously reported in the literature.

Teaching Complex Dynamic Systems to Young Students with StarLogo

ERIC Educational Resources Information Center

Klopfer, Eric; Yoon, Susan; Um, Tricia

2005-01-01

In this paper, we report on a program of study called Adventures in Modeling that challenges the traditional scientific method approach in science classrooms using StarLogo modeling software. Drawing upon previous successful efforts with older students, and the related work of other projects working with younger students, we explore: (a) What can…

Adolescent Aspirations for Change: Creativity as a Life Purpose

ERIC Educational Resources Information Center

Moran, Seana

2015-01-01

Through a cultural dynamics lens, what are the promises and pitfalls of having a life purpose to make a "creative" contribution to one's culture? Purpose is self-regulation that focuses on a personally meaningful intention to accomplish something prosocial. Although previously studied among older adults reflecting on their lives, a more…

Is a Partner's Competence Threatening during Dyadic Cooperative Work? It Depends on Resource Interdependence

ERIC Educational Resources Information Center

Buchs, Celine; Butera, Fabrizio

2009-01-01

Previous studies with university students have shown that resource interdependence during cooperative dyadic work on texts produces two different dynamics in student interaction and learning. Working on complementary information produces positive interactions, but a good quality of information transmission is needed to foster student learning.…

Intra- and intermolecular effects on the Compton profile of the ionic liquid 1,3-dimethylimidazolium chloride

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

Koskelo, J., E-mail: jaakko.koskelo@helsinki.fi; Juurinen, I.; Ruotsalainen, K. O.

2014-12-28

We present a comprehensive simulation study on the solid-liquid phase transition of the ionic liquid 1,3-dimethylimidazolium chloride in terms of the changes in the atomic structure and their effect on the Compton profile. The structures were obtained by using ab initio molecular dynamics simulations. Chosen radial distribution functions of the liquid structure are presented and found generally to be in good agreement with previous ab initio molecular dynamics and neutron scattering studies. The main contributions to the predicted difference Compton profile are found to arise from intermolecular changes in the phase transition. This prediction can be used for interpreting futuremore » experiments.« less

Flight dynamics and control modelling of damaged asymmetric aircraft

NASA Astrophysics Data System (ADS)

Ogunwa, T. T.; Abdullah, E. J.

2016-10-01

This research investigates the use of a Linear Quadratic Regulator (LQR) controller to assist commercial Boeing 747-200 aircraft regains its stability in the event of damage. Damages cause an aircraft to become asymmetric and in the case of damage to a fraction (33%) of its left wing or complete loss of its vertical stabilizer, the loss of stability may lead to a fatal crash. In this study, aircraft models for the two damage scenarios previously mentioned are constructed using stability derivatives. LQR controller is used as a direct adaptive control design technique for the observable and controllable system. Dynamic stability analysis is conducted in the time domain for all systems in this study.

Compartmental and Data-Based Modeling of Cerebral Hemodynamics: Linear Analysis.

PubMed

Henley, B C; Shin, D C; Zhang, R; Marmarelis, V Z

Compartmental and data-based modeling of cerebral hemodynamics are alternative approaches that utilize distinct model forms and have been employed in the quantitative study of cerebral hemodynamics. This paper examines the relation between a compartmental equivalent-circuit and a data-based input-output model of dynamic cerebral autoregulation (DCA) and CO2-vasomotor reactivity (DVR). The compartmental model is constructed as an equivalent-circuit utilizing putative first principles and previously proposed hypothesis-based models. The linear input-output dynamics of this compartmental model are compared with data-based estimates of the DCA-DVR process. This comparative study indicates that there are some qualitative similarities between the two-input compartmental model and experimental results.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; ...

2014-12-01

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

PubMed Central

Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

2014-01-01

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions. PMID:25453071

Dynamics of cancerous tissue correlates with invasiveness

NASA Astrophysics Data System (ADS)

West, Ann-Katrine Vransø; Wullkopf, Lena; Christensen, Amalie; Leijnse, Natascha; Tarp, Jens Magelund; Mathiesen, Joachim; Erler, Janine Terra; Oddershede, Lene Broeng

2017-03-01

Two of the classical hallmarks of cancer are uncontrolled cell division and tissue invasion, which turn the disease into a systemic, life-threatening condition. Although both processes are studied, a clear correlation between cell division and motility of cancer cells has not been described previously. Here, we experimentally characterize the dynamics of invasive and non-invasive breast cancer tissues using human and murine model systems. The intrinsic tissue velocities, as well as the divergence and vorticity around a dividing cell correlate strongly with the invasive potential of the tissue, thus showing a distinct correlation between tissue dynamics and aggressiveness. We formulate a model which treats the tissue as a visco-elastic continuum. This model provides a valid reproduction of the cancerous tissue dynamics, thus, biological signaling is not needed to explain the observed tissue dynamics. The model returns the characteristic force exerted by an invading cell and reveals a strong correlation between force and invasiveness of breast cancer cells, thus pinpointing the importance of mechanics for cancer invasion.

Matrix viscoplasticity and its shielding by active mechanics in microtissue models: experiments and mathematical modeling

NASA Astrophysics Data System (ADS)

Liu, Alan S.; Wang, Hailong; Copeland, Craig R.; Chen, Christopher S.; Shenoy, Vivek B.; Reich, Daniel H.

2016-09-01

The biomechanical behavior of tissues under mechanical stimulation is critically important to physiological function. We report a combined experimental and modeling study of bioengineered 3D smooth muscle microtissues that reveals a previously unappreciated interaction between active cell mechanics and the viscoplastic properties of the extracellular matrix. The microtissues’ response to stretch/unstretch actuations, as probed by microcantilever force sensors, was dominated by cellular actomyosin dynamics. However, cell lysis revealed a viscoplastic response of the underlying model collagen/fibrin matrix. A model coupling Hill-type actomyosin dynamics with a plastic perfectly viscoplastic description of the matrix quantitatively accounts for the microtissue dynamics, including notably the cells’ shielding of the matrix plasticity. Stretch measurements of single cells confirmed the active cell dynamics, and were well described by a single-cell version of our model. These results reveal the need for new focus on matrix plasticity and its interactions with active cell mechanics in describing tissue dynamics.

First-principles quantum dynamical theory for the dissociative chemisorption of H2O on rigid Cu(111)

PubMed Central

Zhang, Zhaojun; Liu, Tianhui; Fu, Bina; Yang, Xueming; Zhang, Dong H.

2016-01-01

Despite significant progress made in the past decades, it remains extremely challenging to investigate the dissociative chemisorption dynamics of molecular species on surfaces at a full-dimensional quantum mechanical level, in particular for polyatomic-surface reactions. Here we report, to the best of our knowledge, the first full-dimensional quantum dynamics study for the dissociative chemisorption of H2O on rigid Cu(111) with all the nine molecular degrees of freedom fully coupled, based on an accurate full-dimensional potential energy surface. The full-dimensional quantum mechanical reactivity provides the dynamics features with the highest accuracy, revealing that the excitations in vibrational modes of H2O are more efficacious than increasing the translational energy in promoting the reaction. The enhancement of the excitation in asymmetric stretch is the largest, but that of symmetric stretch becomes comparable at very low energies. The full-dimensional characterization also allows the investigation of the validity of previous reduced-dimensional and approximate dynamical models. PMID:27283908

Effects of thermal noise on the transitional dynamics of an inextensible elastic filament in stagnation flow.

PubMed

Deng, Mingge; Grinberg, Leopold; Caswell, Bruce; Karniadakis, George Em

2015-06-28

We investigate the dynamics of a single inextensible elastic filament subject to anisotropic friction in a viscous stagnation-point flow, by employing both a continuum model represented by Langevin type stochastic partial differential equations (SPDEs) and a dissipative particle dynamics (DPD) method. Unlike previous works, the filament is free to rotate and the tension along the filament is determined by the local inextensible constraint. The kinematics of the filament is recorded and studied with normal modes analysis. The results show that the filament displays an instability induced by negative tension, which is analogous to Euler buckling of a beam. Symmetry breaking of normal modes dynamics and stretch-coil transitions are observed above the threshold of the buckling instability point. Furthermore, both temporal and spatial noise are amplified resulting from the interaction of thermal fluctuations and nonlinear filament dynamics. Specifically, the spatial noise is amplified with even normal modes being excited due to symmetry breaking, while the temporal noise is amplified with increasing time correlation length and variance.

Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

PubMed Central

Zhou, Yu-Ping; Jiang, Jin-Wu

2017-01-01

While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

Matrix viscoplasticity and its shielding by active mechanics in microtissue models: experiments and mathematical modeling

PubMed Central

Liu, Alan S.; Wang, Hailong; Copeland, Craig R.; Chen, Christopher S.; Shenoy, Vivek B.; Reich, Daniel H.

2016-01-01

The biomechanical behavior of tissues under mechanical stimulation is critically important to physiological function. We report a combined experimental and modeling study of bioengineered 3D smooth muscle microtissues that reveals a previously unappreciated interaction between active cell mechanics and the viscoplastic properties of the extracellular matrix. The microtissues’ response to stretch/unstretch actuations, as probed by microcantilever force sensors, was dominated by cellular actomyosin dynamics. However, cell lysis revealed a viscoplastic response of the underlying model collagen/fibrin matrix. A model coupling Hill-type actomyosin dynamics with a plastic perfectly viscoplastic description of the matrix quantitatively accounts for the microtissue dynamics, including notably the cells’ shielding of the matrix plasticity. Stretch measurements of single cells confirmed the active cell dynamics, and were well described by a single-cell version of our model. These results reveal the need for new focus on matrix plasticity and its interactions with active cell mechanics in describing tissue dynamics. PMID:27671239

Dynamics of 3D Timoshenko gyroelastic beams with large attitude changes for the gyros

NASA Astrophysics Data System (ADS)

Hassanpour, Soroosh; Heppler, G. R.

2016-01-01

This work is concerned with the theoretical development of dynamic equations for undamped gyroelastic beams which are dynamic systems with continuous inertia, elasticity, and gyricity. Assuming unrestricted or large attitude changes for the axes of the gyros and utilizing generalized Hooke's law, Duleau torsion theory, and Timoshenko bending theory, the energy expressions and equations of motion for the gyroelastic beams in three-dimensional space are derived. The so-obtained comprehensive gyroelastic beam model is compared against earlier gyroelastic beam models developed using Euler-Bernoulli beam models and is used to study the dynamics of gyroelastic beams through numerical examples. It is shown that there are significant differences between the developed unrestricted Timoshenko gyroelastic beam model and the previously derived zero-order restricted Euler-Bernoulli gyroelastic beam models. These differences are more pronounced in the short beam and transverse gyricity cases.

Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET.

PubMed

Sikor, Martin; Mapa, Koyeli; von Voithenberg, Lena Voith; Mokranjac, Dejana; Lamb, Don C

2013-05-29

The numerous functions of the important class of molecular chaperones, heat shock proteins 70 (Hsp70), rely on cycles of intricate conformational changes driven by ATP-hydrolysis and regulated by cochaperones and substrates. Here, we used Förster resonance energy transfer to study the conformational dynamics of individual molecules of Ssc1, a mitochondrial Hsp70, in real time. The intrinsic dynamics of the substrate-binding domain of Ssc1 was observed to be uncoupled from the dynamic interactions between substrate- and nucleotide-binding domains. Analysis of the fluctuations in the interdomain separation revealed frequent transitions to a nucleotide-free state. The nucleotide-exchange factor Mge1 did not induce ADP release, as expected, but rather facilitated binding of ATP. These results indicate that the conformational cycle of Ssc1 is more elaborate than previously thought and provide insight into how the Hsp70s can perform a wide variety of functions.

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations.

PubMed

Mei, Longcan; Zhou, Yanping; Zhu, Lizhe; Liu, Changlin; Wu, Zhuo; Wang, Fangkui; Hao, Gefei; Yu, Di; Yuan, Hong; Cui, Yanfang

2018-03-20

A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.

Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics.

PubMed

Chen, Minghan; Li, Fei; Wang, Shuo; Cao, Young

2017-03-14

Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion systems is reaction diffusion master equation (RDME). Previous studies have discovered that for the RDME, when discretization size approaches zero, reaction time for bimolecular reactions in high dimensional domains tends to infinity. In this paper, we demonstrate that in the 1D domain, highly nonlinear reaction dynamics given by Hill function may also have dramatic change when discretization size is smaller than a critical value. Moreover, we discuss methods to avoid this problem: smoothing over space, fixed length smoothing over space and a hybrid method. Our analysis reveals that the switch-like Hill dynamics reduces to a linear function of discretization size when the discretization size is small enough. The three proposed methods could correctly (under certain precision) simulate Hill function dynamics in the microscopic RDME system.

Ab Initio Molecular Dynamics Studies of Pb m Sb n ( m + n ≤ 9) Alloy Clusters

NASA Astrophysics Data System (ADS)

Song, Bingyi; Xu, Baoqiang; Yang, Bin; Jiang, Wenlong; Chen, Xiumin; Xu, Na; Liu, Dachun; Dai, Yongnian

2017-10-01

Structure, stability, and dynamics of Pb m Sb n ( m + n ≤ 9) clusters were investigated using ab initio molecular dynamics. Size dependence of binding energies, the second-order energy difference of clusters, dissociation energy, HOMO-LUMO gaps, Mayer bond order, and the diffusion coefficient of Pb m Sb n clusters were discussed. Results suggest that Pb3Sb2, Pb4Sb2, and Pb5Sb4 ( n = 2 or 4) clusters have higher stability than other clusters, which is consistent with previous findings. In case of Pb-Sb alloy, the dynamics results show that Pb4Sb2 (Pb-22.71 wt pct Sb) can exist in gas phase at 1073 K (800 °C), which reasonably explains the azeotropic phenomenon, and the calculated values are in agreement with the experimental results (Pb-22 wt pct Sb).

Chimera states in nonlocally coupled phase oscillators with biharmonic interaction

NASA Astrophysics Data System (ADS)

Cheng, Hongyan; Dai, Qionglin; Wu, Nianping; Feng, Yuee; Li, Haihong; Yang, Junzhong

2018-03-01

Chimera states, which consist of coexisting domains of coherent and incoherent parts, have been observed in a variety of systems. Most of previous works on chimera states have taken into account specific form of interaction between oscillators, for example, sinusoidal coupling or diffusive coupling. Here, we investigate chimera dynamics in nonlocally coupled phase oscillators with biharmonic interaction. We find novel chimera states with features such as that oscillators in the same coherent cluster may split into two groups with a phase difference around π/2 and that oscillators in adjacent coherent clusters may have a phase difference close to π/2. The different impacts of the coupling ranges in the first and the second harmonic interactions on chimera dynamics are investigated based on the synchronous dynamics in globally coupled phase oscillators. Our study suggests a new direction in the field of chimera dynamics.

Finite-temperature lattice dynamics and superionic transition in ceria from first principles

NASA Astrophysics Data System (ADS)

Klarbring, Johan; Skorodumova, Natalia V.; Simak, Sergei I.

2018-03-01

Ab initio molecular dynamics (AIMD) in combination with the temperature dependent effective potential (TDEP) method has been used to go beyond the quasiharmonic approximation and study the lattice dynamics in ceria, CeO2, at finite temperature. The results indicate that the previously proposed connection between the B1 u phonon mode turning imaginary and the transition to the superionic phase in fluorite structured materials is an artifact of the failure of the quasiharmonic approximation in describing the lattice dynamics at elevated temperatures. We instead show that, in the TDEP picture, a phonon mode coupling to the Eu mode prevents the B1 u mode from becoming imaginary. We directly observe the superionic transition at high temperatures in our AIMD simulations and find that it is initiated by the formation of oxygen Frenkel pairs (FP). These FP are found to form in a collective process involving simultaneous motion of two oxygen ions.

Modes and emergent time scales of embayed beach dynamics

NASA Astrophysics Data System (ADS)

Ratliff, Katherine M.; Murray, A. Brad

2014-10-01

In this study, we use a simple numerical model (the Coastline Evolution Model) to explore alongshore transport-driven shoreline dynamics within generalized embayed beaches (neglecting cross-shore effects). Using principal component analysis (PCA), we identify two primary orthogonal modes of shoreline behavior that describe shoreline variation about its unchanging mean position: the rotation mode, which has been previously identified and describes changes in the mean shoreline orientation, and a newly identified breathing mode, which represents changes in shoreline curvature. Wavelet analysis of the PCA mode time series reveals characteristic time scales of these modes (typically years to decades) that emerge within even a statistically constant white-noise wave climate (without changes in external forcing), suggesting that these time scales can arise from internal system dynamics. The time scales of both modes increase linearly with shoreface depth, suggesting that the embayed beach sediment transport dynamics exhibit a diffusive scaling.

Dynamic Integration of Value Information into a Common Probability Currency as a Theory for Flexible Decision Making

PubMed Central

Christopoulos, Vassilios; Schrater, Paul R.

2015-01-01

Decisions involve two fundamental problems, selecting goals and generating actions to pursue those goals. While simple decisions involve choosing a goal and pursuing it, humans evolved to survive in hostile dynamic environments where goal availability and value can change with time and previous actions, entangling goal decisions with action selection. Recent studies suggest the brain generates concurrent action-plans for competing goals, using online information to bias the competition until a single goal is pursued. This creates a challenging problem of integrating information across diverse types, including both the dynamic value of the goal and the costs of action. We model the computations underlying dynamic decision-making with disparate value types, using the probability of getting the highest pay-off with the least effort as a common currency that supports goal competition. This framework predicts many aspects of decision behavior that have eluded a common explanation. PMID:26394299

Topologically Associating Domains: An invariant framework or a dynamic scaffold?

PubMed

Cubeñas-Potts, Caelin; Corces, Victor G

2015-01-01

Metazoan genomes are organized into regions of topologically associating domains (TADs). TADs are demarcated by border elements, which are enriched for active genes and high occupancy architectural protein binding sites. We recently demonstrated that 3D chromatin architecture is dynamic in response to heat shock, a physiological stress that downregulates transcription and causes a global redistribution of architectural proteins. We utilized a quantitative measure of border strength after heat shock, transcriptional inhibition, and architectural protein knockdown to demonstrate that changes in both transcription and architectural protein occupancy contribute to heat shock-induced TAD dynamics. Notably, architectural proteins appear to play a more important role in altering 3D chromatin architecture. Here, we discuss the implications of our findings on previous studies evaluating the dynamics of TAD structure during cellular differentiation. We propose that the subset of variable TADs observed after differentiation are representative of cell-type specific gene expression and are biologically significant.

How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch.

PubMed

Marucci, Lucia; Barton, David A W; Cantone, Irene; Ricci, Maria Aurelia; Cosma, Maria Pia; Santini, Stefania; di Bernardo, Diego; di Bernardo, Mario

2009-12-07

Systems and Synthetic Biology use computational models of biological pathways in order to study in silico the behaviour of biological pathways. Mathematical models allow to verify biological hypotheses and to predict new possible dynamical behaviours. Here we use the tools of non-linear analysis to understand how to change the dynamics of the genes composing a novel synthetic network recently constructed in the yeast Saccharomyces cerevisiae for In-vivo Reverse-engineering and Modelling Assessment (IRMA). Guided by previous theoretical results that make the dynamics of a biological network depend on its topological properties, through the use of simulation and continuation techniques, we found that the network can be easily turned into a robust and tunable synthetic oscillator or a bistable switch. Our results provide guidelines to properly re-engineering in vivo the network in order to tune its dynamics.

Cluster analysis of word frequency dynamics

NASA Astrophysics Data System (ADS)

Maslennikova, Yu S.; Bochkarev, V. V.; Belashova, I. A.

2015-01-01

This paper describes the analysis and modelling of word usage frequency time series. During one of previous studies, an assumption was put forward that all word usage frequencies have uniform dynamics approaching the shape of a Gaussian function. This assumption can be checked using the frequency dictionaries of the Google Books Ngram database. This database includes 5.2 million books published between 1500 and 2008. The corpus contains over 500 billion words in American English, British English, French, German, Spanish, Russian, Hebrew, and Chinese. We clustered time series of word usage frequencies using a Kohonen neural network. The similarity between input vectors was estimated using several algorithms. As a result of the neural network training procedure, more than ten different forms of time series were found. They describe the dynamics of word usage frequencies from birth to death of individual words. Different groups of word forms were found to have different dynamics of word usage frequency variations.

Verifying detailed fluctuation relations for discrete feedback-controlled quantum dynamics

NASA Astrophysics Data System (ADS)

Camati, Patrice A.; Serra, Roberto M.

2018-04-01

Discrete quantum feedback control consists of a managed dynamics according to the information acquired by a previous measurement. Energy fluctuations along such dynamics satisfy generalized fluctuation relations, which are useful tools to study the thermodynamics of systems far away from equilibrium. Due to the practical challenge to assess energy fluctuations in the quantum scenario, the experimental verification of detailed fluctuation relations in the presence of feedback control remains elusive. We present a feasible method to experimentally verify detailed fluctuation relations for discrete feedback control quantum dynamics. Two detailed fluctuation relations are developed and employed. The method is based on a quantum interferometric strategy that allows the verification of fluctuation relations in the presence of feedback control. An analytical example to illustrate the applicability of the method is discussed. The comprehensive technique introduced here can be experimentally implemented at a microscale with the current technology in a variety of experimental platforms.

Addressing group dynamics in a brief motivational intervention for college student drinkers.

PubMed

Faris, Alexander S; Brown, Janice M

2003-01-01

Previous research indicates that brief motivational interventions for college student drinkers may be less effective in group settings than individual settings. Social psychological theories about counterproductive group dynamics may partially explain this finding. The present study examined potential problems with group motivational interventions by comparing outcomes from a standard group motivational intervention (SGMI; n = 25), an enhanced group motivational intervention (EGMI; n = 27) designed to suppress counterproductive processes, and a no intervention control (n = 23). SGMI and EGMI participants reported disruptive group dynamics as evidenced by low elaboration likelihood, production blocking, and social loafing, though the level of disturbance was significantly lower for EGMI individuals (p = .001). Despite counteracting group dynamics in the EGMI condition, participants in the two interventions were statistically similar in post-intervention problem recognition and future drinking intentions. The results raise concerns over implementing individually-based interventions in group settings without making necessary adjustments.

Dynamic Parameter Identification of Subject-Specific Body Segment Parameters Using Robotics Formalism: Case Study Head Complex.

PubMed

Díaz-Rodríguez, Miguel; Valera, Angel; Page, Alvaro; Besa, Antonio; Mata, Vicente

2016-05-01

Accurate knowledge of body segment inertia parameters (BSIP) improves the assessment of dynamic analysis based on biomechanical models, which is of paramount importance in fields such as sport activities or impact crash test. Early approaches for BSIP identification rely on the experiments conducted on cadavers or through imaging techniques conducted on living subjects. Recent approaches for BSIP identification rely on inverse dynamic modeling. However, most of the approaches are focused on the entire body, and verification of BSIP for dynamic analysis for distal segment or chain of segments, which has proven to be of significant importance in impact test studies, is rarely established. Previous studies have suggested that BSIP should be obtained by using subject-specific identification techniques. To this end, our paper develops a novel approach for estimating subject-specific BSIP based on static and dynamics identification models (SIM, DIM). We test the validity of SIM and DIM by comparing the results using parameters obtained from a regression model proposed by De Leva (1996, "Adjustments to Zatsiorsky-Seluyanov's Segment Inertia Parameters," J. Biomech., 29(9), pp. 1223-1230). Both SIM and DIM are developed considering robotics formalism. First, the static model allows the mass and center of gravity (COG) to be estimated. Second, the results from the static model are included in the dynamics equation allowing us to estimate the moment of inertia (MOI). As a case study, we applied the approach to evaluate the dynamics modeling of the head complex. Findings provide some insight into the validity not only of the proposed method but also of the application proposed by De Leva (1996, "Adjustments to Zatsiorsky-Seluyanov's Segment Inertia Parameters," J. Biomech., 29(9), pp. 1223-1230) for dynamic modeling of body segments.

Dynamic probability of reinforcement for cooperation: Random game termination in the centipede game.

PubMed

Krockow, Eva M; Colman, Andrew M; Pulford, Briony D

2018-03-01

Experimental games have previously been used to study principles of human interaction. Many such games are characterized by iterated or repeated designs that model dynamic relationships, including reciprocal cooperation. To enable the study of infinite game repetitions and to avoid endgame effects of lower cooperation toward the final game round, investigators have introduced random termination rules. This study extends previous research that has focused narrowly on repeated Prisoner's Dilemma games by conducting a controlled experiment of two-player, random termination Centipede games involving probabilistic reinforcement and characterized by the longest decision sequences reported in the empirical literature to date (24 decision nodes). Specifically, we assessed mean exit points and cooperation rates, and compared the effects of four different termination rules: no random game termination, random game termination with constant termination probability, random game termination with increasing termination probability, and random game termination with decreasing termination probability. We found that although mean exit points were lower for games with shorter expected game lengths, the subjects' cooperativeness was significantly reduced only in the most extreme condition with decreasing computer termination probability and an expected game length of two decision nodes. © 2018 Society for the Experimental Analysis of Behavior.

An analytic modeling and system identification study of rotor/fuselage dynamics at hover

NASA Technical Reports Server (NTRS)

Hong, Steven W.; Curtiss, H. C., Jr.

1993-01-01

A combination of analytic modeling and system identification methods have been used to develop an improved dynamic model describing the response of articulated rotor helicopters to control inputs. A high-order linearized model of coupled rotor/body dynamics including flap and lag degrees of freedom and inflow dynamics with literal coefficients is compared to flight test data from single rotor helicopters in the near hover trim condition. The identification problem was formulated using the maximum likelihood function in the time domain. The dynamic model with literal coefficients was used to generate the model states, and the model was parametrized in terms of physical constants of the aircraft rather than the stability derivatives resulting in a significant reduction in the number of quantities to be identified. The likelihood function was optimized using the genetic algorithm approach. This method proved highly effective in producing an estimated model from flight test data which included coupled fuselage/rotor dynamics. Using this approach it has been shown that blade flexibility is a significant contributing factor to the discrepancies between theory and experiment shown in previous studies. Addition of flexible modes, properly incorporating the constraint due to the lag dampers, results in excellent agreement between flight test and theory, especially in the high frequency range.

An analytic modeling and system identification study of rotor/fuselage dynamics at hover

NASA Technical Reports Server (NTRS)

Hong, Steven W.; Curtiss, H. C., Jr.

1993-01-01

A combination of analytic modeling and system identification methods have been used to develop an improved dynamic model describing the response of articulated rotor helicopters to control inputs. A high-order linearized model of coupled rotor/body dynamics including flap and lag degrees of freedom and inflow dynamics with literal coefficients is compared to flight test data from single rotor helicopters in the near hover trim condition. The identification problem was formulated using the maximum likelihood function in the time domain. The dynamic model with literal coefficients was used to generate the model states, and the model was parametrized in terms of physical constants of the aircraft rather than the stability derivatives, resulting in a significant reduction in the number of quantities to be identified. The likelihood function was optimized using the genetic algorithm approach. This method proved highly effective in producing an estimated model from flight test data which included coupled fuselage/rotor dynamics. Using this approach it has been shown that blade flexibility is a significant contributing factor to the discrepancies between theory and experiment shown in previous studies. Addition of flexible modes, properly incorporating the constraint due to the lag dampers, results in excellent agreement between flight test and theory, especially in the high frequency range.

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.

Dynamical analysis and simulation of a 2-dimensional disease model with convex incidence

NASA Astrophysics Data System (ADS)

Yu, Pei; Zhang, Wenjing; Wahl, Lindi M.

2016-08-01

In this paper, a previously developed 2-dimensional disease model is studied, which can be used for both epidemiologic modeling and in-host disease modeling. The main attention of this paper is focused on various dynamical behaviors of the system, including Hopf and generalized Hopf bifurcations which yield bistability and tristability, Bogdanov-Takens bifurcation, and homoclinic bifurcation. It is shown that the Bogdanov-Takens bifurcation and homoclinic bifurcation provide a new mechanism for generating disease recurrence, that is, cycles of remission and relapse such as the viral blips observed in HIV infection.

Molecular dynamics study of melting and fcc-bcc transitions in Xe.

PubMed

Belonoshko, A B; Ahuja, R; Johansson, B

2001-10-15

We have investigated the phase diagram of Xe over a wide pressure-temperature range by molecular dynamics. The calculated melting curve is in good agreement with earlier experimental data. At a pressure of around 25 GPa and a temperature of about 2700 K we find a triple fcc-bcc liquid point. The calculated fcc-bcc boundary is in nice agreement with the experimental points, which, however, were interpreted as melting. This finding suggests that the transition from close-packed to bcc structure might be more common at high pressure and high temperature than was previously anticipated.

Dynamic regimes of local homogeneous population model with time lag

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

Neverova, Galina; Frisman, Efim

We investigated Moran - Ricker model with time lag 1. It is made analytical and numerical study of the model. It is shown there is co-existence of various dynamic regimes under the same values of parameters. The model simultaneously possesses several different limit regimes: stable state, periodic fluctuations, and chaotic attractor. The research results show if present population size substantially depends on population number of previous year then it is observed quasi-periodic oscillations. Fluctuations with period 2 occur when the growth of population size is regulated by density dependence in the current year.

Molecular dynamics study of the solvation of calcium carbonate in water.

PubMed

Bruneval, Fabien; Donadio, Davide; Parrinello, Michele

2007-10-25

We performed molecular dynamics simulations of diluted solutions of calcium carbonate in water. To this end, we combined and tested previous polarizable models. The carbonate anion forms long-living hydrogen bonds with water and shows an amphiphilic character, in which the water molecules are expelled in a region close to its C(3) symmetry axis. The calcium cation forms a strongly bound ion pair with the carbonate. The first hydration shell around the CaCO(3) pair is found to be very similar to the location of the water molecules surrounding CaCO(3) in ikaite, the hydrated mineral.

Gradual Crossover from Subdiffusion to Normal Diffusion: A Many-Body Effect in Protein Surface Water

NASA Astrophysics Data System (ADS)

Tan, Pan; Liang, Yihao; Xu, Qin; Mamontov, Eugene; Li, Jinglai; Xing, Xiangjun; Hong, Liang

2018-06-01

Dynamics of hydration water is essential for the function of biomacromolecules. Previous studies have demonstrated that water molecules exhibit subdiffusion on the surface of biomacromolecules; yet the microscopic mechanism remains vague. Here, by performing neutron scattering, molecular dynamics simulations, and analytic modeling on hydrated perdeuterated protein powders, we found water molecules jump randomly between trapping sites on protein surfaces, whose waiting times obey a broad distribution, resulting in subdiffusion. Moreover, the subdiffusive exponent gradually increases with observation time towards normal diffusion due to a many-body volume-exclusion effect.

A system dynamics approach to develop a recovery model in the Malaysian automotive industry

NASA Astrophysics Data System (ADS)

Mohamad-Ali, N.; Ghazilla, R. A. R.; Abdul-Rashid, S. H.; Sakundarini, N.; Ahmad-Yazid, A.; Stephenie, L.

2017-06-01

Design strategies play a significant role to enhance recovery effectiveness at the end of product life cycle. By reviewing previous study, there are many factors involved to enhance recovery effectiveness but limited to linking design strategies factors in holistic and dynamics view. Proposed method are explained and an initial model for end-of-life vehicles (ELVs) recovery model illustrated in graphical and numerical data is presented. However this is limited to authors understanding and preliminary data which requires collaboration between designers and other stakeholders to develop a model based on actual situation.

Effects of pressure on the dynamics of a hyperthermophilic protein revealed by quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Shrestha, U. R.; Bhowmik, D.; Copley, J. R. D.; Tyagi, M.; Leao, J. B.; Chu, X.-Q.

Inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens is a large oligomeric protein derived from hyperthermophilic microorganism that is found near hydrothermal vents deep under the sea, where the pressure is nearly 100 MPa. Here we study the effects of pressure on the conformational flexibility and relaxation dynamics of IPPase over a wide temperature range using quasielastic neutron scattering (QENS) technique. Two spectrometers were used to investigate the β-relaxation dynamics of proteins in time ranges from 2 to 25 ps, and from 100 ps to 2 ns. Our results reveal that, under the pressure of 100 MPa, IPPase displays much faster relaxation dynamics than a mesophilic model protein, hen egg white lysozyme (HEWL), opposite to what we observed previously under the ambient pressure. These contradictory observations imply that high pressure affects the dynamical properties of proteins by distorting their energy landscapes. Accordingly, we derived a general schematic denaturation phase diagram that can be used as a general picture to understand the effects of pressure on protein dynamics and activities Wayne State Univ Startup Fund.

Dynamic PET Image reconstruction for parametric imaging using the HYPR kernel method

NASA Astrophysics Data System (ADS)

Spencer, Benjamin; Qi, Jinyi; Badawi, Ramsey D.; Wang, Guobao

2017-03-01

Dynamic PET image reconstruction is a challenging problem because of the ill-conditioned nature of PET and the lowcounting statistics resulted from short time-frames in dynamic imaging. The kernel method for image reconstruction has been developed to improve image reconstruction of low-count PET data by incorporating prior information derived from high-count composite data. In contrast to most of the existing regularization-based methods, the kernel method embeds image prior information in the forward projection model and does not require an explicit regularization term in the reconstruction formula. Inspired by the existing highly constrained back-projection (HYPR) algorithm for dynamic PET image denoising, we propose in this work a new type of kernel that is simpler to implement and further improves the kernel-based dynamic PET image reconstruction. Our evaluation study using a physical phantom scan with synthetic FDG tracer kinetics has demonstrated that the new HYPR kernel-based reconstruction can achieve a better region-of-interest (ROI) bias versus standard deviation trade-off for dynamic PET parametric imaging than the post-reconstruction HYPR denoising method and the previously used nonlocal-means kernel.

Superlinearly scalable noise robustness of redundant coupled dynamical systems.

PubMed

Kohar, Vivek; Kia, Behnam; Lindner, John F; Ditto, William L

2016-03-01

We illustrate through theory and numerical simulations that redundant coupled dynamical systems can be extremely robust against local noise in comparison to uncoupled dynamical systems evolving in the same noisy environment. Previous studies have shown that the noise robustness of redundant coupled dynamical systems is linearly scalable and deviations due to noise can be minimized by increasing the number of coupled units. Here, we demonstrate that the noise robustness can actually be scaled superlinearly if some conditions are met and very high noise robustness can be realized with very few coupled units. We discuss these conditions and show that this superlinear scalability depends on the nonlinearity of the individual dynamical units. The phenomenon is demonstrated in discrete as well as continuous dynamical systems. This superlinear scalability not only provides us an opportunity to exploit the nonlinearity of physical systems without being bogged down by noise but may also help us in understanding the functional role of coupled redundancy found in many biological systems. Moreover, engineers can exploit superlinear noise suppression by starting a coupled system near (not necessarily at) the appropriate initial condition.

Effect of retinal defocus on basketball free throw shooting performance.

PubMed

Bulson, Ryan C; Ciuffreda, Kenneth J; Hayes, John; Ludlam, Diana P

2015-07-01

Vision plays a critical role in athletic performance; however, previous studies have demonstrated that a variety of simulated athletic sensorimotor tasks can be surprisingly resilient to retinal defocus (blurred vision). The purpose of the present study was to extend this work to determine the effect of retinal defocus on overall basketball free throw performance, as well as for the factors gender, refractive error and experience. Forty-four young adult participants of both genders were recruited. They had a range of refractive errors and basketball experience. Each performed 20 standard basketball free throws under five lens defocus conditions in a randomised manner: plano, +1.50 D, +3.00 D, +4.50 D and +10.00 D. Overall, free throw performance was significantly reduced under the +10.00 D lens defocus condition only. Previous experience, but neither refractive error nor gender, yielded a statistically significant difference in performance. Consistent with previous studies of complex sensorimotor tasks, basketball free throw performance was resilient to low and moderate levels of retinal defocus. Thus, for a relatively non-dynamic motor task at a fixed far distance, such as the basketball free throw, precise visual clarity was not critical. Other factors such as motor memory may be important. However, in the dynamic athletic competitive environment it is likely that visual clarity plays a more critical role in one's performance level, at least for specific task demands. © 2015 The Authors. Clinical and Experimental Optometry © 2015 Optometry Australia.

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

NASA Astrophysics Data System (ADS)

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

2018-07-01

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

Modeling of silicon in femtosecond laser-induced modification regimes: accounting for ambipolar diffusion

NASA Astrophysics Data System (ADS)

Derrien, Thibault J.-Y.; Bulgakova, Nadezhda M.

2017-05-01

During the last decades, femtosecond laser irradiation of materials has led to the emergence of various applications based on functionalization of surfaces at the nano- and microscale. Via inducing a periodic modification on material surfaces (band gap modification, nanostructure formation, crystallization or amorphization), optical and mechanical properties can be tailored, thus turning femtosecond laser to a key technology for development of nanophotonics, bionanoengineering, and nanomechanics. Although modification of semiconductor surfaces with femtosecond laser pulses has been studied for more than two decades, the dynamics of coupling of intense laser light with excited matter remains incompletely understood. In particular, swift formation of a transient overdense electron-hole plasma dynamically modifies optical properties in the material surface layer and induces large gradients of hot charge carriers, resulting in ultrafast charge-transport phenomena. In this work, the dynamics of ultrafast laser excitation of a semiconductor material is studied theoretically on the example of silicon. A special attention is paid to the electron-hole pair dynamics, taking into account ambipolar diffusion effects. The results are compared with previously developed simulation models, and a discussion of the role of charge-carrier dynamics in localization of material modification is provided.

Nitrogen feedbacks increase future terrestrial ecosystem carbon uptake in an individual-based dynamic vegetation model

NASA Astrophysics Data System (ADS)

Wårlind, D.; Smith, B.; Hickler, T.; Arneth, A.

2014-01-01

Recently a considerable amount of effort has been put into quantifying how interactions of the carbon and nitrogen cycle affect future terrestrial carbon sinks. Dynamic vegetation models, representing the nitrogen cycle with varying degree of complexity, have shown diverging constraints of nitrogen dynamics on future carbon sequestration. In this study, we use the dynamic vegetation model LPJ-GUESS to evaluate how population dynamics and resource competition between plant functional types, combined with nitrogen dynamics, have influenced the terrestrial carbon storage in the past and to investigate how terrestrial carbon and nitrogen dynamics might change in the future (1850 to 2100; one exemplary "business-as-usual" climate scenario). Single factor model experiments of CO2 fertilisation and climate change show generally similar directions of the responses of C-N interactions, compared to the C-only version of the model, as documented in previous studies. Under a RCP 8.5 scenario, nitrogen limitation suppresses potential CO2 fertilisation, reducing the cumulative net ecosystem carbon uptake between 1850 and 2100 by 61%, and soil warming-induced increase in nitrogen mineralisation reduces terrestrial carbon loss by 31%. When environmental changes are considered conjointly, carbon sequestration is limited by nitrogen dynamics until present. However, during the 21st century nitrogen dynamics induce a net increase in carbon sequestration, resulting in an overall larger carbon uptake of 17% over the full period. This contradicts earlier model results that showed an 8 to 37% decrease in carbon uptake, questioning the often stated assumption that projections of future terrestrial C dynamics from C-only models are too optimistic.

Stochastic lattice model of synaptic membrane protein domains.

PubMed

Li, Yiwei; Kahraman, Osman; Haselwandter, Christoph A

2017-05-01

Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments. We show that our stochastic lattice model yields quantitative agreement with mean-field models of nonlinear diffusion in crowded membranes. Through a combination of analytic and numerical solutions of the master equation governing the reaction dynamics at synaptic domains, together with kinetic Monte Carlo simulations, we find substantial discrepancies between mean-field and stochastic models for the reaction dynamics at synaptic domains. Based on the reaction and diffusion properties of synaptic receptors and scaffolds suggested by previous experiments and mean-field calculations, we show that the stochastic reaction-diffusion dynamics of synaptic receptors and scaffolds provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the observed single-molecule trajectories, and spatial heterogeneity in the effective rates at which receptors and scaffolds are recycled at the cell membrane. Our work sheds light on the physical mechanisms and principles linking the collective properties of membrane protein domains to the stochastic dynamics that rule their molecular components.

Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions

PubMed Central

Dzierlenga, M.W.; Varga, M.J.

2016-01-01

The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate the full dynamical properties of enzymatic systems. This can lead to misleading results in cases where enzyme motion plays a significant role in the reaction coordinate, which is especially relevant in particle transfer reactions where nuclear tunneling may occur. In this chapter, we outline previous methods, as well as discuss newly developed dynamical methods to interrogate mechanisms of enzymatic particle transfer reactions. These new methods allow for the calculation of free energy barriers and kinetic isotope effects (KIEs) with the incorporation of quantum effects through centroid molecular dynamics (CMD) and the full complement of enzyme dynamics through transition path sampling (TPS). Recent work, summarized in this chapter, applied the method for calculation of free energy barriers to reaction in lactate dehydrogenase (LDH) and yeast alcohol dehydrogenase (YADH). It was found that tunneling plays an insignificant role in YADH but plays a more significant role in LDH, though not dominant over classical transfer. Additionally, we summarize the application of a TPS algorithm for the calculation of reaction rates in tandem with CMD to calculate the primary H/D KIE of YADH from first principles. It was found that the computationally obtained KIE is within the margin of error of experimentally determined KIEs, and corresponds to the KIE of particle transfer in the enzyme. These methods provide new ways to investigate enzyme mechanism with the inclusion of protein and quantum dynamics. PMID:27497161

Dynamic stability with the disturbance-free payload architecture as applied to the Large UV/Optical/Infrared (LUVOIR) Mission

NASA Astrophysics Data System (ADS)

Dewell, Larry D.; Tajdaran, Kiarash; Bell, Raymond M.; Liu, Kuo-Chia; Bolcar, Matthew R.; Sacks, Lia W.; Crooke, Julie A.; Blaurock, Carl

2017-09-01

The need for high payload dynamic stability and ultra-stable mechanical systems is an overarching technology need for large space telescopes such as the Large Ultraviolet / Optical / Infrared (LUVOIR) Surveyor. Wavefront error stability of less than 10 picometers RMS of uncorrected system WFE per wavefront control step represents a drastic performance improvement over current space-based telescopes being fielded. Previous studies of similar telescope architectures have shown that passive telescope isolation approaches are hard-pressed to meet dynamic stability requirements and usually involve complex actively-controlled elements and sophisticated metrology. To meet these challenging dynamic stability requirements, an isolation architecture that involves no mechanical contact between telescope and the host spacecraft structure has the potential of delivering this needed performance improvement. One such architecture, previously developed by Lockheed Martin called Disturbance Free Payload (DFP), is applied to and analyzed for LUVOIR. In a noncontact DFP architecture, the payload and spacecraft fly in close proximity, and interact via non-contact actuators to allow precision payload pointing and isolation from spacecraft vibration. Because disturbance isolation through non-contact, vibration isolation down to zero frequency is possible, and high-frequency structural dynamics of passive isolators are not introduced into the system. In this paper, the system-level analysis of a non-contact architecture is presented for LUVOIR, based on requirements that are directly traceable to its science objectives, including astrophysics and the direct imaging of habitable exoplanets. Aspects of architecture and how they contribute to system performance are examined and tailored to the LUVOIR architecture and concept of operation.

Massive Black-Hole Binary Mergers: Dynamics, Environments & Expected Detections

NASA Astrophysics Data System (ADS)

Kelley, Luke Zoltan

2018-05-01

This thesis studies the populations and dynamics of massive black-hole binaries and their mergers, and explores the implications for electromagnetic and gravitational-wave signals that will be detected in the near future. Massive black-holes (MBH) reside in the centers of galaxies, and when galaxies merge, their MBH interact and often pair together. We base our study on the populations of MBH and galaxies from the `Illustris' cosmological hydrodynamic simulations. The bulk of the binary merger dynamics, however, are unresolved in cosmological simulations. We implement a suite of comprehensive physical models for the merger process, like dynamical friction and gravitational wave emission, which are added in post-processing. Contrary to many previous studies, we find that the most massive binaries with near equal-mass companions are the most efficient at coalescing; though the process still typically takes gigayears.From the data produced by these MBH binary populations and their dynamics, we calculate the expected gravitational wave (GW) signals: both the stochastic, GW background of countless unresolved sources, and the GW foreground of individually resolvable binaries which resound above the noise. Ongoing experiments, called pulsar timing arrays, are sensitive to both of these types of signals. We find that, while the current lack of detections is unsurprising, both the background and foreground will plausibly be detected in the next decade. Unlike previous studies which have predicted the foreground to be significantly harder to detect than the background, we find their typical amplitudes are comparable.With traditional electromagnetic observations, there has also been a dearth of confirmed detections of MBH binary systems. We use our binaries, combined with models of emission from accreting MBH systems, to make predictions for the occurrence rate of systems observable using photometric, periodic-variability surveys. These variables should be detectable in current surveys, and indeed, we expect many candidates recently identified to be true binaries - though a significant fraction are likely false positives. Overall, this thesis finds the science of MBH binaries at an exciting cusp: just before incredible breakthroughs in observations, both electromagnetically and in the new age of gravitational wave astrophysics.

Multi-period response management to contaminated water distribution networks: dynamic programming versus genetic algorithms

NASA Astrophysics Data System (ADS)

Bashi-Azghadi, Seyyed Nasser; Afshar, Abbas; Afshar, Mohammad Hadi

2018-03-01

Previous studies on consequence management assume that the selected response action including valve closure and/or hydrant opening remains unchanged during the entire management period. This study presents a new embedded simulation-optimization methodology for deriving time-varying operational response actions in which the network topology may change from one stage to another. Dynamic programming (DP) and genetic algorithm (GA) are used in order to minimize selected objective functions. Two networks of small and large sizes are used in order to illustrate the performance of the proposed modelling schemes if a time-dependent consequence management strategy is to be implemented. The results show that for a small number of decision variables even in large-scale networks, DP is superior in terms of accuracy and computer runtime. However, as the number of potential actions grows, DP loses its merit over the GA approach. This study clearly proves the priority of the proposed dynamic operation strategy over the commonly used static strategy.

How good strong union men line it out: explorations of the structure and dynamics of coal-miners' class consciousness

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

Yarrow, M.N.

1982-01-01

This study explores how working-class people apprehend and analyze the class dynamics of their social world. As an exploratory empirical study of the structure and dynamics of working-class consciousness, it seeks to develop the theory of actual class consciousness by bringing previous theories into dialogue with the articulated analyses of coal miners in central Appalachia. Although changing conditions are shown to have a powerful effect on class consciousness, the respondents were found to respond differently to the changing context and to remain loyal to important elements of their earlier perspectives. Suggestions are made for how the theory could be developedmore » further. The data for the study are flexibly structured interviews which were conducted with active, retired, and disabled miners in southern West Virginia and western Virginia. A dozen miners were interviewed during the 1978 strike and again the following summer; during the summer of 1978, nineteen additional miners were interviewed.« less

Social climber attachment in forming networks produces a phase transition in a measure of connectivity

NASA Astrophysics Data System (ADS)

Taylor, Dane; Larremore, Daniel B.

2012-09-01

The formation and fragmentation of networks are typically studied using percolation theory, but most previous research has been restricted to studying a phase transition in cluster size, examining the emergence of a giant component. This approach does not study the effects of evolving network structure on dynamics that occur at the nodes, such as the synchronization of oscillators and the spread of information, epidemics, and neuronal excitations. We introduce and analyze an alternative link-formation rule, called social climber (SC) attachment, that may be combined with arbitrary percolation models to produce a phase transition using the largest eigenvalue of the network adjacency matrix as the order parameter. This eigenvalue is significant in the analyses of many network-coupled dynamical systems in which it measures the quality of global coupling and is hence a natural measure of connectivity. We highlight the important self-organized properties of SC attachment and discuss implications for controlling dynamics on networks.

Exploring spatial evolution of economic clusters: A case study of Beijing

NASA Astrophysics Data System (ADS)

Yang, Zhenshan; Sliuzas, Richard; Cai, Jianming; Ottens, Henk F. L.

2012-10-01

An identification of economic clusters and analysing their changing spatial patterns is important for understanding urban economic space dynamics. Previous studies, however, suffer from limitations as a consequence of using fixed geographically areas and not combining functional and spatial dynamics. The paper presents an approach, based on local spatial statistics and the case of Beijing to understand the spatial clustering of industries that are functionally interconnected by common or complementary patterns of demand or supply relations. Using register data of business establishments, it identifies economic clusters and analyses their pattern based on postcodes at different time slices during the period 1983-2002. The study shows how the advanced services occupy the urban centre and key sub centres. The Information and Communication Technology (ICT) cluster is mainly concentrated in the north part of the city and circles the urban centre, and the main manufacturing clusters are evolved in the key sub centers. This type of outcomes improves understanding of urban-economic dynamics, which can support spatial and economic planning.

A high dynamic range pulse counting detection system for mass spectrometry.

PubMed

Collings, Bruce A; Dima, Martian D; Ivosev, Gordana; Zhong, Feng

2014-01-30

A high dynamic range pulse counting system has been developed that demonstrates an ability to operate at up to 2e8 counts per second (cps) on a triple quadrupole mass spectrometer. Previous pulse counting detection systems have typically been limited to about 1e7 cps at the upper end of the systems dynamic range. Modifications to the detection electronics and dead time correction algorithm are described in this paper. A high gain transimpedance amplifier is employed that allows a multi-channel electron multiplier to be operated at a significantly lower bias potential than in previous pulse counting systems. The system utilises a high-energy conversion dynode, a multi-channel electron multiplier, a high gain transimpedance amplifier, non-paralysing detection electronics and a modified dead time correction algorithm. Modification of the dead time correction algorithm is necessary due to a characteristic of the pulse counting electronics. A pulse counting detection system with the capability to count at ion arrival rates of up to 2e8 cps is described. This is shown to provide a linear dynamic range of nearly five orders of magnitude for a sample of aprazolam with concentrations ranging from 0.0006970 ng/mL to 3333 ng/mL while monitoring the m/z 309.1 → m/z 205.2 transition. This represents an upward extension of the detector's linear dynamic range of about two orders of magnitude. A new high dynamic range pulse counting system has been developed demonstrating the ability to operate at up to 2e8 cps on a triple quadrupole mass spectrometer. This provides an upward extension of the detector's linear dynamic range by about two orders of magnitude over previous pulse counting systems. Copyright © 2013 John Wiley & Sons, Ltd.

Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

PubMed

Frembgen-Kesner, Tamara; Elcock, Adrian H

2010-11-03

Theory and computation have long been used to rationalize the experimental association rate constants of protein-protein complexes, and Brownian dynamics (BD) simulations, in particular, have been successful in reproducing the relative rate constants of wild-type and mutant protein pairs. Missing from previous BD studies of association kinetics, however, has been the description of hydrodynamic interactions (HIs) between, and within, the diffusing proteins. Here we address this issue by rigorously including HIs in BD simulations of the barnase-barstar association reaction. We first show that even very simplified representations of the proteins--involving approximately one pseudoatom for every three residues in the protein--can provide excellent reproduction of the absolute association rate constants of wild-type and mutant protein pairs. We then show that simulations that include intermolecular HIs also produce excellent estimates of association rate constants, but, for a given reaction criterion, yield values that are decreased by ∼35-80% relative to those obtained in the absence of intermolecular HIs. The neglect of intermolecular HIs in previous BD simulation studies, therefore, is likely to have contributed to the somewhat overestimated absolute rate constants previously obtained. Consequently, intermolecular HIs could be an important component to include in accurate modeling of the kinetics of macromolecular association events. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Comparing DNS and Experiments of Subcritical Flow Past an Isolated Surface Roughness Element

NASA Astrophysics Data System (ADS)

Doolittle, Charles; Goldstein, David

2009-11-01

Results are presented from computational and experimental studies of subcritical roughness within a Blasius boundary layer. This work stems from discrepancies presented by Stephani and Goldstein (AIAA Paper 2009-585) where DNS results did not agree with hot-wire measurements. The near wake regions of cylindrical surface roughness elements corresponding to roughness-based Reynolds numbers Rek of about 202 are of specific concern. Laser-Doppler anemometry and flow visualization in water, as well as the same spectral DNS code used by Stephani and Goldstein are used to obtain both quantitative and qualitative comparisons with previous results. Conclusions regarding previous studies will be presented alongside discussion of current work including grid resolution studies and an examination of vorticity dynamics.

The implications of selective attrition for estimates of intergenerational elasticity of family income

PubMed Central

Schoeni, Robert F.

2015-01-01

Numerous studies have estimated a high intergenerational correlation in economic status. Such studies do not typically attend to potential biases that may arise due to survey attrition. Using the Panel Study of Income Dynamics – the data source most commonly used in prior studies – we demonstrate that attrition is particularly high for low-income adult children with low-income parents and particularly low for high-income adult children with high-income parents. Because of this pattern of attrition, intergenerational upward mobility has been overstated for low-income families and downward mobility has been understated for high-income families. The bias among low-income families is greater than the bias among high-income families implying that intergenerational elasticity in family income is higher than previous estimates with the Panel Study of Income Dynamics would suggest. PMID:26251655

Dynamics of regional brain activity in epilepsy: a cross-disciplinary study on both intracranial and scalp-recorded epileptic seizures

NASA Astrophysics Data System (ADS)

Minadakis, George; Ventouras, Errikos; Gatzonis, Stylianos D.; Siatouni, Anna; Tsekou, Hara; Kalatzis, Ioannis; Sakas, Damianos E.; Stonham, John

2014-04-01

Objective. Recent cross-disciplinary literature suggests a dynamical analogy between earthquakes and epileptic seizures. This study extends the focus of inquiry for the applicability of models for earthquake dynamics to examine both scalp-recorded and intracranial electroencephalogram recordings related to epileptic seizures. Approach. First, we provide an updated definition of the electric event in terms of magnitude and we focus on the applicability of (i) a model for earthquake dynamics, rooted in a nonextensive Tsallis framework, (ii) the traditional Gutenberg and Richter law and (iii) an alternative method for the magnitude-frequency relation for earthquakes. Second, we apply spatiotemporal analysis in terms of nonextensive statistical physics and we further examine the behavior of the parameters included in the nonextensive formula for both types of electroencephalogram recordings under study. Main results. We confirm the previously observed power-law distribution, showing that the nonextensive formula can adequately describe the sequences of electric events included in both types of electroencephalogram recordings. We also show the intermittent behavior of the epileptic seizure cycle which is analogous to the earthquake cycles and we provide evidence of self-affinity of the regional electroencephalogram epileptic seizure activity. Significance. This study may provide a framework for the analysis and interpretation of epileptic brain activity and other biological phenomena with similar underlying dynamical mechanisms.

A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

NASA Astrophysics Data System (ADS)

Alavi, Saman; Ohmura, Ryo; Ripmeester, John A.

2011-02-01

Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO2 molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.

Attainment rate as a surrogate indicator of the intervertebral neutral zone length in lateral bending: an in vitro proof of concept study.

PubMed

Breen, Alexander C; Dupac, Mihai; Osborne, Neil

2015-01-01

Lumbar segmental instability is often considered to be a cause of chronic low back pain. However, defining its measurement has been largely limited to laboratory studies. These have characterised segmental stability as the intrinsic resistance of spine specimens to initial bending moments by quantifying the dynamic neutral zone. However these measurements have been impossible to obtain in vivo without invasive procedures, preventing the assessment of intervertebral stability in patients. Quantitative fluoroscopy (QF), measures the initial velocity of the attainment of intervertebral rotational motion in patients, which may to some extent be representative of the dynamic neutral zone. This study sought to explore the possible relationship between the dynamic neutral zone and intervertebral rotational attainment rate as measured with (QF) in an in vitro preparation. The purpose was to find out if further work into this concept is worth pursuing. This study used passive recumbent QF in a multi-segmental porcine model. This assessed the intrinsic intervertebral responses to a minimal coronal plane bending moment as measured with a digital force guage. Bending moments about each intervertebral joint were calculated and correlated with the rate at which global motion was attained at each intervertebral segment in the first 10° of global motion where the intervertebral joint was rotating. Unlike previous studies of single segment specimens, a neutral zone was found to exist during lateral bending. The initial attainment rates for left and right lateral flexion were comparable to previously published in vivo values for healthy controls. Substantial and highly significant levels of correlation between initial attainment rate and neutral zone were found for left (Rho = 0.75, P = 0.0002) and combined left-right bending (Rho = 0.72, P = 0.0001) and moderate ones for right alone (Rho = 0.55, P = 0.0012). This study found good correlation between the initial intervertebral attainment rate and the dynamic neutral zone, thereby opening the possibility to detect segmental instability from clinical studies. However the results must be treated with caution. Further studies with multiple specimens and adding sagittal plane motion are warranted.

A computational study suggests that replacing PEG with PMOZ may increase exposure of hydrophobic targeting moiety.

PubMed

Magarkar, Aniket; Róg, Tomasz; Bunker, Alex

2017-05-30

In a previous study we showed that the cause of failure of a new, proposed, targeting ligand, the AETP moiety, when attached to a PEGylated liposome, was occlusion by the poly(ethylene glycol) (PEG) layer due to its hydrophobic nature, given that PEG is not entirely hydrophilic. At the time we proposed that possible replacement with a more hydrophilic protective polymer could alleviate this problem. In this study we have used computational molecular dynamics modelling, using a model with all atom resolution, to suggest that a specific alternative protective polymer, poly(2-methyloxazoline) (PMOZ), would perform exactly this function. Our results show that when PEG is replaced by PMOZ the relative exposure to the solvent of AETP is increased to a level even greater than that we found in previous simulations for the RGD peptide, a targeting moiety that has previously been used successfully in PEGylated liposome based therapies. While the AETP moiety itself is no longer under consideration, the results of this computational study have broader significance: the use of PMOZ as an alternative polymer coating to PEG could be efficacious in the context of more hydrophobic targeting ligands. In addition to PMOZ we studied another polyoxazoline, poly(2-ethyloxazoline) (PEOZ), that has also been mooted as a possible alternate protective polymer. It was also found that the RDG peptide occlusion was significantly greater for the case of both oxazolines as opposed to PEG and that, unlike PEG, neither oxazoline entered the membrane. As far as we are aware this is the first time that polyoxazolines have been studied using molecular dynamics simulation with all atom resolution. Copyright © 2017 Elsevier B.V. All rights reserved.

Population variation and individual maximum size in two leech populations: energy extraction from cannibalism or niche widening?

PubMed

Persson, Lennart; Elliott, J Malcolm

2013-05-01

The theory of cannibal dynamics predicts a link between population dynamics and individual life history. In particular, increased individual growth has, in both modeling and empirical studies, been shown to result from a destabilization of population dynamics. We used data from a long-term study of the dynamics of two leech (Erpobdella octoculata) populations to test the hypothesis that maximum size should be higher in a cycling population; one of the study populations exhibited a delayed feedback cycle while the other population showed no sign of cyclicity. A hump-shaped relationship between individual mass of 1-year-old leeches and offspring density the previous year was present in both populations. As predicted from the theory, the maximum mass of individuals was much larger in the fluctuating population. In contrast to predictions, the higher growth rate was not related to energy extraction from cannibalism. Instead, the higher individual mass is suggested to be due to increased availability of resources due to a niche widening with increased individual body mass. The larger individual mass in the fluctuating population was related to a stronger correlation between the densities of 1-year-old individuals and 2-year-old individuals the following year in this population. Although cannibalism was the major mechanism regulating population dynamics, its importance was negligible in terms of providing cannibalizing individuals with energy subsequently increasing their fecundity. Instead, the study identifies a need for theoretical and empirical studies on the largely unstudied interplay between ontogenetic niche shifts and cannibalistic population dynamics.

Emergence of scaling in human-interest dynamics.

PubMed

Zhao, Zhi-Dan; Yang, Zimo; Zhang, Zike; Zhou, Tao; Huang, Zi-Gang; Lai, Ying-Cheng

2013-12-11

Human behaviors are often driven by human interests. Despite intense recent efforts in exploring the dynamics of human behaviors, little is known about human-interest dynamics, partly due to the extreme difficulty in accessing the human mind from observations. However, the availability of large-scale data, such as those from e-commerce and smart-phone communications, makes it possible to probe into and quantify the dynamics of human interest. Using three prototypical "Big Data" sets, we investigate the scaling behaviors associated with human-interest dynamics. In particular, from the data sets we uncover fat-tailed (possibly power-law) distributions associated with the three basic quantities: (1) the length of continuous interest, (2) the return time of visiting certain interest, and (3) interest ranking and transition. We argue that there are three basic ingredients underlying human-interest dynamics: preferential return to previously visited interests, inertial effect, and exploration of new interests. We develop a biased random-walk model, incorporating the three ingredients, to account for the observed fat-tailed distributions. Our study represents the first attempt to understand the dynamical processes underlying human interest, which has significant applications in science and engineering, commerce, as well as defense, in terms of specific tasks such as recommendation and human-behavior prediction.

On the relationship between the dynamic behavior and nanoscale staggered structure of the bone

NASA Astrophysics Data System (ADS)

Qwamizadeh, Mahan; Zhang, Zuoqi; Zhou, Kun; Zhang, Yong Wei

2015-05-01

Bone, a typical load-bearing biological material, composed of ordinary base materials such as organic protein and inorganic mineral arranged in a hierarchical architecture, exhibits extraordinary mechanical properties. Up to now, most of previous studies focused on its mechanical properties under static loading. However, failure of the bone occurs often under dynamic loading. An interesting question is: Are the structural sizes and layouts of the bone related or even adapted to the functionalities demanded by its dynamic performance? In the present work, systematic finite element analysis was performed on the dynamic response of nanoscale bone structures under dynamic loading. It was found that for a fixed mineral volume fraction and unit cell area, there exists a nanoscale staggered structure at some specific feature size and layout which exhibits the fastest attenuation of stress waves. Remarkably, these specific feature sizes and layouts are in excellent agreement with those experimentally observed in the bone at the same scale, indicating that the structural size and layout of the bone at the nanoscale are evolutionarily adapted to its dynamic behavior. The present work points out the importance of dynamic effect on the biological evolution of load-bearing biological materials.

Molecular dynamics simulations of thermally activated edge dislocation unpinning from voids in α -Fe

NASA Astrophysics Data System (ADS)

Byggmästar, J.; Granberg, F.; Nordlund, K.

2017-10-01

In this study, thermal unpinning of edge dislocations from voids in α -Fe is investigated by means of molecular dynamics simulations. The activation energy as a function of shear stress and temperature is systematically determined. Simulations with a constant applied stress are compared with dynamic simulations with a constant strain rate. We found that a constant applied stress results in a temperature-dependent activation energy. The temperature dependence is attributed to the elastic softening of iron. If the stress is normalized with the softening of the specific shear modulus, the activation energy is shown to be temperature-independent. From the dynamic simulations, the activation energy as a function of critical shear stress was determined using previously developed methods. The results from the dynamic simulations are in good agreement with the constant stress simulations, after the normalization. This indicates that the computationally more efficient dynamic method can be used to obtain the activation energy as a function of stress and temperature. The obtained relation between stress, temperature, and activation energy can be used to introduce a stochastic unpinning event in larger-scale simulation methods, such as discrete dislocation dynamics.

Emergence of scaling in human-interest dynamics

NASA Astrophysics Data System (ADS)

Zhao, Zhi-Dan; Yang, Zimo; Zhang, Zike; Zhou, Tao; Huang, Zi-Gang; Lai, Ying-Cheng

2013-12-01

Human behaviors are often driven by human interests. Despite intense recent efforts in exploring the dynamics of human behaviors, little is known about human-interest dynamics, partly due to the extreme difficulty in accessing the human mind from observations. However, the availability of large-scale data, such as those from e-commerce and smart-phone communications, makes it possible to probe into and quantify the dynamics of human interest. Using three prototypical ``Big Data'' sets, we investigate the scaling behaviors associated with human-interest dynamics. In particular, from the data sets we uncover fat-tailed (possibly power-law) distributions associated with the three basic quantities: (1) the length of continuous interest, (2) the return time of visiting certain interest, and (3) interest ranking and transition. We argue that there are three basic ingredients underlying human-interest dynamics: preferential return to previously visited interests, inertial effect, and exploration of new interests. We develop a biased random-walk model, incorporating the three ingredients, to account for the observed fat-tailed distributions. Our study represents the first attempt to understand the dynamical processes underlying human interest, which has significant applications in science and engineering, commerce, as well as defense, in terms of specific tasks such as recommendation and human-behavior prediction.

A Longitudinal Study of the Six Degrees of Freedom Cervical Spine Range of Motion During Dynamic Flexion/Extension and Rotation After Single-Level Anterior Arthrodesis

PubMed Central

Anderst, William J.; West, Tyler; Donaldson, William F; Lee, Joon Y.; Kang, James D.

2016-01-01

Study Design A longitudinal study using biplane radiography to measure in vivo intervertebral range of motion (ROM) during dynamic flexion/extension and rotation. Objective To longitudinally compare intervertebral maximal ROM and midrange motion in asymptomatic control subjects and single-level arthrodesis patients. Summary of Background Data In vitro studies consistently report that adjacent segment maximal ROM increases superior and inferior to cervical arthrodesis. Previous in vivo results have been conflicting, indicating that maximal ROM may or may not increase superior and/or inferior to the arthrodesis. There are no previous reports of midrange motion in arthrodesis patients and similar-aged controls. Methods Eight single-level (C5/C6) anterior arthrodesis patients (tested 7±1 months and 28±6 months post-surgery) and six asymptomatic control subjects (tested twice, 58±6 months apart) performed dynamic full ROM flexion/extension and axial rotation while biplane radiographs were collected at 30 images/s. A previously validated tracking process determined three-dimensional vertebral position from each pair of radiographs with sub-millimeter accuracy. The intervertebral maximal ROM and midrange motion in flexion/extension, rotation, lateral bending, and anterior-posterior translation were compared between test dates and between groups. Results Adjacent segment maximal ROM did not increase over time during flexion/extension or rotation movements. Adjacent segment maximal rotational ROM was not significantly greater in arthrodesis patients than in corresponding motion segments of similar-aged controls. C4/C5 adjacent segment rotation during the midrange of head motion and maximal anterior-posterior translation were significantly greater in arthrodesis patients than in the corresponding motion segment in controls on the second test date. Conclusions C5/C6 arthrodesis appears to significantly affect midrange, but not end-range, adjacent segment motions. The effects of arthrodesis on adjacent segment motion may be best evaluated by longitudinal studies that compare maximal and midrange adjacent segment motion to corresponding motion segments of similar-aged controls to determine if the adjacent segment motion is truly excessive. PMID:27831986

A dynamical-systems approach for computing ice-affected streamflow

USGS Publications Warehouse

Holtschlag, David J.

1996-01-01

A dynamical-systems approach was developed and evaluated for computing ice-affected streamflow. The approach provides for dynamic simulation and parameter estimation of site-specific equations relating ice effects to routinely measured environmental variables. Comparison indicates that results from the dynamical-systems approach ranked higher than results from 11 analytical methods previously investigated on the basis of accuracy and feasibility criteria. Additional research will likely lead to further improvements in the approach.

Promotion of cooperation by selective group extinction

NASA Astrophysics Data System (ADS)

Böttcher, Marvin A.; Nagler, Jan

2016-06-01

Multilevel selection is an important organizing principle that crucially underlies evolutionary processes from the emergence of cells to eusociality and the economics of nations. Previous studies on multilevel selection assumed that the effective higher-level selection emerges from lower-level reproduction. This leads to selection among groups, although only individuals reproduce. We introduce selective group extinction, where groups die with a probability inversely proportional to their group fitness. When accounting for this the critical benefit-to-cost ratio is substantially lowered. Because in game theory and evolutionary dynamics the degree of cooperation crucially depends on this ratio above which cooperation emerges, previous studies may have substantially underestimated the establishment and maintenance of cooperation.

A quantum dynamics study of the benzopyran ring opening guided by laser pulses

NASA Astrophysics Data System (ADS)

Saab, Mohamad; Doriol, Loïc Joubert; Lasorne, Benjamin; Guérin, Stéphane; Gatti, Fabien

2014-10-01

The ring-opening photoisomerization of benzopyran, which occurs via a photochemical route involving a conical intersection, has been studied with quantum dynamics calculations using the multi-configuration time-dependent Hartree method (MCTDH). We introduce a mechanistic strategy to control the conversion of benzopyran to merocyanine with laser pulses. We use a six-dimensional model developed in a previous work for the potential energy surfaces (PES) based on an extension of the vibronic-coupling Hamiltonian model (diabatization method by ansatz), which depends on the most active degrees of freedom. The main objective of these quantum dynamics simulations is to provide a set of strategies that could help experimentalists to control the photoreactivity vs. photostability ratio (selectivity). In this work we present: (i) a pump-dump technique used to control the photostability, (ii) a two-step strategy to enhance the reactivity of the system: first, a pure vibrational excitation in the electronic ground state that prepares the system and, second, an ultraviolet excitation that brings the system to the first adiabatic electronic state; (iii) finally the effect of a non-resonant pulse (Stark effect) on the dynamics.

Probing Dynamics in Granular Media of Contrasting Geometries via X-Ray Phase Contrast Imaging and PDV

NASA Astrophysics Data System (ADS)

Crum, Ryan; Pagan, Darren; Lind, Jon; Homel, Michael; Hurley, Ryan; Herbold, Eric; Akin, Minta

Granular systems are ubiquitous in our everyday world and play a central role in many dynamic scientific problems including mine blasting, projectile penetration, astrophysical collisions, explosions, and dynamic compaction. An understanding of granular media's behavior under various loading conditions is an ongoing scientific grand challenge. This is partly due to the intricate interplay between material properties, loading conditions, grain geometry, and grain connectivity. Previous dynamic studies in granular media predominantly utilize the macro-scale analyses VISAR or PDV, diagnostics that are not sensitive to the many degrees of freedom and their interactions, focusing instead on their aggregate effect. Results of a macro-scale analysis leave the principal interactions of these degrees of freedom too entangled to elucidate. To isolate the significance of grain geometry, this study probes various geometries of granular media subjected to gas gun generated waves via in-situ X-ray analysis. Analyses include evaluating displacement fields, grain fracture, inter- and intra-granular densification, and wave front motion. Phase Contrast Imaging (PCI) and PDV analyses feed directly into our concurrent meso-scale granular media modeling efforts to enhance our predictive capabilities.

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes.

PubMed

Kürten, Charlotte; Syrén, Per-Olof

2016-01-16

Enzyme catalysis evolved in an aqueous environment. The influence of solvent dynamics on catalysis is, however, currently poorly understood and usually neglected. The study of water dynamics in enzymes and the associated thermodynamical consequences is highly complex and has involved computer simulations, nuclear magnetic resonance (NMR) experiments, and calorimetry. Water tunnels that connect the active site with the surrounding solvent are key to solvent displacement and dynamics. The protocol herein allows for the engineering of these motifs for water transport, which affects specificity, activity and thermodynamics. By providing a biophysical framework founded on theory and experiments, the method presented herein can be used by researchers without previous expertise in computer modeling or biophysical chemistry. The method will advance our understanding of enzyme catalysis on the molecular level by measuring the enthalpic and entropic changes associated with catalysis by enzyme variants with obstructed water tunnels. The protocol can be used for the study of membrane-bound enzymes and other complex systems. This will enhance our understanding of the importance of solvent reorganization in catalysis as well as provide new catalytic strategies in protein design and engineering.

Using experimental human influenza infections to validate a viral dynamic model and the implications for prediction.

PubMed

Chen, S C; You, S H; Liu, C Y; Chio, C P; Liao, C M

2012-09-01

The aim of this work was to use experimental infection data of human influenza to assess a simple viral dynamics model in epithelial cells and better understand the underlying complex factors governing the infection process. The developed study model expands on previous reports of a target cell-limited model with delayed virus production. Data from 10 published experimental infection studies of human influenza was used to validate the model. Our results elucidate, mechanistically, the associations between epithelial cells, human immune responses, and viral titres and were supported by the experimental infection data. We report that the maximum total number of free virions following infection is 10(3)-fold higher than the initial introduced titre. Our results indicated that the infection rates of unprotected epithelial cells probably play an important role in affecting viral dynamics. By simulating an advanced model of viral dynamics and applying it to experimental infection data of human influenza, we obtained important estimates of the infection rate. This work provides epidemiologically meaningful results, meriting further efforts to understand the causes and consequences of influenza A infection.

The Effects of Aging and Dual Tasking on Human Gait Complexity During Treadmill Walking: A Comparative Study Using Quantized Dynamical Entropy and Sample Entropy.

PubMed

Ahmadi, Samira; Wu, Christine; Sepehri, Nariman; Kantikar, Anuprita; Nankar, Mayur; Szturm, Tony

2018-01-01

Quantized dynamical entropy (QDE) has recently been proposed as a new measure to quantify the complexity of dynamical systems with the purpose of offering a better computational efficiency. This paper further investigates the viability of this method using five different human gait signals. These signals are recorded while normal walking and while performing secondary tasks among two age groups (young and older age groups). The results are compared with the outcomes of previously established sample entropy (SampEn) measure for the same signals. We also study how analyzing segmented and spatially and temporally normalized signal differs from analyzing whole data. Our findings show that human gait signals become more complex as people age and while they are cognitively loaded. Center of pressure (COP) displacement in mediolateral direction is the best signal for showing the gait changes. Moreover, the results suggest that by segmenting data, more information about intrastride dynamical features are obtained. Most importantly, QDE is shown to be a reliable measure for human gait complexity analysis.

Multi-channel dynamics in high harmonic generation of aligned CO2: ab initio analysis with time-dependent B-spline algebraic diagrammatic construction.

PubMed

Ruberti, M; Decleva, P; Averbukh, V

2018-03-28

Here we present a fully ab initio study of the high-order harmonic generation (HHG) spectrum of aligned CO 2 molecules. The calculations have been performed by using the molecular time-dependent (TD) B-spline algebraic diagrammatic construction (ADC) method. We quantitatively study how the sub-cycle laser-driven multi-channel dynamics, as reflected in the position of the dynamical minimum in the HHG spectrum, is affected by the full inclusion of both correlation-driven and laser-driven dipole interchannel couplings. We calculate channel-resolved spectral intensities as well as the phase differences between contributions of the different ionization-recombination channels to the total HHG spectrum. Our results show that electron correlation effectively controls the relative contributions of the different channels to the total HHG spectrum, leading to the opening of the new ones (1 2 Π u , 1 2 Σ), previously disregarded for the aligned molecular setup. We conclude that inclusion of many-electron effects into the theoretical interpretation of molecular HHG spectra is essential in order to correctly extract ultrafast electron dynamics using HHG spectroscopy.

In vivo imaging of emerging endocrine cells reveals a requirement for PI3K-regulated motility in pancreatic islet morphogenesis

PubMed Central

Freudenblum, Julia; Iglesias, José A.; Hermann, Martin; Walsen, Tanja; Wilfinger, Armin; Meyer, Dirk

2018-01-01

ABSTRACT The three-dimensional architecture of the pancreatic islet is integral to beta cell function, but the process of islet formation remains poorly understood due to the difficulties of imaging internal organs with cellular resolution. Within transparent zebrafish larvae, the developing pancreas is relatively superficial and thus amenable to live imaging approaches. We performed in vivo time-lapse and longitudinal imaging studies to follow islet development, visualizing both naturally occurring islet cells and cells arising with an accelerated timecourse following an induction approach. These studies revealed previously unappreciated fine dynamic protrusions projecting between neighboring and distant endocrine cells. Using pharmacological compound and toxin interference approaches, and single-cell analysis of morphology and cell dynamics, we determined that endocrine cell motility is regulated by phosphoinositide 3-kinase (PI3K) and G-protein-coupled receptor (GPCR) signaling. Linking cell dynamics to islet formation, perturbation of protrusion formation disrupted endocrine cell coalescence, and correlated with decreased islet cell differentiation. These studies identified novel cell behaviors contributing to islet morphogenesis, and suggest a model in which dynamic exploratory filopodia establish cell-cell contacts that subsequently promote cell clustering. PMID:29386244

The allosteric communication pathways in KIX domain of CBP.

PubMed

Palazzesi, Ferruccio; Barducci, Alessandro; Tollinger, Martin; Parrinello, Michele

2013-08-27

Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics. Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). In this work, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID), by combing all-atom molecular dynamics with enhanced sampling methods recently developed in our group. We discuss our results in relation to previous NMR studies. We also develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale.

Dynamical analysis of uterine cell electrical activity model.

PubMed

Rihana, S; Santos, J; Mondie, S; Marque, C

2006-01-01

The uterus is a physiological system consisting of a large number of interacting smooth muscle cells. The uterine excitability changes remarkably with time, generally quiescent during pregnancy, the uterus exhibits forceful synchronized contractions at term leading to fetus expulsion. These changes characterize thus a dynamical system susceptible of being studied through formal mathematical tools. Multiple physiological factors are involved in the regulation process of this complex system. Our aim is to relate the physiological factors to the uterine cell dynamic behaviors. Taking into account a previous work presented, in which the electrical activity of a uterine cell is described by a set of ordinary differential equations, we analyze the impact of physiological parameters on the response of the model, and identify the main subsystems generating the complex uterine electrical activity, with respect to physiological data.

Communication: Heterogeneous water dynamics on a clathrate hydrate lattice detected by multidimensional oxygen nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Adjei-Acheamfour, Mischa; Storek, Michael; Böhmer, Roland

2017-05-01

Previous deuteron nuclear magnetic resonance studies revealed conflicting evidence regarding the possible motional heterogeneity of the water dynamics on the hydrate lattice of an ice-like crystal. Using oxygen-17 nuclei as a sensitive quadrupolar probe, the reorientational two-time correlation function displays a clear nonexponentiality. To check whether this dispersive behavior is a consequence of dynamic heterogeneity or rather of an intrinsic nonexponentiality, a multidimensional, four-time magnetic resonance experiment was devised that is generally applicable to strongly quadrupolarly perturbed half-integer nuclei such as oxygen-17. Measurements of an appropriate four-time function demonstrate that it is possible to select a subensemble of slow water molecules. Its mean time scale is compared to theoretical predictions and evidence for significant motional heterogeneity is found.

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations.

PubMed

Lenski, Richard E

2017-10-01

Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.

Classification of small lesions on dynamic breast MRI: Integrating dimension reduction and out-of-sample extension into CADx methodology

PubMed Central

Nagarajan, Mahesh B.; Huber, Markus B.; Schlossbauer, Thomas; Leinsinger, Gerda; Krol, Andrzej; Wismüller, Axel

2014-01-01

Objective While dimension reduction has been previously explored in computer aided diagnosis (CADx) as an alternative to feature selection, previous implementations of its integration into CADx do not ensure strict separation between training and test data required for the machine learning task. This compromises the integrity of the independent test set, which serves as the basis for evaluating classifier performance. Methods and Materials We propose, implement and evaluate an improved CADx methodology where strict separation is maintained. This is achieved by subjecting the training data alone to dimension reduction; the test data is subsequently processed with out-of-sample extension methods. Our approach is demonstrated in the research context of classifying small diagnostically challenging lesions annotated on dynamic breast magnetic resonance imaging (MRI) studies. The lesions were dynamically characterized through topological feature vectors derived from Minkowski functionals. These feature vectors were then subject to dimension reduction with different linear and non-linear algorithms applied in conjunction with out-of-sample extension techniques. This was followed by classification through supervised learning with support vector regression. Area under the receiver-operating characteristic curve (AUC) was evaluated as the metric of classifier performance. Results Of the feature vectors investigated, the best performance was observed with Minkowski functional ’perimeter’ while comparable performance was observed with ’area’. Of the dimension reduction algorithms tested with ’perimeter’, the best performance was observed with Sammon’s mapping (0.84 ± 0.10) while comparable performance was achieved with exploratory observation machine (0.82 ± 0.09) and principal component analysis (0.80 ± 0.10). Conclusions The results reported in this study with the proposed CADx methodology present a significant improvement over previous results reported with such small lesions on dynamic breast MRI. In particular, non-linear algorithms for dimension reduction exhibited better classification performance than linear approaches, when integrated into our CADx methodology. We also note that while dimension reduction techniques may not necessarily provide an improvement in classification performance over feature selection, they do allow for a higher degree of feature compaction. PMID:24355697

Estimation of Dynamic Friction Process of the Akatani Landslide Based on the Waveform Inversion and Numerical Simulation

NASA Astrophysics Data System (ADS)

Yamada, M.; Mangeney, A.; Moretti, L.; Matsushi, Y.

2014-12-01

Understanding physical parameters, such as frictional coefficients, velocity change, and dynamic history, is important issue for assessing and managing the risks posed by deep-seated catastrophic landslides. Previously, landslide motion has been inferred qualitatively from topographic changes caused by the event, and occasionally from eyewitness reports. However, these conventional approaches are unable to evaluate source processes and dynamic parameters. In this study, we use broadband seismic recordings to trace the dynamic process of the deep-seated Akatani landslide that occurred on the Kii Peninsula, Japan, which is one of the best recorded large slope failures. Based on the previous results of waveform inversions and precise topographic surveys done before and after the event, we applied numerical simulations using the SHALTOP numerical model (Mangeney et al., 2007). This model describes homogeneous continuous granular flows on a 3D topography based on a depth averaged thin layer approximation. We assume a Coulomb's friction law with a constant friction coefficient, i. e. the friction is independent of the sliding velocity. We varied the friction coefficients in the simulation so that the resulting force acting on the surface agrees with the single force estimated from the seismic waveform inversion. Figure shows the force history of the east-west components after the band-pass filtering between 10-100 seconds. The force history of the simulation with frictional coefficient 0.27 (thin red line) the best agrees with the result of seismic waveform inversion (thick gray line). Although the amplitude is slightly different, phases are coherent for the main three pulses. This is an evidence that the point-source approximation works reasonably well for this particular event. The friction coefficient during the sliding was estimated to be 0.38 based on the seismic waveform inversion performed by the previous study and on the sliding block model (Yamada et al., 2013), whereas the frictional coefficient estimated from the numerical simulation was about 0.27. This discrepancy may be due to the digital elevation model, to the other forces such as pressure gradients and centrifugal acceleration included in the model. However, quantitative interpretation of this difference requires further investigation.

Dynamical Constraints on the Seasonal Migration of the ITCZ Using a Moist GCM

NASA Astrophysics Data System (ADS)

Faulk, S.; Mitchell, J.; Bordoni, S.

2015-12-01

One of the most prominent features of the Earth's large-scale circulation in low latitudes is the intertropical convergence zone (ITCZ), where tropical precipitation is concentrated in a relatively narrow latitudinal band that moves seasonally. On Earth, the ITCZ is limited to low latitudes; however on Mars and Titan, it has been argued that analagous convergence zones can migrate significantly off the equator into the summer hemisphere, perhaps even reaching the summer pole in the case of Titan. Previous studies of the ITCZ's extent have focused primarily on thermodynamics, particularly emphasizing its collocation with maximum moist static energy (MSE) and its response to local surface heat capacity. Here, we focus on the dynamical mechanisms controlling ITCZ migrations, examining the ITCZ's extent through the perspective of the momentum budget rather than through thermal forces or land-sea changes. We study a wide range of atmospheric circulations with an idealized General Circulation Model (GCM), in which an atmospheric model with idealized physics is coupled to an aquaplanet slab ocean of fixed depth and top-of-atmosphere insolation is varied seasonally as well as held fixed at the pole in "eternal solstice" runs. We explore a range of surface heat capacities and rotation rates, keeping all other parameters Earth-like. We find that for rotation rates ΩE/8 and slower, the seasonal ITCZ reaches the summer pole. Additionally, in contrast to previous thermodynamic arguments, we find that the ITCZ does not follow the maximum MSE, remaining at low latitudes in the eternal solstice case for Earth's rotation rate. Furthermore, we find that significantly decreasing the surface heat capacity does little to extend the ITCZ's summer migration off the equator. These results suggest that the ITCZ may be more controlled by dynamical mechanisms than previously thought; however, we also find that baroclinic instability, often invoked as a limiter on the extent of the summer Hadley cell, appears to play only a minor role in limiting the ITCZ's extent. We develop a theory for constraining the ITCZ's position based on top-of-atmosphere energetics and boundary layer dynamics, offering a new perspective on the seasonal weather patterns of terrestrial planets.

Child Labor in the World Polity: Decline and Persistence, 1980-2000

ERIC Educational Resources Information Center

Clark, Rob

2011-01-01

From 1980 to 2000, child labor rates across the world fell by more than a quarter. Much of the explanation for this decrease resides in development processes broadly associated with the demographic transition. Net of these internal dynamics, however, globalization may also have played a role. Previous studies have examined the effect of trade and…

"I Just Want to Be 'Me' When I Am Exercising": Adrianna's Construction of a Vulnerable Exercise Identity

ERIC Educational Resources Information Center

Rossing, Hilde; Ronglan, Lars-Tore; Scott, Susie

2016-01-01

This study explores the social and dynamic aspects of the concept "exercise identity". Previous research, mainly in psychology, has documented a link between exercise identity and exercise behaviour. However, the process of identity formation is not straightforward but rather something that can change with time, context and interaction…

Patterns of Word Reading Skill, Interest and Self-Concept of Ability

ERIC Educational Resources Information Center

Viljaranta, Jaana; Kiuru, Noona; Lerkkanen, Marja-Kristiina; Silinskas, Gintautas; Poikkeus, Anna-Maija; Nurmi, Jari-Erik

2017-01-01

The majority of previous research on academic skills, self-concept of ability and interest has deployed the variable-oriented approach and focused on self-concept, or ability, or interest only. This study examined the patterns and dynamics of pattern change in Finnish children's word reading skill, self-concept of ability and interest from…

Toward a Dynamic Interactive Model of Non-Native Chinese Character Processing

ERIC Educational Resources Information Center

Tong, Xiuli; Kwan, Joyce Lok Yin; Wong, Denise Wai Man; Lee, Stephen Man Kit; Yip, Joanna Hew Yan

2016-01-01

Previous studies have suggested that word processing in English as a second language (L2) is affected by first language (L1) orthographic features. However, little is known about what affects L2 Chinese character processing in adult Chinese learners with different L1 orthographies such as Japanese, Korean, and English. With a picture-character…

The Importance of "What": Infants Use Featural Information to Index Events

ERIC Educational Resources Information Center

Kirkham, Natasha Z.; Richardson, Daniel C.; Wu, Rachel; Johnson, Scott P.

2012-01-01

Dynamic spatial indexing is the ability to encode, remember, and track the location of complex events. For example, in a previous study, 6-month-old infants were familiarized to a toy making a particular sound in a particular location, and later they fixated that empty location when they heard the sound presented alone ("Journal of Experimental…

Monitoring land surface albedo and vegetation dynamics using high spatial and temporal resolution synthetic data from Landsat and MODIS BRDF/albedo product

USDA-ARS?s Scientific Manuscript database

Climate warming over the past half century has led to observable changes in vegetation phenology and growing season length; which can be measured globally using remote sensing derived vegetation indices. Previous studies in mid- and high northern latitude systems show temperature driven earlier spri...

Stabilizing coherence with nested environments: a numerical study using kicked Ising models

NASA Astrophysics Data System (ADS)

González-Gutiérrez, C.; Villaseñor, E.; Pineda, C.; Seligman, T. H.

2016-08-01

We study a tripartite system of coupled spins, where a first set of one or two spins is our central system which is coupled to another set considered, the near environment, in turn coupled to the third set, the far environment. The dynamics considered are those of a generalized kicked spin chain in the regime of quantum chaotic dynamics. This allows us to test recent results that suggest that the presence of a far environment, coupled to the near environment, slows decoherence of the central system. After an extensive numerical study, we confirm previous results for extreme values and special cases. In particular, under a wide variety of circumstances an increasing coupling between near and far environment, slows decoherence, as measured by purity, and protects internal entanglement.

Time-dependent variational principle in matrix-product state manifolds: Pitfalls and potential

NASA Astrophysics Data System (ADS)

Kloss, Benedikt; Lev, Yevgeny Bar; Reichman, David

2018-01-01

We study the applicability of the time-dependent variational principle in matrix-product state manifolds for the long time description of quantum interacting systems. By studying integrable and nonintegrable systems for which the long time dynamics are known we demonstrate that convergence of long time observables is subtle and needs to be examined carefully. Remarkably, for the disordered nonintegrable system we consider the long time dynamics are in good agreement with the rigorously obtained short time behavior and with previous obtained numerically exact results, suggesting that at least in this case, the apparent convergence of this approach is reliable. Our study indicates that, while great care must be exercised in establishing the convergence of the method, it may still be asymptotically accurate for a class of disordered nonintegrable quantum systems.

Multi-kw dc power distribution system study program

NASA Technical Reports Server (NTRS)

Berkery, E. A.; Krausz, A.

1974-01-01

The first phase of the Multi-kw dc Power Distribution Technology Program is reported and involves the test and evaluation of a technology breadboard in a specifically designed test facility according to design concepts developed in a previous study on space vehicle electrical power processing, distribution, and control. The static and dynamic performance, fault isolation, reliability, electromagnetic interference characterisitics, and operability factors of high distribution systems were studied in order to gain a technology base for the use of high voltage dc systems in future aerospace vehicles. Detailed technical descriptions are presented and include data for the following: (1) dynamic interactions due to operation of solid state and electromechanical switchgear; (2) multiplexed and computer controlled supervision and checkout methods; (3) pulse width modulator design; and (4) cable design factors.

Hybrid finite element and Brownian dynamics method for charged particles

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

Huber, Gary A., E-mail: ghuber@ucsd.edu; Miao, Yinglong; Zhou, Shenggao

2016-04-28

Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced a new hybrid diffusion method that couples the strengths of each of these two methods, but was limited by the lack of interactions among the particles; the force on each particle had to be from an external field. This study further develops the method to allow charged particles. The method is derived for a general multidimensional system and is presented usingmore » a basic test case for a one-dimensional linear system with one charged species and a radially symmetric system with three charged species.« less

Packaging stiff polymers in small containers: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

2016-09-01

The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of the system—the DNA polymer and the spherical viral capsid—has been studied by molecular dynamics simulation. The results, involving longer polymers than in earlier work, show that as polymers become more rigid there is an increasing tendency to self-organize as spools that wrap from the inside out, rather than the inverse direction seen previously. In the final state, a substantial part of the polymer is packed into one or more coaxial spools, concentrically layered with different orientations, a form of packaging achievable without twisting the polymer.

Simulation of in vivo dynamics during robot assisted joint movement.

PubMed

Bobrowitsch, Evgenij; Lorenz, Andrea; Wülker, Nikolaus; Walter, Christian

2014-12-16

Robots are very useful tools in orthopedic research. They can provide force/torque controlled specimen motion with high repeatability and precision. A method to analyze dissipative energy outcome in an entire joint was developed in our group. In a previous study, a sheep knee was flexed while axial load remained constant during the measurement of dissipated energy. We intend to apply this method for the investigation of osteoarthritis. Additionally, the method should be improved by simulation of in vivo knee dynamics. Thus, a new biomechanical testing tool will be developed for analyzing in vitro joint properties after different treatments. Discretization of passive knee flexion was used to construct a complex flexion movement by a robot and simulate altering axial load similar to in vivo sheep knee dynamics described in a previous experimental study. The robot applied an in vivo like axial force profile with high reproducibility during the corresponding knee flexion (total standard deviation of 0.025 body weight (BW)). A total residual error between the in vivo and simulated axial force was 0.16 BW. Posterior-anterior and medio-lateral forces were detected by the robot as a backlash of joint structures. Their curve forms were similar to curve forms of corresponding in vivo measured forces, but in contrast to the axial force, they showed higher total standard deviation of 0.118 and 0.203 BW and higher total residual error of 0.79 and 0.21 BW for posterior-anterior and medio-lateral forces respectively. We developed and evaluated an algorithm for the robotic simulation of complex in vivo joint dynamics using a joint specimen. This should be a new biomechanical testing tool for analyzing joint properties after different treatments.

Analysis of 15N-1H NMR relaxation in proteins by a combined experimental and molecular dynamics simulation approach: picosecond-nanosecond dynamics of the Rho GTPase binding domain of plexin-B1 in the dimeric state indicates allosteric pathways.

PubMed

Zerbetto, Mirco; Anderson, Ross; Bouguet-Bonnet, Sabine; Rech, Mariano; Zhang, Liqun; Meirovitch, Eva; Polimeno, Antonino; Buck, Matthias

2013-01-10

We investigate picosecond–nanosecond dynamics of the Rho-GTPase Binding Domain (RBD) of plexin-B1, which plays a key role in plexin-mediated cell signaling. Backbone 15N relaxation data of the dimeric RBD are analyzed with the model-free (MF) method, and with the slowly relaxing local structure/molecular dynamics (SRLS-MD) approach. Independent analysis of the MD trajectories, based on the MF paradigm, is also carried out. MF is a widely popular and simple method, SRLS is a general approach, and SRLS-MD is an integrated approach we developed recently. Corresponding parameters from the RBD dimer, a previously studied RBD monomer mutant, and the previously studied complex of the latter with the GTPase Rac1, are compared. The L2, L3, and L4 loops of the plexin-B1 RBD are involved in interactions with other plexin domains, GTPase binding, and RBD dimerization, respectively. Peptide groups in the loops of both the monomeric and dimeric RBD are found to experience weak and moderately asymmetric local ordering centered approximately at the C(i–1)(α)–C(i)(α) axes, and nanosecond backbone motion. Peptide groups in the α-helices and the β-strands of the dimer (the β-strands of the monomer) experience strong and highly asymmetric local ordering centered approximately at the C(i–1)(α)–C(i)(α) axes (N–H bonds). N–H fluctuations occur on the picosecond time scale. An allosteric pathway for GTPase binding, providing new insights into plexin function, is delineated.

Preictal dynamics of EEG complexity in intracranially recorded epileptic seizure: a case report.

PubMed

Bob, Petr; Roman, Robert; Svetlak, Miroslav; Kukleta, Miloslav; Chladek, Jan; Brazdil, Milan

2014-11-01

Recent findings suggest that neural complexity reflecting a number of independent processes in the brain may characterize typical changes during epileptic seizures and may enable to describe preictal dynamics. With respect to previously reported findings suggesting specific changes in neural complexity during preictal period, we have used measure of pointwise correlation dimension (PD2) as a sensitive indicator of nonstationary changes in complexity of the electroencephalogram (EEG) signal. Although this measure of complexity in epileptic patients was previously reported by Feucht et al (Applications of correlation dimension and pointwise dimension for non-linear topographical analysis of focal onset seizures. Med Biol Comput. 1999;37:208-217), it was not used to study changes in preictal dynamics. With this aim to study preictal changes of EEG complexity, we have examined signals from 11 multicontact depth (intracerebral) EEG electrodes located in 108 cortical and subcortical brain sites, and from 3 scalp EEG electrodes in a patient with intractable epilepsy, who underwent preoperative evaluation before epilepsy surgery. From those 108 EEG contacts, records related to 44 electrode contacts implanted into lesional structures and white matter were not included into the experimental analysis.The results show that in comparison to interictal period (at about 8-6 minutes before seizure onset), there was a statistically significant decrease in PD2 complexity in the preictal period at about 2 minutes before seizure onset in all 64 intracranial channels localized in various brain sites that were included into the analysis and in 3 scalp EEG channels as well. Presented results suggest that using PD2 in EEG analysis may have significant implications for research of preictal dynamics and prediction of epileptic seizures.

Chenciner bubbles and torus break-up in a periodically forced delay differential equation

NASA Astrophysics Data System (ADS)

Keane, A.; Krauskopf, B.

2018-06-01

We study a generic model for the interaction of negative delayed feedback and periodic forcing that was first introduced by Ghil et al (2008 Nonlinear Process. Geophys. 15 417–33) in the context of the El Niño Southern Oscillation climate system. This model takes the form of a delay differential equation and has been shown in previous work to be capable of producing complicated dynamics, which is organised by resonances between the external forcing and dynamics induced by feedback. For certain parameter values, we observe in simulations the sudden disappearance of (two-frequency dynamics on) tori. This can be explained by the folding of invariant tori and their associated resonance tongues. It is known that two smooth tori cannot simply meet and merge; they must actually break up in complicated bifurcation scenarios that are organised within so-called resonance bubbles first studied by Chenciner. We identify and analyse such a Chenciner bubble in order to understand the dynamics at folds of tori. We conduct a bifurcation analysis of the Chenciner bubble by means of continuation software and dedicated simulations, whereby some bifurcations involve tori and are detected in appropriate two-dimensional projections associated with Poincaré sections. We find close agreement between the observed bifurcation structure in the Chenciner bubble and a previously suggested theoretical picture. As far as we are aware, this is the first time the bifurcation structure associated with a Chenciner bubble has been analysed in a delay differential equation and, in fact, for a flow rather than an explicit map. Following our analysis, we briefly discuss the possible role of folding tori and Chenciner bubbles in the context of tipping.

Snap, Crackle, Pop: Dilational fault breccias record seismic slip below the brittle-plastic transition

NASA Astrophysics Data System (ADS)

Melosh, Ben L.; Rowe, Christie D.; Smit, Louis; Groenewald, Conrad; Lambert, Christopher W.; Macey, Paul

2014-10-01

Off-fault dynamic tensile cracks form behind an earthquake rupture front with distinct orientation and spacing. These cracks explode the wall rock and create breccias, which we hypothesize will preserve a unique fingerprint of dynamic rupture. Identification of these characteristic breccias may enable a new tool for identifying paleoseismic slip surfaces in the rock record. Using previous experimental and theoretical predictions, we develop a field-based model of dynamic dilational breccia formation. Experimental studies find that secondary tensile fracture networks comprise closely spaced fractures at angles of 70-90° from a slip surface, as well as fractures that branch at angles of ∼ 30 ° from a primary mode I fracture. The Pofadder Shear Zone, in Namibia and South Africa, preserves breccias formed in the brittle-ductile transition zone displaying fracture patterns consistent with those described above. Fracture spacing is approximately two orders of magnitude less than predicted by quasi-static models. Breccias are clast-supported, monomict and can display an abrupt transition from fracture network crackle breccia to mosaic breccia textures. Brecciation occurs by the intersection of off-fault dynamic fractures and wall rock fabric; this is in contrast to previous models of fluid pressure gradient-driven failure ;implosion breccias;. This mechanism tends to form many similar sized clasts with particle size distributions that may not display self-similarity; where self-similarity is observed the distributions have relatively low D-values of 1.47 ± 0.37, similar to other studies of dynamic processes. We measure slip distances at dilational breccia stepovers, estimating earthquake magnitudes between Mw 2.8-5.8 and associated rupture lengths of 0.023-3.3 km. The small calculated rupture dimensions, in combination with our geologic observations, suggest that some earthquakes nucleated within the quartz-plastic transitional zone and potentially record deep seismic slip.

Validity of thermally-driven small-scale ventilated filling box models

NASA Astrophysics Data System (ADS)

Partridge, Jamie L.; Linden, P. F.

2013-11-01

The majority of previous work studying building ventilation flows at laboratory scale have used saline plumes in water. The production of buoyancy forces using salinity variations in water allows dynamic similarity between the small-scale models and the full-scale flows. However, in some situations, such as including the effects of non-adiabatic boundaries, the use of a thermal plume is desirable. The efficacy of using temperature differences to produce buoyancy-driven flows representing natural ventilation of a building in a small-scale model is examined here, with comparison between previous theoretical and new, heat-based, experiments.

A Theory of Electrical Conductivity of Pseudo-Binary Equivalent Molten Salt

NASA Astrophysics Data System (ADS)

Matsunaga, Shigeki; Koishi, Takahiro; Tamaki, Shigeru

2008-02-01

Many years ago, Sundheim proposed the "universal golden rule" by experiments, i.e. the ratio of the partial ionic conductivities in molten binary salt is equal to the inverse mass ratio of each ions, σ+/σ- = m-/m-. In the previous works, we have proved this relation by the theory using Langevin equation, and by molecular dynamics simulations (MD). In this study, the pseudo binary molten salt NaCl-KCl system is investigated in the same theoretical framework as previous works as the serial work in molten salts. The MD results are also reported in connection with the theoretical analysis.

Two-dimensional electronic spectra from the hierarchical equations of motion method: Application to model dimers

NASA Astrophysics Data System (ADS)

Chen, Liping; Zheng, Renhui; Shi, Qiang; Yan, YiJing

2010-01-01

We extend our previous study of absorption line shapes of molecular aggregates using the Liouville space hierarchical equations of motion (HEOM) method [L. P. Chen, R. H. Zheng, Q. Shi, and Y. J. Yan, J. Chem. Phys. 131, 094502 (2009)] to calculate third order optical response functions and two-dimensional electronic spectra of model dimers. As in our previous work, we have focused on the applicability of several approximate methods related to the HEOM method. We show that while the second order perturbative quantum master equations are generally inaccurate in describing the peak shapes and solvation dynamics, they can give reasonable peak amplitude evolution even in the intermediate coupling regime. The stochastic Liouville equation results in good peak shapes, but does not properly describe the excited state dynamics due to the lack of detailed balance. A modified version of the high temperature approximation to the HEOM gives the best agreement with the exact result.

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

An automated detection for axonal boutons in vivo two-photon imaging of mouse

NASA Astrophysics Data System (ADS)

Li, Weifu; Zhang, Dandan; Xie, Qiwei; Chen, Xi; Han, Hua

2017-02-01

Activity-dependent changes in the synaptic connections of the brain are tightly related to learning and memory. Previous studies have shown that essentially all new synaptic contacts were made by adding new partners to existing synaptic elements. To further explore synaptic dynamics in specific pathways, concurrent imaging of pre and postsynaptic structures in identified connections is required. Consequently, considerable attention has been paid for the automated detection of axonal boutons. Different from most previous methods proposed in vitro data, this paper considers a more practical case in vivo neuron images which can provide real time information and direct observation of the dynamics of a disease process in mouse. Additionally, we present an automated approach for detecting axonal boutons by starting with deconvolving the original images, then thresholding the enhanced images, and reserving the regions fulfilling a series of criteria. Experimental result in vivo two-photon imaging of mouse demonstrates the effectiveness of our proposed method.

Multiobjective Resource-Constrained Project Scheduling with a Time-Varying Number of Tasks

PubMed Central

Abello, Manuel Blanco

2014-01-01

In resource-constrained project scheduling (RCPS) problems, ongoing tasks are restricted to utilizing a fixed number of resources. This paper investigates a dynamic version of the RCPS problem where the number of tasks varies in time. Our previous work investigated a technique called mapping of task IDs for centroid-based approach with random immigrants (McBAR) that was used to solve the dynamic problem. However, the solution-searching ability of McBAR was investigated over only a few instances of the dynamic problem. As a consequence, only a small number of characteristics of McBAR, under the dynamics of the RCPS problem, were found. Further, only a few techniques were compared to McBAR with respect to its solution-searching ability for solving the dynamic problem. In this paper, (a) the significance of the subalgorithms of McBAR is investigated by comparing McBAR to several other techniques; and (b) the scope of investigation in the previous work is extended. In particular, McBAR is compared to a technique called, Estimation Distribution Algorithm (EDA). As with McBAR, EDA is applied to solve the dynamic problem, an application that is unique in the literature. PMID:24883398

Transient absorption microscopy studies of energy relaxation in graphene oxide thin film.

PubMed

Murphy, Sean; Huang, Libai

2013-04-10

Spatial mapping of energy relaxation in graphene oxide (GO) thin films has been imaged using transient absorption microscopy (TAM). Correlated AFM images allow us to accurately determine the thickness of the GO films. In contrast to previous studies, correlated TAM-AFM allows determination of the effect of interactions of GO with the substrate and between stacked GO layers on the relaxation dynamics. Our results show that energy relaxation in GO flakes has little dependence on the substrate, number of stacked layers, and excitation intensity. This is in direct contrast to pristine graphene, where these factors have great consequences in energy relaxation. This suggests intrinsic factors rather than extrinsic ones dominate the excited state dynamics of GO films.

Black Hole Formation in Randall-Sundrum II Braneworlds.

PubMed

Wang, Daoyan; Choptuik, Matthew W

2016-07-01

We present the first numerical study of the full dynamics of a braneworld scenario, working within the framework of the single brane model of Randall and Sundrum. In particular, we study the process of gravitational collapse driven by a massless scalar field which is confined to the brane. Imposing spherical symmetry on the brane, we show that the evolutions of sufficiently strong initial configurations of the scalar field result in black holes that have finite extension into the bulk. Furthermore, we find preliminary evidence that the black holes generated form a unique sequence, irrespective of the details of the initial data. The black hole solutions we obtain from dynamical evolutions are consistent with those previously computed from a static vacuum ansatz.

An understanding of human dynamics in urban subway traffic from the Maximum Entropy Principle

NASA Astrophysics Data System (ADS)

Yong, Nuo; Ni, Shunjiang; Shen, Shifei; Ji, Xuewei

2016-08-01

We studied the distribution of entry time interval in Beijing subway traffic by analyzing the smart card transaction data, and then deduced the probability distribution function of entry time interval based on the Maximum Entropy Principle. Both theoretical derivation and data statistics indicated that the entry time interval obeys power-law distribution with an exponential cutoff. In addition, we pointed out the constraint conditions for the distribution form and discussed how the constraints affect the distribution function. It is speculated that for bursts and heavy tails in human dynamics, when the fitted power exponent is less than 1.0, it cannot be a pure power-law distribution, but with an exponential cutoff, which may be ignored in the previous studies.

Study of Geometric Porosity on Static Stability and Drag Using Computational Fluid Dynamics for Rigid Parachute Shapes

NASA Technical Reports Server (NTRS)

Greathouse, James S.; Schwing, Alan M.

2015-01-01

This paper explores use of computational fluid dynamics to study the e?ect of geometric porosity on static stability and drag for NASA's Multi-Purpose Crew Vehicle main parachute. Both of these aerodynamic characteristics are of interest to in parachute design, and computational methods promise designers the ability to perform detailed parametric studies and other design iterations with a level of control previously unobtainable using ground or flight testing. The approach presented here uses a canopy structural analysis code to define the inflated parachute shapes on which structured computational grids are generated. These grids are used by the computational fluid dynamics code OVERFLOW and are modeled as rigid, impermeable bodies for this analysis. Comparisons to Apollo drop test data is shown as preliminary validation of the technique. Results include several parametric sweeps through design variables in order to better understand the trade between static stability and drag. Finally, designs that maximize static stability with a minimal loss in drag are suggested for further study in subscale ground and flight testing.

Childhood Obesity and Interpersonal Dynamics During Family Meals

PubMed Central

Rowley, Seth; Trofholz, Amanda; Hanson, Carrie; Rueter, Martha; MacLehose, Richard F.; Neumark-Sztainer, Dianne

2014-01-01

BACKGROUND: Family meals have been found to be associated with a number of health benefits for children; however, associations with obesity have been less consistent, which raises questions about the specific characteristics of family meals that may be protective against childhood obesity. The current study examined associations between interpersonal and food-related family dynamics at family meals and childhood obesity status. METHODS: The current mixed-methods, cross-sectional study included 120 children (47% girls; mean age: 9 years) and parents (92% women; mean age: 35 years) from low-income and minority communities. Families participated in an 8-day direct observational study in which family meals were video-recorded in their homes. Family meal characteristics (eg, length of the meal, types of foods served) were described and associations between dyadic (eg, parent-child, child-sibling) and family-level interpersonal and food-related dynamics (eg, communication, affect management, parental food control) during family meals and child weight status were examined. RESULTS: Significant associations were found between positive family- and parent-level interpersonal dynamics (ie, warmth, group enjoyment, parental positive reinforcement) at family meals and reduced risk of childhood overweight. In addition, significant associations were found between positive family- and parent-level food-related dynamics (ie, food warmth, food communication, parental food positive reinforcement) and reduced risk of childhood obesity. CONCLUSIONS: Results extend previous findings on family meals by providing a better understanding of interpersonal and food-related family dynamics at family meals by childhood weight status. Findings suggest the importance of working with families to improve the dyadic and family-level interpersonal and food-related dynamics at family meals. PMID:25311603

Dynamic light scattering study on phase separation of a protein-water mixture: Application on cold cataract development in the ocular lens

NASA Astrophysics Data System (ADS)

Petta, V.; Pharmakakis, N.; Papatheodorou, G. N.; Yannopoulos, S. N.

2008-06-01

We present a detailed dynamic light scattering study of the phase separation in the ocular lens emerging during cold cataract development. Cold cataract is a phase separation effect that proceeds via spinodal decomposition of the lens cytoplasm with cooling. The intensity autocorrelation functions of the lens protein content are analyzed with the aid of two methods, providing information on the populations and dynamics of the scattering elements associated with cold cataract. It is found that the temperature dependence of many measurable parameters changes appreciably at the characteristic temperature ˜16±1°C which is associated with the onset of cold cataract. By extending the temperature range of this work to previously inaccessible regimes, i.e., well below the phase separation or coexistence curve at Tcc , we have been able to accurately determine the temperature dependence of the collective and self-diffusion coefficients of proteins near the spinodal. The analysis showed that the dynamics of proteins bears some resemblance to the dynamics of structural glasses, where the apparent activation energy for particle diffusion increases below Tcc , indicating a highly cooperative motion. Application of ideas developed for studying the critical dynamics of binary protein-solvent mixtures, as well as the use of a modified Arrhenius equation, enabled us to estimate the spinodal temperature Tsp of the lens nucleus. The applicability of dynamic light scattering as a noninvasive, early-diagnostic tool for ocular diseases is also demonstrated in light of the findings of the present paper.

Constraining hot Jupiter’s atmospheric structure and dynamics through Doppler shifted emission spectra

NASA Astrophysics Data System (ADS)

Zhang, Jisheng; Kempton, Eliza; Rauscher, Emily

2017-01-01

In recent years, astronomers have begun successfully observing the atmospheres of extrasolar planets using ground-based telescopes equipped with spectrographs capable of observing at high spectral resolution (R~105). Such studies are capable of diagnosing the atmospheric structure, composition, and dynamics (winds and rotation) of both transiting and non-transiting exoplanets. However, few studies have examined how the 3-D atmospheric dynamics could alter the emitted light of hot Jupiters at such high spectral resolution. Here, we present a model to explore such influence on the hot Jupiters’ thermal emission spectra. Our aim is to investigate the extent to which the effects of 3-D atmospheric dynamics are imprinted on planet-averaged thermal emission spectra. We couple together a 3-D general circulation model of hot Jupiter atmospheric dynamics (Rauscher & Menou, 2012) with a radiative transfer solver to predict the planet’s disk-integrated emission spectrum as a function of its orbital phase. For the first time, we self-consistently include the effects of the line-of-sight atmospheric motions (resulting from winds and rotation) in the calculation to produce Doppler-shifted spectral line profiles that result from the atmospheric dynamics. We focus our study on three benchmark hot Jupiters, HD 189733b, HD 209458b, and WASP-43b which have been the focus of previous detailed observational studies. We find that the high-resolution Doppler shifted thermal emission spectra can be used to diagnose key properties of the dynamical atmosphere - the planet’s longitudinal temperature and wind structure, and its rotation rate.

A generalized procedure for analyzing sustained and dynamic vocal fold vibrations from laryngeal high-speed videos using phonovibrograms.

PubMed

Unger, Jakob; Schuster, Maria; Hecker, Dietmar J; Schick, Bernhard; Lohscheller, Jörg

2016-01-01

This work presents a computer-based approach to analyze the two-dimensional vocal fold dynamics of endoscopic high-speed videos, and constitutes an extension and generalization of a previously proposed wavelet-based procedure. While most approaches aim for analyzing sustained phonation conditions, the proposed method allows for a clinically adequate analysis of both dynamic as well as sustained phonation paradigms. The analysis procedure is based on a spatio-temporal visualization technique, the phonovibrogram, that facilitates the documentation of the visible laryngeal dynamics. From the phonovibrogram, a low-dimensional set of features is computed using a principle component analysis strategy that quantifies the type of vibration patterns, irregularity, lateral symmetry and synchronicity, as a function of time. Two different test bench data sets are used to validate the approach: (I) 150 healthy and pathologic subjects examined during sustained phonation. (II) 20 healthy and pathologic subjects that were examined twice: during sustained phonation and a glissando from a low to a higher fundamental frequency. In order to assess the discriminative power of the extracted features, a Support Vector Machine is trained to distinguish between physiologic and pathologic vibrations. The results for sustained phonation sequences are compared to the previous approach. Finally, the classification performance of the stationary analyzing procedure is compared to the transient analysis of the glissando maneuver. For the first test bench the proposed procedure outperformed the previous approach (proposed feature set: accuracy: 91.3%, sensitivity: 80%, specificity: 97%, previous approach: accuracy: 89.3%, sensitivity: 76%, specificity: 96%). Comparing the classification performance of the second test bench further corroborates that analyzing transient paradigms provides clear additional diagnostic value (glissando maneuver: accuracy: 90%, sensitivity: 100%, specificity: 80%, sustained phonation: accuracy: 75%, sensitivity: 80%, specificity: 70%). The incorporation of parameters describing the temporal evolvement of vocal fold vibration clearly improves the automatic identification of pathologic vibration patterns. Furthermore, incorporating a dynamic phonation paradigm provides additional valuable information about the underlying laryngeal dynamics that cannot be derived from sustained conditions. The proposed generalized approach provides a better overall classification performance than the previous approach, and hence constitutes a new advantageous tool for an improved clinical diagnosis of voice disorders. Copyright © 2015 Elsevier B.V. All rights reserved.

The Complexity of Dynamics in Small Neural Circuits

PubMed Central

Panzeri, Stefano

2016-01-01

Mean-field approximations are a powerful tool for studying large neural networks. However, they do not describe well the behavior of networks composed of a small number of neurons. In this case, major differences between the mean-field approximation and the real behavior of the network can arise. Yet, many interesting problems in neuroscience involve the study of mesoscopic networks composed of a few tens of neurons. Nonetheless, mathematical methods that correctly describe networks of small size are still rare, and this prevents us to make progress in understanding neural dynamics at these intermediate scales. Here we develop a novel systematic analysis of the dynamics of arbitrarily small networks composed of homogeneous populations of excitatory and inhibitory firing-rate neurons. We study the local bifurcations of their neural activity with an approach that is largely analytically tractable, and we numerically determine the global bifurcations. We find that for strong inhibition these networks give rise to very complex dynamics, caused by the formation of multiple branching solutions of the neural dynamics equations that emerge through spontaneous symmetry-breaking. This qualitative change of the neural dynamics is a finite-size effect of the network, that reveals qualitative and previously unexplored differences between mesoscopic cortical circuits and their mean-field approximation. The most important consequence of spontaneous symmetry-breaking is the ability of mesoscopic networks to regulate their degree of functional heterogeneity, which is thought to help reducing the detrimental effect of noise correlations on cortical information processing. PMID:27494737

Quantifying Factors That Impact Riverbed Dynamic Permeability at a Riverbank Filtration Facility

NASA Astrophysics Data System (ADS)

Ulrich, C.; Hubbard, S. S.; Florsheim, J. L.; Rosenberry, D. O.; Borglin, S. E.; Zhang, Y.; Seymour, D.; Trotta, M.

2012-12-01

Previous modeling studies of the Wohler riverbank filtration system on the Russian River, California suggested that riverbed and aquifer permeability both influence the development of a pumping-induced unsaturated zone below the riverbed, which affects water produced through large radial water-supply collector wells that extend beneath and adjacent to the river. In particular, previous work suggests that riverbed permeability is influenced by interaction between pumping and river stage that is controlled by a downstream temporary inflatable dam during the summer low flow period. We hypothesize that raising the dam may instead lead to deposition of fine-grained sediment and/or accumulation of biota, both of which decrease riverbed permeability in the vicinity of the collector wells. To test this hypothesis, we are monitoring streambed permeability and seepage as a function of river stage and dam operation. We are using multiple methods to monitor the hydrological, sedimentological and geomorphic dynamics, including: seepage meters, sediment traps, cryogenic coring, ground penetrating radar, electrical resistance tomography, riverbed topography, piezometers, and thermistors. Here we discuss the use of this novel suite of methods to quantify dynamic riverbed permeability, how it relates to dam operation, and determine the key controls on permeability (i.e., biotic or abiotic). These results are expected to improve the overall understanding of riverbed permeability dynamics associated with Riverbank filtration. The results are also expected to be transferable to the project sponsors, the Sonoma County Water Agency, toward the development of an optimal pumping and dam operation schedule.

The diffusion dynamics of PEGylated liposomes in the intact vitreous of the ex vivo porcine eye: A fluorescence correlation spectroscopy and biodistribution study.

PubMed

Eriksen, Anne Z; Brewer, Jonathan; Andresen, Thomas L; Urquhart, Andrew J

2017-04-30

The diffusion dynamics of nanocarriers in the vitreous and the influence of nanocarrier physicochemical properties on these dynamics is an important aspect of the efficacy of intravitreal administered nanomedicines for the treatment of posterior segment eye diseases. Here we use fluorescence correlation spectroscopy (FCS) to determine liposome diffusion coefficients in the intact vitreous (D Vit ) of ex vivo porcine eyes using a modified Miyake-Apple technique to minimize the disruption of the vitreous fine structure. We chose to investigate whether the zeta potential of polyethylene glycol functionalized (i.e. PEGylated) liposomes altered liposome in situ diffusion dynamics in the vitreous. Non-PEGylated cationic nanocarriers have previously shown little to no diffusion in the vitreous, whilst neutral and anionic have shown diffusion. The liposomes investigated had diameters below 150nm and zeta potentials ranging from -20 to +12mV. We observed that PEGylated cationic liposomes had significantly lower D Vit values (1.14μm 2 s -1 ) than PEGylated neutral and anionic liposomes (2.78 and 2.87μm 2 s -1 ). However, PEGylated cationic liposomes had a similar biodistribution profile across the vitreous to the other systems. These results show that PEGylated cationic liposomes with limited cationic charge can diffuse across the vitreous and indicate that the vitreous as a barrier to nanocarriers (Ø<500nm) is more complicated than simply an electrostatic barrier as previously suggested. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of resource quality on the population dynamics of the Indian meal moth Plodia interpunctella and its granulovirus.

PubMed

McVean, Ross I; Sait, Steve M; Thompson, David J; Begon, Mike

2002-03-01

Although the Plodia interpunctella-granulovirus system is one of the most studied models for insect-pathogen interactions, there are relatively few precise data on the dynamics of the virus in coexisting populations of these two organisms. Previous work has suggested that resource quality, in terms of the diet supplied to P. interpunctella, has a strong effect on the population dynamics of host and pathogen. Here we investigate the impact of resource-dependent host patterns of abundance on pathogen dynamics and prevalence. In the laboratory, three populations of P. interpunctella feeding on a good quality food and infected with a granulovirus were compared with three populations also infected with a granulovirus but feeding on poor quality food. Populations feeding on good quality food produced larger adult moths, and had greater numbers of adult moths, healthy larvae, and virus-infected larvae. A higher proportion of larvae in these good quality populations were infected with virus, and adult moths exhibited cyclic fluctuations in abundance, unlike those on poor quality food. This cyclic behaviour was shown to be associated with cycles in the age structure of the larval population. Previous theoretical work suggests that these cycles may result from asymmetric competition between young and old larvae. Cyclic fluctuations in the proportion of infected larvae, that occurred on good, but not on poor quality food, were also shown to be related to cycles in the age structure of the larval population.

Heuristic reusable dynamic programming: efficient updates of local sequence alignment.

PubMed

Hong, Changjin; Tewfik, Ahmed H

2009-01-01

Recomputation of the previously evaluated similarity results between biological sequences becomes inevitable when researchers realize errors in their sequenced data or when the researchers have to compare nearly similar sequences, e.g., in a family of proteins. We present an efficient scheme for updating local sequence alignments with an affine gap model. In principle, using the previous matching result between two amino acid sequences, we perform a forward-backward alignment to generate heuristic searching bands which are bounded by a set of suboptimal paths. Given a correctly updated sequence, we initially predict a new score of the alignment path for each contour to select the best candidates among them. Then, we run the Smith-Waterman algorithm in this confined space. Furthermore, our heuristic alignment for an updated sequence shows that it can be further accelerated by using reusable dynamic programming (rDP), our prior work. In this study, we successfully validate "relative node tolerance bound" (RNTB) in the pruned searching space. Furthermore, we improve the computational performance by quantifying the successful RNTB tolerance probability and switch to rDP on perturbation-resilient columns only. In our searching space derived by a threshold value of 90 percent of the optimal alignment score, we find that 98.3 percent of contours contain correctly updated paths. We also find that our method consumes only 25.36 percent of the runtime cost of sparse dynamic programming (sDP) method, and to only 2.55 percent of that of a normal dynamic programming with the Smith-Waterman algorithm.

Teasing apart the anticipatory and consummatory processing of monetary incentives: An event-related potential study of reward dynamics.

PubMed

Novak, Keisha D; Foti, Dan

2015-11-01

The monetary incentive delay (MID) task has been widely used in fMRI studies to investigate the neural networks involved in anticipatory and consummatory reward processing. Previous efforts to adapt the MID task for use with ERPs, however, have had limited success. Here, we sought to further decompose reward dynamics using a comprehensive set of anticipatory (cue-N2, cue-P3, contingent negative variation [CNV]) and consummatory ERPs (feedback negativity [FN], feedback P3 [fb-P3]). ERP data was recorded during adapted versions of the MID task across two experiments. Unlike previous studies, monetary incentive cues modulated the cue-N2, cue-P3, and CNV; however, cue-related ERPs and the CNV were uncorrelated with one another, indicating distinct anticipatory subprocesses. With regard to consummatory processing, FN amplitude primarily tracked outcome valence (reward vs. nonreward), whereas fb-P3 amplitude primarily tracked outcome salience (uncertain vs. certain). Independent modulation of the cue-P3 and fb-P3 was observed, indicating that these two P3 responses may uniquely capture the allocation of attention during anticipatory and consummatory reward processing, respectively. Overall, across two samples, consistent evidence of both anticipatory and consummatory ERP activity was observed on an adapted version of the MID paradigm, demonstrating for the first time how these ERP components may be integrated with one another to more fully characterize the time course of reward processing. This ERP-MID paradigm is well suited to parsing reward dynamics, and can be applied to both healthy and clinical populations. © 2015 Society for Psychophysiological Research.

Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel

PubMed Central

Liang, Ruibin; Li, Hui; Swanson, Jessica M. J.; Voth, Gregory A.

2014-01-01

The influenza A virus M2 channel (AM2) is crucial in the viral life cycle. Despite many previous experimental and computational studies, the mechanism of the activating process in which proton permeation acidifies the virion to release the viral RNA and core proteins is not well understood. Herein the AM2 proton permeation process has been systematically characterized using multiscale computer simulations, including quantum, classical, and reactive molecular dynamics methods. We report, to our knowledge, the first complete free-energy profiles for proton transport through the entire AM2 transmembrane domain at various pH values, including explicit treatment of excess proton charge delocalization and shuttling through the His37 tetrad. The free-energy profiles reveal that the excess proton must overcome a large free-energy barrier to diffuse to the His37 tetrad, where it is stabilized in a deep minimum reflecting the delocalization of the excess charge among the histidines and the cost of shuttling the proton past them. At lower pH values the His37 tetrad has a larger total charge that increases the channel width, hydration, and solvent dynamics, in agreement with recent 2D-IR spectroscopic studies. The proton transport barrier becomes smaller, despite the increased charge repulsion, due to backbone expansion and the more dynamic pore water molecules. The calculated conductances are in quantitative agreement with recent experimental measurements. In addition, the free-energy profiles and conductances for proton transport in several mutants provide insights for explaining our findings and those of previous experimental mutagenesis studies. PMID:24979779

Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel.

PubMed

Liang, Ruibin; Li, Hui; Swanson, Jessica M J; Voth, Gregory A

2014-07-01

The influenza A virus M2 channel (AM2) is crucial in the viral life cycle. Despite many previous experimental and computational studies, the mechanism of the activating process in which proton permeation acidifies the virion to release the viral RNA and core proteins is not well understood. Herein the AM2 proton permeation process has been systematically characterized using multiscale computer simulations, including quantum, classical, and reactive molecular dynamics methods. We report, to our knowledge, the first complete free-energy profiles for proton transport through the entire AM2 transmembrane domain at various pH values, including explicit treatment of excess proton charge delocalization and shuttling through the His37 tetrad. The free-energy profiles reveal that the excess proton must overcome a large free-energy barrier to diffuse to the His37 tetrad, where it is stabilized in a deep minimum reflecting the delocalization of the excess charge among the histidines and the cost of shuttling the proton past them. At lower pH values the His37 tetrad has a larger total charge that increases the channel width, hydration, and solvent dynamics, in agreement with recent 2D-IR spectroscopic studies. The proton transport barrier becomes smaller, despite the increased charge repulsion, due to backbone expansion and the more dynamic pore water molecules. The calculated conductances are in quantitative agreement with recent experimental measurements. In addition, the free-energy profiles and conductances for proton transport in several mutants provide insights for explaining our findings and those of previous experimental mutagenesis studies.

Computational Investigation of Cerebrospinal Fluid Dynamics in the Posterior Cranial Fossa and Cervical Subarachnoid Space in Patients with Chiari I Malformation.

PubMed

Støverud, Karen-Helene; Langtangen, Hans Petter; Ringstad, Geir Andre; Eide, Per Kristian; Mardal, Kent-Andre

2016-01-01

Previous computational fluid dynamics (CFD) studies have demonstrated that the Chiari malformation is associated with abnormal cerebrospinal fluid (CSF) flow in the cervical part of the subarachnoid space (SAS), but the flow in the SAS of the posterior cranial fossa has received little attention. This study extends previous modelling efforts by including the cerebellomedullary cistern, pontine cistern, and 4th ventricle in addition to the cervical subarachnoid space. The study included one healthy control, Con1, and two patients with Chiari I malformation, P1 and P2. Meshes were constructed by segmenting images obtained from T2-weighted turbo spin-echo sequences. CFD simulations were performed with a previously verified and validated code. Patient-specific flow conditions in the aqueduct and the cervical SAS were used. Two patients with the Chiari malformation and one control were modelled. The results demonstrated increased maximal flow velocities in the Chiari patients, ranging from factor 5 in P1 to 14.8 in P2, when compared to Con1 at the level of Foramen Magnum (FM). Maximal velocities in the cervical SAS varied by a factor 2.3, while the maximal flow in the aqueduct varied by a factor 3.5. The pressure drop from the pontine cistern to the cervical SAS was similar in Con1 and P1, but a factor two higher in P2. The pressure drop between the aqueduct and the cervical SAS varied by a factor 9.4 where P1 was the one with the lowest pressure jump and P2 and Con1 differed only by a factor 1.6. This pilot study demonstrates that including the posterior cranial fossa is feasible and suggests that previously found flow differences between Chiari I patients and healthy individuals in the cervical SAS may be present also in the SAS of the posterior cranial fossa.

Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis

PubMed Central

Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D

2014-01-01

Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent interactions with nearby structural elements. PMID:24403092

Long-term monitoring of glacier dynamics of Fleming Glacier after the disintegration of Wordie Ice Shelf, Antarctic Peninsula

NASA Astrophysics Data System (ADS)

Friedl, Peter; Seehaus, Thorsten; Wendt, Anja; Braun, Matthias

2017-04-01

The Antarctic Peninsula is one of the world`s most affected regions by Climate Change. Dense and long time series of remote sensing data enable detailed studies of the rapid glaciological changes in this area. We present results of a study on Fleming Glacier, which was the major tributary glacier of former Wordie Ice Shelf, located at the south-western side of the Antarctic Peninsula. Since the ice shelf disintegrated in a series of events starting in the 1970s, only disconnected tidewater glaciers have remained today. As a reaction to the loss of the buttressing force of the ice shelf, Fleming Glacier accelerated and dynamically thinned. However, all previous studies conducted at Wordie Bay covered only relatively short investigation periods and ended in 2008 the latest. Hence it was not well known how long the process of adaption to the changing boundary conditions exactly lasts and how it is characterized in detail. We provide long time series (1994 - 2016) of glaciological parameters (i.e. ice extent, velocity, grounding line position, ice elevation) for Fleming Glacier obtained from multi-mission remote sensing data. For this purpose large datasets of previously active (e.g. ERS, Envisat, ALOS PALSAR, Radarsat-1) as well as currently recording SAR sensors (e.g. Sentinel-1, TerraSAR-X, TanDEM-X) were processed and combined with data from other sources (e.g. optical images, laser altimeter and ice thickness data). The high temporal resolution of our dataset enables us to present a detailed history of 22 years of glacial dynamics at Fleming Glacier after the disintegration of Wordie Ice Shelf. We found strong evidence for a rapid grounding line retreat of up to 13 km between 2008 and 2011, which led to a further amplification of dynamic ice thinning. Today Fleming Glacier seems to be far away from approaching a new equilibrium. Our data show that the current glacier dynamics of Fleming Glacier are not primarily controlled by the loss of the ice shelf anymore, but by other sources of external forcing, such as oceanic warming.

Fine-scale analysis of genetic structure in the brooding coral Seriatopora hystrix from the Red Sea

NASA Astrophysics Data System (ADS)

Maier, E.; Tollrian, R.; Nürnberger, B.

2009-09-01

The dispersal of gametes and larvae plays a key role in the population dynamics of sessile marine invertebrates. Species with internal fertilisation are often associated with very localised larval dispersal, which may cause small-scale patterns of neutral genetic variation. This study on the brooding coral Seriatopora hystrix from the Red Sea focused on the smallest possible scale: Two S. hystrix stands (~100 colonies each) near Dahab were completely sampled, mapped and analysed at five microsatellite markers. The sexual mode of reproduction, the likely occurrence of selfing and the level of immigration were in agreement with previous studies on this species. Contrary to previous findings, both stands were in Hardy-Weinberg proportions. Also, no evidence for spatially restricted larval dispersal within the sampled areas was found. Differences between this and previous studies on S. hystrix could reflect variation in life history or varying environmental conditions, which opens intriguing questions for future research.

On-line implementation of nonlinear parameter estimation for the Space Shuttle main engine

NASA Technical Reports Server (NTRS)

Buckland, Julia H.; Musgrave, Jeffrey L.; Walker, Bruce K.

1992-01-01

We investigate the performance of a nonlinear estimation scheme applied to the estimation of several parameters in a performance model of the Space Shuttle Main Engine. The nonlinear estimator is based upon the extended Kalman filter which has been augmented to provide estimates of several key performance variables. The estimated parameters are directly related to the efficiency of both the low pressure and high pressure fuel turbopumps. Decreases in the parameter estimates may be interpreted as degradations in turbine and/or pump efficiencies which can be useful measures for an online health monitoring algorithm. This paper extends previous work which has focused on off-line parameter estimation by investigating the filter's on-line potential from a computational standpoint. ln addition, we examine the robustness of the algorithm to unmodeled dynamics. The filter uses a reduced-order model of the engine that includes only fuel-side dynamics. The on-line results produced during this study are comparable to off-line results generated previously. The results show that the parameter estimates are sensitive to dynamics not included in the filter model. Off-line results using an extended Kalman filter with a full order engine model to address the robustness problems of the reduced-order model are also presented.

The relationship between crystal structure and methyl and t-butyl group dynamics in van der Waals organic solids

NASA Astrophysics Data System (ADS)

Beckmann, Peter A.; Paty, Carol; Allocco, Elizabeth; Herd, Maria; Kuranz, Carolyn; Rheingold, Arnold L.

2004-03-01

We report x-ray diffractometry in a single crystal of 2-t-butyl-4-methylphenol (TMP) and low-frequency solid state nuclear magnetic resonance (NMR) proton relaxometry in a polycrystalline sample of TMP. The x-ray data show TMP to have a monoclinic, P21/c, structure with eight molecules per unit cell and two crystallographically inequivalent t-butyl group (C(CH3)3) sites. The proton spin-lattice relaxation rates were measured between 90 and 310 K at NMR frequencies of 8.50, 22.5, and 53.0 MHz. The relaxometry data is fitted with two models characterizing the dynamics of the t-butyl groups and their constituent methyl groups, both of which are consistent with the determined x-ray structure. In addition to presenting results for TMP, we review previously reported x-ray diffractometry and low-frequency NMR relaxometry in two other van der Waals solids which have a simpler structure. In both cases, a unique model for the reorientational dynamics was found. Finally, we review a similar previously reported analysis in a van der Waals solid with a very complex structure in which case fitting the NMR relaxometry requires very many parameters and serves mainly as a flag for a careful x-ray diffraction study.

Dynamic stability during running gait termination: Predictors for successful control of forward momentum in children and adults.

PubMed

Cesar, Guilherme M; Sigward, Susan M

2016-08-01

Reported differences between children and adults with respect to COM horizontal and vertical position to maintain dynamic stability during running deceleration suggest that this relationship may not be as important in children. This study challenged the current dynamic stability paradigm by determining the features of whole body posture that predicted forward velocity and momentum of running gait termination in adults and children. Sixteen adults and 15 children ran as fast as possible and stopped at pre-determined location. Separate regression analyses determined whether COM posterior and vertical positions and functional limb length (distance between COM and stance foot) predicted velocity and momentum for adults and children. COM posterior position was the strongest predictor of forward velocity and momentum in both groups supporting the previously established relationship during slower tasks. COM vertical position also predicted momentum in children, not adults. Higher COM position in children was related to greater momentum; consistent with previously reported differences between children and adults in COM position across running deceleration. COM vertical position was related to momentum but not velocity in children suggesting that strategies used to terminate running may be driven by demands imposed not just by velocity, but also the mass being decelerated. Copyright © 2016. Published by Elsevier B.V.

Osmolyte cooperation affects turgor dynamics in plants

NASA Astrophysics Data System (ADS)

Argiolas, Alfredo; Puleo, Gian Luigi; Sinibaldi, Edoardo; Mazzolai, Barbara

2016-07-01

Scientists have identified turgor-based actuation as a fundamental mechanism in plant movements. Plant cell turgor is generated by water influx due to the osmolyte concentration gradient through the cell wall and the plasma membrane behaving as an osmotic barrier. Previous studies have focused on turgor modulation with respect to potassium chloride (KCl) concentration changes, although KCl is not efficiently retained in the cell, and many other compounds, including L-glutamine (L-Gln) and D-glucose (D-Glc), are present in the cytosol. In fact, the contributions of other osmolytes to turgor dynamics remain to be elucidated. Here, we show the association of osmolytes and their consequent cooperative effects on the time-dependent turgor profile generated in a model cytosol consisting of KCl, D-Glc and L-Gln at experimentally measured plant motor/generic cell concentrations and at modified concentrations. We demonstrate the influence and association of the osmolytes using osmometry and NMR measurements. We also show, using a plant cell-inspired device we previously developed, that osmolyte complexes, rather than single osmolytes, permit to obtain higher turgor required by plant movements. We provide quantitative cues for deeper investigations of osmolyte transport for plant movement, and reveal the possibility of developing osmotic actuators exploiting a dynamically varying concentration of osmolytes.

Osmolyte cooperation affects turgor dynamics in plants.

PubMed

Argiolas, Alfredo; Puleo, Gian Luigi; Sinibaldi, Edoardo; Mazzolai, Barbara

2016-07-22

Scientists have identified turgor-based actuation as a fundamental mechanism in plant movements. Plant cell turgor is generated by water influx due to the osmolyte concentration gradient through the cell wall and the plasma membrane behaving as an osmotic barrier. Previous studies have focused on turgor modulation with respect to potassium chloride (KCl) concentration changes, although KCl is not efficiently retained in the cell, and many other compounds, including L-glutamine (L-Gln) and D-glucose (D-Glc), are present in the cytosol. In fact, the contributions of other osmolytes to turgor dynamics remain to be elucidated. Here, we show the association of osmolytes and their consequent cooperative effects on the time-dependent turgor profile generated in a model cytosol consisting of KCl, D-Glc and L-Gln at experimentally measured plant motor/generic cell concentrations and at modified concentrations. We demonstrate the influence and association of the osmolytes using osmometry and NMR measurements. We also show, using a plant cell-inspired device we previously developed, that osmolyte complexes, rather than single osmolytes, permit to obtain higher turgor required by plant movements. We provide quantitative cues for deeper investigations of osmolyte transport for plant movement, and reveal the possibility of developing osmotic actuators exploiting a dynamically varying concentration of osmolytes.

Osmolyte cooperation affects turgor dynamics in plants

PubMed Central

Argiolas, Alfredo; Puleo, Gian Luigi; Sinibaldi, Edoardo; Mazzolai, Barbara

2016-01-01

Scientists have identified turgor-based actuation as a fundamental mechanism in plant movements. Plant cell turgor is generated by water influx due to the osmolyte concentration gradient through the cell wall and the plasma membrane behaving as an osmotic barrier. Previous studies have focused on turgor modulation with respect to potassium chloride (KCl) concentration changes, although KCl is not efficiently retained in the cell, and many other compounds, including L-glutamine (L-Gln) and D-glucose (D-Glc), are present in the cytosol. In fact, the contributions of other osmolytes to turgor dynamics remain to be elucidated. Here, we show the association of osmolytes and their consequent cooperative effects on the time-dependent turgor profile generated in a model cytosol consisting of KCl, D-Glc and L-Gln at experimentally measured plant motor/generic cell concentrations and at modified concentrations. We demonstrate the influence and association of the osmolytes using osmometry and NMR measurements. We also show, using a plant cell-inspired device we previously developed, that osmolyte complexes, rather than single osmolytes, permit to obtain higher turgor required by plant movements. We provide quantitative cues for deeper investigations of osmolyte transport for plant movement, and reveal the possibility of developing osmotic actuators exploiting a dynamically varying concentration of osmolytes. PMID:27445173

Longitudinal Study of the Six Degrees of Freedom Cervical Spine Range of Motion During Dynamic Flexion, Extension, and Rotation After Single-level Anterior Arthrodesis.

PubMed

Anderst, William J; West, Tyler; Donaldson, William F; Lee, Joon Y; Kang, James D

2016-11-15

A longitudinal study using biplane radiography to measure in vivo intervertebral range of motion (ROM) during dynamic flexion/extension, and rotation. To longitudinally compare intervertebral maximal ROM and midrange motion in asymptomatic control subjects and single-level arthrodesis patients. In vitro studies consistently report that adjacent segment maximal ROM increases superior and inferior to cervical arthrodesis. Previous in vivo results have been conflicting, indicating that maximal ROM may or may not increase superior and/or inferior to the arthrodesis. There are no previous reports of midrange motion in arthrodesis patients and similar-aged controls. Eight single-level (C5/C6) anterior arthrodesis patients (tested 7 ± 1 months and 28 ± 6 months postsurgery) and six asymptomatic control subjects (tested twice, 58 ± 6 months apart) performed dynamic full ROM flexion/extension and axial rotation whereas biplane radiographs were collected at 30 images per second. A previously validated tracking process determined three-dimensional vertebral position from each pair of radiographs with submillimeter accuracy. The intervertebral maximal ROM and midrange motion in flexion/extension, rotation, lateral bending, and anterior-posterior translation were compared between test dates and between groups. Adjacent segment maximal ROM did not increase over time during flexion/extension, or rotation movements. Adjacent segment maximal rotational ROM was not significantly greater in arthrodesis patients than in corresponding motion segments of similar-aged controls. C4/C5 adjacent segment rotation during the midrange of head motion and maximal anterior-posterior translation were significantly greater in arthrodesis patients than in the corresponding motion segment in controls on the second test date. C5/C6 arthrodesis appears to significantly affect midrange, but not end-range, adjacent segment motions. The effects of arthrodesis on adjacent segment motion may be best evaluated by longitudinal studies that compare maximal and midrange adjacent segment motion to corresponding motion segments of similar-aged controls to determine if the adjacent segment motion is truly excessive. 3.

Optimization of multi-stage dynamic treatment regimes utilizing accumulated data.

PubMed

Huang, Xuelin; Choi, Sangbum; Wang, Lu; Thall, Peter F

2015-11-20

In medical therapies involving multiple stages, a physician's choice of a subject's treatment at each stage depends on the subject's history of previous treatments and outcomes. The sequence of decisions is known as a dynamic treatment regime or treatment policy. We consider dynamic treatment regimes in settings where each subject's final outcome can be defined as the sum of longitudinally observed values, each corresponding to a stage of the regime. Q-learning, which is a backward induction method, is used to first optimize the last stage treatment then sequentially optimize each previous stage treatment until the first stage treatment is optimized. During this process, model-based expectations of outcomes of late stages are used in the optimization of earlier stages. When the outcome models are misspecified, bias can accumulate from stage to stage and become severe, especially when the number of treatment stages is large. We demonstrate that a modification of standard Q-learning can help reduce the accumulated bias. We provide a computational algorithm, estimators, and closed-form variance formulas. Simulation studies show that the modified Q-learning method has a higher probability of identifying the optimal treatment regime even in settings with misspecified models for outcomes. It is applied to identify optimal treatment regimes in a study for advanced prostate cancer and to estimate and compare the final mean rewards of all the possible discrete two-stage treatment sequences. Copyright © 2015 John Wiley & Sons, Ltd.

Live-cell and super-resolution imaging reveal that the distribution of wall-associated protein A is correlated with the cell chain integrity of Streptococcus mutans.

PubMed

Li, Y; Liu, Z; Zhang, Y; Su, Q P; Xue, B; Shao, S; Zhu, Y; Xu, X; Wei, S; Sun, Y

2015-10-01

Streptococcus mutans is a primary pathogen responsible for dental caries. It has an outstanding ability to form biofilm, which is vital for virulence. Previous studies have shown that knockout of Wall-associated protein A (WapA) affects cell chain and biofilm formation of S. mutans. As a surface protein, the distribution of WapA remains unknown, but it is important to understand the mechanism underlying the function of WapA. This study applied the fluorescence protein mCherry as a reporter gene to characterize the dynamic distribution of WapA in S. mutans via time-lapse and super-resolution fluorescence imaging. The results revealed interesting subcellular distribution patterns of WapA in single, dividing and long chains of S. mutans cells. It appears at the middle of the cell and moves to the poles as the cell grows and divides. In a cell chain, after each round of cell division, such dynamic relocation results in WapA distribution at the previous cell division sites, resulting in a pattern where WapA is located at the boundary of two adjacent cell pairs. This WapA distribution pattern corresponds to the breaking segmentation of wapA deletion cell chains. The dynamic relocation of WapA through the cell cycle increases our understanding of the mechanism of WapA in maintaining cell chain integrity and biofilm formation. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Precipitation Dynamical Downscaling Over the Great Plains

NASA Astrophysics Data System (ADS)

Hu, Xiao-Ming; Xue, Ming; McPherson, Renee A.; Martin, Elinor; Rosendahl, Derek H.; Qiao, Lei

2018-02-01

Detailed, regional climate projections, particularly for precipitation, are critical for many applications. Accurate precipitation downscaling in the United States Great Plains remains a great challenge for most Regional Climate Models, particularly for warm months. Most previous dynamic downscaling simulations significantly underestimate warm-season precipitation in the region. This study aims to achieve a better precipitation downscaling in the Great Plains with the Weather Research and Forecast (WRF) model. To this end, WRF simulations with different physics schemes and nudging strategies are first conducted for a representative warm season. Results show that different cumulus schemes lead to more pronounced difference in simulated precipitation than other tested physics schemes. Simply choosing different physics schemes is not enough to alleviate the dry bias over the southern Great Plains, which is related to an anticyclonic circulation anomaly over the central and western parts of continental U.S. in the simulations. Spectral nudging emerges as an effective solution for alleviating the precipitation bias. Spectral nudging ensures that large and synoptic-scale circulations are faithfully reproduced while still allowing WRF to develop small-scale dynamics, thus effectively suppressing the large-scale circulation anomaly in the downscaling. As a result, a better precipitation downscaling is achieved. With the carefully validated configurations, WRF downscaling is conducted for 1980-2015. The downscaling captures well the spatial distribution of monthly climatology precipitation and the monthly/yearly variability, showing improvement over at least two previously published precipitation downscaling studies. With the improved precipitation downscaling, a better hydrological simulation over the trans-state Oologah watershed is also achieved.

Early Warning Signals for Regime Transition in the Stable Boundary Layer: A Model Study

NASA Astrophysics Data System (ADS)

van Hooijdonk, I. G. S.; Moene, A. F.; Scheffer, M.; Clercx, H. J. H.; van de Wiel, B. J. H.

2017-02-01

The evening transition is investigated in an idealized model for the nocturnal boundary layer. From earlier studies it is known that the nocturnal boundary layer may manifest itself in two distinct regimes, depending on the ambient synoptic conditions: strong-wind or overcast conditions typically lead to weakly stable, turbulent nights; clear-sky and weak-wind conditions, on the other hand, lead to very stable, weakly turbulent conditions. Previously, the dynamical behaviour near the transition between these regimes was investigated in an idealized setting, relying on Monin-Obukhov (MO) similarity to describe turbulent transport. Here, we investigate a similar set-up, using direct numerical simulation; in contrast to MO-based models, this type of simulation does not need to rely on turbulence closure assumptions. We show that previous predictions are verified, but now independent of turbulence parametrizations. Also, it appears that a regime shift to the very stable state is signaled in advance by specific changes in the dynamics of the turbulent boundary layer. Here, we show how these changes may be used to infer a quantitative estimate of the transition point from the weakly stable boundary layer to the very stable boundary layer. In addition, it is shown that the idealized, nocturnal boundary-layer system shares important similarities with generic non-linear dynamical systems that exhibit critical transitions. Therefore, the presence of other, generic early warning signals is tested as well. Indeed, indications are found that such signals are present in stably stratified turbulent flows.

Modeling the Complexity of Post-Treatment Drinking: It’s a Rocky Road to Relapse

PubMed Central

Witkiewitz, Katie; Marlatt, G. Alan

2007-01-01

The most widely cited road block to successful treatment outcomes for psychological and substance use disorders has been described as the return to the previous behavior, or “relapse.” The operational definition of “relapse” varies from study to study and between clinicians, but in general the term is used to indicate the return to previous levels of symptomatic behavior. One explanation for the variation in the operationalization of relapse is the wide variety of behaviors for which the term is applied, including (but not limited to): depression, substance abuse, schizophrenia, mania, sexual offending, risky sexual behavior, dieting, and the anxiety disorders. A second explanation for the multitude of definitions for relapse is the inherent complexity in the process of behavior change. In this paper we present the most recent treatment outcome research evaluating relapse rates, with a special focus on the substance use disorders. Following this review of the literature we present an argument for the operationalization of relapse as a dynamic process, which can be empirically characterized using dynamical systems theory. We support this argument by presenting results from the analysis of alcohol treatment outcomes using catastrophe modeling techniques. These results demonstrate the utility of catastrophe theory in modeling the alcohol relapse process. The implications of these analyses for the treatment of alcohol use disorders, as well as a discussion of future research incorporating nonlinear dynamical systems theory is provided. PMID:17355897

Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA

PubMed Central

Muniyappa, Kalappa; Yan, Jie

2013-01-01

The RecA filament formed on double-stranded (ds) DNA is proposed to be a functional state analogous to that generated during the process of DNA strand exchange. RecA polymerization and de-polymerization on dsDNA is governed by multiple physiological factors. However, a comprehensive understanding of how these factors regulate the processes of polymerization and de-polymerization of RecA filament on dsDNA is still evolving. Here, we investigate the effects of temperature, pH, tensile force, and DNA ends (in particular ssDNA overhang) on the polymerization and de-polymerization dynamics of the E. coli RecA filament at a single-molecule level. Our results identified the optimal conditions that permitted spontaneous RecA nucleation and polymerization, as well as conditions that could maintain the stability of a preformed RecA filament. Further examination at a nano-meter spatial resolution, by stretching short DNA constructs, revealed a striking dynamic RecA polymerization and de-polymerization induced saw-tooth pattern in DNA extension fluctuation. In addition, we show that RecA does not polymerize on S-DNA, a recently identified novel base-paired elongated DNA structure that was previously proposed to be a possible binding substrate for RecA. Overall, our studies have helped to resolve several previous single-molecule studies that reported contradictory and inconsistent results on RecA nucleation, polymerization and stability. Furthermore, our findings also provide insights into the regulatory mechanisms of RecA filament formation and stability in vivo. PMID:23825559

Activation induced changes in GABA: Functional MRS at 7T with MEGA-sLASER.

PubMed

Chen, Chen; Sigurdsson, Hilmar P; Pépés, Sophia E; Auer, Dorothee P; Morris, Peter G; Morgan, Paul S; Gowland, Penny A; Jackson, Stephen R

2017-08-01

Functional magnetic resonance spectroscopy (fMRS) has been used to assess the dynamic metabolic responses of the brain to a physiological stimulus non-invasively. However, only limited information on the dynamic functional response of γ-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the brain, is available. We aimed to measure the activation-induced changes in GABA unambiguously using a spectral editing method, instead of the conventional direct detection techniques used in previous fMRS studies. The Mescher-Garwood-semi-localised by adiabatic selective refocusing (MEGA-sLASER) sequence was developed at 7T to obtain the time course of GABA concentration without macromolecular contamination. A significant decrease (-12±5%) in the GABA to total creatine ratio (GABA/tCr) was observed in the motor cortex during a period of 10min of hand-clenching, compared to an initial baseline level (GABA/tCr =0.11±0.02) at rest. An increase in the Glx (glutamate and glutamine) to tCr ratio was also found, which is in agreement with previous findings. In contrast, no significant changes in NAA/tCr and tCr were detected. With consistent and highly efficient editing performance for GABA detection and the advantage of visually identifying GABA resonances in the spectra, MEGA-sLASER is demonstrated to be an effective method for studying of dynamic changes in GABA at 7T. Copyright © 2017 Elsevier Inc. All rights reserved.

Testing the generality of a trophic-cascade model for plague

USGS Publications Warehouse

Collinge, S.K.; Johnson, W.C.; Ray, C.; Matchett, R.; Grensten, J.; Cully, J.F.; Gage, K.L.; Kosoy, M.Y.; Loye, J.E.; Martin, A.P.

2005-01-01

Climate may affect the dynamics of infectious diseases by shifting pathogen, vector, or host species abundance, population dynamics, or community interactions. Black-tailed prairie dogs (Cynomys ludovicianus) are highly susceptible to plague, yet little is known about factors that influence the dynamics of plague epizootics in prairie dogs. We investigated temporal patterns of plague occurrence in black-tailed prairie dogs to assess the generality of links between climate and plague occurrence found in previous analyses of human plague cases. We examined long-term data on climate and plague occurrence in prairie dog colonies within two study areas. Multiple regression analyses revealed that plague occurrence in prairie dogs was not associated with climatic variables in our Colorado study area. In contrast, plague occurrence was strongly associated with climatic variables in our Montana study area. The models with most support included a positive association with precipitation in April-July of the previous year, in addition to a positive association with the number of "warm" days and a negative association with the number of "hot" days in the same year as reported plague events. We conclude that the timing and magnitude of precipitation and temperature may affect plague occurrence in some geographic areas. The best climatic predictors of plague occurrence in prairie dogs within our Montana study area are quite similar to the best climatic predictors of human plague cases in the southwestern United States. This correspondence across regions and species suggests support for a (temperature-modulated) trophic-cascade model for plague, including climatic effects on rodent abundance, flea abundance, and pathogen transmission, at least in regions that experience strong climatic signals. ?? 2005 EcoHealth Journal Consortium.

IDENTIFICATION OF REGIME SHIFTS IN TIME SERIES USING NEIGHBORHOOD STATISTICS

EPA Science Inventory

The identification of alternative dynamic regimes in ecological systems requires several lines of evidence. Previous work on time series analysis of dynamic regimes includes mainly model-fitting methods. We introduce two methods that do not use models. These approaches use state-...

Dynamics of Metabolism and Decision Making During Alcohol Consumption: Modeling and Analysis.

PubMed

Giraldo, Luis Felipe; Passino, Kevin M; Clapp, John D; Ruderman, Danielle

2017-11-01

Heavy alcohol consumption is considered an important public health issue in the United States as over 88 000 people die every year from alcohol-related causes. Research is being conducted to understand the etiology of alcohol consumption and to develop strategies to decrease high-risk consumption and its consequences, but there are still important gaps in determining the main factors that influence the consumption behaviors throughout the drinking event. There is a need for methodologies that allow us not only to identify such factors but also to have a comprehensive understanding of how they are connected and how they affect the dynamical evolution of a drinking event. In this paper, we use previous empirical findings from laboratory and field studies to build a mathematical model of the blood alcohol concentration dynamics in individuals that are in drinking events. We characterize these dynamics as the result of the interaction between a decision-making system and the metabolic process for alcohol. We provide a model of the metabolic process for arbitrary alcohol intake patterns and a characterization of the mechanisms that drive the decision-making process of a drinker during the drinking event. We use computational simulations and Lyapunov stability theory to analyze the effects of the parameters of the model on the blood alcohol concentration dynamics that are characterized. Also, we propose a methodology to inform the model using data collected in situ and to make estimations that provide additional information to the analysis. We show how this model allows us to analyze and predict previously observed behaviors, to design new approaches for the collection of data that improves the construction of the model, and help with the design of interventions.

Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions

NASA Astrophysics Data System (ADS)

Fernandes, R.; Braunschweig, F.; Lourenço, F.; Neves, R.

2015-07-01

The technological evolution in terms of computational capacity, data acquisition systems, numerical modelling and operational oceanography is supplying opportunities for designing and building holistic approaches and complex tools for newer and more efficient management (planning, prevention and response) of coastal water pollution risk events. A combined methodology to dynamically estimate time and space variable shoreline risk levels from ships has been developed, integrating numerical metocean forecasts and oil spill simulations with vessel tracking automatic identification systems (AIS). The risk rating combines the likelihood of an oil spill occurring from a vessel navigating in a study area - Portuguese Continental shelf - with the assessed consequences to the shoreline. The spill likelihood is based on dynamic marine weather conditions and statistical information from previous accidents. The shoreline consequences reflect the virtual spilled oil amount reaching shoreline and its environmental and socio-economic vulnerabilities. The oil reaching shoreline is quantified with an oil spill fate and behaviour model running multiple virtual spills from vessels along time. Shoreline risks can be computed in real-time or from previously obtained data. Results show the ability of the proposed methodology to estimate the risk properly sensitive to dynamic metocean conditions and to oil transport behaviour. The integration of meteo-oceanic + oil spill models with coastal vulnerability and AIS data in the quantification of risk enhances the maritime situational awareness and the decision support model, providing a more realistic approach in the assessment of shoreline impacts. The risk assessment from historical data can help finding typical risk patterns, "hot spots" or developing sensitivity analysis to specific conditions, whereas real time risk levels can be used in the prioritization of individual ships, geographical areas, strategic tug positioning and implementation of dynamic risk-based vessel traffic monitoring.

Diverse roles of actin in C. elegans early embryogenesis

PubMed Central

Velarde, Nathalie; Gunsalus, Kristin C; Piano, Fabio

2007-01-01

Background The actin cytoskeleton plays critical roles in early development in Caenorhabditis elegans. To further understand the complex roles of actin in early embryogenesis we use RNAi and in vivo imaging of filamentous actin (F-actin) dynamics. Results Using RNAi, we found processes that are differentially sensitive to levels of actin during early embryogenesis. Mild actin depletion shows defects in cortical ruffling, pseudocleavage, and establishment of polarity, while more severe depletion shows defects in polar body extrusion, cytokinesis, chromosome segregation, and eventually, egg production. These defects indicate that actin is required for proper oocyte development, fertilization, and a wide range of important events during early embryogenesis, including proper chromosome segregation. In vivo visualization of the cortical actin cytoskeleton shows dynamics that parallel but are distinct from the previously described myosin dynamics. Two distinct types of actin organization are observed at the cortex. During asymmetric polarization to the anterior, or the establishment phase (Phase I), actin forms a meshwork of microfilaments and focal accumulations throughout the cortex, while during the anterior maintenance phase (Phase II) it undergoes a morphological transition to asymmetrically localized puncta. The proper asymmetric redistribution is dependent on the PAR proteins, while both asymmetric redistribution and morphological transitions are dependent upon PFN-1 and NMY-2. Just before cytokinesis, actin disappears from most of the cortex and is only found around the presumptive cytokinetic furrow. Finally, we describe dynamic actin-enriched comets in the early embryo. Conclusion During early C. elegans embryogenesis actin plays more roles and its organization is more dynamic than previously described. Morphological transitions of F-actin, from meshwork to puncta, as well as asymmetric redistribution, are regulated by the PAR proteins. Results from this study indicate new insights into the cellular and developmental roles of the actin cytoskeleton. PMID:18157918

Modeling Endoplasmic Reticulum Network Maintenance in a Plant Cell.

PubMed

Lin, Congping; White, Rhiannon R; Sparkes, Imogen; Ashwin, Peter

2017-07-11

The endoplasmic reticulum (ER) in plant cells forms a highly dynamic network of complex geometry. ER network morphology and dynamics are influenced by a number of biophysical processes, including filament/tubule tension, viscous forces, Brownian diffusion, and interactions with many other organelles and cytoskeletal elements. Previous studies have indicated that ER networks can be thought of as constrained minimal-length networks acted on by a variety of forces that perturb and/or remodel the network. Here, we study two specific biophysical processes involved in remodeling. One is the dynamic relaxation process involving a combination of tubule tension and viscous forces. The other is the rapid creation of cross-connection tubules by direct or indirect interactions with cytoskeletal elements. These processes are able to remodel the ER network: the first reduces network length and complexity whereas the second increases both. Using live cell imaging of ER network dynamics in tobacco leaf epidermal cells, we examine these processes on ER network dynamics. Away from regions of cytoplasmic streaming, we suggest that the dynamic network structure is a balance between the two processes, and we build an integrative model of the two processes for network remodeling. This model produces quantitatively similar ER networks to those observed in experiments. We use the model to explore the effect of parameter variation on statistical properties of the ER network. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

NASA Astrophysics Data System (ADS)

Naritomi, Yusuke; Fuchigami, Sotaro

2013-12-01

We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of Cα atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

Dynamic portrait of the region occupied by the Hungaria Asteroids: The influence of Mars

NASA Astrophysics Data System (ADS)

Correa-Otto, J. A.; Cañada-Assandri, M.

2018-06-01

The region occupied by the Hungaria asteroids has a high dynamical complexity. In this paper, we analyse the main dynamic structures and their influence on the known asteroids through the construction of maps of initial conditions. We evolve a set of test particles placed on a perfectly rectangular grid of initial conditions during 3 Myr under the gravitational influence of the Sun and eight planets, from Mercury to Neptune. Moreover, we use the method MEGNO in order to obtain a complete dynamical portrait of the region. A comparison of our maps with the distribution of real objects allows us to detect the main dynamical mechanisms acting in the domain under study such as mean-motion and secular resonances. Our main results is the existence of a small area inside a stable region where are placed the Hungaria asteroids. We found that the influence of Mars has an important role for the dynamic structure of the region, defining the limits for this population of asteroids. Our result is in agreement with previous studies, which have indicated the importance of the eccentricity of Mars for the stability of Hungaria asteroids. However, we found that the secular resonance resulting from the precession of perihelion due to a coupling with that of Jupiter proposed as limit for the Hungaria region could not be determinant for this population of asteroids.

Coupled Ocean-Atmosphere Dynamics and Predictability of MJO’s

DTIC Science & Technology

2012-09-30

developed. b. Modeling study of the mechanisms of surface chlorophyll modulation by the MJO Previous studies analyzed ocean color satellite data and...to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data ...with Gupta, SIO) e. Run SCOAR2 in downscaling mode for the 2nd MJO event during the DYNAMO period (led by Seo, WHOI, with Miller, SIO) f. Run and

Wave packet dynamics, time scales and phase diagram in the IBM-Lipkin-Meshkov-Glick model

NASA Astrophysics Data System (ADS)

Castaños, Octavio; de los Santos, Francisco; Yáñez, Rafael; Romera, Elvira

2018-02-01

We derive the phase diagram of a scalar two-level boson model by studying the equilibrium and stability properties of its energy surface. The plane of control parameters is enlarged with respect to previous studies. We then analyze the time evolution of wave packets centered around the ground state at various quantum phase transition boundary lines. In particular, classical and revival times are computed numerically.

Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge.

PubMed

Pervin, Hasina M; Batstone, Damien J; Bond, Philip L

2013-06-01

Thermophilic biological pre-treatment enables enhanced anaerobic digestion for treatment of wastewater sludges but, at present, there is limited understanding of the hydrolytic-acidogenic microbial composition and its contribution to this process. In this study, the process was assessed by comparing the microbiology of thermophilic (50-65 °C) and mesophilic (35 °C) pre-treatment reactors treating primary sludge. A full-cycle approach for the 16S rRNA genes was applied in order to monitor the diversity of bacteria and their abundance in a thermophilic pre-treatment reactor treating primary sludge. For the thermophilic pre-treatment (TP), over 90% of the sequences were previously undetected and these had less than 97% sequence similarity to cultured organisms. During the first 83 days, members of the Betaproteobacteria dominated the community sequences and a newly designed probe was used to monitor a previously unknown bacterium affiliated with the genus Brachymonas. Between days 85 and 183, three phylotypes that affiliated with the genera Comamonas, Clostridium and Lysobacter were persistently dominant in the TP community, as revealed by terminal-restriction fragment length polymorphism (T-RFLP). Hydrolytic and fermentative functions have been speculated for these bacteria. Mesophilic pre-treatment (MP) and TP communities were different but they were both relatively dynamic. Statistical correlation analysis and the function of closely allied reference organisms indicated that previously unclassified bacteria dominated the TP community and may have been functionally involved in the enhanced hydrolytic performance of thermophilic anaerobic pre-treatment. This study is the first to reveal the diversity and dynamics of bacteria during anaerobic digestion of primary sludge. Copyright © 2013 Elsevier GmbH. All rights reserved.

A reassessment of the emergence time of European bat lyssavirus type 1.

PubMed

Hughes, Gareth J

2008-12-01

The previous study of the evolutionary rates of European bat lyssavirus type 1 (EBLV-1) used a strict molecular clock to estimate substitution rates of the nucleoprotein gene and in turn times of the most recent common ancestor (tMRCA) of the entire genotype and the two major EBLV-1 lineages (EBLV-1A and EBLV-1B). The results of that study suggested that the evolutionary rate of EBLV-1 was one of the lowest recorded for RNA viruses and that genetic diversity of EBLV-1 arose 500-750 years ago. Here I have shown that the use of a relaxed molecular clock (allowing branch rates to vary within a phylogeny) shows that these previous estimates should be revised. The relaxed clock provides a significantly better fit to all datasets. The substitution rate of EBLV-1B is compatible to that expected given previous estimates for the N gene of rabies virus whilst rate estimations for EBLV-1A appear to be confounded by substantial rate variation within the phylogeny. The relaxed clock substitution rate for EBLV-1 (1.1 x 10(-4)) is higher than had been estimated previously, and closer to that expected for the N gene. Moreover, tMRCA estimates for EBLV-1 are substantially reduced using the relaxed molecular clock (70-300 years) although the differing dynamics of EBLV-1A and EBLV-1B confound the confidence in this estimate. Current diversity of both EBLV-1A and EBLV-1B appears to have emerged within the last 100 years. Reconstruction of the population histories suggests that EBLV-1B may be emerging whilst the signal derived from the EBLV-1A phylogeny may be dampened by clade-specific dynamics.

A single-rate context-dependent learning process underlies rapid adaptation to familiar object dynamics.

PubMed

Ingram, James N; Howard, Ian S; Flanagan, J Randall; Wolpert, Daniel M

2011-09-01

Motor learning has been extensively studied using dynamic (force-field) perturbations. These induce movement errors that result in adaptive changes to the motor commands. Several state-space models have been developed to explain how trial-by-trial errors drive the progressive adaptation observed in such studies. These models have been applied to adaptation involving novel dynamics, which typically occurs over tens to hundreds of trials, and which appears to be mediated by a dual-rate adaptation process. In contrast, when manipulating objects with familiar dynamics, subjects adapt rapidly within a few trials. Here, we apply state-space models to familiar dynamics, asking whether adaptation is mediated by a single-rate or dual-rate process. Previously, we reported a task in which subjects rotate an object with known dynamics. By presenting the object at different visual orientations, adaptation was shown to be context-specific, with limited generalization to novel orientations. Here we show that a multiple-context state-space model, with a generalization function tuned to visual object orientation, can reproduce the time-course of adaptation and de-adaptation as well as the observed context-dependent behavior. In contrast to the dual-rate process associated with novel dynamics, we show that a single-rate process mediates adaptation to familiar object dynamics. The model predicts that during exposure to the object across multiple orientations, there will be a degree of independence for adaptation and de-adaptation within each context, and that the states associated with all contexts will slowly de-adapt during exposure in one particular context. We confirm these predictions in two new experiments. Results of the current study thus highlight similarities and differences in the processes engaged during exposure to novel versus familiar dynamics. In both cases, adaptation is mediated by multiple context-specific representations. In the case of familiar object dynamics, however, the representations can be engaged based on visual context, and are updated by a single-rate process.

Agent-based model for rural-urban migration: A dynamic consideration

NASA Astrophysics Data System (ADS)

Cai, Ning; Ma, Hai-Ying; Khan, M. Junaid

2015-10-01

This paper develops a dynamic agent-based model for rural-urban migration, based on the previous relevant works. The model conforms to the typical dynamic linear multi-agent systems model concerned extensively in systems science, in which the communication network is formulated as a digraph. Simulations reveal that consensus of certain variable could be harmful to the overall stability and should be avoided.

Dynamic Accuracy of Inertial Magnetic Sensor Modules

DTIC Science & Technology

2016-12-01

and the cost of the YEI 3-space data-logging sensor was justified. C. PREVIOUS WORK In [7], Jeremy Cookson built a low-cost pendulum with an optical...encoder to test the dynamic accuracy of MARG sensor modules. The pendulum was designed in order to execute dynamic, repeatable tests in a single...3DM-GX1 and 3DM-GX3-25 sensors. In [8], Leslie Landry developed similar repeatable tests and utilized the pendulum to test the dynamic accuracy of

Rotor-Bearing Dynamics Technology Design Guide. Part 8. A computerized Data Retrieval System for Fluid Film Bearings

DTIC Science & Technology

1980-10-01

AFAPL-TR-78-6 ’: Part Vill (U ROTOR -BEARING DYNAMICS - TECHNOLOGY DESIGN GUIDE ¢ Part Vil A Comput eri eval Syteftor Fluid Film Bearings SHAKER...Protection," Task 304806, "Aerospace Lubrication," Work Unit 30480685, " Rotor -Bearing Dynamics Design." The work reported herein was performed during the...the previous issue of the Rotor -Bearing Dynamics Technology Design Guide, - one volume dealt with the calculation of performance parameters and pertur

Flight Dynamics and Controls Discipline Overview

NASA Technical Reports Server (NTRS)

Theodore, Colin R.

2012-01-01

This presentation will touch topics, including but not limited to, the objectives and challenges of flight dynamics and controls that deal with the pilot and the cockpit's technology, the flight dynamics and controls discipline tasks, and the full envelope of flight dynamics modeling. In addition, the LCTR 7x10-ft wind tunnel test will also be included along with the optimal trajectories for noise abatement and its investigations on handling quality. Furthermore, previous experiments and their complying results will also be discussed.

Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making

PubMed Central

Niyogi, Ritwik K.; Wong-Lin, KongFatt

2013-01-01

Behavioural and neurophysiological studies in primates have increasingly shown the involvement of urgency signals during the temporal integration of sensory evidence in perceptual decision-making. Neuronal correlates of such signals have been found in the parietal cortex, and in separate studies, demonstrated attention-induced gain modulation of both excitatory and inhibitory neurons. Although previous computational models of decision-making have incorporated gain modulation, their abstract forms do not permit an understanding of the contribution of inhibitory gain modulation. Thus, the effects of co-modulating both excitatory and inhibitory neuronal gains on decision-making dynamics and behavioural performance remain unclear. In this work, we incorporate time-dependent co-modulation of the gains of both excitatory and inhibitory neurons into our previous biologically based decision circuit model. We base our computational study in the context of two classic motion-discrimination tasks performed in animals. Our model shows that by simultaneously increasing the gains of both excitatory and inhibitory neurons, a variety of the observed dynamic neuronal firing activities can be replicated. In particular, the model can exhibit winner-take-all decision-making behaviour with higher firing rates and within a significantly more robust model parameter range. It also exhibits short-tailed reaction time distributions even when operating near a dynamical bifurcation point. The model further shows that neuronal gain modulation can compensate for weaker recurrent excitation in a decision neural circuit, and support decision formation and storage. Higher neuronal gain is also suggested in the more cognitively demanding reaction time than in the fixed delay version of the task. Using the exact temporal delays from the animal experiments, fast recruitment of gain co-modulation is shown to maximize reward rate, with a timescale that is surprisingly near the experimentally fitted value. Our work provides insights into the simultaneous and rapid modulation of excitatory and inhibitory neuronal gains, which enables flexible, robust, and optimal decision-making. PMID:23825935

Symbolic dynamics techniques for complex systems: Application to share price dynamics

NASA Astrophysics Data System (ADS)

Xu, Dan; Beck, Christian

2017-05-01

The symbolic dynamics technique is well known for low-dimensional dynamical systems and chaotic maps, and lies at the roots of the thermodynamic formalism of dynamical systems. Here we show that this technique can also be successfully applied to time series generated by complex systems of much higher dimensionality. Our main example is the investigation of share price returns in a coarse-grained way. A nontrivial spectrum of Rényi entropies is found. We study how the spectrum depends on the time scale of returns, the sector of stocks considered, as well as the number of symbols used for the symbolic description. Overall our analysis confirms that in the symbol space transition probabilities of observed share price returns depend on the entire history of previous symbols, thus emphasizing the need for a modelling based on non-Markovian stochastic processes. Our method allows for quantitative comparisons of entirely different complex systems, for example the statistics of symbol sequences generated by share price returns using 4 symbols can be compared with that of genomic sequences.

Dynamic image reconstruction: MR movies from motion ghosts.

PubMed

Xiang, Q S; Henkelman, R M

1992-01-01

It has been previously shown that an image with motion ghost artifacts can be decomposed into a ghost mask superimposed over a ghost-free image. The present study demonstrates that the ghost components carry useful dynamic information and should not be discarded. Specifically, ghosts of different orders indicate the intensity and phase of the corresponding harmonics contained in the quasi-periodically varying spin-density distribution. A summation of the ghosts weighted by appropriate temporal phase factors can give a time-dependent dynamic image that is a movie of the object motion. This dynamic image reconstruction technique does not necessarily require monitoring of the motion and thus is easy to implement and operate. It also has a shorter imaging time than point-by-point imaging of temporal variation, because the periodic motion is more efficiently sampled with a limited number of harmonics recorded in the motion ghosts. This technique was tested in both moving phantoms and volunteers. It is believed to be useful for dynamic imaging of time-varying anatomic structures, such as in the cardiovascular system.

Emotion recognition in Parkinson's disease: Static and dynamic factors.

PubMed

Wasser, Cory I; Evans, Felicity; Kempnich, Clare; Glikmann-Johnston, Yifat; Andrews, Sophie C; Thyagarajan, Dominic; Stout, Julie C

2018-02-01

The authors tested the hypothesis that Parkinson's disease (PD) participants would perform better in an emotion recognition task with dynamic (video) stimuli compared to a task using only static (photograph) stimuli and compared performances on both tasks to healthy control participants. In a within-subjects study, 21 PD participants and 20 age-matched healthy controls performed both static and dynamic emotion recognition tasks. The authors used a 2-way analysis of variance (controlling for individual participant variance) to determine the effect of group (PD, control) on emotion recognition performance in static and dynamic facial recognition tasks. Groups did not significantly differ in their performances on the static and dynamic tasks; however, the trend was suggestive that PD participants performed worse than controls. PD participants may have subtle emotion recognition deficits that are not ameliorated by the addition of contextual cues, similar to those found in everyday scenarios. Consistent with previous literature, the results suggest that PD participants may have underlying emotion recognition deficits, which may impact their social functioning. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Effects of Thermal Noise on the Transitional Dynamics of an Inextensible Elastic Filament in Stagnation Flow

PubMed Central

Deng, Mingge; Grinberg, Leopold; Caswell, Bruce

2015-01-01

We investigate the dynamics of a single inextensible elastic filament subject to anisotropic friction in a viscous stagnation-point flow, by employing both a continuum model represented by Langevin type stochastic partial differential equations (SPDEs) and a Dissipative Particle Dynamics (DPD) method. Unlike previous works1, the filament is free to rotate and the tension along the filament is determined by the local inextensible constraint. The kinematics of the filament is recorded and studied with normal modes analysis. The results show that the filament displays an instability induced by negative tension, which is analogous to Euler buckling of a beam. Symmetry breaking of normal modes dynamics and stretch-coil transitions are observed above the threshold of the buckling instability point. Furthermore, both temporal and spatial noise are amplified resulting from the interaction of thermal fluctuations and nonlinear filament dynamics. Specifically, the spatial noise is amplified with even normal modes being excited due to symmetry breaking, while the temporal noise is amplified with increasing time correlation length and variance. PMID:26023834

Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.

PubMed

Zanchi, Fernando Berton; Caceres, Rafael Andrade; Stabeli, Rodrigo Guerino; de Azevedo, Walter Filgueira

2010-03-01

Purine nucleoside phosphorylase (PNP) (EC.2.4.2.1) is an enzyme that catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is involved in purine-salvage pathway and has been proposed as a promising target for design and development of antimalarial and antibacterial drugs. Recent elucidation of the three-dimensional structure of PNP by X-ray protein crystallography left open the possibility of structure-based virtual screening initiatives in combination with molecular dynamics simulations focused on identification of potential new antimalarial drugs. Most of the previously published molecular dynamics simulations of PNP were carried out on human PNP, a trimeric PNP. The present article describes for the first time molecular dynamics simulations of hexameric PNP from Plasmodium falciparum (PfPNP). Two systems were simulated in the present work, PfPNP in ligand free form, and in complex with immucillin and sulfate. Based on the dynamical behavior of both systems the main results related to structural stability and protein-drug interactions are discussed.

Towards a physics of evolution: Critical diversity dynamics at the edges of collapse and bursts of diversification

NASA Astrophysics Data System (ADS)

Hanel, Rudolf; Kauffman, Stuart A.; Thurner, Stefan

2007-09-01

Systems governed by the standard mechanisms of biological or technological evolution are often described by catalytic evolution equations. We study the structure of these equations and find an analogy with classical thermodynamic systems. In particular, we can demonstrate the existence of several distinct phases of evolutionary dynamics: a phase of fast growing diversity, one of stationary, finite diversity, and one of rapidly decaying diversity. While the first two phases have been subject to previous work, here we focus on the destructive aspects—in particular the phase diagram—of evolutionary dynamics. The main message is that within a critical region, massive loss of diversity can be triggered by very small external fluctuations. We further propose a dynamical model of diversity which captures spontaneous creation and destruction processes fully respecting the phase diagrams of evolutionary systems. The emergent time series show rich diversity dynamics, including power laws as observed in actual economical data, e.g., firm bankruptcy data. We believe the present model presents a possibility to cast the famous qualitative picture of Schumpeterian economic evolution, into a quantifiable and testable framework.