Performance analysis of jump-gliding locomotion for miniature robotics.

PubMed

Vidyasagar, A; Zufferey, Jean-Christohphe; Floreano, Dario; Kovač, M

2015-03-26

Recent work suggests that jumping locomotion in combination with a gliding phase can be used as an effective mobility principle in robotics. Compared to pure jumping without a gliding phase, the potential benefits of hybrid jump-gliding locomotion includes the ability to extend the distance travelled and reduce the potentially damaging impact forces upon landing. This publication evaluates the performance of jump-gliding locomotion and provides models for the analysis of the relevant dynamics of flight. It also defines a jump-gliding envelope that encompasses the range that can be achieved with jump-gliding robots and that can be used to evaluate the performance and improvement potential of jump-gliding robots. We present first a planar dynamic model and then a simplified closed form model, which allow for quantification of the distance travelled and the impact energy on landing. In order to validate the prediction of these models, we validate the model with experiments using a novel jump-gliding robot, named the 'EPFL jump-glider'. It has a mass of 16.5 g and is able to perform jumps from elevated positions, perform steered gliding flight, land safely and traverse on the ground by repetitive jumping. The experiments indicate that the developed jump-gliding model fits very well with the measured flight data using the EPFL jump-glider, confirming the benefits of jump-gliding locomotion to mobile robotics. The jump-glide envelope considerations indicate that the EPFL jump-glider, when traversing from a 2 m height, reaches 74.3% of optimal jump-gliding distance compared to pure jumping without a gliding phase which only reaches 33.4% of the optimal jump-gliding distance. Methods of further improving flight performance based on the models and inspiration from biological systems are presented providing mechanical design pathways to future jump-gliding robot designs.

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

PubMed Central

Zheng, Wenjun

2010-01-01

Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

Individual movement behavior, matrix heterogeneity, and the dynamics of spatially structured populations.

PubMed

Revilla, Eloy; Wiegand, Thorsten

2008-12-09

The dynamics of spatially structured populations is characterized by within- and between-patch processes. The available theory describes the latter with simple distance-dependent functions that depend on landscape properties such as interpatch distance or patch size. Despite its potential role, we lack a good mechanistic understanding of how the movement of individuals between patches affects the dynamics of these populations. We used the theoretical framework provided by movement ecology to make a direct representation of the processes determining how individuals connect local populations in a spatially structured population of Iberian lynx. Interpatch processes depended on the heterogeneity of the matrix where patches are embedded and the parameters defining individual movement behavior. They were also very sensitive to the dynamic demographic variables limiting the time moving, the within-patch dynamics of available settlement sites (both spatiotemporally heterogeneous) and the response of individuals to the perceived risk while moving. These context-dependent dynamic factors are an inherent part of the movement process, producing connectivities and dispersal kernels whose variability is affected by other demographic processes. Mechanistic representations of interpatch movements, such as the one provided by the movement-ecology framework, permit the dynamic interaction of birth-death processes and individual movement behavior, thus improving our understanding of stochastic spatially structured populations.

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.

On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems

NASA Astrophysics Data System (ADS)

Junge, Oliver; Kevrekidis, Ioannis G.

2017-06-01

We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.

On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems.

PubMed

Junge, Oliver; Kevrekidis, Ioannis G

2017-06-01

We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.

Detecting changes in forced climate attractors with Wasserstein distance

NASA Astrophysics Data System (ADS)

Robin, Yoann; Yiou, Pascal; Naveau, Philippe

2017-07-01

The climate system can been described by a dynamical system and its associated attractor. The dynamics of this attractor depends on the external forcings that influence the climate. Such forcings can affect the mean values or variances, but regions of the attractor that are seldom visited can also be affected. It is an important challenge to measure how the climate attractor responds to different forcings. Currently, the Euclidean distance or similar measures like the Mahalanobis distance have been favored to measure discrepancies between two climatic situations. Those distances do not have a natural building mechanism to take into account the attractor dynamics. In this paper, we argue that a Wasserstein distance, stemming from optimal transport theory, offers an efficient and practical way to discriminate between dynamical systems. After treating a toy example, we explore how the Wasserstein distance can be applied and interpreted to detect non-autonomous dynamics from a Lorenz system driven by seasonal cycles and a warming trend.

Comparison Between Self-Guided Langevin Dynamics and Molecular Dynamics Simulations for Structure Refinement of Protein Loop Conformations

DTIC Science & Technology

2011-01-01

SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18 . NUMBER OF PAGES 9 19a. NAME OF RESPONSIBLE PERSON a. REPORT...unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39- 18 sampling is based on...atom distance-scaled ideal-gas reference state (DFIRE-AA) statistical potential func- tion.[ 18 ] The third approach is the Rosetta all-atom energy func

Acoustic variation of spider monkeys' contact calls (whinnies) is related to distance between vocalizing individuals and immediate caller behavior.

PubMed

Ordóñez-Gómez, José D; Santillán-Doherty, Ana M; Fischer, Julia; Hammerschmidt, Kurt

2018-04-01

Due to several factors such as ecological conditions, group size, and social organization, primates frequently spend time out of visual contact with individuals of their own group. Through the use of long-distance vocalizations, often termed "contact calls," primates are able to maintain contact with out-of-sight individuals. Contact calls have been shown to be individually distinct, and reverberation and attenuation provide information about caller distance. It is less clear, however, whether callers actively change the structure of contact calls depending on the distance to the presumed listeners. We studied this question in spider monkeys (Ateles geoffroyi), a species with complex spatial dynamics (fission-fusion society) that produces highly frequency modulated contact calls, denominated "whinnies." We determined the acoustic characteristics of 566 whinnies recorded from 35 free-ranging spider monkeys that belong to a community located in Mexico, and used cluster analyses, discriminant function analyses, and generalized linear mixed models to assess if they varied in relation to the presumed distance to the listener. Whinnies could be grouped into five subtypes. Since the lowest frequency subtype was mainly produced by spider monkeys that exchanged whinnies at longer distances, and lower frequency calls propagate across longer distances, our results suggest that whinnies vary in order to enhance vocal contact between individuals separated by different distances. Our results also revealed that whinnies convey potential information about caller immediate behaviors and corroborated that these calls are individually distinct. Overall, our results suggest that whinny acoustic variation facilitates the maintenance of vocal contact between individuals living in a society with complex spatial dynamics. © 2018 Wiley Periodicals, Inc.

A fast community detection method in bipartite networks by distance dynamics

NASA Astrophysics Data System (ADS)

Sun, Hong-liang; Ch'ng, Eugene; Yong, Xi; Garibaldi, Jonathan M.; See, Simon; Chen, Duan-bing

2018-04-01

Many real bipartite networks are found to be divided into two-mode communities. In this paper, we formulate a new two-mode community detection algorithm BiAttractor. It is based on distance dynamics model Attractor proposed by Shao et al. with extension from unipartite to bipartite networks. Since Jaccard coefficient of distance dynamics model is incapable to measure distances of different types of vertices in bipartite networks, our main contribution is to extend distance dynamics model from unipartite to bipartite networks using a novel measure Local Jaccard Distance (LJD). Furthermore, distances between different types of vertices are not affected by common neighbors in the original method. This new idea makes clear assumptions and yields interpretable results in linear time complexity O(| E |) in sparse networks, where | E | is the number of edges. Experiments on synthetic networks demonstrate it is capable to overcome resolution limit compared with existing other methods. Further research on real networks shows that this model can accurately detect interpretable community structures in a short time.

Differential morphology and image processing.

PubMed

Maragos, P

1996-01-01

Image processing via mathematical morphology has traditionally used geometry to intuitively understand morphological signal operators and set or lattice algebra to analyze them in the space domain. We provide a unified view and analytic tools for morphological image processing that is based on ideas from differential calculus and dynamical systems. This includes ideas on using partial differential or difference equations (PDEs) to model distance propagation or nonlinear multiscale processes in images. We briefly review some nonlinear difference equations that implement discrete distance transforms and relate them to numerical solutions of the eikonal equation of optics. We also review some nonlinear PDEs that model the evolution of multiscale morphological operators and use morphological derivatives. Among the new ideas presented, we develop some general 2-D max/min-sum difference equations that model the space dynamics of 2-D morphological systems (including the distance computations) and some nonlinear signal transforms, called slope transforms, that can analyze these systems in a transform domain in ways conceptually similar to the application of Fourier transforms to linear systems. Thus, distance transforms are shown to be bandpass slope filters. We view the analysis of the multiscale morphological PDEs and of the eikonal PDE solved via weighted distance transforms as a unified area in nonlinear image processing, which we call differential morphology, and briefly discuss its potential applications to image processing and computer vision.

A Critical Interpersonal Distance Switches between Two Coordination Modes in Kendo Matches

PubMed Central

Okumura, Motoki; Kijima, Akifumi; Kadota, Koji; Yokoyama, Keiko; Suzuki, Hiroo; Yamamoto, Yuji

2012-01-01

In many competitive sports, players need to quickly and continuously execute movements that co-adapt to various movements executed by their opponents and physical objects. In a martial art such as kendo, players must be able to skillfully change interpersonal distance in order to win. However, very little information about the task and expertise properties of the maneuvers affecting interpersonal distance is available. This study investigated behavioral dynamics underlying opponent tasks by analyzing changes in interpersonal distance made by expert players in kendo matches. Analysis of preferred interpersonal distances indicated that players tended to step toward and away from their opponents based on two distances. The most preferred distance enabled the players to execute both striking and defensive movements immediately. The relative phase analysis of the velocities at which players executed steps toward and away revealed that players developed anti-phase synchronizations at near distances to maintain safe distances from their opponents. Alternatively, players shifted to in-phase synchronization to approach their opponents from far distances. This abrupt phase-transition phenomenon constitutes a characteristic bifurcation dynamics that regularly and instantaneously occurs between in- and anti-phase synchronizations at a critical interpersonal distance. These dynamics are profoundly affected by the task constraints of kendo and the physical constraints of the players. Thus, the current study identifies the clear behavioral dynamics that emerge in a sport setting. PMID:23284799

Tests of general relativity using Starprobe radio metric tracking data

NASA Technical Reports Server (NTRS)

Mease, K. D.; Anderson, J. D.; Wood, L. J.; White, L. K.

1982-01-01

The potential of a proposed spacecraft mission, called Starprobe, for testing general relativity and providing information on the interior structure and dynamics of the sun is investigated. Parametric, gravitational perturbation terms are derived which represent relativistic effects and effects due to spatial and temporal variations in the solar potential at a given radial distance. A covariance analysis based on Kalman filtering theory predicts the accuracies with which the free parameters in the perturbation terms can be estimated with radio metric tracking data through the process of trajectory reconstruction. It is concluded that Starprobe can contribute significant information on both the nature of gravitation and the structure and dynamics of the solar interior.

The need for speed: escape velocity and dynamical mass measurements of the Andromeda galaxy

NASA Astrophysics Data System (ADS)

Kafle, Prajwal R.; Sharma, Sanjib; Lewis, Geraint F.; Robotham, Aaron S. G.; Driver, Simon P.

2018-04-01

Our nearest large cosmological neighbour, the Andromeda galaxy (M31), is a dynamical system, and an accurate measurement of its total mass is central to our understanding of its assembly history, the life-cycles of its satellite galaxies, and its role in shaping the Local Group environment. Here, we apply a novel approach to determine the dynamical mass of M31 using high-velocity Planetary Nebulae, establishing a hierarchical Bayesian model united with a scheme to capture potential outliers and marginalize over tracers unknown distances. With this, we derive the escape velocity run of M31 as a function of galactocentric distance, with both parametric and non-parametric approaches. We determine the escape velocity of M31 to be 470 ± 40 km s-1 at a galactocentric distance of 15 kpc, and also, derive the total potential of M31, estimating the virial mass and radius of the galaxy to be 0.8 ± 0.1 × 1012 M⊙ and 240 ± 10 kpc, respectively. Our M31 mass is on the low side of the measured range, this supports the lower expected mass of the M31-Milky Way system from the timing and momentum arguments, satisfying the H I constraint on circular velocity between 10 ≲ R/ kpc < 35, and agreeing with the stellar mass Tully-Fisher relation. To place these results in a broader context, we compare them to the key predictions of the ΛCDM cosmological paradigm, including the stellar-mass-halo-mass and the dark matter halo concentration-virial mass correlation, and finding it to be an outlier to this relation.

Long-Distance Rescue and Slow Extinction Dynamics Govern Multiscale Metapopulations.

PubMed

Huth, Géraldine; Haegeman, Bart; Pitard, Estelle; Munoz, François

2015-10-01

Rare long-distance dispersal is known to be critical for species dynamics, but how the interplay between short- and long-distance colonization influences regional persistence in a fragmented habitat remains poorly understood. We propose a metapopulation model that combines local colonization within habitat islands and long-distance colonization between islands. We study how regional occupancy dynamics are affected by the multiscale colonization process. We find that the island size distribution (ISD) is a key driver of the long-term occupancy dynamics. When the ISD is heterogeneous-that is, when the size of islands is variable-we show that extinction dynamics become very slow. We demonstrate that this behavior is unrelated to the well-known extinction debt near the critical extinction threshold. Hence, this finding questions the equivalence between extinction debt and critical transitions in the context of metapopulation collapse. Furthermore, we show that long-distance colonization can rescue small islands from extinction and sustain a steady regional occupancy. These results provide novel theoretical and practical insights into extinction dynamics and persistence in fragmented habitats and are thus relevant for the design of conservation strategies.

Geographical variation in the spatial synchrony of a forest-defoliating insect: isolation of environmental and spatial drivers

Treesearch

K.yle J. Haynes; Ottar N. Bjornstad; Andrew J. Allstadt; Andrew M. Liebhold

2012-01-01

Despite the pervasiveness of spatial synchrony of population fluctuations in virtually every taxon, it remains difficult to disentangle its underlying mechanisms, such as environmental perturbations and dispersal. We used multiple regression of distance matrices (MRMs) to statistically partition the importance of several factors potentially synchronizing the dynamics...

Dust characteristics of dusty plasma ring of Saturn

NASA Astrophysics Data System (ADS)

Morooka, M.; Wahlund, J.-E.; Ye, S.-Y.; Persoon, A. M.; Kurth, W. S.

2017-09-01

During the Ring Grazing orbit, starting from December 2016, Cassini carried out twenty of the faint Saturn ring crossing observations at the distance of 2.45-2.51 RS (1RS 60,268 km) from Saturn center. We will show the electron and the ion density measurements of the RPWS/Langmuir Probe (LP) during these orbits. In most of the orbits significant ion/electron density differences have been observed, which indicates the presence of the charged nm and µm sized grains. The relationship between the observed charge densities and the electrical potential of the grains shows that the grains and the ambient electrons and ions are electro dynamical ensemble, a dusty plasma. The results show that characteristic dust size changes depending on the distance from the ring center. The result suggests that a dusty plasma state is related to the dynamics of the grain sizes.

Euclidean distance and Kolmogorov-Smirnov analyses of multi-day auditory event-related potentials: a longitudinal stability study

NASA Astrophysics Data System (ADS)

Durato, M. V.; Albano, A. M.; Rapp, P. E.; Nawang, S. A.

2015-06-01

The validity of ERPs as indices of stable neurophysiological traits is partially dependent on their stability over time. Previous studies on ERP stability, however, have reported diverse stability estimates despite using the same component scoring methods. This present study explores a novel approach in investigating the longitudinal stability of average ERPs—that is, by treating the ERP waveform as a time series and then applying Euclidean Distance and Kolmogorov-Smirnov analyses to evaluate the similarity or dissimilarity between the ERP time series of different sessions or run pairs. Nonlinear dynamical analysis show that in the absence of a change in medical condition, the average ERPs of healthy human adults are highly longitudinally stable—as evaluated by both the Euclidean distance and the Kolmogorov-Smirnov test.

Learning Human Actions by Combining Global Dynamics and Local Appearance.

PubMed

Luo, Guan; Yang, Shuang; Tian, Guodong; Yuan, Chunfeng; Hu, Weiming; Maybank, Stephen J

2014-12-01

In this paper, we address the problem of human action recognition through combining global temporal dynamics and local visual spatio-temporal appearance features. For this purpose, in the global temporal dimension, we propose to model the motion dynamics with robust linear dynamical systems (LDSs) and use the model parameters as motion descriptors. Since LDSs live in a non-Euclidean space and the descriptors are in non-vector form, we propose a shift invariant subspace angles based distance to measure the similarity between LDSs. In the local visual dimension, we construct curved spatio-temporal cuboids along the trajectories of densely sampled feature points and describe them using histograms of oriented gradients (HOG). The distance between motion sequences is computed with the Chi-Squared histogram distance in the bag-of-words framework. Finally we perform classification using the maximum margin distance learning method by combining the global dynamic distances and the local visual distances. We evaluate our approach for action recognition on five short clips data sets, namely Weizmann, KTH, UCF sports, Hollywood2 and UCF50, as well as three long continuous data sets, namely VIRAT, ADL and CRIM13. We show competitive results as compared with current state-of-the-art methods.

A theoretical Deduction from the Hubble law based on a Modified Newtonian Dynamics with field of Yukawa inverse

NASA Astrophysics Data System (ADS)

Falcon, N.

2017-07-01

At cosmic scales the dynamics of the Universe are almost exclusively prescribed by the force of gravity; however the assumption of the law of gravitation, depending on the inverse of the distance, leads to the known problems of the rotation curves of galaxies and missing mass (dark matter). The problem of the coupling of gravity to changes in scale and deviations from the law of the inverse square is an old problem (Laplace, 1805; Seeliger 1898), which has motivated alternatives to Newtonian dynamics compatible with observations. The present paper postulates a modified Newtonian dynamics by adding an inverse Yukawa potential: U(r)≡U0(M)(r-r0)e-α/r is the the potential per unit mass (in N/kg) as a function of the barionic mass that causes the field, r0 is of the order of 50h-1 Mpc and alpha is a coupling constant of the order of 2.5 h-1 Mpc. This potential is zero within the solar system, slightly attractive at interstellar distances, very attractive in galactic range and repulsive at cosmic scales. Its origin is the barionic matter, it allows to include the Milgrow MoND theory to explain the rotation curves, it is compatible with the experiments Eovos type, and allows to deduce the law of Hubble to cosmic scales, in the form H0=100h km/s Mpc≍U0(M)/c, where U0(M)≍ 4pi×6.67 10-11m/s2, is obtained from the Laplace's equation, assuming that the gravitational force is the law of the inverse of the square plus a non-linear term type Yukawa inverse. It is concluded that the modification of the law of gravity with nonlinear terms, allows to model the dynamics of the Universe on a large scale and include non-locality without dark matter. (See Falcon et al. 2014, International Journal of Astronomy and Astrophysics, 4, 551-559).

Potential for the dynamics of pedestrians in a socially interacting group

NASA Astrophysics Data System (ADS)

Zanlungo, Francesco; Ikeda, Tetsushi; Kanda, Takayuki

2014-01-01

We introduce a simple potential to describe the dynamics of the relative motion of two pedestrians socially interacting in a walking group. We show that the proposed potential, based on basic empirical observations and theoretical considerations, can qualitatively describe the statistical properties of pedestrian behavior. In detail, we show that the two-dimensional probability distribution of the relative distance is determined by the proposed potential through a Boltzmann distribution. After calibrating the parameters of the model on the two-pedestrian group data, we apply the model to three-pedestrian groups, showing that it describes qualitatively and quantitatively well their behavior. In particular, the model predicts that three-pedestrian groups walk in a V-shaped formation and provides accurate values for the position of the three pedestrians. Furthermore, the model correctly predicts the average walking velocity of three-person groups based on the velocity of two-person ones. Possible extensions to larger groups, along with alternative explanations of the social dynamics that may be implied by our model, are discussed at the end of the paper.

Performance evaluation of the zero-multipole summation method in modern molecular dynamics software.

PubMed

Sakuraba, Shun; Fukuda, Ikuo

2018-05-04

The zero-multiple summation method (ZMM) is a cutoff-based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS. Extensive performance comparisons against a highly optimized, parameter-tuned SPME implementation are performed for various-sized water systems and two protein-water systems. We analyze in detail the dependence of the performance on the potential parameters and the number of CPU cores. Even though the ZMM uses a larger cutoff distance than the SPME does, the performance of the ZMM is comparable to or better than that of the SPME. This is because the ZMM does not require a time-consuming electrostatic convolution and because the ZMM gains short neighbor-list distances due to the smooth damping feature of the pairwise potential function near the cutoff length. We found, in particular, that the ZMM with quadrupole or octupole cancellation and no damping factor is an excellent candidate for the fast calculation of electrostatic interactions. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

SODA Repuslive Function Shaping

NASA Image and Video Library

2017-06-16

SODA, Swarm Orbital Dynamics Advisor, a tool that provides the orbital maneuvers required to achieve a desired type of relative swarm motion. The SODA algorithm uses a repulsive potential that is a function of the distances between each pair of satellites. Choosing the parameters of the function is a swarm design choice, as different values can yield very different maneuvers and thus impact fuel use and mission life. This is an animation illustrating how the peaks of the repulsive potential function vary when varying certain parameters.

Phase structure of completely asymptotically free SU(Nc) models with quarks and scalar quarks

NASA Astrophysics Data System (ADS)

Hansen, F. F.; Janowski, T.; Langæble, K.; Mann, R. B.; Sannino, F.; Steele, T. G.; Wang, Z. W.

2018-03-01

We determine the phase diagram of completely asymptotically free SU (Nc) gauge theories featuring Ns complex scalars and Nf Dirac quarks transforming according to the fundamental representation of the gauge group. The analysis is performed at the maximum known order in perturbation theory. We unveil a very rich dynamics and associated phase structure. Intriguingly, we discover that the completely asymptotically free conditions guarantee that the infrared dynamics displays long-distance conformality, and in a regime when perturbation theory is applicable. We conclude our analysis by determining the quantum corrected potential of the model and summarizing the possible patterns of radiative symmetry breaking. These models are of potential phenomenological interest as either elementary or composite ultraviolet finite extensions of the standard model.

Directed Magnetic Particle Transport above Artificial Magnetic Domains Due to Dynamic Magnetic Potential Energy Landscape Transformation.

PubMed

Holzinger, Dennis; Koch, Iris; Burgard, Stefan; Ehresmann, Arno

2015-07-28

An approach for a remotely controllable transport of magnetic micro- and/or nanoparticles above a topographically flat exchange-bias (EB) thin film system, magnetically patterned into parallel stripe domains, is presented where the particle manipulation is achieved by sub-mT external magnetic field pulses. Superparamagnetic core-shell particles are moved stepwise by the dynamic transformation of the particles' magnetic potential energy landscape due to the external magnetic field pulses without affecting the magnetic state of the thin film system. The magnetic particle velocity is adjustable in the range of 1-100 μm/s by the design of the substrate's magnetic field landscape (MFL), the particle-substrate distance, and the magnitude of the applied external magnetic field pulses. The agglomeration of magnetic particles is avoided by the intrinsic magnetostatic repulsion of particles due to the parallel alignment of the particles' magnetic moments perpendicular to the transport direction and parallel to the surface normal of the substrate during the particle motion. The transport mechanism is modeled by a quantitative theory based on the precise knowledge of the sample's MFL and the particle-substrate distance.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

Discovery of long-distance gamete dispersal in a lichen-forming ascomycete.

PubMed

Ronnås, Cecilia; Werth, Silke; Ovaskainen, Otso; Várkonyi, Gergely; Scheidegger, Christoph; Snäll, Tord

2017-10-01

Accurate estimates of gamete and offspring dispersal range are required for the understanding and prediction of spatial population dynamics and species persistence. Little is known about gamete dispersal in fungi, especially in lichen-forming ascomycetes. Here, we estimate the dispersal functions of clonal propagules, gametes and ascospores of the epiphytic lichen Lobaria pulmonaria. We use hierarchical Bayesian parentage analysis, which integrates genetic and ecological information from multiannual colonization and dispersal source data collected in a large, old-growth forest landscape. The effective dispersal range of gametes is several hundred metres to kilometres from potential paternal individuals. By contrast, clonal propagules disperse only tens of metres, and ascospores disperse over several thousand metres. Our study reveals the dispersal distances of individual reproductive units; clonal propagules, gametes and ascospores, which is of great importance for a thorough understanding of the spatial dynamics of ascomycetes. Sexual reproduction occurs between distant individuals. However, whereas gametes and ascospores disperse over long distances, the overall rate of colonization of trees is low. Hence, establishment is the limiting factor for the colonization of new host trees by the lichen in old-growth landscapes. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Effect of Strain Field on Threshold Displacement Energy of Tungsten Studied by Molecular Dynamics Simulation

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

Wang, Dong; Gao, Ning; Setyawan, W.

The influence of strain field on defect formation energy and threshold displacement energy (Ed) in body-centered cubic (BCC) tungsten (W) has been studied with molecular dynamics simulations. Two different W potentials (Fikar and Juslin) were compared and the results indicate that the connection distance and selected function linking the short-range and long-range portions of the potentials affects the threshold displacement energy and its direction-specific values. The minimum Ed direction calculated with the Fikar-potential is <100> and with the Juslin-potential is <111>. Nevertheless, the most stable self-interstitial configuration is found to be a <111>-crowdion for both potentials. This stable configuration doesmore » not change with applied strain. Varying the strain from compression to tension increases the vacancy formation energy but decreases the self-interstitial formation energy. The formation energy of a self-interstitial changes more significantly than a vacancy such that Ed decreases with applied hydrostatic strain from compression to tension.« less

Angular Declination and the Dynamic Perception of Egocentric Distance

PubMed Central

Gajewski, Daniel A.; Philbeck, John W.; Wirtz, Philip W.; Chichka, David

2014-01-01

The extraction of the distance between an object and an observer is fast when angular declination is informative, as it is with targets placed on the ground. To what extent does angular declination drive performance when viewing time is limited? Participants judged target distances in a real-world environment with viewing durations ranging from 36–220 ms. An important role for angular declination was supported by experiments showing that the cue provides information about egocentric distance even on the very first glimpse, and that it supports a sensitive response to distance in the absence of other useful cues. Performance was better at 220 ms viewing durations than for briefer glimpses, suggesting that the perception of distance is dynamic even within the time frame of a typical eye fixation. Critically, performance in limited viewing trials was better when preceded by a 15 second preview of the room without a designated target. The results indicate that the perception of distance is powerfully shaped by memory from prior visual experience with the scene. A theoretical framework for the dynamic perception of distance is presented. PMID:24099588

A Novel Dynamic Update Framework for Epileptic Seizure Prediction

PubMed Central

Wang, Minghui; Hong, Xiaojun; Han, Jie

2014-01-01

Epileptic seizure prediction is a difficult problem in clinical applications, and it has the potential to significantly improve the patients' daily lives whose seizures cannot be controlled by either drugs or surgery. However, most current studies of epileptic seizure prediction focus on high sensitivity and low false-positive rate only and lack the flexibility for a variety of epileptic seizures and patients' physical conditions. Therefore, a novel dynamic update framework for epileptic seizure prediction is proposed in this paper. In this framework, two basic sample pools are constructed and updated dynamically. Furthermore, the prediction model can be updated to be the most appropriate one for the prediction of seizures' arrival. Mahalanobis distance is introduced in this part to solve the problem of side information, measuring the distance between two data sets. In addition, a multichannel feature extraction method based on Hilbert-Huang transform and extreme learning machine is utilized to extract the features of a patient's preseizure state against the normal state. At last, a dynamic update epileptic seizure prediction system is built up. Simulations on Freiburg database show that the proposed system has a better performance than the one without update. The research of this paper is significantly helpful for clinical applications, especially for the exploitation of online portable devices. PMID:25050381

A novel dynamic update framework for epileptic seizure prediction.

PubMed

Han, Min; Ge, Sunan; Wang, Minghui; Hong, Xiaojun; Han, Jie

2014-01-01

Epileptic seizure prediction is a difficult problem in clinical applications, and it has the potential to significantly improve the patients' daily lives whose seizures cannot be controlled by either drugs or surgery. However, most current studies of epileptic seizure prediction focus on high sensitivity and low false-positive rate only and lack the flexibility for a variety of epileptic seizures and patients' physical conditions. Therefore, a novel dynamic update framework for epileptic seizure prediction is proposed in this paper. In this framework, two basic sample pools are constructed and updated dynamically. Furthermore, the prediction model can be updated to be the most appropriate one for the prediction of seizures' arrival. Mahalanobis distance is introduced in this part to solve the problem of side information, measuring the distance between two data sets. In addition, a multichannel feature extraction method based on Hilbert-Huang transform and extreme learning machine is utilized to extract the features of a patient's preseizure state against the normal state. At last, a dynamic update epileptic seizure prediction system is built up. Simulations on Freiburg database show that the proposed system has a better performance than the one without update. The research of this paper is significantly helpful for clinical applications, especially for the exploitation of online portable devices.

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

PubMed Central

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic. PMID:26177039

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.

PubMed

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.

Survival of extrasolar giant planet moons in planet-planet scattering

NASA Astrophysics Data System (ADS)

CIAN HONG, YU; Lunine, Jonathan; Nicholson, Phillip; Raymond, Sean

2015-12-01

Planet-planet scattering is the best candidate mechanism for explaining the eccentricity distribution of exoplanets. Here we study the survival and dynamics of exomoons under strong perturbations during giant planet scattering. During close encounters, planets and moons exchange orbital angular momentum and energy. The most common outcomes are the destruction of moons by ejection from the system, collision with the planets and the star, and scattering of moons onto perturbed but still planet-bound orbits. A small percentage of interesting moons can remain bound to ejected (free-floating) planets or be captured by a different planet. Moons' survival rate is correlated with planet observables such as mass, semi-major axis, eccentricity and inclination, as well as the close encounter distance and the number of close encounters. In addition, moons' survival rate and dynamical outcomes are predetermined by the moons' initial semi-major axes. The survival rate drops quickly as moons' distances increase, but simulations predict a good chance of survival for the Galilean moons. Moons with different dynamical outcomes occupy different regions of orbital parameter space, which may enable the study of moons' past evolution. Potential effects of planet obliquity evolution caused by close encounters on the satellites’ stability and dynamics will be reported, as well as detailed and systematic studies of individual close encounter events.

Wake-sleep transition as a noisy bifurcation

NASA Astrophysics Data System (ADS)

Yang, Dong-Ping; McKenzie-Sell, Lauren; Karanjai, Angela; Robinson, P. A.

2016-08-01

A recent physiologically based model of the ascending arousal system is used to analyze the dynamics near the transition from wake to sleep, which corresponds to a saddle-node bifurcation at a critical point. A normal form is derived by approximating the dynamics by those of a particle in a parabolic potential well with dissipation. This mechanical analog is used to calculate the power spectrum of fluctuations in response to a white noise drive, and the scalings of fluctuation variance and spectral width are derived versus distance from the critical point. The predicted scalings are quantitatively confirmed by numerical simulations, which show that the variance increases and the spectrum undergoes critical slowing, both in accord with theory. These signals can thus serve as potential precursors to indicate imminent wake-sleep transition, with potential application to safety-critical occupations in transport, air-traffic control, medicine, and heavy industry.

Influence of the distance between target surface and focal point on the expansion dynamics of a laser-induced silicon plasma with spatial confinement

NASA Astrophysics Data System (ADS)

Zhang, Dan; Chen, Anmin; Wang, Xiaowei; Wang, Ying; Sui, Laizhi; Ke, Da; Li, Suyu; Jiang, Yuanfei; Jin, Mingxing

2018-05-01

Expansion dynamics of a laser-induced plasma plume, with spatial confinement, for various distances between the target surface and focal point were studied by the fast photography technique. A silicon wafer was ablated to induce the plasma with a Nd:YAG laser in an atmospheric environment. The expansion dynamics of the plasma plume depended on the distance between the target surface and focal point. In addition, spatially confined time-resolved images showed the different structures of the plasma plumes at different distances between the target surface and focal point. By analyzing the plume images, the optimal distance for emission enhancement was found to be approximately 6 mm away from the geometrical focus using a 10 cm focal length lens. This optimized distance resulted in the strongest compression ratio of the plasma plume by the reflected shock wave. Furthermore, the duration of the interaction between the reflected shock wave and the plasma plume was also prolonged.

Angular declination and the dynamic perception of egocentric distance.

PubMed

Gajewski, Daniel A; Philbeck, John W; Wirtz, Philip W; Chichka, David

2014-02-01

The extraction of the distance between an object and an observer is fast when angular declination is informative, as it is with targets placed on the ground. To what extent does angular declination drive performance when viewing time is limited? Participants judged target distances in a real-world environment with viewing durations ranging from 36-220 ms. An important role for angular declination was supported by experiments showing that the cue provides information about egocentric distance even on the very first glimpse, and that it supports a sensitive response to distance in the absence of other useful cues. Performance was better at 220-ms viewing durations than for briefer glimpses, suggesting that the perception of distance is dynamic even within the time frame of a typical eye fixation. Critically, performance in limited viewing trials was better when preceded by a 15-s preview of the room without a designated target. The results indicate that the perception of distance is powerfully shaped by memory from prior visual experience with the scene. A theoretical framework for the dynamic perception of distance is presented. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Treelike networks accelerating capillary flow.

PubMed

Shou, Dahua; Ye, Lin; Fan, Jintu

2014-05-01

Transport in treelike networks has received wide attention in natural systems, oil recovery, microelectronic cooling systems, and textiles. Existing studies are focused on transport behaviors under a constant potential difference (including pressure, temperature, and voltage) in a steady state [B. Yu and B. Li, Phys. Rev. E 73, 066302 (2006); J. Chen, B. Yu, P. Xu, and Y. Li, Phys. Rev. E 75, 056301 (2007)]. However, dynamic (time-dependent) transport in such systems has rarely been concerned. In this work, we theoretically investigate the dynamics of capillary flow in treelike networks and design the distribution of radius and length of local branches for the fastest capillary flow. It is demonstrated that capillary flow in the optimized tree networks is faster than in traditional parallel tube nets under fixed constraints. As well, the flow time of the liquid is found to increase approximately linearly with penetration distance, which differs from Washburn's classic description that flow time increases as the square of penetration distance in a uniform tube.

Preserving photon qubits in an unknown quantum state with Knill Dynamical Decoupling - Towards an all optical quantum memory

NASA Astrophysics Data System (ADS)

Gupta, Manish K.; Navarro, Erik J.; Moulder, Todd A.; Mueller, Jason D.; Balouchi, Ashkan; Brown, Katherine L.; Lee, Hwang; Dowling, Jonathan P.

2015-05-01

The storage of quantum states and its distribution over long distances is essential for emerging quantum technologies such as quantum networks and long distance quantum cryptography. The implementation of polarization-based quantum communication is limited by signal loss and decoherence caused by the birefringence of a single-mode fiber. We investigate the Knill dynamical decoupling scheme, implemented using half-wave plates in a single mode fiber, to minimize decoherence of polarization qubit and show that a fidelity greater than 99 % can be achieved in absence of rotation error and fidelity greater than 96 % can be achieved in presence of rotation error. Such a scheme can be used to preserve any quantum state with high fidelity and has potential application for constructing all optical quantum memory, quantum delay line, and quantum repeater. The authors would like to acknowledge the support from the Air Force office of Scientific Research, the Army Research office, and the National Science Foundation.

Mapping photometric metallicities in the Galactic halo using broadband photometry

NASA Astrophysics Data System (ADS)

Hebenstreit, Samuel David; Nidever, David L.; Munn, Jeffrey A.; Majewski, Steven R.

2018-06-01

An important objective of modern Astrophysics is to trace the history of galaxies and the dynamics of their formations. The outer regions of the Milky Way, including the Galactic halo, could potentially elucidate the evolutionary history of our galaxy. In this study, we make use of extensive DDO51 photometry combined with SDSS broadband photometry to select giant stars reaching to 90 kpc. Photometric metallicities, calibrated by overlapping spectroscopic data (SDSS, APOGEE and LAMOST), and distances are calculated for all giant stars. Using these metallicities and distances, we construct metallicity distribution functions (MDFs) from these stars. We study the MDFs for information pertaining to the accretion history of the Milky Way.

Role of vaccination-induced immunity and antigenic distance in the transmission dynamics of highly pathogenic avian influenza H5N1

PubMed Central

Rousou, Xanthoula; Kalthoff, Donata; Beer, Martin

2016-01-01

Highly pathogenic avian influenza (HPAI) H5N1 epidemics in poultry cause huge economic losses as well as sporadic human morbidity and mortality. Vaccination in poultry has often been reported as being ineffective in preventing transmission and as a potential driving force in the selection of immune escape mutants. We conducted transmission experiments to evaluate the transmission dynamics of HPAI H5N1 strains in chickens vaccinated with high and low doses of immune escape mutants we have previously selected, and analysed the data using mathematical models. Remarkably, we demonstrate that the effect of antigenic distances between the vaccine and challenge strains used in this study is too small to influence the transmission dynamics of the strains used. This is because the effect of a sufficient vaccine dose on antibody levels against the challenge viruses is large enough to compensate for any decrease in antibody titres due to antigenic differences between vaccine and challenge strains. Our results show that at least under experimental conditions, vaccination will remain effective even after antigenic changes as may be caused by the initial selection in vaccinated birds. PMID:26763336

Spatiotemporal dynamics of surface water networks across a global biodiversity hotspot—implications for conservation

NASA Astrophysics Data System (ADS)

Tulbure, Mirela G.; Kininmonth, Stuart; Broich, Mark

2014-11-01

The concept of habitat networks represents an important tool for landscape conservation and management at regional scales. Previous studies simulated degradation of temporally fixed networks but few quantified the change in network connectivity from disintegration of key features that undergo naturally occurring spatiotemporal dynamics. This is particularly of concern for aquatic systems, which typically show high natural spatiotemporal variability. Here we focused on the Swan Coastal Plain, a bioregion that encompasses a global biodiversity hotspot in Australia with over 1500 water bodies of high biodiversity. Using graph theory, we conducted a temporal analysis of water body connectivity over 13 years of variable climate. We derived large networks of surface water bodies using Landsat data (1999-2011). We generated an ensemble of 278 potential networks at three dispersal distances approximating the maximum dispersal distance of different water dependent organisms. We assessed network connectivity through several network topology metrics and quantified the resilience of the network topology during wet and dry phases. We identified ‘stepping stone’ water bodies across time and compared our networks with theoretical network models with known properties. Results showed a highly dynamic seasonal pattern of variability in network topology metrics. A decline in connectivity over the 13 years was noted with potential negative consequences for species with limited dispersal capacity. The networks described here resemble theoretical scale-free models, also known as ‘rich get richer’ algorithm. The ‘stepping stone’ water bodies are located in the area around the Peel-Harvey Estuary, a Ramsar listed site, and some are located in a national park. Our results describe a powerful approach that can be implemented when assessing the connectivity for a particular organism with known dispersal distance. The approach of identifying the surface water bodies that act as ‘stepping stone’ over time may help prioritize surface water bodies that are essential for maintaining regional scale connectivity.

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

Structure of Poly(dialkylsiloxane) Melts:  Comparisons of Wide-Angle X-ray Scattering, Molecular Dynamics Simulations, and Integral Equation Theory

DOE PAGES

Habenschuss, Anton; Tsige, Mesfin; Curro, John G.; ...

2007-08-21

Here, wide-angle X-ray scattering, molecular dynamics (MD) simulations, and integral equation theory are used to study the structure of poly(diethylsiloxane) (PDES), poly(ethylmethylsiloxane) (PEMS), and poly(dimethylsiloxane) (PDMS) melts. The structure functions of PDES, PEMS, and PDMS are similar, but systematic trends in the intermolecular packing are observed. The local intramolecular structure is extracted from the experimental structure functions. The bond distances and bond angles obtained, including the large Si-O-Si angle, are in good agreement with the explicit atom (EA) and united atom (UA) potentials used in the simulations and theory and from other sources. Very good agreement is found between themore » MD simulations using the EA potentials and the experimental scattering results. Good agreement is also found between the polymer reference interaction site model (PRISM theory) and the UA MD simulations. The intermolecular structure is examined experimentally using an appropriately weighted radial distribution function and with theory and simulation using intermolecular site/site pair correlation functions. Finally, experiment, simulation, and theory show systematic increases in the chain/chain packing distances in the siloxanes as the number of sites in the pendant side chains is increased.« less

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

PubMed Central

Abriata, Luciano A.; Dal Peraro, Matteo

2015-01-01

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin’s noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations. PMID:26023027

Evidence for asymptotic safety from lattice quantum gravity.

PubMed

Laiho, J; Coumbe, D

2011-10-14

We calculate the spectral dimension for nonperturbative quantum gravity defined via Euclidean dynamical triangulations. We find that it runs from a value of ∼3/2 at short distance to ∼4 at large distance scales, similar to results from causal dynamical triangulations. We argue that the short-distance value of 3/2 for the spectral dimension may resolve the tension between asymptotic safety and the holographic principle.

Timing of transients: quantifying reaching times and transient behavior in complex systems

NASA Astrophysics Data System (ADS)

Kittel, Tim; Heitzig, Jobst; Webster, Kevin; Kurths, Jürgen

2017-08-01

In dynamical systems, one may ask how long it takes for a trajectory to reach the attractor, i.e. how long it spends in the transient phase. Although for a single trajectory the mathematically precise answer may be infinity, it still makes sense to compare different trajectories and quantify which of them approaches the attractor earlier. In this article, we categorize several problems of quantifying such transient times. To treat them, we propose two metrics, area under distance curve and regularized reaching time, that capture two complementary aspects of transient dynamics. The first, area under distance curve, is the distance of the trajectory to the attractor integrated over time. It measures which trajectories are ‘reluctant’, i.e. stay distant from the attractor for long, or ‘eager’ to approach it right away. Regularized reaching time, on the other hand, quantifies the additional time (positive or negative) that a trajectory starting at a chosen initial condition needs to approach the attractor as compared to some reference trajectory. A positive or negative value means that it approaches the attractor by this much ‘earlier’ or ‘later’ than the reference, respectively. We demonstrated their substantial potential for application with multiple paradigmatic examples uncovering new features.

Effective field theories for van der Waals interactions

NASA Astrophysics Data System (ADS)

Brambilla, Nora; Shtabovenko, Vladyslav; Tarrús Castellà, Jaume; Vairo, Antonio

2017-06-01

Van der Waals interactions between two neutral but polarizable systems at a separation R much larger than the typical size of the systems are at the core of a broad sweep of contemporary problems in settings ranging from atomic, molecular and condensed matter physics to strong interactions and gravity. In this paper, we reexamine the dispersive van der Waals interactions between two hydrogen atoms. The novelty of the analysis resides in the usage of nonrelativistic effective field theories of quantum electrodynamics. In this framework, the van der Waals potential acquires the meaning of a matching coefficient in an effective field theory, dubbed van der Waals effective field theory, suited to describe the low-energy dynamics of an atom pair. It may be computed systematically as a series in R times some typical atomic scale and in the fine-structure constant α . The van der Waals potential gets short-range contributions and radiative corrections, which we compute in dimensional regularization and renormalize here for the first time. Results are given in d space-time dimensions. One can distinguish among different regimes depending on the relative size between 1 /R and the typical atomic bound-state energy, which is of order m α2. Each regime is characterized by a specific hierarchy of scales and a corresponding tower of effective field theories. The short-distance regime is characterized by 1 /R ≫m α2 and the leading-order van der Waals potential is the London potential. We also compute next-to-next-to-next-to-leading-order corrections. In the long-distance regime we have 1 /R ≪m α2. In this regime, the van der Waals potential contains contact terms, which are parametrically larger than the Casimir-Polder potential that describes the potential at large distances. In the effective field theory, the Casimir-Polder potential counts as a next-to-next-to-next-to-leading-order effect. In the intermediate-distance regime, 1 /R ˜m α2, a significantly more complex potential is obtained. We compare this exact result with the two previous limiting cases. We conclude by commenting on the van der Waals interactions in the hadronic case.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

Characteristics and Drivers of High-Altitude Ladybird Flight: Insights from Vertical-Looking Entomological Radar

PubMed Central

Jeffries, Daniel L.; Chapman, Jason; Roy, Helen E.; Humphries, Stuart; Harrington, Richard; Brown, Peter M. J.; Handley, Lori-J. Lawson

2013-01-01

Understanding the characteristics and drivers of dispersal is crucial for predicting population dynamics, particularly in range-shifting species. Studying long-distance dispersal in insects is challenging, but recent advances in entomological radar offer unique insights. We analysed 10 years of radar data collected at Rothamsted Research, U.K., to investigate characteristics (altitude, speed, seasonal and annual trends) and drivers (aphid abundance, air temperature, wind speed and rainfall) of high-altitude flight of the two most abundant U.K. ladybird species (native Coccinella septempunctata and invasive Harmonia axyridis). These species cannot be distinguished in the radar data since their reflectivity signals overlap, and they were therefore analysed together. However, their signals do not overlap with other, abundant insects so we are confident they constitute the overwhelming majority of the analysed data. The target species were detected up to ∼1100 m above ground level, where displacement speeds of up to ∼60 km/h were recorded, however most ladybirds were found between ∼150 and 500 m, and had a mean displacement of 30 km/h. Average flight time was estimated, using tethered flight experiments, to be 36.5 minutes, but flights of up to two hours were observed. Ladybirds are therefore potentially able to travel 18 km in a “typical” high-altitude flight, but up to 120 km if flying at higher altitudes, indicating a high capacity for long-distance dispersal. There were strong seasonal trends in ladybird abundance, with peaks corresponding to the highest temperatures of mid-summer, and warm air temperature was the key driver of ladybird flight. Climatic warming may therefore increase the potential for long-distance dispersal in these species. Low aphid abundance was a second significant factor, highlighting the important role of aphid population dynamics in ladybird dispersal. This research illustrates the utility of radar for studying high-altitude insect flight and has important implications for predicting long-distance dispersal. PMID:24367512

Contact- and distance-based principal component analysis of protein dynamics.

PubMed

Ernst, Matthias; Sittel, Florian; Stock, Gerhard

2015-12-28

To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal coordinates, e.g., backbone dihedral angles or various kinds of distances, may be used as input data in a PCA. Adopting two well-known model problems, folding of villin headpiece and the functional dynamics of BPTI, a systematic study of PCA using distance-based measures is presented which employs distances between Cα-atoms as well as distances between inter-residue contacts including side chains. While this approach seems prohibitive for larger systems due to the quadratic scaling of the number of distances with the size of the molecule, it is shown that it is sufficient (and sometimes even better) to include only relatively few selected distances in the analysis. The quality of the PCA is assessed by considering the resolution of the resulting free energy landscape (to identify metastable conformational states and barriers) and the decay behavior of the corresponding autocorrelation functions (to test the time scale separation of the PCA). By comparing results obtained with distance-based, dihedral angle, and Cartesian coordinates, the study shows that the choice of input variables may drastically influence the outcome of a PCA.

Contact- and distance-based principal component analysis of protein dynamics

NASA Astrophysics Data System (ADS)

Ernst, Matthias; Sittel, Florian; Stock, Gerhard

2015-12-01

To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal coordinates, e.g., backbone dihedral angles or various kinds of distances, may be used as input data in a PCA. Adopting two well-known model problems, folding of villin headpiece and the functional dynamics of BPTI, a systematic study of PCA using distance-based measures is presented which employs distances between Cα-atoms as well as distances between inter-residue contacts including side chains. While this approach seems prohibitive for larger systems due to the quadratic scaling of the number of distances with the size of the molecule, it is shown that it is sufficient (and sometimes even better) to include only relatively few selected distances in the analysis. The quality of the PCA is assessed by considering the resolution of the resulting free energy landscape (to identify metastable conformational states and barriers) and the decay behavior of the corresponding autocorrelation functions (to test the time scale separation of the PCA). By comparing results obtained with distance-based, dihedral angle, and Cartesian coordinates, the study shows that the choice of input variables may drastically influence the outcome of a PCA.

Kantorovich-Wasserstein Distance for Identifying the Dynamic of Some Compartmental Models in Biology

NASA Astrophysics Data System (ADS)

Pousin, Jérôme

2008-09-01

Determining the influence of a biological species to the evolution of an other one strongly depends on the choice of mathematical models in biology. In this work we consider the case of distribution of lipids (docosahexaenoic acid (DHA)) in two compartments of the plasma, the platelets and the erythrocytes, and we compare three different mathematical approaches. The first one, consists of a system of differential equations the coefficients of which are identified through a least square procedure. The second one is made of a system of differential equations on a graph, the adjacency matrix of which represents the interplay between the species. The third one consists of mapping the provider curves to the target curves. Thus we have a distance between two families of curves, the curves of providers and the curves of targets, and by comparing the distances, we are able to decide which provider delivers preferentially to a target according to cumulative species mass curves. Numerical results are presented, and we show that the ordinary differential least square model provides qualitatively the same result as the Kantorovich-Wasserstein distance strategy. Finally, we discuss the potential ability of the presented Kantorovich-Wasserstein distance to perform the biological properties of a system.

Tracking the dynamics of divergent thinking via semantic distance: Analytic methods and theoretical implications.

PubMed

Hass, Richard W

2017-02-01

Divergent thinking has often been used as a proxy measure of creative thinking, but this practice lacks a foundation in modern cognitive psychological theory. This article addresses several issues with the classic divergent-thinking methodology and presents a new theoretical and methodological framework for cognitive divergent-thinking studies. A secondary analysis of a large dataset of divergent-thinking responses is presented. Latent semantic analysis was used to examine the potential changes in semantic distance between responses and the concept represented by the divergent-thinking prompt across successive response iterations. The results of linear growth modeling showed that although there is some linear increase in semantic distance across response iterations, participants high in fluid intelligence tended to give more distant initial responses than those with lower fluid intelligence. Additional analyses showed that the semantic distance of responses significantly predicted the average creativity rating given to the response, with significant variation in average levels of creativity across participants. Finally, semantic distance does not seem to be related to participants' choices of their own most creative responses. Implications for cognitive theories of creativity are discussed, along with the limitations of the methodology and directions for future research.

Dynamic Parameters of the 2015 Nepal Gorkha Mw7.8 Earthquake Constrained by Multi-observations

NASA Astrophysics Data System (ADS)

Weng, H.; Yang, H.

2017-12-01

Dynamic rupture model can provide much detailed insights into rupture physics that is capable of assessing future seismic risk. Many studies have attempted to constrain the slip-weakening distance, an important parameter controlling friction behavior of rock, for several earthquakes based on dynamic models, kinematic models, and direct estimations from near-field ground motion. However, large uncertainties of the values of the slip-weakening distance still remain, mostly because of the intrinsic trade-offs between the slip-weakening distance and fault strength. Here we use a spontaneously dynamic rupture model to constrain the frictional parameters of the 25 April 2015 Mw7.8 Nepal earthquake, by combining with multiple seismic observations such as high-rate cGPS data, strong motion data, and kinematic source models. With numerous tests we find the trade-off patterns of final slip, rupture speed, static GPS ground displacements, and dynamic ground waveforms are quite different. Combining all the seismic constraints we can conclude a robust solution without a substantial trade-off of average slip-weakening distance, 0.6 m, in contrast to previous kinematical estimation of 5 m. To our best knowledge, this is the first time to robustly determine the slip-weakening distance on seismogenic fault from seismic observations. The well-constrained frictional parameters may be used for future dynamic models to assess seismic hazard, such as estimating the peak ground acceleration (PGA) etc. Similar approach could also be conducted for other great earthquakes, enabling broad estimations of the dynamic parameters in global perspectives that can better reveal the intrinsic physics of earthquakes.

Impacts of land cover data selection and trait parameterisation on dynamic modelling of species' range expansion.

PubMed

Heikkinen, Risto K; Bocedi, Greta; Kuussaari, Mikko; Heliölä, Janne; Leikola, Niko; Pöyry, Juha; Travis, Justin M J

2014-01-01

Dynamic models for range expansion provide a promising tool for assessing species' capacity to respond to climate change by shifting their ranges to new areas. However, these models include a number of uncertainties which may affect how successfully they can be applied to climate change oriented conservation planning. We used RangeShifter, a novel dynamic and individual-based modelling platform, to study two potential sources of such uncertainties: the selection of land cover data and the parameterization of key life-history traits. As an example, we modelled the range expansion dynamics of two butterfly species, one habitat specialist (Maniola jurtina) and one generalist (Issoria lathonia). Our results show that projections of total population size, number of occupied grid cells and the mean maximal latitudinal range shift were all clearly dependent on the choice made between using CORINE land cover data vs. using more detailed grassland data from three alternative national databases. Range expansion was also sensitive to the parameterization of the four considered life-history traits (magnitude and probability of long-distance dispersal events, population growth rate and carrying capacity), with carrying capacity and magnitude of long-distance dispersal showing the strongest effect. Our results highlight the sensitivity of dynamic species population models to the selection of existing land cover data and to uncertainty in the model parameters and indicate that these need to be carefully evaluated before the models are applied to conservation planning.

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

PubMed Central

Guenot, J.; Kollman, P. A.

1992-01-01

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable. PMID:1304396

Molecular simulation of disjoining-pressure isotherms for free liquid , Lennard-Jones thin films

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

Bhatt, Divesh; Newman, John; Radke, C.J.

2001-10-01

We present canonical-ensemble molecular-dynamics simulations of disjoining-pressure isotherms in Lennard-Jones free liquid films. Thermodynamics demands that the disjoining pressure is determined uniquely as a function of the chemical potential purely from the phase diagram of the fluid. Our results from molecular dynamics validate this argument. The inverse-sixth-power distance term in the Lennard-Jones intermolecular potential represents van der Waals dispersion forces. Hence, we compare our results with classical Hamaker theory that is based on dispersion forces but assumes a slab geometry for the density profile and completely neglects fluid structure and entropy. We find that the Hamaker constant obtained from ourmore » simulations is about an order of magnitude larger than that from classical theory. To investigate the origin of this discrepancy, we calculate the disjoining-pressure isotherm using a density-functional theory relaxing the inherent assumptions in the Hamaker theory and imparting to the fluid an approximate structure. For disjoining pressure as a function of chemical potential, the results of density-functional theory and molecular dynamics are very close. Even for disjoining-pressure isotherms, and the subsequently calculated Hamaker constant, results of the density-functional theory are closer to the molecular-dynamics simulations by about a factor of 4 compared to Hamaker theory. [References: 44]« less

Photoluminescence decay dynamics in γ-Ga2O3 nanocrystals: The role of exclusion distance at short time scales

NASA Astrophysics Data System (ADS)

Fernandes, Brian; Hegde, Manu; Stanish, Paul C.; Mišković, Zoran L.; Radovanovic, Pavle V.

2017-09-01

We developed a comprehensive theoretical model describing the photoluminescence decay dynamics at short and long time scales based on the donor-acceptor defect interactions in γ-Ga2O3 nanocrystals, and quantitatively determined the importance of exclusion distance and spatial distribution of defects. We allowed for donors and acceptors to be adjacent to each other or separated by different exclusion distances. The optimal exclusion distance was found to be comparable to the donor Bohr radius and have a strong effect on the photoluminescence decay curve at short times. The importance of the exclusion distance at short time scales was confirmed by Monte Carlo simulations.

Distance geometry protocol to generate conformations of natural products to structurally interpret ion mobility-mass spectrometry collision cross sections.

PubMed

Stow, Sarah M; Goodwin, Cody R; Kliman, Michal; Bachmann, Brian O; McLean, John A; Lybrand, Terry P

2014-12-04

Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to the ion conformation and hence molecular size and shape. Studying the conformational landscape of these ionized molecules computationally provides interpretation to delineate the potential structures that these CCS values could represent, or conversely, structural motifs not consistent with the IM data. A challenge in the IM-MS community is the ability to rapidly compute conformations to interpret natural product data, a class of molecules exhibiting a broad range of biological activity. The diversity of biological activity is, in part, related to the unique structural characteristics often observed for natural products. Contemporary approaches to structurally interpret IM-MS data for peptides and proteins typically utilize molecular dynamics (MD) simulations to sample conformational space. However, MD calculations are computationally expensive, they require a force field that accurately describes the molecule of interest, and there is no simple metric that indicates when sufficient conformational sampling has been achieved. Distance geometry is a computationally inexpensive approach that creates conformations based on sampling different pairwise distances between the atoms within the molecule and therefore does not require a force field. Progressively larger distance bounds can be used in distance geometry calculations, providing in principle a strategy to assess when all plausible conformations have been sampled. Our results suggest that distance geometry is a computationally efficient and potentially superior strategy for conformational analysis of natural products to interpret gas-phase CCS data.

Distance Geometry Protocol to Generate Conformations of Natural Products to Structurally Interpret Ion Mobility-Mass Spectrometry Collision Cross Sections

PubMed Central

2015-01-01

Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to the ion conformation and hence molecular size and shape. Studying the conformational landscape of these ionized molecules computationally provides interpretation to delineate the potential structures that these CCS values could represent, or conversely, structural motifs not consistent with the IM data. A challenge in the IM-MS community is the ability to rapidly compute conformations to interpret natural product data, a class of molecules exhibiting a broad range of biological activity. The diversity of biological activity is, in part, related to the unique structural characteristics often observed for natural products. Contemporary approaches to structurally interpret IM-MS data for peptides and proteins typically utilize molecular dynamics (MD) simulations to sample conformational space. However, MD calculations are computationally expensive, they require a force field that accurately describes the molecule of interest, and there is no simple metric that indicates when sufficient conformational sampling has been achieved. Distance geometry is a computationally inexpensive approach that creates conformations based on sampling different pairwise distances between the atoms within the molecule and therefore does not require a force field. Progressively larger distance bounds can be used in distance geometry calculations, providing in principle a strategy to assess when all plausible conformations have been sampled. Our results suggest that distance geometry is a computationally efficient and potentially superior strategy for conformational analysis of natural products to interpret gas-phase CCS data. PMID:25360896

Dynamic frequency-domain interferometer for absolute distance measurements with high resolution

NASA Astrophysics Data System (ADS)

Weng, Jidong; Liu, Shenggang; Ma, Heli; Tao, Tianjiong; Wang, Xiang; Liu, Cangli; Tan, Hua

2014-11-01

A unique dynamic frequency-domain interferometer for absolute distance measurement has been developed recently. This paper presents the working principle of the new interferometric system, which uses a photonic crystal fiber to transmit the wide-spectrum light beams and a high-speed streak camera or frame camera to record the interference stripes. Preliminary measurements of harmonic vibrations of a speaker, driven by a radio, and the changes in the tip clearance of a rotating gear wheel show that this new type of interferometer has the ability to perform absolute distance measurements both with high time- and distance-resolution.

Climate change effects on migration phenology may mismatch brood parasitic cuckoos and their hosts.

PubMed

Saino, Nicola; Rubolini, Diego; Lehikoinen, Esa; Sokolov, Leonid V; Bonisoli-Alquati, Andrea; Ambrosini, Roberto; Boncoraglio, Giuseppe; Møller, Anders P

2009-08-23

Phenological responses to climate change vary among taxa and across trophic levels. This can lead to a mismatch between the life cycles of ecologically interrelated populations (e.g. predators and prey), with negative consequences for population dynamics of some of the interacting species. Here we provide, to our knowledge, the first evidence that climate change might disrupt the association between the life cycles of the common cuckoo (Cuculus canorus), a migratory brood parasitic bird, and its hosts. We investigated changes in timing of spring arrival of the cuckoo and its hosts throughout Europe over six decades, and found that short-distance, but not long-distance, migratory hosts have advanced their arrival more than the cuckoo. Hence, cuckoos may keep track of phenological changes of long-distance, but not short-distance migrant hosts, with potential consequences for breeding of both cuckoo and hosts. The mismatch to some of the important hosts may contribute to the decline of cuckoo populations and explain some of the observed local changes in parasitism rates of migratory hosts.

Hadronic and nuclear interactions in QCD

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

Not Available

Despite the evidence that QCD - or something close to it - gives a correct description of the structure of hadrons and their interactions, it seems paradoxical that the theory has thus far had very little impact in nuclear physics. One reason for this is that the application of QCD to distances larger than 1 fm involves coherent, non-perturbative dynamics which is beyond present calculational techniques. For example, in QCD the nuclear force can evidently be ascribed to quark interchange and gluon exchange processes. These, however, are as complicated to analyze from a fundamental point of view as is themore » analogous covalent bond in molecular physics. Since a detailed description of quark-quark interactions and the structure of hadronic wavefunctions is not yet well-understood in QCD, it is evident that a quantitative first-principle description of the nuclear force will require a great deal of theoretical effort. Another reason for the limited impact of QCD in nuclear physics has been the conventional assumption that nuclear interactions can for the most part be analyzed in terms of an effective meson-nucleon field theory or potential model in isolation from the details of short distance quark and gluon structure of hadrons. These lectures, argue that this view is untenable: in fact, there is no correspondence principle which yields traditional nuclear physics as a rigorous large-distance or non-relativistic limit of QCD dynamics. On the other hand, the distinctions between standard nuclear physics dynamics and QCD at nuclear dimensions are extremely interesting and illuminating for both particle and nuclear physics.« less

System Dynamics in Distance Education and a Call to Develop a Standard Model

ERIC Educational Resources Information Center

Shaffer, Steven C.

2005-01-01

This paper describes systems dynamics, reviews the literature of uses of systems concepts in distance education (DE), presents a preliminary model, and ends in a call to researchers to contribute to the building of a standard model of DE. (Contains 4 figures.)

Comparison of Dynamic Balance in Collegiate Field Hockey and Football Players Using Star Excursion Balance Test

PubMed Central

Bhat, Rashi; Moiz, Jamal Ali

2013-01-01

Purpose The preliminary study aimed to compare dynamic balance between collegiate athletes competing or training in football and hockey using star excursion balance test. Methods A total thirty university level players, football (n = 15) and field hockey (n = 15) were participated in the study. Dynamic balance was assessed by using star excursion balance test. The testing grid consists of 8 lines each 120 cm in length extending from a common point at 45° increments. The subjects were instructed to maintain a stable single leg stance with the test leg with shoes off and to reach for maximal distance with the other leg in each of the 8 directions. A pencil was used to point and read the distance to which each subject's foot reached. The normalized leg reach distances in each direction were summed for both limbs and the total sum of the mean of summed normalized distances of both limbs were calculated. Results There was no significant difference in all the directions of star excursion balance test scores in both the groups. Additionally, composite reach distances of both groups also found non-significant (P=0.5). However, the posterior (P=0.05) and lateral (P=0.03) normalized reach distances were significantly more in field hockey players. Conclusion Field hockey players and football players did not differ in terms of dynamic balance. PMID:24427482

Comparison of dynamic balance in collegiate field hockey and football players using star excursion balance test.

PubMed

Bhat, Rashi; Moiz, Jamal Ali

2013-09-01

The preliminary study aimed to compare dynamic balance between collegiate athletes competing or training in football and hockey using star excursion balance test. A total thirty university level players, football (n = 15) and field hockey (n = 15) were participated in the study. Dynamic balance was assessed by using star excursion balance test. The testing grid consists of 8 lines each 120 cm in length extending from a common point at 45° increments. The subjects were instructed to maintain a stable single leg stance with the test leg with shoes off and to reach for maximal distance with the other leg in each of the 8 directions. A pencil was used to point and read the distance to which each subject's foot reached. The normalized leg reach distances in each direction were summed for both limbs and the total sum of the mean of summed normalized distances of both limbs were calculated. There was no significant difference in all the directions of star excursion balance test scores in both the groups. Additionally, composite reach distances of both groups also found non-significant (P=0.5). However, the posterior (P=0.05) and lateral (P=0.03) normalized reach distances were significantly more in field hockey players. Field hockey players and football players did not differ in terms of dynamic balance.

A Qualitative Analysis of Loneliness Dynamics Involved with College Long-Distance Relationships

ERIC Educational Resources Information Center

Firmin, Michael W.; Firmin, Ruth L.; Lorenzen, Kailee

2014-01-01

The present phenomenological, qualitative research study involved in-depth interviews of all 16 female, sophomore students involved in respective distance relationships at a private, selective, comprehensive, Midwest university. Among other results found in the study, the present article specifically addressed the loneliness dynamics involved with…

Distance Teacher Education in Pakistan

ERIC Educational Resources Information Center

Jumani, Nabi Bux; Zai, Zafar Iqbal Yousuf

2009-01-01

Distance education means instruction in which the instructor and student are separated by distance and interact through the assistance of communication technology. Distance education changes the learning relationship from the common, centralized school model to a more decentralized, flexible model. It also reverses social dynamics by bringing…

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

PubMed

Ostermeir, Katja; Zacharias, Martin

2014-12-01

Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations. © 2014 Wiley Periodicals, Inc.

Graph distance for complex networks

NASA Astrophysics Data System (ADS)

Shimada, Yutaka; Hirata, Yoshito; Ikeguchi, Tohru; Aihara, Kazuyuki

2016-10-01

Networks are widely used as a tool for describing diverse real complex systems and have been successfully applied to many fields. The distance between networks is one of the most fundamental concepts for properly classifying real networks, detecting temporal changes in network structures, and effectively predicting their temporal evolution. However, this distance has rarely been discussed in the theory of complex networks. Here, we propose a graph distance between networks based on a Laplacian matrix that reflects the structural and dynamical properties of networked dynamical systems. Our results indicate that the Laplacian-based graph distance effectively quantifies the structural difference between complex networks. We further show that our approach successfully elucidates the temporal properties underlying temporal networks observed in the context of face-to-face human interactions.

Dynamics of statistical distance: Quantum limits for two-level clocks

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

Braunstein, S.L.; Milburn, G.J.

1995-03-01

We study the evolution of statistical distance on the Bloch sphere under unitary and nonunitary dynamics. This corresponds to studying the limits to clock precision for a clock constructed from a two-state system. We find that the initial motion away from pure states under nonunitary dynamics yields the greatest accuracy for a one-tick'' clock; in this case the clock's precision is not limited by the largest frequency of the system.

Seascape dynamics of a coral disease outbreak in Hawaii

NASA Astrophysics Data System (ADS)

Sziklay, J.; Donahue, M. J.

2016-02-01

When trying to understand patterns of disease transmission, it is essential to estimate the rate at which individuals become infected. Over the past five years, there have been three coral disease outbreaks of tissue loss diseases in Kaneohe Bay, Oahu, Hawaii resulting in localized mass mortality of the host coral species Montipora capitata. These progressive tissue loss diseases cause coral tissue to disassociate with the coral skeleton, usually resulting in total colony mortality. During the most recent outbreak (winter 2015) we designed a natural experiment to estimate force of infection in the field, and determine whether benthic characteristics of the coral community (size of host, distance from host to infected individuals, coral community composition) increased or decreased the probability of survival. We determined that colony size and distance to infected neighbors were the most important determinants of infection likelihood and calculated a force of infection, which is key to understanding epidemiology in any disease and for modeling potential intervention strategies. We plan to use this information to better understand disease dynamics for tissue loss diseases in coral more broadly and to identify putative vectors of disease transmission.

Orbits of Selected Globular Clusters in the Galactic Bulge

NASA Astrophysics Data System (ADS)

Pérez-Villegas, A.; Rossi, L.; Ortolani, S.; Casotto, S.; Barbuy, B.; Bica, E.

2018-05-01

We present orbit analysis for a sample of eight inner bulge globular clusters, together with one reference halo object. We used proper motion values derived from long time base CCD data. Orbits are integrated in both an axisymmetric model and a model including the Galactic bar potential. The inclusion of the bar proved to be essential for the description of the dynamical behaviour of the clusters. We use the Monte Carlo scheme to construct the initial conditions for each cluster, taking into account the uncertainties in the kinematical data and distances. The sample clusters show typically maximum height to the Galactic plane below 1.5 kpc, and develop rather eccentric orbits. Seven of the bulge sample clusters share the orbital properties of the bar/bulge, having perigalactic and apogalatic distances, and maximum vertical excursion from the Galactic plane inside the bar region. NGC 6540 instead shows a completely different orbital behaviour, having a dynamical signature of the thick disc. Both prograde and prograde-retrograde orbits with respect to the direction of the Galactic rotation were revealed, which might characterise a chaotic behaviour.

Molecular dynamics simulation of membrane in room temperature ionic liquids

NASA Astrophysics Data System (ADS)

Theng, Soong Guan; Jumbri, Khairulazhar bin; Wirzal, Mohd Dzul Hakim

2017-10-01

The polyvinylidene difluoride (PVDF) membrane has been a popular material in membrane separation process. In this work, molecular dynamic simulation was done on the PVDF membrane with 100 wt% IL and 50 wt% IL in GROningen MAchine for Chemical Simulations (GROMACS). The results was evaluated based on potential energy, root mean square deviation (RMSD) and radial distribution function (RDF). The stability and interaction of PVDF were evaluated. Results reveal that PVDF has a stronger interaction to [C2bim]+ cation compared to water and bromine anion. Both potential energy and RMSD were lower when the weight percentage of IL is higher. This indicates that the IL is able to stabilize the PVDF structure. RMSD reveals that [C2bim]+ cation is dominant at short distance (less than 1 nm), indicating that strong interaction of cation to PVDF. This understanding of the behavior of PVDF-IL could be used as a reference for future development of stronger membrane.

Counter-rotating effects and entanglement dynamics in strongly coupled quantum-emitter-metallic-nanoparticle structures

NASA Astrophysics Data System (ADS)

Iliopoulos, Nikos; Thanopulos, Ioannis; Yannopapas, Vassilios; Paspalakis, Emmanuel

2018-03-01

We study the spontaneous emission of a two-level quantum emitter next to a plasmonic nanoparticle beyond the Markovian approximation and the rotating-wave approximation (RWA) by combining quantum dynamics and classical electromagnetic calculations. For emitters with decay times in the picosecond to nanosecond time regime, as well as located at distances from the nanoparticle up to its radius, the dynamics with and without the RWA and the transition from the non-Markovian to the Markovian regime are investigated. For emitters with longer decay times, the Markov approximation proves to be adequate for distances larger than half the nanoparticle radius. However, the RWA is correct for all distances of the emitter from the nanoparticle. For short decay time emitters, the Markov approximation and RWA are both inadequate, with only the RWA becoming valid again at a distance larger than half the nanoparticle radius. We also show that the entanglement dynamics of two initially entangled qubits interacting independently with the nanoparticle may have a strong non-Markovian character when counter-rotating effects are included. Interesting effects such as entanglement sudden death, periodic entanglement revival, entanglement oscillations, and entanglement trapping are further observed when different initial two-qubit states and different distances between the qubit and the nanoparticle are considered.

Neuronal avalanches and coherence potentials

NASA Astrophysics Data System (ADS)

Plenz, D.

2012-05-01

The mammalian cortex consists of a vast network of weakly interacting excitable cells called neurons. Neurons must synchronize their activities in order to trigger activity in neighboring neurons. Moreover, interactions must be carefully regulated to remain weak (but not too weak) such that cascades of active neuronal groups avoid explosive growth yet allow for activity propagation over long-distances. Such a balance is robustly realized for neuronal avalanches, which are defined as cortical activity cascades that follow precise power laws. In experiments, scale-invariant neuronal avalanche dynamics have been observed during spontaneous cortical activity in isolated preparations in vitro as well as in the ongoing cortical activity of awake animals and in humans. Theory, models, and experiments suggest that neuronal avalanches are the signature of brain function near criticality at which the cortex optimally responds to inputs and maximizes its information capacity. Importantly, avalanche dynamics allow for the emergence of a subset of avalanches, the coherence potentials. They emerge when the synchronization of a local neuronal group exceeds a local threshold, at which the system spawns replicas of the local group activity at distant network sites. The functional importance of coherence potentials will be discussed in the context of propagating structures, such as gliders in balanced cellular automata. Gliders constitute local population dynamics that replicate in space after a finite number of generations and are thought to provide cellular automata with universal computation. Avalanches and coherence potentials are proposed to constitute a modern framework of cortical synchronization dynamics that underlies brain function.

Quantitative phase microscopy for cellular dynamics based on transport of intensity equation.

PubMed

Li, Ying; Di, Jianglei; Ma, Chaojie; Zhang, Jiwei; Zhong, Jinzhan; Wang, Kaiqiang; Xi, Teli; Zhao, Jianlin

2018-01-08

We demonstrate a simple method for quantitative phase imaging of tiny transparent objects such as living cells based on the transport of intensity equation. The experiments are performed using an inverted bright field microscope upgraded with a flipping imaging module, which enables to simultaneously create two laterally separated images with unequal defocus distances. This add-on module does not include any lenses or gratings and is cost-effective and easy-to-alignment. The validity of this method is confirmed by the measurement of microlens array and human osteoblastic cells in culture, indicating its potential in the applications of dynamically measuring living cells and other transparent specimens in a quantitative, non-invasive and label-free manner.

Imbibition dynamics on surfaces of legs of a small animal and on artificial surfaces mimicking them

NASA Astrophysics Data System (ADS)

Tani, Marie; Ishii, Daisuke; Ito, Shuto; Hariyama, Takahiko; Shimomura, Masatsugu; Okumura, Ko

2014-03-01

Recently, imbibition of textured surfaces covered with homogeneous micro-pillar arrays has been actively studied partly because of the potential for transport of a small amount of liquids. In most cases, the dynamics is described by the Washburn law, in which the imbibition distance scales with the square root of elapsed time, while a different scaling law has been recently found. In this study, we studied imbibition on legs of a small animal that absorbs water via its legs to find yet another scaling law. Furthermore, imbibition of artificial surfaces mimicking the leg surface was found to be described well by a composite theory.

The ecological forecast horizon, and examples of its uses and determinants

PubMed Central

Petchey, Owen L; Pontarp, Mikael; Massie, Thomas M; Kéfi, Sonia; Ozgul, Arpat; Weilenmann, Maja; Palamara, Gian Marco; Altermatt, Florian; Matthews, Blake; Levine, Jonathan M; Childs, Dylan Z; McGill, Brian J; Schaepman, Michael E; Schmid, Bernhard; Spaak, Piet; Beckerman, Andrew P; Pennekamp, Frank; Pearse, Ian S; Vasseur, David

2015-01-01

Forecasts of ecological dynamics in changing environments are increasingly important, and are available for a plethora of variables, such as species abundance and distribution, community structure and ecosystem processes. There is, however, a general absence of knowledge about how far into the future, or other dimensions (space, temperature, phylogenetic distance), useful ecological forecasts can be made, and about how features of ecological systems relate to these distances. The ecological forecast horizon is the dimensional distance for which useful forecasts can be made. Five case studies illustrate the influence of various sources of uncertainty (e.g. parameter uncertainty, environmental variation, demographic stochasticity and evolution), level of ecological organisation (e.g. population or community), and organismal properties (e.g. body size or number of trophic links) on temporal, spatial and phylogenetic forecast horizons. Insights from these case studies demonstrate that the ecological forecast horizon is a flexible and powerful tool for researching and communicating ecological predictability. It also has potential for motivating and guiding agenda setting for ecological forecasting research and development. PMID:25960188

Jets in a strongly coupled anisotropic plasma

NASA Astrophysics Data System (ADS)

Fadafan, Kazem Bitaghsir; Morad, Razieh

2018-01-01

In this paper, we study the dynamics of the light quark jet moving through the static, strongly coupled N=4, anisotropic plasma with and without charge. The light quark is presented by a 2-parameters point-like initial condition falling string in the context of the AdS/CFT. We calculate the stopping distance of the light quark in the anisotropic medium and compare it with its isotropic value. We study the dependency of the stopping distance to the both string initial conditions and background parameters such as anisotropy parameter or chemical potential. Although the typical behavior of the string in the anisotropic medium is similar to the one in the isotropic AdS-Sch background, the string falls faster to the horizon depending on the direction of moving. Particularly, the enhancement of quenching is larger in the beam direction. We find that the suppression of stopping distance is more prominent when the anisotropic plasma have the same temperature as the isotropic plasma.

A dual systems account of visual perception: Predicting candy consumption from distance estimates.

PubMed

Krpan, Dario; Schnall, Simone

2017-04-01

A substantial amount of evidence shows that visual perception is influenced by forces that control human actions, ranging from motivation to physiological potential. However, studies have not yet provided convincing evidence that perception itself is directly involved in everyday behaviors such as eating. We suggest that this issue can be resolved by employing the dual systems account of human behavior. We tested the link between perceived distance to candies and their consumption for participants who were tired or depleted (impulsive system), versus those who were not (reflective system). Perception predicted eating only when participants were tired (Experiment 1) or depleted (Experiments 2 and 3). In contrast, a rational determinant of behavior-eating restraint towards candies-predicted eating for non-depleted individuals (Experiment 2). Finally, Experiment 3 established that perceived distance was correlated with participants' self-reported motivation to consume candies. Overall, these findings suggest that the dynamics between perception and behavior depend on the interplay of the two behavioral systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Potentially Extreme Population Displacement and Concentration in the Tropics Under Non-Extreme Warming

NASA Astrophysics Data System (ADS)

Hsiang, Solomon M.; Sobel, Adam H.

2016-06-01

Evidence increasingly suggests that as climate warms, some plant, animal, and human populations may move to preserve their environmental temperature. The distances they must travel to do this depends on how much cooler nearby surfaces temperatures are. Because large-scale atmospheric dynamics constrain surface temperatures to be nearly uniform near the equator, these displacements can grow to extreme distances in the tropics, even under relatively mild warming scenarios. Here we show that in order to preserve their annual mean temperatures, tropical populations would have to travel distances greater than 1000 km over less than a century if global mean temperature rises by 2 °C over the same period. The disproportionately rapid evacuation of the tropics under such a scenario would cause migrants to concentrate in tropical margins and the subtropics, where population densities would increase 300% or more. These results may have critical consequences for ecosystem and human wellbeing in tropical contexts where alternatives to geographic displacement are limited.

Geography and distance effect on financial dynamics in the Chinese stock market

NASA Astrophysics Data System (ADS)

Li, Xing; Qiu, Tian; Chen, Guang; Zhong, Li-Xin; Jiang, Xiong-Fei

2016-09-01

Geography effect is investigated for the Chinese stock market including the Shanghai and Shenzhen stock markets, based on the daily data of individual stocks. The stocks in the Shanghai city and the Guangdong province are found to greatly contribute to the Shanghai and Shenzhen markets in the geographical sector, respectively. By investigating a geographical correlation on a geographical parameter, the stock location is found to have an impact on the financial dynamics, except for the financial crisis time of the Shenzhen market. Stock distance effect is further studied, with the probability of the short distance observed to be much greater than that of the long distance. The distance is found to only affect the stock correlation of the Shanghai stock market, but has no effect on the Shenzhen stock market.

New method for distance-based close following safety indicator.

PubMed

Sharizli, A A; Rahizar, R; Karim, M R; Saifizul, A A

2015-01-01

The increase in the number of fatalities caused by road accidents involving heavy vehicles every year has raised the level of concern and awareness on road safety in developing countries like Malaysia. Changes in the vehicle dynamic characteristics such as gross vehicle weight, travel speed, and vehicle classification will affect a heavy vehicle's braking performance and its ability to stop safely in emergency situations. As such, the aim of this study is to establish a more realistic new distance-based safety indicator called the minimum safe distance gap (MSDG), which incorporates vehicle classification (VC), speed, and gross vehicle weight (GVW). Commercial multibody dynamics simulation software was used to generate braking distance data for various heavy vehicle classes under various loads and speeds. By applying nonlinear regression analysis to the simulation results, a mathematical expression of MSDG has been established. The results show that MSDG is dynamically changed according to GVW, VC, and speed. It is envisaged that this new distance-based safety indicator would provide a more realistic depiction of the real traffic situation for safety analysis.

Local stellar kinematics from RAVE data—VIII. Effects of the Galactic disc perturbations on stellar orbits of red clump stars

NASA Astrophysics Data System (ADS)

Önal Taş, Ö.; Bilir, S.; Plevne, O.

2018-02-01

We aim to probe the dynamic structure of the extended Solar neighborhood by calculating the radial metallicity gradients from orbit properties, which are obtained for axisymmetric and non-axisymmetric potential models, of red clump (RC) stars selected from the RAdial Velocity Experiment's Fourth Data Release. Distances are obtained by assuming a single absolute magnitude value in near-infrared, i.e. M_{Ks}=-1.54±0.04 mag, for each RC star. Stellar orbit parameters are calculated by using the potential functions: (i) for the MWPotential2014 potential, (ii) for the same potential with perturbation functions of the Galactic bar and transient spiral arms. The stellar age is calculated with a method based on Bayesian statistics. The radial metallicity gradients are evaluated based on the maximum vertical distance (z_{max}) from the Galactic plane and the planar eccentricity (ep) of RC stars for both of the potential models. The largest radial metallicity gradient in the 0< z_{max} ≤0.5 kpc distance interval is -0.065±0.005 dex kpc^{-1} for a subsample with ep≤0.1, while the lowest value is -0.014±0.006 dex kpc^{-1} for the subsample with ep≤0.5. We find that at z_{max}>1 kpc, the radial metallicity gradients have zero or positive values and they do not depend on ep subsamples. There is a large radial metallicity gradient for thin disc, but no radial gradient found for thick disc. Moreover, the largest radial metallicity gradients are obtained where the outer Lindblad resonance region is effective. We claim that this apparent change in radial metallicity gradients in the thin disc is a result of orbital perturbation originating from the existing resonance regions.

Modeling the erosion risk potential induced by terraces and their condition in a highly dynamic watershed close to the Three-Gorges-Dam

NASA Astrophysics Data System (ADS)

Schönbrodt, S.; Behrens, T.; Imbery, S.; Scholten, T.

2010-03-01

Globally, the Three-Gorges Ecosystem is currently one of the most anthropogenic influenced regions. Due to the Three-Gorges Dam large areas in the upper catchment of the Yangtze and its major tributaries become inundated. Consequently, high land-use dynamic with resettlements, construction of infrastructure, and new land reclamation for smallholder agriculture and cash crops characterize this area. Therefore, ecological impacts are expected in an unforeseeable dimension. Soil loss is one of the major threats and its control an enormous challenge. Even existing erosion control measures like dry-stone walling bench terraces have to be adapted to this new situation in order to keep their effectiveness. In the highly dynamic watershed of the Xiangxi, a first class tributary to the Yangtze, this study aims to assess and predict the spatial and temporal varying dam-caused soil erosion risk potential. Using a multi-level and multi-scale approach this study seeks to develop an integrative data-based methodology for soil erosion assessment by means of GIS-based erosion modeling using relevant digital terrain data, field investigations and remote sensing. The different scales considered cover the Xiangxi watershed (3.100 km²), the highly dynamic backwater area (500 km²), and two micro-scale study sites (3 km² and 88 km²) subject to flooding and high land-use dynamic. Central features of the Xiangxi watershed are steep slopes artificially fractured by terraces. A preliminary erosion survey has shown a strong connection of the frequency and intensity of erosion and the quality of terrace-maintenance. Terraces with wall disorders and technically poor constructed design show higher soil loss and runoff than well-maintained terraces. Their condition is regarded as a driving erosion factor. Therefore, a conceptual Terrace-Condition-Erosion model (TerraCE) was developed in order to assess to what extent soil erosion depends on the quality of terraces. Central aspects are the distance to the inundated area, to the road network, and to the settlements. Four classes of terrace-maintenance are analyzed: well-maintained (20 %), badly-maintained (48 %), partially collapsed (15 %), and completely collapsed (6 %). Unterraced farmland (7 %) is regarded as an extra class. First results of TerraCE indicate that with increasing distance from the highly dynamic inundated area and the main roads the better is the quality of terrace-maintenance with less wall disorders and less soil erosion potential. It is concluded that the construction of infrastructure and the artificially fluctuating water level at the dam lead to a degradation of terraces within close distances to the Xiangxi and the main road network. Terraced farmland that is more remote to the main transportation routes seems to be less influenced by the high land-use dynamic. The mean distance of (a) well-/badly-maintainedand(b)partially-/completely collapsed terraces from the Xiangxi is(a) 613.8 m with SD 318.2 m/474.4 m with SD 291.6 m and (b) 208.6m with SD 292.1 m/127.6 m with SD 81.7 m. In average, unterraced farmland is 261.9 m (SD 286.2 m) located from the new shoreline of the Xiangxi. By combining the model results with DEM-analysis and remote sensing data a high-resolution soil erosion risk model will be computed using spatial regression approaches. It aims to assess the soil erosion as a function of natural factors and anthropogenic impacts in an increasingly complex system. Especially against the background of global change and the increasing demand for water and energy the study aims at enhancing the understanding of the ecological consequences of large dam projects.

Development of Time-Distance Helioseismology Data Analysis Pipeline for SDO/HMI

NASA Technical Reports Server (NTRS)

DuVall, T. L., Jr.; Zhao, J.; Couvidat, S.; Parchevsky, K. V.; Beck, J.; Kosovichev, A. G.; Scherrer, P. H.

2008-01-01

The Helioseismic and Magnetic Imager of SDO will provide uninterrupted 4k x 4k-pixel Doppler-shift images of the Sun with approximately 40 sec cadence. These data will have a unique potential for advancing local helioseismic diagnostics of the Sun's interior structure and dynamics. They will help to understand the basic mechanisms of solar activity and develop predictive capabilities for NASA's Living with a Star program. Because of the tremendous amount of data the HMI team is developing a data analysis pipeline, which will provide maps of subsurface flows and sound-speed distributions inferred form the Doppler data by the time-distance technique. We discuss the development plan, methods, and algorithms, and present the status of the pipeline, testing results and examples of the data products.

A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes.

PubMed Central

Klenin, K; Merlitz, H; Langowski, J

1998-01-01

For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation of such DNAs, we have developed an efficient and easy way to set up a program based on a second-order explicit Brownian dynamics algorithm. The DNA is modeled by a chain of rigid segments interacting through harmonic spring potentials for bending, torsion, and stretching. The electrostatics are handled using precalculated energy tables for the interactions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prager tensor. While maintaining acceptable precision, the simulation can be accelerated by recalculating this tensor only once in a certain number of steps. PMID:9533691

Calibration of the Tip of the Red Giant Branch Distance Method in IR

NASA Astrophysics Data System (ADS)

Sakai, Shoko

1999-02-01

We propose to investigate the feasibility of the tip of the red giant branch (TRGB) as a distance indicator in IR wavelength. The TRGB has been shown both observationally and theoretically to be an excellent distance indicator in I-band, mainly because of its insensitivity to both metallicity and age. Its accuracy is comparable to that of the Cepheid variable stars. The TRGB method in I-band is currently calibrated by Galactic globular clusters whose distances have been measured with RR Lyrae variables. The main objective of this proposal is to calibrate this method in IR by obtaining JHK photometry for a number of Galactic globular clusters. This is motivated by two related scientific goals: (1) It will be possible in the future to obtain direct distances to galaxies even in Coma cluster using the NGST, but only if the TRGB method has been calibrated accurately in IR filters. If the method is proven reliable, then it can be a powerful tool to map out the density and velocity fields of the local Universe in three dimensions. (2) A considerable amount of effort has been spent on obtaining accurate, direct distances to nearby galaxies. However, this has been difficult for a number of galaxies, including IC 342, because they are located at very low Galactic latitude. These galaxies could potentially have a tremendous effect on the dynamics of the Local Group, depending on their distances. Using the calibrated IR TRGB method, we could solve this uncertainty by measuring their distances directly.

Dissociation dynamics of simple chlorine containing molecules upon resonant Cl K-σ{sup *} excitation

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

Bohinc, R., E-mail: rok.bohinc@ijs.si; Bučar, K.; Kavčič, M.

2014-04-28

A theoretical analysis of dissociation dynamics of chlorine K-σ{sup *} core-excited molecules is performed. The potential energy surfaces of HCl, Cl{sub 2}, CH{sub 3}Cl, CH{sub 2}Cl{sub 2}, CHCl{sub 3}, CCl{sub 4}, CFCl{sub 3}, CF{sub 2}Cl{sub 2}, and CF{sub 3}Cl are calculated along the normal vibrational modes of the ground electronic state yielding the widths of the corresponding Franck-Condon distributions. An insight into the potential energy surface of 1st σ{sup *} resonances shows that the initial dissociation dynamics of chloro(fluoro)methanes mainly involves the distancing of the carbon and the core-excited chlorine atom and is practically independent of other atoms in themore » molecule, which is in agreement with the recent experimental findings. The carbon atom pulls out the remaining three atoms shortly after piercing the three-atom plane resulting in a high vibrationally excited state of the fragment if the reconnection time is smaller than the lifetime of the L shell.« less

A Novel Concept for a Deformable Membrane Mirror for Correction of Large Amplitude Aberrations

NASA Technical Reports Server (NTRS)

Moore, Jim; Patrick, Brian

2006-01-01

Very large, light weight mirrors are being developed for applications in space. Due to launch mass and volume restrictions these mirrors will need to be much more flexible than traditional optics. The use of primary mirrors with these characteristics will lead to requirements for adaptive optics capable of correcting wave front errors with large amplitude relatively low spatial frequency aberrations. The use of low modulus membrane mirrors actuated with electrostatic attraction forces is a potential solution for this application. Several different electrostatic membrane mirrors are now available commercially. However, as the dynamic range requirement of the adaptive mirror is increased the separation distance between the membrane and the electrodes must increase to accommodate the required face sheet deformations. The actuation force applied to the mirror decreases inversely proportional to the square of the separation distance; thus for large dynamic ranges the voltage requirement can rapidly increase into the high voltage regime. Experimentation with mirrors operating in the KV range has shown that at the higher voltages a serious problem with electrostatic field cross coupling between actuators can occur. Voltage changes on individual actuators affect the voltage of other actuators making the system very difficult to control. A novel solution has been proposed that combines high voltage electrodes with mechanical actuation to overcome this problem. In this design an array of electrodes are mounted to a backing structure via light weight large dynamic range flextensional actuators. With this design the control input becomes the separation distance between the electrode and the mirror. The voltage on each of the actuators is set to a uniform relatively high voltage, thus the problem of cross talk between actuators is avoided and the favorable distributed load characteristic of electrostatic actuation is retained. Initial testing and modeling of this concept demonstrates that this is an attractive concept for increasing the dynamic range capability of electrostatic deformable mirrors.

How Markovian is exciton dynamics in purple bacteria?

NASA Astrophysics Data System (ADS)

Vaughan, Felix; Linden, Noah; Manby, Frederick R.

2017-03-01

We investigate the extent to which the dynamics of excitons in the light-harvesting complex LH2 of purple bacteria can be described using a Markovian approximation. To analyse the degree of non-Markovianity in these systems, we introduce a measure based on fitting Lindblad dynamics, as well as employing a recently introduced trace-distance measure. We apply these measures to a chromophore-dimer model of exciton dynamics and use the hierarchical equation-of-motion method to take into account the broad, low-frequency phonon bath. With a smooth phonon bath, small amounts of non-Markovianity are present according to the trace-distance measure, but the dynamics is poorly described by a Lindblad master equation unless the excitonic dimer coupling strength is modified. Inclusion of underdamped, high-frequency modes leads to significant deviations from Markovian evolution in both measures. In particular, we find that modes that are nearly resonant with gaps in the excitonic spectrum produce dynamics that deviate most strongly from the Lindblad approximation, despite the trace distance measuring larger amounts of non-Markovianity for higher frequency modes. Overall we find that the detailed structure in the high-frequency region of the spectral density has a significant impact on the nature of the dynamics of excitons.

Wavelet transform analysis of dynamic speckle patterns texture

NASA Astrophysics Data System (ADS)

Limia, Margarita Fernandez; Nunez, Adriana Mavilio; Rabal, Hector; Trivi, Marcelo

2002-11-01

We propose the use of the wavelet transform to characterize the time evolution of dynamic speckle patterns. We describe it by using as an example a method used for the assessment of the drying of paint. Optimal texture features are determined and the time evolution is described in terms of the Mahalanobis distance to the final (dry) state. From the behavior of this distance function, two parameters are defined that characterize the evolution. Because detailed knowledge of the involved dynamics is not required, the methodology could be implemented for other complex or poorly understood dynamic phenomena.

Age-Related Changes in Dynamic Postural Control and Attentional Demands are Minimally Affected by Local Muscle Fatigue

PubMed Central

Remaud, Anthony; Thuong-Cong, Cécile; Bilodeau, Martin

2016-01-01

Normal aging results in alterations in the visual, vestibular and somtaosensory systems, which in turn modify the control of balance. Muscle fatigue may exacerbate these age-related changes in sensory and motor functions, and also increase the attentional demands associated with dynamic postural control. The purpose of this study was to investigate the effect of aging on dynamic postural control and posture-related attentional demands before and after a plantar flexor fatigue protocol. Participants (young adults: n = 15; healthy seniors: n = 13) performed a dynamic postural task along the antero-posterior (AP) and the medio-lateral (ML) axes, with and without the addition of a simple reaction time (RT) task. The dynamic postural task consisted in following a moving circle on a computer screen with the representation of the center of pressure (COP). This protocol was repeated before and after a fatigue task where ankle plantar flexor muscles were targeted. The mean COP-target distance and the mean COP velocity were calculated for each trial. Cross-correlation analyses between the COP and target displacements were also performed. RTs were recorded during dual-task trials. Results showed that while young adults adopted an anticipatory control mode to move their COP as close as possible to the target center, seniors adopted a reactive control mode, lagging behind the target center. This resulted in longer COP-target distance and higher COP velocity in the latter group. Concurrently, RT increased more in seniors when switching from static stance to dynamic postural conditions, suggesting potential alterations in the central nervous system (CNS) functions. Finally, plantar flexor muscle fatigue and dual-tasking had only minor effects on dynamic postural control of both young adults and seniors. Future studies should investigate why the fatigue-induced changes in quiet standing postural control do not seem to transfer to dynamic balance tasks. PMID:26834626

Supporting Dynamic Quantization for High-Dimensional Data Analytics.

PubMed

Guzun, Gheorghi; Canahuate, Guadalupe

2017-05-01

Similarity searches are at the heart of exploratory data analysis tasks. Distance metrics are typically used to characterize the similarity between data objects represented as feature vectors. However, when the dimensionality of the data increases and the number of features is large, traditional distance metrics fail to distinguish between the closest and furthest data points. Localized distance functions have been proposed as an alternative to traditional distance metrics. These functions only consider dimensions close to query to compute the distance/similarity. Furthermore, in order to enable interactive explorations of high-dimensional data, indexing support for ad-hoc queries is needed. In this work we set up to investigate whether bit-sliced indices can be used for exploratory analytics such as similarity searches and data clustering for high-dimensional big-data. We also propose a novel dynamic quantization called Query dependent Equi-Depth (QED) quantization and show its effectiveness on characterizing high-dimensional similarity. When applying QED we observe improvements in kNN classification accuracy over traditional distance functions. Gheorghi Guzun and Guadalupe Canahuate. 2017. Supporting Dynamic Quantization for High-Dimensional Data Analytics. In Proceedings of Ex-ploreDB'17, Chicago, IL, USA, May 14-19, 2017, 6 pages. https://doi.org/http://dx.doi.org/10.1145/3077331.3077336.

A dust-parallax distance of 19 megaparsecs to the supermassive black hole in NGC 4151.

PubMed

Hönig, Sebastian F; Watson, Darach; Kishimoto, Makoto; Hjorth, Jens

2014-11-27

The active galaxy NGC 4151 has a crucial role as one of only two active galactic nuclei for which black hole mass measurements based on emission line reverberation mapping can be calibrated against other dynamical techniques. Unfortunately, effective calibration requires accurate knowledge of the distance to NGC 4151, which is not at present available. Recently reported distances range from 4 to 29 megaparsecs. Strong peculiar motions make a redshift-based distance very uncertain, and the geometry of the galaxy and its nucleus prohibit accurate measurements using other techniques. Here we report a dust-parallax distance to NGC 4151 of 19.0(+2.4)(-2.6) megaparsecs. The measurement is based on an adaptation of a geometric method that uses the emission line regions of active galaxies. Because these regions are too small to be imaged with present technology, we use instead the ratio of the physical and angular sizes of the more extended hot-dust emission as determined from time delays and infrared interferometry. This distance leads to an approximately 1.4-fold increase in the dynamical black hole mass, implying a corresponding correction to emission line reverberation masses of black holes if they are calibrated against the two objects with additional dynamical masses.

Quasispecies in population of compositional assemblies.

PubMed

Gross, Renan; Fouxon, Itzhak; Lancet, Doron; Markovitch, Omer

2014-12-30

The quasispecies model refers to information carriers that undergo self-replication with errors. A quasispecies is a steady-state population of biopolymer sequence variants generated by mutations from a master sequence. A quasispecies error threshold is a minimal replication accuracy below which the population structure breaks down. Theory and experimentation of this model often refer to biopolymers, e.g. RNA molecules or viral genomes, while its prebiotic context is often associated with an RNA world scenario. Here, we study the possibility that compositional entities which code for compositional information, intrinsically different from biopolymers coding for sequential information, could show quasispecies dynamics. We employed a chemistry-based model, graded autocatalysis replication domain (GARD), which simulates the network dynamics within compositional molecular assemblies. In GARD, a compotype represents a population of similar assemblies that constitute a quasi-stationary state in compositional space. A compotype's center-of-mass is found to be analogous to a master sequence for a sequential quasispecies. Using single-cycle GARD dynamics, we measured the quasispecies transition matrix (Q) for the probabilities of transition from one center-of-mass Euclidean distance to another. Similarly, the quasispecies' growth rate vector (A) was obtained. This allowed computing a steady state distribution of distances to the center of mass, as derived from the quasispecies equation. In parallel, a steady state distribution was obtained via the GARD equation kinetics. Rewardingly, a significant correlation was observed between the distributions obtained by these two methods. This was only seen for distances to the compotype center-of-mass, and not to randomly selected compositions. A similar correspondence was found when comparing the quasispecies time dependent dynamics towards steady state. Further, changing the error rate by modifying basal assembly joining rate of GARD kinetics was found to display an error catastrophe, similar to the standard quasispecies model. Additional augmentation of compositional mutations leads to the complete disappearance of the master-like composition. Our results show that compositional assemblies, as simulated by the GARD formalism, portray significant attributes of quasispecies dynamics. This expands the applicability of the quasispecies model beyond sequence-based entities, and potentially enhances validity of GARD as a model for prebiotic evolution.

Variable population exposure and distributed travel speeds in least-cost tsunami evacuation modelling

NASA Astrophysics Data System (ADS)

Fraser, S. A.; Wood, N. J.; Johnston, D. M.; Leonard, G. S.; Greening, P. D.; Rossetto, T.

2014-11-01

Evacuation of the population from a tsunami hazard zone is vital to reduce life-loss due to inundation. Geospatial least-cost distance modelling provides one approach to assessing tsunami evacuation potential. Previous models have generally used two static exposure scenarios and fixed travel speeds to represent population movement. Some analyses have assumed immediate departure or a common evacuation departure time for all exposed population. Here, a method is proposed to incorporate time-variable exposure, distributed travel speeds, and uncertain evacuation departure time into an existing anisotropic least-cost path distance framework. The method is demonstrated for hypothetical local-source tsunami evacuation in Napier City, Hawke's Bay, New Zealand. There is significant diurnal variation in pedestrian evacuation potential at the suburb level, although the total number of people unable to evacuate is stable across all scenarios. Whilst some fixed travel speeds approximate a distributed speed approach, others may overestimate evacuation potential. The impact of evacuation departure time is a significant contributor to total evacuation time. This method improves least-cost modelling of evacuation dynamics for evacuation planning, casualty modelling, and development of emergency response training scenarios. However, it requires detailed exposure data, which may preclude its use in many situations.

Variable population exposure and distributed travel speeds in least-cost tsunami evacuation modelling

NASA Astrophysics Data System (ADS)

Fraser, S. A.; Wood, N. J.; Johnston, D. M.; Leonard, G. S.; Greening, P. D.; Rossetto, T.

2014-06-01

Evacuation of the population from a tsunami hazard zone is vital to reduce life-loss due to inundation. Geospatial least-cost distance modelling provides one approach to assessing tsunami evacuation potential. Previous models have generally used two static exposure scenarios and fixed travel speeds to represent population movement. Some analyses have assumed immediate evacuation departure time or assumed a common departure time for all exposed population. In this paper, a method is proposed to incorporate time-variable exposure, distributed travel speeds, and uncertain evacuation departure time into an existing anisotropic least-cost path distance framework. The model is demonstrated for a case study of local-source tsunami evacuation in Napier City, Hawke's Bay, New Zealand. There is significant diurnal variation in pedestrian evacuation potential at the suburb-level, although the total number of people unable to evacuate is stable across all scenarios. Whilst some fixed travel speeds can approximate a distributed speed approach, others may overestimate evacuation potential. The impact of evacuation departure time is a significant contributor to total evacuation time. This method improves least-cost modelling of evacuation dynamics for evacuation planning, casualty modelling, and development of emergency response training scenarios.

Variable population exposure and distributed travel speeds in least-cost tsunami evacuation modelling

USGS Publications Warehouse

Fraser, Stuart A.; Wood, Nathan J.; Johnston, David A.; Leonard, Graham S.; Greening, Paul D.; Rossetto, Tiziana

2014-01-01

Evacuation of the population from a tsunami hazard zone is vital to reduce life-loss due to inundation. Geospatial least-cost distance modelling provides one approach to assessing tsunami evacuation potential. Previous models have generally used two static exposure scenarios and fixed travel speeds to represent population movement. Some analyses have assumed immediate departure or a common evacuation departure time for all exposed population. Here, a method is proposed to incorporate time-variable exposure, distributed travel speeds, and uncertain evacuation departure time into an existing anisotropic least-cost path distance framework. The method is demonstrated for hypothetical local-source tsunami evacuation in Napier City, Hawke's Bay, New Zealand. There is significant diurnal variation in pedestrian evacuation potential at the suburb level, although the total number of people unable to evacuate is stable across all scenarios. Whilst some fixed travel speeds approximate a distributed speed approach, others may overestimate evacuation potential. The impact of evacuation departure time is a significant contributor to total evacuation time. This method improves least-cost modelling of evacuation dynamics for evacuation planning, casualty modelling, and development of emergency response training scenarios. However, it requires detailed exposure data, which may preclude its use in many situations.

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

PubMed

Cossio, Pilar; Laio, Alessandro; Pietrucci, Fabio

2011-06-14

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are different. By analyzing microseconds-long all-atom molecular dynamics simulations of a polypeptide, we find that a distance based on backbone dihedral angles performs very well in distinguishing structures that are kinetically correlated from those that are not, while the widely used C(α) root mean square distance performs more poorly. The root mean square difference between contact matrices turns out instead to be the metric providing the highest clustering coefficient, namely, according to this similarity measure, the neighbors of a structure are also, on average, neighbors among themselves. We also propose a combined distance measure which, for the system considered here, performs well both for distinguishing structures which are distant in time and for giving a consistent cluster analysis. This journal is © the Owner Societies 2011

Functional near-infrared spectroscopy at small source-detector distance by means of high dynamic-range fast-gated SPAD acquisitions: first in-vivo measurements

NASA Astrophysics Data System (ADS)

Di Sieno, L.; Contini, D.; Dalla Mora, A.; Torricelli, A.; Spinelli, L.; Cubeddu, R.; Tosi, A.; Boso, G.; Pifferi, A.

2013-06-01

In this article, we show experimental results of time-resolved optical spectroscopy performed with small distance between launching and detecting fibers. It was already demonstrated that depth discrimination is independent of source-detector separation and that measurements at small source detector distance provide better contrast and spatial resolution. The main disadvantage is represent by the huge increase in early photons (scarcely diffused by tissue) peak that can saturate the dynamic range of most detectors, hiding information carried by late photons. Thanks to a fast-gated Single- Photon Avalanche Diode (SPAD) module, we are able to reject the peak of early photons and to obtain high-dynamic range acquisitions. We exploit fast-gated SPAD module to perform for the first time functional near-infrared spectroscopy (fNIRS) at small source-detector distance for in vivo measurements and we demonstrate the possibility to detect non-invasively the dynamics of oxygenated and deoxygenated haemoglobin occurring in the motor cortex during a motor task. We also show the improvement in terms of signal amplitude and Signal-to-Noise Ratio (SNR) obtained exploiting fast-gated SPAD performances with respect to "non-gated" measurements.

Brazilian Amazon Roads and Parks: Temporal & Spatial Deforestation Dynamics

NASA Astrophysics Data System (ADS)

Pfaff, A.; Robalino, J.

2011-12-01

Heterogeneous Forest Impacts of Transport Infrastructure: spatial frontier dynamics & impacts of Brazilian Amazon road changes Prior research on road impacts has almost completely ignored heterogeneity of impacts and as a result both empirically understated potential impact and missed policy potential. We note von Thunen's model suggests not only heterogeneity with distance from market but also specifically road impacts rising then falling with distance ('non-monoThunicity') Endogenous development and partial adjustment dynamics support this for the short run. Causal effects result from studying Brazilian Amazon deforestation (1976-87, 2000-04) using matching for short-run responses to lagged new roads changes (1968-75, 1985-00). We show the critical role of prior development, proxied by 1968 and 1985 road distances, for which exact matching addresses development trends and transforms impact estimates. Splitting the sample on this measure finds confirmation of the nonmonotonic predictions: new road impacts are relatively low if a prior road was close, such that prior transport access and endogenous development dynamics compete with the new road for influence, but also if a prior road was far, since first-decade adjustment in pristine areas is limited; yet in between these bounds, investments immediately raise deforestation significantly. This pattern helps to explain lower estimates within research on a single average impact. It suggests potential for REDD if a country chooses to shift its spatial transport networks. Protected Areas & Brazilian Amazon Deforestation: modeling and testing the impacts of varied PA strategies We model and then estimate the impacts of multiple types of protected areas upon 2000 - 2004 deforestation in the Brazilian Amazon. Our modeling starts with federal versus state objectives and predicts differences in both choice and implementation of each PA strategy that we examine. Our empirical examination brings not only breakdowns sufficient to test the model's implications but also, critically, explicit controls for the influences of the characteristics of protected lands. Controlling for how PAs differ from unprotected lands cuts impact estimates roughly in half, implying that accounting for and planning around site characteristics should be a part of REDD. For instance, we highlight differences among the improved impacts estimates across PA subsets: Federal vs. State vs. Indigenous; 1980s vs. 1990s; and Integral Protection vs. Sustainable Use. Without correcting for the differences in land characteristics, each of the subsets we examine is estimated to cause significant reduction in deforestation. Corrections find Federal and Indigenous prevented more clearing than did State, while Sustainable Use areas blocked more deforestation than Integral Protection. The reason for these unequal shifts in estimates is that the different PA subsets were allocated to different types of locations. That protection's impact is not uniform is important for REDD and those designing institutions should note what local planners may favor.

Tunable Excited-State Properties and Dynamics as a Function of Pt–Pt Distance in Pyrazolate-Bridged Pt(II) Dimers

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

Brown-Xu, Samantha E.; Kelley, Matthew S. J.; Fransted, Kelly A.

The influence of molecular structure on excited state properties and dynamics of a series of cyclometalated platinum dimers was investigated through a combined experimental and theoretical approach using femtosecond transient absorption (fs TA) spectroscopy and density functional theory (DFT) calculations. The molecules have the general formula [Pt(ppy)(µ-R2pz)]2 where ppy = 2-phenylpyridine, pz = pyrazolate and R = H, Me, Ph, or tBu, and are strongly photoluminescent at room temperature. The distance between the platinum centers in this A frame geometry can be varied depending on the steric bulk of the bridging pyrazolate ligands that exert structural constraints and compress themore » Pt-Pt distance. At large Pt-Pt distances there is little interaction between the subunits and the chromophore behaves similar to a monomer with excited states described as mixtures of ligand-centered and metal-to-ligand charge transfer (LC/MLCT) transitions. When the Pt(II) centers are brought closer together with bulky bridging ligands, they interact through their orbitals and the S1 and T1 states are best characterized as metal metal to ligand charge transfer (MMLCT) in character. The results of the fs TA experiments reveal that intersystem crossing (ISC) occurs on ultrafast timescales (τS1 < 200 fs) while there are two relaxation processes occurring within the triplet manifold, τ1 = 0.5 – 3.2 ps and τ2 = 20 – 70 ps; the longer time constants correspond to the presence of bulkier bridging ligands. DFT calculations illustrate that the Pt-Pt distances further contract in the T1 3MMLCT states, therefore slower relaxation may be related to a larger structural reorganization. Subsequent investigations using faster time resolution are planned to measure the ISC process as well as to identify any potential coherent interaction(s) between the platinum centers that may occur.« less

The Importance of Seed Characteristics in the Dispersal of Splash-Cup Plants

NASA Astrophysics Data System (ADS)

Eklof, Joel; Pepper, Rachel Pepper; Echternach, Juliana

2016-11-01

Splash-cup plants disperse their seeds by exploiting the kinetic energy of raindrops. When raindrops impact the splash-cup, a 3-5 mm vessel that holds seeds, the seeds are projected up to 1 m away from the parent plant. It has been established, using 3D printed models, that a 40°cone angle maximizes dispersal distance when seeds are not present in the cup. We therefore use 40°cups with the addition of different types of seeds to determine the effect that seeds of varying characteristics have on the dispersal and splash dynamics of splash-cup plants. Splash characteristics and dispersal distances of seeds with differing characteristics such as size, shape, texture, density, and hydrophobicity were compared to one another, as well as to the case of having no seeds present. We found that the presence of seeds dramatically decreased dispersal distance and changed splash characteristics (are measured by the angle and velocity of the resulting splash). In addition, different types of seeds yielded splashes with differing dispersal distance and splash characteristics. Splash characteristics and dispersal distances of glass beads of differing hydrophobicity were compared to determine the effect hydrophobicity has on dispersal and splash dynamics. These beads yielded some differences in dispersal distance, but no notable difference in splash dynamics. Models of the conical fruit bodies of the splash-cups were 3D printed and high-speed video was used to find splash characteristics, and dispersal distance was calculated by measuring the distance from the model to the final resting position of the seeds and droplets.

A Short-Range Distance Sensor with Exceptional Linearity

NASA Technical Reports Server (NTRS)

Simmons, Steven; Youngquist, Robert

2013-01-01

A sensor has been demonstrated that can measure distance over a total range of about 300 microns to an accuracy of about 0.1 nm (resolution of about 0.01 nm). This represents an exceptionally large dynamic range of operation - over 1,000,000. The sensor is optical in nature, and requires the attachment of a mirror to the object whose distance is being measured. This work resulted from actively developing a white light interferometric system to be used to measure the depths of defects in the Space Shuttle Orbiter windows. The concept was then applied to measuring distance. The concept later expanded to include spectrometer calibration. In summary, broadband (i.e., white) light is launched into a Michelson interferometer, one mirror of which is fixed and one of which is attached to the object whose distance is to be measured. The light emerging from the interferometer has traveled one of two distances: either the distance to the fixed mirror and back, or the distance to the moving mirror and back. These two light beams mix and produce an interference pattern where some wavelengths interfere constructively and some destructively. Sending this light into a spectrometer allows this interference pattern to be analyzed, yielding the net distance difference between the two paths. The unique feature of this distance sensor is its ability to measure accurately distance over a dynamic range of more than one million, the ratio of its range (about 300 microns) to its accuracy (about 0.1 nanometer). Such a large linear operating range is rare and arises here because both amplitude and phase-matching algorithms contribute to the performance. The sensor is limited by the need to attach a mirror of some kind to the object being tracked, and by the fairly small total range, but the exceptional dynamic range should make it of interest.

Decay of aftershock density with distance does not indicate triggering by dynamic stress

USGS Publications Warehouse

Richards-Dinger, K.; Stein, R.S.; Toda, S.

2010-01-01

Resolving whether static or dynamic stress triggers most aftershocks and subsequent mainshocks is essential to understand earthquake interaction and to forecast seismic hazard. Felzer and Brodsky examined the distance distribution of earthquakes occurring in the first five minutes after 2 ≤ M  M  M ≥ 2 aftershocks showed a uniform power-law decay with slope −1.35 out to 50 km from the mainshocks. From this they argued that the distance decay could be explained only by dynamic triggering. Here we propose an alternative explanation for the decay, and subject their hypothesis to a series of tests, none of which it passes. At distances more than 300 m from the 2 ≤  M< 3 mainshocks, the seismicity decay 5 min before the mainshocks is indistinguishable from the decay five minutes afterwards, indicating that the mainshocks have no effect at distances outside their static triggering range. Omori temporal decay, the fundamental signature of aftershocks, is absent at distances exceeding 10 km from the mainshocks. Finally, the distance decay is found among aftershocks that occur before the arrival of the seismic wave front from the mainshock, which violates causality. We argue that Felzer and Brodsky implicitly assume that the first of two independent aftershocks along a fault rupture triggers the second, and that the first of two shocks in a creep- or intrusion-driven swarm triggers the second, when this need not be the case.

MOLECULAR DYNAMICS OF CASCADES OVERLAP IN TUNGSTEN WITH 20-KEV PRIMARY KNOCK-ON ATOMS

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

Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.

2015-04-16

Molecular dynamics simulations are performed to investigate the mutual influence of two subsequent cascades in tungsten. The influence is studied using 20-keV primary knock-on atoms, to induce one cascade after another separated by 15 ps, in a lattice temperature of 1025 K (i.e. 0.25 of the melting temperature of the interatomic potential). The center of mass of the vacancies at the peak damage during the cascade is taken as the location of the cascade. The distance between this location to that of the next cascade is taken as the overlap parameter. Empirical fits describing the number of surviving vacancies andmore » interstitial atoms as a function of overlap are presented.« less

Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Hung, Shih-Wei; Hsiao, Pai-Yi; Chieng, Ching-Chang

2011-05-01

Dynamic information, such as force, structural change, interaction energy, and potential of mean force (PMF), about the desorption of a single cardiotoxin (CTX) protein from a methyl-terminated self-assembled monolayer (SAM) surface was investigated by means of steered molecular dynamics (SMD) simulations. The simulation results indicated that Loop I is the first loop to depart from the SAM surface, which is in good agreement with the results of the nuclear magnetic resonance spectroscopy experiment. The free energy landscape and the thermodynamic force of the CTX desorption process was represented by the PMF and by the derivative of PMF with respect to distance, respectively. By applying Jarzynski's equality, the PMF can be reconstructed from the SMD simulation. The PMFs, calculated by different estimators based upon Jarzynski's equality, were compared with the conventional umbrella sampling method. The best estimation was obtained by using the fluctuation-dissipation estimator with a pulling velocity of v = 0.25 nm/ns for the present study.

Nuclear Quantum Effects in H+ and OH- Diffusion Along Confined Water Wires from Ab Initio Path Integral Molecular Dyanmics

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Ceriotti, Michele; Manolopoulos, David

Diffusion of H+ and OH- along water wires provides an efficient mechanism for charge transport that is exploited by biological systems and shows promise in technological applications. However, what is lacking for a better control and design of these systems is a thorough theoretical understanding of the diffusion process at the atomic scale. Here we consider H+ and OH- in finite water wires using density functional theory. We employ machine learning techniques to identify the charged species, thus obtaining an agnostic definition of the charge. We employ thermostated ring polymer molecular dynamics and extract a ``universal'' diffusion coefficient from simulations with different wire sizes by considering Langevin dynamics on the potential of mean force of the charged species. In the classical case, diffusion coefficients depend significantly on the potential energy surface, in particular on how dispersion forces modulate O-O distances. NQEs, however, make the diffusion less sensitive to the underlying potential and geometry of the wire, presumably making them more robust to environment fluctuations.

Local and global dynamical effects of dark energy

NASA Astrophysics Data System (ADS)

Chernin, A. D.

Local expansion flows of galaxies were discovered by Lemaitre and Hubble in 1927-29 at distances of less than 25-30 Mpc. The global expansion of the Universe as a whole was predicted theoretically by Friedmann in 1922-24 and discovered in the 1990s in observations at truly cosmological distances of more than 1 000 Mpc. On all these spatial scales, the flows follow a (nearly) linear velocity-distance relation, known now as Hubble's law. This similarity of local and global phenomena is due to the universal dark energy antigravity which dominates the cosmic dynamics on both local and global spatial scales.

Optical dynamic deformation measurements at translucent materials.

PubMed

Philipp, Katrin; Koukourakis, Nektarios; Kuschmierz, Robert; Leithold, Christoph; Fischer, Andreas; Czarske, Jürgen

2015-02-15

Due to their high stiffness-to-weight ratio, glass fiber-reinforced polymers are an attractive material for rotors, e.g., in the aerospace industry. A fundamental understanding of the material behavior requires non-contact, in-situ dynamic deformation measurements. The high surface speeds and particularly the translucence of the material limit the usability of conventional optical measurement techniques. We demonstrate that the laser Doppler distance sensor provides a powerful and reliable tool for monitoring radial expansion at fast rotating translucent materials. We find that backscattering in material volume does not lead to secondary signals as surface scattering results in degradation of the measurement volume inside the translucent medium. This ensures that the acquired signal contains information of the rotor surface only, as long as the sample surface is rough enough. Dynamic deformation measurements of fast-rotating fiber-reinforced polymer composite rotors with surface speeds of more than 300 m/s underline the potential of the laser Doppler sensor.

Clinical balance tests, proprioceptive system and adolescent idiopathic scoliosis.

PubMed

Le Berre, Morgane; Guyot, Marc-Alexandre; Agnani, Olivier; Bourdeauducq, Isabelle; Versyp, Marie-Christine; Donze, Cécile; Thévenon, André; Catanzariti, Jean-Francois

2017-06-01

Adolescent idiopathic scoliosis (AIS) is a three-dimensional deformity of the spinal column of unknown etiology. Multiple factors could be involved, including neurosensory pathways and, potentially, an elective disorder of dynamic proprioception. The purpose of this study was to determine whether routine balance tests could be used to demonstrate an elective alteration of dynamic proprioception in AIS. This was a multicentre case-control study based on prospectively collected clinical data, in three hospitals pediatric, with spine consultation, from January 2013 through April 2015. From an original population of 547 adolescents, inclusion and non-inclusion criteria indentified 114 adolescents with right thoracic AIS (mean age 14.5 ± 1.9 years, Cobb angle 35.7 ± 15.3°) and 81 matched adolescents without scoliosis (mean age 14.1 ± 1.9 years). Participants performed three routine clinical balance tests to assess the static and dynamic proprioception: the Fukuda-Utenberger stepping test (angle of rotation in degrees and distance of displacement in cm) to assess dynamic balance; the sharpened Romberg test and the unipedal stance test (eyes closed) to assess static balance. There was no significant difference between AIS subjects and controls for the static tests, but there was a significant difference for the dynamic test for both measures: distance of displacement (p < 0.01) and angle of rotation (p < 0.0001). This result confirms our initial these: the dynamic proprioception is altered electively in AIS. These findings confirm recent AIS studies. Our results might be related to immature central integration of dynamic proprioceptive input leading to a poorly adapted motor response, particularly for postural control of the, in AIS. These balance tests can be performed in routine practice. Their validity as a biomarker for screening and monitoring purposes should be assessed.

Modeling the spatio-temporal dynamics of porcine reproductive & respiratory syndrome cases at farm level using geographical distance and pig trade network matrices.

PubMed

Amirpour Haredasht, Sara; Polson, Dale; Main, Rodger; Lee, Kyuyoung; Holtkamp, Derald; Martínez-López, Beatriz

2017-06-07

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically devastating infectious diseases for the swine industry. A better understanding of the disease dynamics and the transmission pathways under diverse epidemiological scenarios is a key for the successful PRRS control and elimination in endemic settings. In this paper we used a two step parameter-driven (PD) Bayesian approach to model the spatio-temporal dynamics of PRRS and predict the PRRS status on farm in subsequent time periods in an endemic setting in the US. For such purpose we used information from a production system with 124 pig sites that reported 237 PRRS cases from 2012 to 2015 and from which the pig trade network and geographical location of farms (i.e., distance was used as a proxy of airborne transmission) was available. We estimated five PD models with different weights namely: (i) geographical distance weight which contains the inverse distance between each pair of farms in kilometers, (ii) pig trade weight (PT ji ) which contains the absolute number of pig movements between each pair of farms, (iii) the product between the distance weight and the standardized relative pig trade weight, (iv) the product between the standardized distance weight and the standardized relative pig trade weight, and (v) the product of the distance weight and the pig trade weight. The model that included the pig trade weight matrix provided the best fit to model the dynamics of PRRS cases on a 6-month basis from 2012 to 2015 and was able to predict PRRS outbreaks in the subsequent time period with an area under the ROC curve (AUC) of 0.88 and the accuracy of 85% (105/124). The result of this study reinforces the importance of pig trade in PRRS transmission in the US. Methods and results of this study may be easily adapted to any production system to characterize the PRRS dynamics under diverse epidemic settings to more timely support decision-making.

An integrated system for dynamic control of auditory perspective in a multichannel sound field

NASA Astrophysics Data System (ADS)

Corey, Jason Andrew

An integrated system providing dynamic control of sound source azimuth, distance and proximity to a room boundary within a simulated acoustic space is proposed for use in multichannel music and film sound production. The system has been investigated, implemented, and psychoacoustically tested within the ITU-R BS.775 recommended five-channel (3/2) loudspeaker layout. The work brings together physical and perceptual models of room simulation to allow dynamic placement of virtual sound sources at any location of a simulated space within the horizontal plane. The control system incorporates a number of modules including simulated room modes, "fuzzy" sources, and tracking early reflections, whose parameters are dynamically changed according to sound source location within the simulated space. The control functions of the basic elements, derived from theories of perception of a source in a real room, have been carefully tuned to provide efficient, effective, and intuitive control of a sound source's perceived location. Seven formal listening tests were conducted to evaluate the effectiveness of the algorithm design choices. The tests evaluated: (1) loudness calibration of multichannel sound images; (2) the effectiveness of distance control; (3) the resolution of distance control provided by the system; (4) the effectiveness of the proposed system when compared to a commercially available multichannel room simulation system in terms of control of source distance and proximity to a room boundary; (5) the role of tracking early reflection patterns on the perception of sound source distance; (6) the role of tracking early reflection patterns on the perception of lateral phantom images. The listening tests confirm the effectiveness of the system for control of perceived sound source distance, proximity to room boundaries, and azimuth, through fine, dynamic adjustment of parameters according to source location. All of the parameters are grouped and controlled together to create a perceptually strong impression of source location and movement within a simulated space.

Secondary coordination sphere interactions within the biomimetic iron azadithiolate complexes related to Fe-only hydrogenase: dynamic measure of electron density about the Fe sites.

PubMed

Liu, Yu-Chiao; Tu, Ling-Kuang; Yen, Tao-Hung; Lee, Gene-Hsiang; Yang, Shu-Ting; Chiang, Ming-Hsi

2010-07-19

A series of iron azadithiolate complexes possessing an intramolecular secondary coordination sphere interaction and an ability to reduce HOAc at the potential near the first electron-transfer process are reported. A unique structural feature in which the aza nitrogen has its lone pair point toward the apical carbonyl carbon is observed in [Fe(2)(mu-S(CH(2))(2)NR(CH(2))(2)S)(CO)(6-x)L(x)](2) (R = (n)Pr, x = 0, 1a; R = (i)Pr, x = 0, 1b; R = (n)Pr, L = PPh(3), x = 1, 2; R = (n)Pr, L = P(n)Bu(3), x = 1, 3) as biomimetic models of the active site of Fe-only hydrogenase. The presence of this weak N...C(CO(ap)) interaction provides electronic perturbation at the Fe center. The distance of the N...C(CO(ap)) contact is 3.497 A in 1a. It increases by 0.455 A in 2 when electronic density of the Fe site is slightly enriched by a weak sigma-donating ligand, PPh(3). A longer distance (4.040 A) is observed for the P(n)Bu(3) derivative, 3. This N...C(CO(ap)) distance is thus a dynamic measure of electronic nature of the Fe(2) core. Variation of electronic richness within the Fe(2) moiety among the complexes reflects on their electrochemical response. Reduction of 2 is recorded at the potential of -2.17 V, which is 270 mV more negative than that of 1. Complex 3 requires additional 150 mV for the same reduction. Such cathodic shift results from CO substitution by phosphines. Electrocatalytic hydrogen production from HOAc by both kinds of complexes (all-CO and phosphine-substituted species) requires the potential close to that for reduction of the parent molecules in the absence of acids. The catalytic mechanism of 1a is proposed to involve proton uptake at the Fe(0)Fe(I) redox level instead of the Fe(0)Fe(0) level. This result is the first observation among the all-CO complexes with respect to electrocatalysis of HOAc.

Implications of recurrent disturbance for genetic diversity.

PubMed

Davies, Ian D; Cary, Geoffrey J; Landguth, Erin L; Lindenmayer, David B; Banks, Sam C

2016-02-01

Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.

The effects of dication symmetry on ionic liquid electrolytes in supercapacitors.

PubMed

Li, Song; Zhu, Mengyang; Feng, Guang

2016-11-23

The effects of dication symmetry on the structure and capacitance of the electrical double layers (EDLs) of dicationic ionic liquids (DILs) near graphene electrodes were investigated by molecular dynamics (MD) simulation in this work. Symmetrical 1-hexyl-3-dimethylimidazolium di[bis(trifluoromethyl)imide]([C6(mim)2](Tf2N)2) and asymmetrical 1-(1-trimethylammonium-yl-hexyl)-3-methylimidazolium di[bis(trifluoro-methanesulfonyl)-imide] ([C6(tma)(mim)](Tf2N)2) were both employed. Radial distribution function (RDF) analysis of the two DILs revealed a shorter distance between the cation-anion pairs in symmetrical [C6(mim)2](Tf2N)2), which was attributed to the closely packed imidazolium ring-anion pairs. In contrast, the trimethylammonium head groups and anions exhibit a relatively longer distance, but a stronger correlation in asymmetrical [C6(tma)(mim)](Tf2N)2. In addition, it was illustrated that more symmetrical DIL ions in EDLs are distributed near graphite electrodes and exhibit closer distances to the electrode, which is most probably due to the parallel orientation of imidazolium rings, reducing the distance between the cation and the graphene. In contrast, asymmetrical DILs, with one trimethylammonium head group and one imidazolium ring in the dications, are loosely packed due to their tilting orientation near graphene surfaces. However, the capacitance-potential (C-V) curves of the two DILs are almost the same, regardless of the opposite sign of potential of zero charge (PZC), indicating the insignificant influence of dication symmetry on the capacitance of DIL-based supercapacitors.

The effects of dication symmetry on ionic liquid electrolytes in supercapacitors

NASA Astrophysics Data System (ADS)

Li, Song; Zhu, Mengyang; Feng, Guang

2016-11-01

The effects of dication symmetry on the structure and capacitance of the electrical double layers (EDLs) of dicationic ionic liquids (DILs) near graphene electrodes were investigated by molecular dynamics (MD) simulation in this work. Symmetrical 1-hexyl-3-dimethylimidazolium di[bis(trifluoromethyl)imide]([C6(mim)2](Tf2N)2) and asymmetrical 1-(1-trimethylammonium-yl-hexyl)-3-methylimidazolium di[bis(trifluoro-methanesulfonyl)-imide] ([C6(tma)(mim)](Tf2N)2) were both employed. Radial distribution function (RDF) analysis of the two DILs revealed a shorter distance between the cation-anion pairs in symmetrical [C6(mim)2](Tf2N)2), which was attributed to the closely packed imidazolium ring-anion pairs. In contrast, the trimethylammonium head groups and anions exhibit a relatively longer distance, but a stronger correlation in asymmetrical [C6(tma)(mim)](Tf2N)2. In addition, it was illustrated that more symmetrical DIL ions in EDLs are distributed near graphite electrodes and exhibit closer distances to the electrode, which is most probably due to the parallel orientation of imidazolium rings, reducing the distance between the cation and the graphene. In contrast, asymmetrical DILs, with one trimethylammonium head group and one imidazolium ring in the dications, are loosely packed due to their tilting orientation near graphene surfaces. However, the capacitance-potential (C-V) curves of the two DILs are almost the same, regardless of the opposite sign of potential of zero charge (PZC), indicating the insignificant influence of dication symmetry on the capacitance of DIL-based supercapacitors.

A CONTINUUM HARD-SPHERE MODEL OF PROTEIN ADSORPTION

PubMed Central

Finch, Craig; Clarke, Thomas; Hickman, James J.

2012-01-01

Protein adsorption plays a significant role in biological phenomena such as cell-surface interactions and the coagulation of blood. Two-dimensional random sequential adsorption (RSA) models are widely used to model the adsorption of proteins on solid surfaces. Continuum equations have been developed so that the results of RSA simulations can be used to predict the kinetics of adsorption. Recently, Brownian dynamics simulations have become popular for modeling protein adsorption. In this work a continuum model was developed to allow the results from a Brownian dynamics simulation to be used as the boundary condition in a computational fluid dynamics (CFD) simulation. Brownian dynamics simulations were used to model the diffusive transport of hard-sphere particles in a liquid and the adsorption of the particles onto a solid surface. The configuration of the adsorbed particles was analyzed to quantify the chemical potential near the surface, which was found to be a function of the distance from the surface and the fractional surface coverage. The near-surface chemical potential was used to derive a continuum model of adsorption that incorporates the results from the Brownian dynamics simulations. The equations of the continuum model were discretized and coupled to a CFD simulation of diffusive transport to the surface. The kinetics of adsorption predicted by the continuum model closely matched the results from the Brownian dynamics simulation. This new model allows the results from mesoscale simulations to be incorporated into micro- or macro-scale CFD transport simulations of protein adsorption in practical devices. PMID:23729843

Dynamic behaviour of a two-microbubble system under ultrasonic wave excitation.

PubMed

Huang, Xiao; Wang, Qian-Xi; Zhang, A-Man; Su, Jian

2018-05-01

Acoustic bubbles have wide and important applications in ultrasonic cleaning, sonochemistry and medical ultrasonics. A two-microbubble system (TMS) under ultrasonic wave excitation is explored in the present study, by using the boundary element method (BEM) based on the potential flow theory. A parametric study of the behaviour of a TMS has been carried out in terms of the amplitude and direction of ultrasound as well as the sizes and separation distance of the two bubbles. Three regimes of the dynamic behaviour of the TMS have been identified in terms of the pressure amplitude of the ultrasonic wave. When subject to a strong wave with the pressure amplitude of 1 atm or larger, the two microbubbles become non-spherical during the first cycle of oscillation, with two counter liquid jets formed. When subject to a weak wave with the pressure amplitude of less than 0.5 atm, two microbubbles may be attracted, repelled, or translate along the wave direction with periodic stable separation distance, depending on their size ratio. However, for the TMS under moderate waves, bubbles undergo both non-spherical oscillation and translation as well as liquid jet rebounding. Copyright © 2018 Elsevier B.V. All rights reserved.

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study.

PubMed

Bandyopadhyay, Dibyendu; Choudhury, Niharendu

2012-06-14

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.

Holographic self-tuning of the cosmological constant

NASA Astrophysics Data System (ADS)

Charmousis, Christos; Kiritsis, Elias; Nitti, Francesco

2017-09-01

We propose a brane-world setup based on gauge/gravity duality in which the four-dimensional cosmological constant is set to zero by a dynamical self-adjustment mechanism. The bulk contains Einstein gravity and a scalar field. We study holographic RG flow solutions, with the standard model brane separating an infinite volume UV region and an IR region of finite volume. For generic values of the brane vacuum energy, regular solutions exist such that the four-dimensional brane is flat. Its position in the bulk is determined dynamically by the junction conditions. Analysis of linear fluctuations shows that a regime of 4-dimensional gravity is possible at large distances, due to the presence of an induced gravity term. The graviton acquires an effective mass, and a five-dimensional regime may exist at large and/or small scales. We show that, for a broad choice of potentials, flat-brane solutions are manifestly stable and free of ghosts. We compute the scalar contribution to the force between brane-localized sources and show that, in certain models, the vDVZ discontinuity is absent and the effective interaction at short distances is mediated by two transverse graviton helicities.

Anti-gravity training improves walking capacity and postural balance in patients with muscular dystrophy.

PubMed

Berthelsen, Martin Peter; Husu, Edith; Christensen, Sofie Bouschinger; Prahm, Kira Philipsen; Vissing, John; Jensen, Bente Rona

2014-06-01

Recent studies in patients with muscular dystrophies suggest positive effects of aerobic and strength training. These studies focused training on using bicycle ergometers and conventional strength training, which precludes more severely affected patients from participating, because of their weakness. We investigated the functional effects of combined aerobic and strength training in patients with Becker and limb-girdle muscular dystrophies with knee muscle strength levels as low as 3% of normal strength. Eight patients performed 10 weeks of aerobic and strength training on an anti-gravity treadmill, which offered weight support up to 80% of their body weight. Six minute walking distance, dynamic postural balance, and plasma creatine kinase were assessed 10 weeks prior to training, immediately before training and after 10 weeks of training. Training elicited an improvement of walking distance by 8±2% and dynamic postural balance by 13±4%, indicating an improved physical function. Plasma creatine kinase remained unchanged. These results provide evidence that a combination of aerobic and strength training during anti-gravity has the potential to safely improve functional ability in severely affected patients with Becker and limb-girdle muscular dystrophies. Copyright © 2014 Elsevier B.V. All rights reserved.

Dynamic response characteristics of the high-temperature superconducting maglev system under lateral eccentric distance

NASA Astrophysics Data System (ADS)

Wang, Bo; Zheng, Jun; Si, Shuaishuai; Qian, Nan; Li, Haitao; Li, Jipeng; Deng, Zigang

2016-07-01

Off-centre operation of high-temperature superconducting (HTS) maglev systems caused by inevitable conditions such as the misregistration of vehicle, crosswind and curve negotiation, may change the distribution of the trapped flux in the HTS bulks and the magnetic interaction between HTS bulks and the PMG. It impacts on the performance of HTS maglev, and more seriously makes the maglev vehicle overturned. Therefore, understanding the performance of the HTS maglev in off-center operation is very important. In this paper, the dynamic response characteristics of a cryostat with twenty-four onboard YBaCuO superconductor bulks were experimentally investigated at different eccentric distances under loads before the initial FC process. Parameters such as vibration accelerations, displacement, natural frequency and dynamic stiffness were acquired and analyzed via the B&K vibration analyzer and laser displacement sensors. Results suggest that the natural frequency and dynamic stiffness of the maglev vehicle would be obviously reduced with the eccentric distance, posing negative effects on the stability of HTS maglev.

Nonlinear Gap Junctions Enable Long-Distance Propagation of Pulsating Calcium Waves in Astrocyte Networks

PubMed Central

Goldberg, Mati; De Pittà, Maurizio; Volman, Vladislav; Berry, Hugues; Ben-Jacob, Eshel

2010-01-01

A new paradigm has recently emerged in brain science whereby communications between glial cells and neuron-glia interactions should be considered together with neurons and their networks to understand higher brain functions. In particular, astrocytes, the main type of glial cells in the cortex, have been shown to communicate with neurons and with each other. They are thought to form a gap-junction-coupled syncytium supporting cell-cell communication via propagating Ca2+ waves. An identified mode of propagation is based on cytoplasm-to-cytoplasm transport of inositol trisphosphate (IP3) through gap junctions that locally trigger Ca2+ pulses via IP3-dependent Ca2+-induced Ca2+ release. It is, however, currently unknown whether this intracellular route is able to support the propagation of long-distance regenerative Ca2+ waves or is restricted to short-distance signaling. Furthermore, the influence of the intracellular signaling dynamics on intercellular propagation remains to be understood. In this work, we propose a model of the gap-junctional route for intercellular Ca2+ wave propagation in astrocytes. Our model yields two major predictions. First, we show that long-distance regenerative signaling requires nonlinear coupling in the gap junctions. Second, we show that even with nonlinear gap junctions, long-distance regenerative signaling is favored when the internal Ca2+ dynamics implements frequency modulation-encoding oscillations with pulsating dynamics, while amplitude modulation-encoding dynamics tends to restrict the propagation range. As a result, spatially heterogeneous molecular properties and/or weak couplings are shown to give rise to rich spatiotemporal dynamics that support complex propagation behaviors. These results shed new light on the mechanisms implicated in the propagation of Ca2+ waves across astrocytes and the precise conditions under which glial cells may participate in information processing in the brain. PMID:20865153

The many faces of graph dynamics

NASA Astrophysics Data System (ADS)

Pignolet, Yvonne Anne; Roy, Matthieu; Schmid, Stefan; Tredan, Gilles

2017-06-01

The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is known today about the network dynamics: indeed, complex networks in reality are not static, but rather dynamically evolve over time. Our paper is motivated by the empirical observation that network evolution patterns seem far from random, but exhibit structure. Moreover, the specific patterns appear to depend on the network type, contradicting the existence of a ‘one fits it all’ model. However, we still lack observables to quantify these intuitions, as well as metrics to compare graph evolutions. Such observables and metrics are needed for extrapolating or predicting evolutions, as well as for interpolating graph evolutions. To explore the many faces of graph dynamics and to quantify temporal changes, this paper suggests to build upon the concept of centrality, a measure of node importance in a network. In particular, we introduce the notion of centrality distance, a natural similarity measure for two graphs which depends on a given centrality, characterizing the graph type. Intuitively, centrality distances reflect the extent to which (non-anonymous) node roles are different or, in case of dynamic graphs, have changed over time, between two graphs. We evaluate the centrality distance approach for five evolutionary models and seven real-world social and physical networks. Our results empirically show the usefulness of centrality distances for characterizing graph dynamics compared to a null-model of random evolution, and highlight the differences between the considered scenarios. Interestingly, our approach allows us to compare the dynamics of very different networks, in terms of scale and evolution speed.

Research in Distance Education: A System Modeling Approach.

ERIC Educational Resources Information Center

Saba, Farhad; Twitchell, David

1988-01-01

Describes how a computer simulation research method can be used for studying distance education systems. Topics discussed include systems research in distance education; a technique of model development using the System Dynamics approach and DYNAMO simulation language; and a computer simulation of a prototype model. (18 references) (LRW)

Research in Distance Education: A System Modeling Approach.

ERIC Educational Resources Information Center

Saba, Farhad; Twitchell, David

This demonstration of the use of a computer simulation research method based on the System Dynamics modeling technique for studying distance education reviews research methods in distance education, including the broad categories of conceptual and case studies, and presents a rationale for the application of systems research in this area. The…

The Evaluation of Foam Performance and Flooding Efficiency

NASA Astrophysics Data System (ADS)

Keliang, Wang; Yuhao, Chen; Gang, Wang; Gen, Li

2017-12-01

ROSS-Miles and spinning drop interfacial tensionmeter are used to select suitable foam system through foam composite index (FCI) and interfacial tension (IT). The selected foam system are taken to conduct further test. The further tests are evaluating the foam system resistance to adsorption with multi-round core flooding dynamic adsorption test and evaluating the performance of foam system with four kinds of different transport distance, quantitatively analyzing the foam system effective distance after dynamic adsorption. The result shows that the foaming ability and the mobilizing ability of the foam system decrease with the increase of the round of dynamic adsorption. As the transport distance increases, the foaming ability and the mobilizing ability of the foam system decrease. This result further reveals the flooding characteristics of nitrogen foam flooding, which provides a reference for the implementation of nitrogen foam flooding technology.

Application of digital image correlation for long-distance bridge deflection measurement

NASA Astrophysics Data System (ADS)

Tian, Long; Pan, Bing; Cai, Youfa; Liang, Hui; Zhao, Yan

2013-06-01

Due to its advantages of non-contact, full-field and high-resolution measurement, digital image correlation (DIC) method has gained wide acceptance and found numerous applications in the field of experimental mechanics. In this paper, the application of DIC for real-time long-distance bridge deflection detection in outdoor environments is studied. Bridge deflection measurement using DIC in outdoor environments is more challenging than regular DIC measurements performed under laboratory conditions. First, much more image noise due to variations in ambient light will be presented in the images recorded in outdoor environments. Second, how to select the target area becomes a key factor because long-distance imaging results in a large field of view of the test object. Finally, the image acquisition speed of the camera must be high enough (larger than 100 fps) to capture the real-time dynamic motion of a bridge. In this work, the above challenging issues are addressed and several improvements were made to DIC method. The applicability was demonstrated by real experiments. Experimental results indicate that the DIC method has great potentials in motion measurement in various large building structures.

Evolution of dispersal and life history interact to drive accelerating spread of an invasive species.

PubMed

Perkins, T Alex; Phillips, Benjamin L; Baskett, Marissa L; Hastings, Alan

2013-08-01

Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life-history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life-history and dispersal evolution during range shift. In roughly equal parts, life-history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion. © 2013 John Wiley & Sons Ltd/CNRS.

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

NASA Astrophysics Data System (ADS)

Kawaguchi, Kazutomo; Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.

Physical Forces between Humans and How Humans Attract and Repel Each Other Based on Their Social Interactions in an Online World

PubMed Central

Thurner, Stefan; Fuchs, Benedikt

2015-01-01

Physical interactions between particles are the result of the exchange of gauge bosons. Human interactions are mediated by the exchange of messages, goods, money, promises, hostilities, etc. While in the physical world interactions and their associated forces have immediate dynamical consequences (Newton’s laws) the situation is not clear for human interactions. Here we quantify the relative acceleration between humans who interact through the exchange of messages, goods and hostilities in a massive multiplayer online game. For this game we have complete information about all interactions (exchange events) between about 430,000 players, and about their trajectories (movements) in the metric space of the game universe at any point in time. We use this information to derive “interaction potentials" for communication, trade and attacks and show that they are harmonic in nature. Individuals who exchange messages and trade goods generally attract each other and start to separate immediately after exchange events end. The form of the interaction potential for attacks mirrors the usual “hit-and-run" tactics of aggressive players. By measuring interaction intensities as a function of distance, velocity and acceleration, we show that “forces" between players are directly related to the number of exchange events. We find an approximate power-law decay of the likelihood for interactions as a function of distance, which is in accordance with previous real world empirical work. We show that the obtained potentials can be understood with a simple model assuming an exchange-driven force in combination with a distance-dependent exchange rate. PMID:26196505

Physical Forces between Humans and How Humans Attract and Repel Each Other Based on Their Social Interactions in an Online World.

PubMed

Thurner, Stefan; Fuchs, Benedikt

2015-01-01

Physical interactions between particles are the result of the exchange of gauge bosons. Human interactions are mediated by the exchange of messages, goods, money, promises, hostilities, etc. While in the physical world interactions and their associated forces have immediate dynamical consequences (Newton's laws) the situation is not clear for human interactions. Here we quantify the relative acceleration between humans who interact through the exchange of messages, goods and hostilities in a massive multiplayer online game. For this game we have complete information about all interactions (exchange events) between about 430,000 players, and about their trajectories (movements) in the metric space of the game universe at any point in time. We use this information to derive "interaction potentials" for communication, trade and attacks and show that they are harmonic in nature. Individuals who exchange messages and trade goods generally attract each other and start to separate immediately after exchange events end. The form of the interaction potential for attacks mirrors the usual "hit-and-run" tactics of aggressive players. By measuring interaction intensities as a function of distance, velocity and acceleration, we show that "forces" between players are directly related to the number of exchange events. We find an approximate power-law decay of the likelihood for interactions as a function of distance, which is in accordance with previous real world empirical work. We show that the obtained potentials can be understood with a simple model assuming an exchange-driven force in combination with a distance-dependent exchange rate.

Feature integration across space, time, and orientation

PubMed Central

Otto, Thomas U.; Öğmen, Haluk; Herzog, Michael H.

2012-01-01

The perception of a visual target can be strongly influenced by flanking stimuli. In static displays, performance on the target improves when the distance to the flanking elements increases- proposedly because feature pooling and integration vanishes with distance. Here, we studied feature integration with dynamic stimuli. We show that features of single elements presented within a continuous motion stream are integrated largely independent of spatial distance (and orientation). Hence, space based models of feature integration cannot be extended to dynamic stimuli. We suggest that feature integration is guided by perceptual grouping operations that maintain the identity of perceptual objects over space and time. PMID:19968428

Functional organization of primate translational vestibulo-ocular reflexes and effects of unilateral labyrinthectomy

NASA Technical Reports Server (NTRS)

Angelaki, D. E.; McHenry, M. Q.; Newlands, S. D.; Dickman, J. D.

1999-01-01

Translational vestibulo-ocular reflexes (trVORs) are characterized by distinct spatio-temporal properties and sensitivities that are proportional to the inverse of viewing distance. Anodal (inhibitory) labyrinthine stimulation (100 microA, < 2 s) during motion decreased the high-pass filtered dynamics, as well as horizontal trVOR sensitivity and its dependence on viewing distance. Cathodal (excitatory) currents had opposite effects. Translational VORs were also affected after unilateral labyrinthectomy. Animals lost their ability to modulate trVOR sensitivity as a function of viewing distance acutely after the lesion. These deficits partially recovered over time, albeit a significant reduction in trVOR sensitivity as a function of viewing distance remained in compensated animals. During fore-aft motion, the effects of unilateral labyrinthectomy were more dramatic. Both acute and compensated animals permanently lost their ability to modulate fore-aft trVOR responses as a function of target eccentricity. These results suggest that (1) the dynamics and viewing distance-dependent properties of the trVORs are very sensitive to changes in the resting firing rate of vestibular afferents and, consequently, vestibular nuclei neurons; (2) the most irregularly firing primary otolith afferents that are most sensitive to labyrinthine electrical stimulation might contribute to reflex dynamics and sensitivity; (3) inputs from both labyrinths are necessary for the generation of the translational VORs.

Role of density modulation in the spatially resolved dynamics of strongly confined liquids

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

Saw, Shibu, E-mail: shibu.saw@sydney.edu.au; Dasgupta, Chandan, E-mail: cdgupta@physics.iisc.ernet.in

Confinement by walls usually produces a strong modulation in the density of dense liquids near the walls. Using molecular dynamics simulations, we examine the effects of the density modulation on the spatially resolved dynamics of a liquid confined between two parallel walls, using a resolution of a fraction of the interparticle distance in the liquid. The local dynamics is quantified by the relaxation time associated with the temporal autocorrelation function of the local density. We find that this local relaxation time varies in phase with the density modulation. The amplitude of the spatial modulation of the relaxation time can bemore » quite large, depending on the characteristics of the wall and thermodynamic parameters of the liquid. To disentangle the effects of confinement and density modulation on the spatially resolved dynamics, we compare the dynamics of a confined liquid with that of an unconfined one in which a similar density modulation is induced by an external potential. We find several differences indicating that density modulation alone cannot account for all the features seen in the spatially resolved dynamics of confined liquids. We also examine how the dynamics near a wall depends on the separation between the two walls and show that the features seen in our simulations persist in the limit of large wall separation.« less

Spatial Distribution of Coffee Wilt Disease Under Roguing and Replanting Conditions: A Case Study from Kaweri Estate in Uganda.

PubMed

Pinard, F; Makune, S E; Campagne, P; Mwangi, J

2016-11-01

Based on time and spatial dynamic considerations, this study evaluates the potential role of short- and long-distance dispersal in the spread of coffee wilt disease (CWD) in a large commercial Robusta coffee estate in Uganda (Kaweri, 1,755 ha) over a 4-year period (2008 to 2012). In monthly surveys, total disease incidence, expansion of infection foci, and the occurrence of isolated infected trees were recorded and submitted to spatial analysis. Incidence was higher and disease progression faster in old coffee plantings compared with young plantings, indicating a lack of efficiency of roguing for reducing disease development in old plantings. At large spatial scale (approximately 1 km), Moran indices (both global and local) revealed the existence of clusters characterized by contrasting disease incidences. This suggested that local environmental conditions were heterogeneous or there were spatial interactions among blocks. At finer spatial scale (approximately 200 m), O-ring statistics revealed positive correlation between distant infection sites across distances as great as 60 m. Although these observations indicate the role of short-distance dispersal in foci expansion, dispersal at greater distances (>20 m) appeared to also contribute to both initiation of new foci and disease progression at coarser spatial scales. Therefore, our results suggested the role of aerial dispersal in CWD progression.

Nanopowder synthesis based on electric explosion technology

NASA Astrophysics Data System (ADS)

Kryzhevich, D. S.; Zolnikov, K. P.; Korchuganov, A. V.; Psakhie, S. G.

2017-10-01

A computer simulation of the bicomponent nanoparticle formation during the electric explosion of copper and nickel wires was carried out. The calculations were performed in the framework of the molecular dynamics method using many-body potentials of interatomic interaction. As a result of an electric explosion of dissimilar metal wires, bicomponent nanoparticles having different stoichiometry and a block structure can be formed. It is possible to control the process of destruction and the structure of the formed bicomponent nanoparticles by varying the distance between the wires and the loading parameters.

Interacting quantum walkers: two-body bosonic and fermionic bound states

NASA Astrophysics Data System (ADS)

Krapivsky, P. L.; Luck, J. M.; Mallick, K.

2015-11-01

We investigate the dynamics of bound states of two interacting particles, either bosons or fermions, performing a continuous-time quantum walk on a one-dimensional lattice. We consider the situation where the distance between both particles has a hard bound, and the richer situation where the particles are bound by a smooth confining potential. The main emphasis is on the velocity characterizing the ballistic spreading of these bound states, and on the structure of the asymptotic distribution profile of their center-of-mass coordinate. The latter profile generically exhibits many internal fronts.

Charge independence, charge symmetry breaking in the S-wave nucleon-nucleon interaction, and renormalization

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

Alvaro Calle Cordon,Manuel Pavon Valderrama,Enrique Ruiz Arriola

2012-02-01

We study the interplay between charge symmetry breaking and renormalization in the NN system for S-waves. We find a set of universality relations which disentangle explicitly the known long distance dynamics from low energy parameters and extend them to the Coulomb case. We analyze within such an approach the One-Boson-Exchange potential and the theoretical conditions which allow to relate the proton-neutron, proton-proton and neutron-neutron scattering observables without the introduction of extra new parameters and providing good phenomenological success.

Differentially Private Histogram Publication For Dynamic Datasets: An Adaptive Sampling Approach

PubMed Central

Li, Haoran; Jiang, Xiaoqian; Xiong, Li; Liu, Jinfei

2016-01-01

Differential privacy has recently become a de facto standard for private statistical data release. Many algorithms have been proposed to generate differentially private histograms or synthetic data. However, most of them focus on “one-time” release of a static dataset and do not adequately address the increasing need of releasing series of dynamic datasets in real time. A straightforward application of existing histogram methods on each snapshot of such dynamic datasets will incur high accumulated error due to the composibility of differential privacy and correlations or overlapping users between the snapshots. In this paper, we address the problem of releasing series of dynamic datasets in real time with differential privacy, using a novel adaptive distance-based sampling approach. Our first method, DSFT, uses a fixed distance threshold and releases a differentially private histogram only when the current snapshot is sufficiently different from the previous one, i.e., with a distance greater than a predefined threshold. Our second method, DSAT, further improves DSFT and uses a dynamic threshold adaptively adjusted by a feedback control mechanism to capture the data dynamics. Extensive experiments on real and synthetic datasets demonstrate that our approach achieves better utility than baseline methods and existing state-of-the-art methods. PMID:26973795

Dynamic clearance measure to evaluate locomotor and perceptuo-motor strategies used for obstacle circumvention in a virtual environment.

PubMed

Darekar, Anuja; Lamontagne, Anouk; Fung, Joyce

2015-04-01

Circumvention around an obstacle entails a dynamic interaction with the obstacle to maintain a safe clearance. We used a novel mathematical interpolation method based on the modified Shepard's method of Inverse Distance Weighting to compute dynamic clearance that reflected this interaction as well as minimal clearance. This proof-of-principle study included seven young healthy, four post-stroke and four healthy age-matched individuals. A virtual environment designed to assess obstacle circumvention was used to administer a locomotor (walking) and a perceptuo-motor (navigation with a joystick) task. In both tasks, participants were asked to navigate towards a target while avoiding collision with a moving obstacle that approached from either head-on, or 30° left or right. Among young individuals, dynamic clearance did not differ significantly between obstacle approach directions in both tasks. Post-stroke individuals maintained larger and smaller dynamic clearance during the locomotor and the perceptuo-motor task respectively as compared to age-matched controls. Dynamic clearance was larger than minimal distance from the obstacle irrespective of the group, task and obstacle approach direction. Also, in contrast to minimal distance, dynamic clearance can respond differently to different avoidance behaviors. Such a measure can be beneficial in contrasting obstacle avoidance behaviors in different populations with mobility problems. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de; Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial chargesmore » within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.« less

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

NASA Astrophysics Data System (ADS)

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.

2015-11-01

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase.

PubMed

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H L

2015-11-07

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

Interactions in charged colloidal suspensions: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Padidela, Uday Kumar; Behera, Raghu Nath

2017-07-01

Colloidal suspensions are extensively used in everyday life and find several applications in the pharmaceutical, chemical, food industries, etc. We present the classical molecular dynamics simulation results of the structural and transport properties of charged colloidal suspensions as a function of its size, charge and concentration. The system is viewed as a two-component (colloids and counterions) primitive model consisting of spherical colloid particle (macroion) and the counterions (micro-particles), which are treated explicitly. The solvent is treated as dielectric continuum. A systematic trend in the radial distribution functions g(r), potential of mean force W(r), different thermodynamic properties and diffusion coefficients is obtained as a function of colloid charge, size and concentration. An attractive minimum in W(r) is obtained at short interparticle distance.

New Results on Short-Range Correlations in Nuclei

DOE PAGES

Fomin, Nadia; Higinbotham, Douglas; Sargsian, Misak; ...

2017-10-12

Nuclear dynamics at short distances is one of the most fascinating topics of strong interaction physics. The physics of it is closely related to the understanding of the role of the QCD in generating nuclear forces at short distances, as well as of the dynamics of the superdense cold nuclear matter relevant to the interior of neutron stars. The emergence of high-energy electron and proton beams has led to significant recent progress in high-energy nuclear scattering experiments investigating the short-range structure of nuclei. These experiments, in turn, have stimulated new theoretical studies resulting in the observation of several new phenomenamore » specific to the short-range structure of nuclei. In this article, we review recent theoretical and experimental progress in studies of short-range correlations in nuclei and discuss their importance for advancing our understanding of the dynamics of nuclear interactions at short distances.« less

New Results on Short-Range Correlations in Nuclei

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

Fomin, Nadia; Higinbotham, Douglas; Sargsian, Misak

Nuclear dynamics at short distances is one of the most fascinating topics of strong interaction physics. The physics of it is closely related to the understanding of the role of the QCD in generating nuclear forces at short distances, as well as of the dynamics of the superdense cold nuclear matter relevant to the interior of neutron stars. The emergence of high-energy electron and proton beams has led to significant recent progress in high-energy nuclear scattering experiments investigating the short-range structure of nuclei. These experiments, in turn, have stimulated new theoretical studies resulting in the observation of several new phenomenamore » specific to the short-range structure of nuclei. In this article, we review recent theoretical and experimental progress in studies of short-range correlations in nuclei and discuss their importance for advancing our understanding of the dynamics of nuclear interactions at short distances.« less

Dynamics of Polarons in Organic Conjugated Polymers with Side Radicals.

PubMed

Liu, J J; Wei, Z J; Zhang, Y L; Meng, Y; Di, B

2017-03-16

Based on the one-dimensional tight-binding Su-Schrieffer-Heeger (SSH) model, and using the molecular dynamics method, we discuss the dynamics of electron and hole polarons propagating along a polymer chain, as a function of the distance between side radicals and the magnitude of the transfer integrals between the main chain and the side radicals. We first discuss the average velocities of electron and hole polarons as a function of the distance between side radicals. It is found that the average velocities of the electron polarons remain almost unchanged, while the average velocities of hole polarons decrease significantly when the radical distance is comparable to the polaron width. Second, we have found that the average velocities of electron polarons decrease with increasing transfer integral, but the average velocities of hole polarons increase. These results may provide a theoretical basis for understanding carriers transport properties in polymers chain with side radicals.

Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations.

PubMed

Blöchliger, Nicolas; Caflisch, Amedeo; Vitalis, Andreas

2015-11-10

Data mining techniques depend strongly on how the data are represented and how distance between samples is measured. High-dimensional data often contain a large number of irrelevant dimensions (features) for a given query. These features act as noise and obfuscate relevant information. Unsupervised approaches to mine such data require distance measures that can account for feature relevance. Molecular dynamics simulations produce high-dimensional data sets describing molecules observed in time. Here, we propose to globally or locally weight simulation features based on effective rates. This emphasizes, in a data-driven manner, slow degrees of freedom that often report on the metastable states sampled by the molecular system. We couple this idea to several unsupervised learning protocols. Our approach unmasks slow side chain dynamics within the native state of a miniprotein and reveals additional metastable conformations of a protein. The approach can be combined with most algorithms for clustering or dimensionality reduction.

High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid.

PubMed

Vanden Broeck, An; Van Landuyt, Wouter; Cox, Karen; De Bruyn, Luc; Gyselings, Ralf; Oostermeijer, Gerard; Valentin, Bertille; Bozic, Gregor; Dolinar, Branko; Illyés, Zoltán; Mergeay, Joachim

2014-07-07

Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) 'outlier' loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe.

Multiple Weather Factors Affect Apparent Survival of European Passerine Birds

PubMed Central

Salewski, Volker; Hochachka, Wesley M.; Fiedler, Wolfgang

2013-01-01

Weather affects the demography of animals and thus climate change will cause local changes in demographic rates. In birds numerous studies have correlated demographic factors with weather but few of those examined variation in the impacts of weather in different seasons and, in the case of migrants, in different regions. Using capture-recapture models we correlated weather with apparent survival of seven passerine bird species with different migration strategies to assess the importance of selected facets of weather throughout the year on apparent survival. Contrary to our expectations weather experienced during the breeding season did not affect apparent survival of the target species. However, measures for winter severity were associated with apparent survival of a resident species, two short-distance/partial migrants and a long-distance migrant. Apparent survival of two short distance migrants as well as two long-distance migrants was further correlated with conditions experienced during the non-breeding season in Spain. Conditions in Africa had statistically significant but relatively minor effects on the apparent survival of the two long-distance migrants but also of a presumably short-distance migrant and a short-distance/partial migrant. In general several weather effects independently explained similar amounts of variation in apparent survival for the majority of species and single factors explained only relatively low amounts of temporal variation of apparent survival. Although the directions of the effects on apparent survival mostly met our expectations and there are clear predictions for effects of future climate we caution against simple extrapolations of present conditions to predict future population dynamics. Not only did weather explains limited amounts of variation in apparent survival, but future demographics will likely be affected by changing interspecific interactions, opposing effects of weather in different seasons, and the potential for phenotypic and microevolutionary adaptations. PMID:23593131

High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid

PubMed Central

2014-01-01

Background Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. Results We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. Conclusions The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe. PMID:24998243

Concentration and biochemical gradients of seston in Lake Ontario

USGS Publications Warehouse

Kelly, Patrick T.; Weidel, Brian C.; Paufve, Matthew R.; O'Malley, Brian P.; Watkins, James M.; Rudstam, Lars G.; Jones, Stuart E.

2017-01-01

Spatial variability in resource quantity and quality may have important implications for the distribution and productivity of primary consumers. In Lake Ontario, ecosystem characteristics suggest the potential for significant spatial heterogeneity in seston quantity and quality, particularly due to the potential for nearshore-offshore gradients in allochthonous nutrient supply, and the formation of a deep chlorophyll layer (DCL) in July. We assessed total and zooplankton food particle size-fractionated chlorophyll a concentrations, as well as carbon-to-phosphorus stoichiometry and essential fatty acid composition of seston across a distance-from-shore and depth transect. We observed time, sampling depth, and distance from shore to be the best predictors of chlorophyll a concentration. Resource quality was much more homogenous in space, but there were strong patterns through time, as both stoichiometric and fatty acid qualities in general were greatest in May, and lowest in July/August. We did observe a peak in essential fatty acid concentration near the DCL in during time of formation, possibly due to differences in phytoplankton community composition between the DCL and epilimnion. These results suggest the potential for a spatially and temporally dynamic resource base for consumers in Lake Ontario, which may be important in developing a broader understanding of variable consumer productivity.

Hydrogen bonds in concreto and in computro

NASA Astrophysics Data System (ADS)

Stouten, Pieter F. W.; Kroon, Jan

1988-07-01

Molecular dynamics simulations of liquid water and liquid methanol have been carried out. For both liquids an effective pair potential was used. The models were fitted to the heat of vaporization, pressure and various radial distribution functions resulting from diffraction experiments on liquids. In both simulations 216 molecules were put in a cubic periodical ☐. The system was loosely coupled to a temperature bath and to a pressure bath. Following an initial equilibration period relevant data were sampled during 15 ps. The distributions of oxygen—oxygen distances in hydrogen bonds obtained from the two simulations are essentially the same. The distribution obtained from crystal data is somewhat different: the maximum has about the same position, but the curve is much narrower, which can be expected merely from the fact that diffraction experiments only supply average atomic positions and hence average interatomic distances. When thermal motion is taken into account a closer likeness is observed.

Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics.

PubMed

Straka, Michal; Lantto, Perttu; Vaara, Juha

2008-03-27

We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized continuum model are found to be very small.

Exploring the Angstrom Excursion of Au Nanoparticles Excited away from a Metal Surface by an Impulsive Acoustic Perturbation.

PubMed

Kim, Ji-Wan; Kovalenko, Oleksandr; Liu, Yu; Bigot, Jean-Yves

2016-12-27

We report the anharmonic angstrom dynamics of self-assembled Au nanoparticles (Au:NPs) away from a nickel surface on top of which they are coupled by their near-field interaction. The deformation and the oscillatory excursion away from the surface are induced by picosecond acoustic pulses and probed at the surface plasmon resonance with femtosecond laser pulses. The overall dynamics are due to an efficient transfer of translational momentum from the Ni surface to the Au:NPs, therefore avoiding usual thermal effects and energy redistribution among the electronic states. Two modes are clearly revealed by the oscillatory shift of the Au:NPs surface plasmon resonance-the quadrupole deformation mode due to the transient ellipsoid shape and the excursion mode when the Au:NPs bounce away from the surface. We find that, contrary to the quadrupole mode, the excursion mode is sensitive to the distance between Au:NPs and Ni. Importantly, the excursion dynamics display a nonsinusoidal motion that cannot be explained by a standard harmonic potential model. A detailed modeling of the dynamics using a Hamaker-type Lennard-Jones potential between two media is performed, showing that each Au:NPs coherently evolves in a nearly one-dimensional anharmonic potential with a total excursion of ∼1 Å. This excursion induces a shift of the surface plasmon resonance detectable because of the strong near-field interaction. This general method of observing the spatiotemporal dynamics with angstrom and picosecond resolutions can be directly transposed to many nanostructures or biosystems to reveal the interaction and contact mechanism with their surrounding medium while remaining in their fundamental electronic states.

Acute effects of rearfoot manipulation on dynamic standing balance in healthy individuals.

PubMed

Wassinger, Craig A; Rockett, Ariel; Pitman, Lucas; Murphy, Matthew Matt; Peters, Charles

2014-06-01

Dynamic standing balance is essential to perform functional activities and is included in the treatment of many lower extremity injuries. Physiotherapists utilize many methods to restore standing balance including stability exercises, functional retraining, and manual therapy. The purpose of this study was to investigate the effects of a rearfoot distraction manipulation on dynamic standing balance. Twenty healthy participants (age: 24.4 ± 2.8 years; height: 162.9 ± 37.7 cm; mass: 68.0 ± 4.8 kg; right leg dominant = 20) completed this study. Following familiarization, dynamic standing balance was assessed during: (1) an experimental condition immediately following a rearfoot distraction manipulation, and (2) a control condition. Dominant leg balance was quantified using the Y-balance test which measures lower extremity reach distances. Reach distances were normalized to leg length and measured in the anterior, posteromedial and posterolateral directions. Overall balance was calculated through the summing of all normalized directions. Paired t-tests and Wilcoxon rank tests were used to compare balance scores for parametric and non-parametric data as appropriate. Significance was set at 0.05 a priori. Effect size (ES) was calculated to determine the clinical impact of the manipulation. Increased reach distances (indicating improved balance) were noted following manipulation for overall balance (p = 0.03, ES = 0.26) and in the posteromedial direction (p = 0.01, ES = 0.42). Reach distances did not differ for the anterior (p = 0.11, ES = 0.16) or posterolateral (p = 0.11, ES = 0.25) components. Dynamic standing balance improved after a rearfoot distraction manipulation in healthy participants. It is hypothesized that manual therapy applied to the foot and ankle may be beneficial to augment other therapeutic modalities when working with patients to improve dynamic standing balance. Copyright © 2013 Elsevier Ltd. All rights reserved.

CAT & MAUS: A novel system for true dynamic motion measurement of underlying bony structures with compensation for soft tissue movement.

PubMed

Jia, Rui; Monk, Paul; Murray, David; Noble, J Alison; Mellon, Stephen

2017-09-06

Optoelectronic motion capture systems are widely employed to measure the movement of human joints. However, there can be a significant discrepancy between the data obtained by a motion capture system (MCS) and the actual movement of underlying bony structures, which is attributed to soft tissue artefact. In this paper, a computer-aided tracking and motion analysis with ultrasound (CAT & MAUS) system with an augmented globally optimal registration algorithm is presented to dynamically track the underlying bony structure during movement. The augmented registration part of CAT & MAUS was validated with a high system accuracy of 80%. The Euclidean distance between the marker-based bony landmark and the bony landmark tracked by CAT & MAUS was calculated to quantify the measurement error of an MCS caused by soft tissue artefact during movement. The average Euclidean distance between the target bony landmark measured by each of the CAT & MAUS system and the MCS alone varied from 8.32mm to 16.87mm in gait. This indicates the discrepancy between the MCS measured bony landmark and the actual underlying bony landmark. Moreover, Procrustes analysis was applied to demonstrate that CAT & MAUS reduces the deformation of the body segment shape modeled by markers during motion. The augmented CAT & MAUS system shows its potential to dynamically detect and locate actual underlying bony landmarks, which reduces the MCS measurement error caused by soft tissue artefact during movement. Copyright © 2017 Elsevier Ltd. All rights reserved.

"Distance Education: An International Journal"-- Reflections on How It All Began

ERIC Educational Resources Information Center

Mitchell, Ian McD.

2009-01-01

In this article, the author reflects on the historical context of the Australian distance education environment that led to the establishment of the journal "Distance Education." He deals with the dynamics of and the decisions made about the journal, in the light of that environment. He also asks readers to share their stance on the…

A variational dynamic programming approach to robot-path planning with a distance-safety criterion

NASA Technical Reports Server (NTRS)

Suh, Suk-Hwan; Shin, Kang G.

1988-01-01

An approach to robot-path planning is developed by considering both the traveling distance and the safety of the robot. A computationally-efficient algorithm is developed to find a near-optimal path with a weighted distance-safety criterion by using a variational calculus and dynamic programming (VCDP) method. The algorithm is readily applicable to any factory environment by representing the free workspace as channels. A method for deriving these channels is also proposed. Although it is developed mainly for two-dimensional problems, this method can be easily extended to a class of three-dimensional problems. Numerical examples are presented to demonstrate the utility and power of this method.

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

PubMed Central

Brodie, Nicholas I.; Popov, Konstantin I.; Petrotchenko, Evgeniy V.; Dokholyan, Nikolay V.; Borchers, Christoph H.

2017-01-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein—models for α helix–rich and β sheet–rich proteins, respectively—and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures. PMID:28695211

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

PubMed

Brodie, Nicholas I; Popov, Konstantin I; Petrotchenko, Evgeniy V; Dokholyan, Nikolay V; Borchers, Christoph H

2017-07-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures.

Sexual Segregation in Juvenile New Zealand Sea Lion Foraging Ranges: Implications for Intraspecific Competition, Population Dynamics and Conservation

PubMed Central

Leung, Elaine S.; Chilvers, B. Louise; Nakagawa, Shinichi; Moore, Antoni B.; Robertson, Bruce C.

2012-01-01

Sexual segregation (sex differences in spatial organisation and resource use) is observed in a large range of taxa. Investigating causes for sexual segregation is vital for understanding population dynamics and has important conservation implications, as sex differences in foraging ecology may affect vulnerability to area-specific human activities. Although behavioural ecologists have proposed numerous hypotheses for this phenomenon, the underlying causes of sexual segregation are poorly understood. We examined the size-dimorphism and niche divergence hypotheses as potential explanations for sexual segregation in the New Zealand (NZ) sea lion (Phocarctos hookeri), a nationally critical, declining species impacted by trawl fisheries. We used satellite telemetry and linear mixed effects models to investigate sex differences in the foraging ranges of juvenile NZ sea lions. Male trip distances and durations were almost twice as long as female trips, with males foraging over the Auckland Island shelf and in further locations than females. Sex was the most important variable in trip distance, maximum distance travelled from study site, foraging cycle duration and percent time at sea whereas mass and age had small effects on these characteristics. Our findings support the predictions of the niche divergence hypothesis, which suggests that sexual segregation acts to decrease intraspecific resource competition. As a consequence of sexual segregation in foraging ranges, female foraging grounds had proportionally double the overlap with fisheries operations than males. This distribution exposes female juvenile NZ sea lions to a greater risk of resource competition and bycatch from fisheries than males, which can result in higher female mortality. Such sex-biased mortality could impact population dynamics, because female population decline can lead to decreased population fecundity. Thus, effective conservation and management strategies must take into account sex differences in foraging behaviour, as well as differential threat-risk to external impacts such as fisheries bycatch. PMID:23028978

Seasonal Food Scarcity Prompts Long-Distance Foraging by a Wild Social Bee.

PubMed

Pope, Nathaniel S; Jha, Shalene

2018-01-01

Foraging is an essential process for mobile animals, and its optimization serves as a foundational theory in ecology and evolution; however, drivers of foraging are rarely investigated across landscapes and seasons. Using a common bumblebee species from the western United States (Bombus vosnesenskii), we ask whether seasonal decreases in food resources prompt changes in foraging behavior and space use. We employ a unique integration of population genetic tools and spatially explicit foraging models to estimate foraging distances and rates of patch visitation for wild bumblebee colonies across three study regions and two seasons. By mapping the locations of 669 wild-caught individual foragers, we find substantial variation in colony-level foraging distances, often exhibiting a 60-fold difference within a study region. Our analysis of visitation rates indicates that foragers display a preference for destination patches with high floral cover and forage significantly farther for these patches, but only in the summer, when landscape-level resources are low. Overall, these results indicate that an increasing proportion of long-distance foraging bouts take place in the summer. Because wild bees are pollinators, their foraging dynamics are of urgent concern, given the potential impacts of global change on their movement and services. The behavioral shift toward long-distance foraging with seasonal declines in food resources suggests a novel, phenologically directed approach to landscape-level pollinator conservation and greater consideration of late-season floral resources in pollinator habitat management.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

PubMed

Gil-Ley, Alejandro; Bussi, Giovanni

2015-03-10

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

Evaluation of TEAM dynamics before and after remote simulation training utilizing CERTAIN platform.

PubMed

Pennington, Kelly M; Dong, Yue; Coville, Hongchuan H; Wang, Bo; Gajic, Ognjen; Kelm, Diana J

2018-12-01

The current study examines the feasibility and potential effects of long distance, remote simulation training on team dynamics. The study design was a prospective study evaluating team dynamics before and after remote simulation. Study subjects consisted of interdisciplinary teams (attending physicians, physicians in training, advanced care practitioners, and/or nurses). The study was conducted at nine training sites in eight countries. Study subjects completed 2-3 simulation scenarios of acute crises before and after training with the Checklist for Early Recognition and Treatment of Acute Illness (CERTAIN). Pre- and post-CERTAIN training simulations were evaluated by two independent reviewers utilizing the Team Emergency Assessment Measure (TEAM), which is a 11-item questionnaire that has been validated for assessing teamwork in the intensive care unit. Any discrepancies of greater than 1 point between the two reviewers on any question on the TEAM assessment were sent to a third reviewer to judge. The score that was deemed discordant by the third judge was eliminated. Pre- and post-CERTAIN training TEAM scores were averaged and compared. Of the nine teams evaluated, six teams demonstrated an overall improvement in global team performance following CERTAIN virtual training. For each of the 11 TEAM assessments, a trend toward improvement following CERTAIN training was noted; however, no assessment had universal improvement. 'Team composure and control' had the least absolute score improvement following CERTAIN training. The greatest improvement in the TEAM assessment scores was in the 'team's ability to complete tasks in a timely manner' and in the 'team leader's communication to the team'. The assessment of team dynamics using long distance, virtual simulation training appears to be feasible and may result in improved team performance during simulated patient crises; however, language and video quality were the two largest barriers noted during the review process.

Influence of surface morphology on adsorption of potassium stearate molecules on diamond-like carbon substrate: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Guo, Shusen; Cao, Yongzhi; Sun, Tao; Zhang, Junjie; Gu, Le; Zhang, Chuanwei; Xu, Zhiqiang

2018-05-01

Molecular dynamics (MD) simulations were used to provide insights into the influence of nano-scale surface morphology on adsorptive behavior of Potassium stearate molecules on diamond-like carbon (DLC) substrates. Particular focus was given to explain that how the distinctive geometric properties of different surface morphologies affect the equilibrium structures and substrate-molecules interactions of monolayers, which was achieved through adsorptive analysis methods including adsorptive process, density profile, density distribution and surface potential energy. Analysis on surface potential energy demonstrated that the adsorptivity of amorphous smooth substrate is uniformly distributed over the surface, while DLC substrates with different surface morphologies appear to be more potentially corrugated, which improves the adsorptivity significantly. Because of the large distance of molecules from carbon atoms located at the square groove bottom, substrate-molecules interactions vanish significantly, and thus potassium stearate molecules cannot penetrate completely into the square groove. It can be observed that the equilibrium substrate-molecules interactions of triangle groove and semi-circle groove are much more powerful than that of square groove due to geometrically advantageous properties. These findings provided key information of optimally design of solid substrates with controllable adsorptivity.

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Surface diffusion of Si, Ge and C adatoms on Si (001) substrate studied by the molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Chen, Zhi-Hui; Yu, Zhong-Yuan; Lu, Peng-Fei; Liu, Yu-Min

2009-10-01

Depositions of Si, Ge and C atoms onto a preliminary Si (001) substrate at different temperatures are investigated by using the molecular dynamics method. The mechanism of atomic self-assembling occurring locally on the flat terraces between steps is suggested. Diffusion and arrangement patterns of adatoms at different temperatures are observed. At 900 K, the deposited atoms are more likely to form dimers in the perpendicular [110] direction due to the more favourable movement along the perpendicular [110] direction. C adatoms are more likely to break or reconstruct the dimers on the substrate surface and have larger diffusion distances than Ge and Si adatoms. Exchange between C adatoms and substrate atoms are obvious and the epitaxial thickness is small. Total potential energies of adatoms and substrate atoms involved in the simulation cell are computed. When a newly arrived adatom reaches the stable position, the potential energy of the system will decrease and the curves turns into a ladder-like shape. It is found that C adatoms can lead to more reduction of the system energy and the potential energy of the system will increase as temperature increases.

Phase space barriers and dividing surfaces in the absence of critical points of the potential energy: Application to roaming in ozone

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

Mauguière, Frédéric A. L., E-mail: frederic.mauguiere@bristol.ac.uk; Collins, Peter, E-mail: peter.collins@bristol.ac.uk; Wiggins, Stephen, E-mail: stephen.wiggins@mac.com

We examine the phase space structures that govern reaction dynamics in the absence of critical points on the potential energy surface. We show that in the vicinity of hyperbolic invariant tori, it is possible to define phase space dividing surfaces that are analogous to the dividing surfaces governing transition from reactants to products near a critical point of the potential energy surface. We investigate the problem of capture of an atom by a diatomic molecule and show that a normally hyperbolic invariant manifold exists at large atom-diatom distances, away from any critical points on the potential. This normally hyperbolic invariantmore » manifold is the anchor for the construction of a dividing surface in phase space, which defines the outer or loose transition state governing capture dynamics. We present an algorithm for sampling an approximate capture dividing surface, and apply our methods to the recombination of the ozone molecule. We treat both 2 and 3 degrees of freedom models with zero total angular momentum. We have located the normally hyperbolic invariant manifold from which the orbiting (outer) transition state is constructed. This forms the basis for our analysis of trajectories for ozone in general, but with particular emphasis on the roaming trajectories.« less

Detecting Intramolecular Conformational Dynamics of Single Molecules in Short Distance Range with Sub-Nanometer Sensitivity

PubMed Central

Zhou, Ruobo; Kunzelmann, Simone; Webb, Martin R.; Ha, Taekjip

2011-01-01

Single molecule detection is useful for characterizing nanoscale objects such as biological macromolecules, nano-particles and nano-devices with nano-meter spatial resolution. Fluorescence resonance energy transfer (FRET) is widely used as a single-molecule assay to monitor intramolecular dynamics in the distance range of 3–8 nm. Here we demonstrate that self-quenching of two rhodamine derivatives can be used to detect small conformational dynamics corresponding to sub-nanometer distance changes in a FRET-insensitive short range at the single molecule level. A ParM protein mutant labeled with two rhodamines works as a single molecule ADP sensor which has 20 times brighter fluorescence signal in the ADP bound state than the unbound state. Single molecule time trajectories show discrete transitions between fluorescence on and off states that can be directly ascribed to ADP binding and dissociation events. The conformational changes observed with 20:1 contrast are only 0.5 nm in magnitude and are between crystallographic distances of 1.6 nm and 2.1 nm, demonstrating exquisite sensitivity to short distance scale changes. The systems also allowed us to gain information on the photophysics of self-quenching induced by rhodamine stacking: (1) photobleaching of either of the two rhodamines eliminates quenching of the other rhodamine fluorophore and (2) photobleaching from the highly quenched, stacked state is only two-fold slower than from the unstacked state. PMID:22023515

Electromyographic Patterns during Golf Swing: Activation Sequence Profiling and Prediction of Shot Effectiveness.

PubMed

Verikas, Antanas; Vaiciukynas, Evaldas; Gelzinis, Adas; Parker, James; Olsson, M Charlotte

2016-04-23

This study analyzes muscle activity, recorded in an eight-channel electromyographic (EMG) signal stream, during the golf swing using a 7-iron club and exploits information extracted from EMG dynamics to predict the success of the resulting shot. Muscles of the arm and shoulder on both the left and right sides, namely flexor carpi radialis, extensor digitorum communis, rhomboideus and trapezius, are considered for 15 golf players (∼5 shots each). The method using Gaussian filtering is outlined for EMG onset time estimation in each channel and activation sequence profiling. Shots of each player revealed a persistent pattern of muscle activation. Profiles were plotted and insights with respect to player effectiveness were provided. Inspection of EMG dynamics revealed a pair of highest peaks in each channel as the hallmark of golf swing, and a custom application of peak detection for automatic extraction of swing segment was introduced. Various EMG features, encompassing 22 feature sets, were constructed. Feature sets were used individually and also in decision-level fusion for the prediction of shot effectiveness. The prediction of the target attribute, such as club head speed or ball carry distance, was investigated using random forest as the learner in detection and regression tasks. Detection evaluates the personal effectiveness of a shot with respect to the player-specific average, whereas regression estimates the value of target attribute, using EMG features as predictors. Fusion after decision optimization provided the best results: the equal error rate in detection was 24.3% for the speed and 31.7% for the distance; the mean absolute percentage error in regression was 3.2% for the speed and 6.4% for the distance. Proposed EMG feature sets were found to be useful, especially when used in combination. Rankings of feature sets indicated statistics for muscle activity in both the left and right body sides, correlation-based analysis of EMG dynamics and features derived from the properties of two highest peaks as important predictors of personal shot effectiveness. Activation sequence profiles helped in analyzing muscle orchestration during golf shot, exposing a specific avalanche pattern, but data from more players are needed for stronger conclusions. Results demonstrate that information arising from an EMG signal stream is useful for predicting golf shot success, in terms of club head speed and ball carry distance, with acceptable accuracy. Surface EMG data, collected with a goal to automatically evaluate golf player's performance, enables wearable computing in the field of ambient intelligence and has potential to enhance exercising of a long carry distance drive.

Electromyographic Patterns during Golf Swing: Activation Sequence Profiling and Prediction of Shot Effectiveness

PubMed Central

Verikas, Antanas; Vaiciukynas, Evaldas; Gelzinis, Adas; Parker, James; Olsson, M. Charlotte

2016-01-01

This study analyzes muscle activity, recorded in an eight-channel electromyographic (EMG) signal stream, during the golf swing using a 7-iron club and exploits information extracted from EMG dynamics to predict the success of the resulting shot. Muscles of the arm and shoulder on both the left and right sides, namely flexor carpi radialis, extensor digitorum communis, rhomboideus and trapezius, are considered for 15 golf players (∼5 shots each). The method using Gaussian filtering is outlined for EMG onset time estimation in each channel and activation sequence profiling. Shots of each player revealed a persistent pattern of muscle activation. Profiles were plotted and insights with respect to player effectiveness were provided. Inspection of EMG dynamics revealed a pair of highest peaks in each channel as the hallmark of golf swing, and a custom application of peak detection for automatic extraction of swing segment was introduced. Various EMG features, encompassing 22 feature sets, were constructed. Feature sets were used individually and also in decision-level fusion for the prediction of shot effectiveness. The prediction of the target attribute, such as club head speed or ball carry distance, was investigated using random forest as the learner in detection and regression tasks. Detection evaluates the personal effectiveness of a shot with respect to the player-specific average, whereas regression estimates the value of target attribute, using EMG features as predictors. Fusion after decision optimization provided the best results: the equal error rate in detection was 24.3% for the speed and 31.7% for the distance; the mean absolute percentage error in regression was 3.2% for the speed and 6.4% for the distance. Proposed EMG feature sets were found to be useful, especially when used in combination. Rankings of feature sets indicated statistics for muscle activity in both the left and right body sides, correlation-based analysis of EMG dynamics and features derived from the properties of two highest peaks as important predictors of personal shot effectiveness. Activation sequence profiles helped in analyzing muscle orchestration during golf shot, exposing a specific avalanche pattern, but data from more players are needed for stronger conclusions. Results demonstrate that information arising from an EMG signal stream is useful for predicting golf shot success, in terms of club head speed and ball carry distance, with acceptable accuracy. Surface EMG data, collected with a goal to automatically evaluate golf player’s performance, enables wearable computing in the field of ambient intelligence and has potential to enhance exercising of a long carry distance drive. PMID:27120604

Obtaining information by dynamic (effortful) touching

PubMed Central

Turvey, M. T.; Carello, Claudia

2011-01-01

Dynamic touching is effortful touching. It entails deformation of muscles and fascia and activation of the embedded mechanoreceptors, as when an object is supported and moved by the body. It is realized as exploratory activities that can vary widely in spatial and temporal extents (a momentary heft, an extended walk). Research has revealed the potential of dynamic touching for obtaining non-visual information about the body (e.g. limb orientation), attachments to the body (e.g. an object's height and width) and the relation of the body both to attachments (e.g. hand's location on a grasped object) and surrounding surfaces (e.g. places and their distances). Invariants over the exploratory activity (e.g. moments of a wielded object's mass distribution) seem to ground this ‘information about’. The conception of a haptic medium as a nested tensegrity structure has been proposed to express the obtained information realized by myofascia deformation, by its invariants and transformations. The tensegrity proposal rationalizes the relative indifference of dynamic touch to the site of mechanical contact (hand, foot, torso or probe) and the overtness of exploratory activity. It also provides a framework for dynamic touching's fractal nature, and the finding that its degree of fractality may matter to its accomplishments. PMID:21969694

Bifurcation analysis of an automatic dynamic balancing mechanism for eccentric rotors

NASA Astrophysics Data System (ADS)

Green, K.; Champneys, A. R.; Lieven, N. J.

2006-04-01

We present a nonlinear bifurcation analysis of the dynamics of an automatic dynamic balancing mechanism for rotating machines. The principle of operation is to deploy two or more masses that are free to travel around a race at a fixed distance from the hub and, subsequently, balance any eccentricity in the rotor. Mathematically, we start from a Lagrangian description of the system. It is then shown how under isotropic conditions a change of coordinates into a rotating frame turns the problem into a regular autonomous dynamical system, amenable to a full nonlinear bifurcation analysis. Using numerical continuation techniques, curves are traced of steady states, limit cycles and their bifurcations as parameters are varied. These results are augmented by simulations of the system trajectories in phase space. Taking the case of a balancer with two free masses, broad trends are revealed on the existence of a stable, dynamically balanced steady-state solution for specific rotation speeds and eccentricities. However, the analysis also reveals other potentially attracting states—non-trivial steady states, limit cycles, and chaotic motion—which are not in balance. The transient effects which lead to these competing states, which in some cases coexist, are investigated.

A Predictive Model for Submarine Canyon Type Based on the Relative Influence of Rivers, Waves and Tides.

NASA Astrophysics Data System (ADS)

Sumner, E.; Paull, C. K.

2017-12-01

In recent years progress has been achieved in directly measuring turbidity currents in submarine canyons and channels. It is useful to consider how representative these observations are of the diversity that potentially exists in the dynamics of turbidity currents among different canyons and channels. Firstly, we integrate sediment core, bathymetric and (in a limited number of cases) direct observations of turbidity current dynamics from 20 submarine canyons on the northern California Margin. We use this dataset to construct a diagram that explains canyon type, and thus turbidity current characteristics (grain-size carried, flow power, relative frequency of flows), based on the relative influence of rivers, waves and tides at the canyon head. This diagram enables prediction of canyon type and thus processes using three easily measurable characteristics: (i) distance of the canyon head from the shoreline; (ii) distance of the canyon head from the nearest river mouth; and (iii) local shelf width. Secondly, we test and refine the diagram using published data on submarine canyons from around the world. We also discuss the influence of outsized events such as earthquakes on submarine canyons. Finally, we demonstrate the location within the diagram of current monitoring studies and thus suggest where it might be fruitful to focus future monitoring efforts.

Dynamic feet distance: A new functional assessment during treadmill locomotion in normal and thoracic spinal cord injured rats.

PubMed

Diogo, Camila Cardoso; Costa, Luís Maltez da; Pereira, José Eduardo; Filipe, Vítor; Couto, Pedro Alexandre; Magalhães, Luís G; Geuna, Stefano; Armada-da-Silva, Paulo A; Maurício, Ana Colette; Varejão, Artur Severo

2017-09-29

Of all the detrimental effects of spinal cord injury (SCI), one of the most devastating is the disruption of the ability to perform functional movement. Very little is known on the recovery of hindlimb joint kinematics after clinically-relevant contusive thoracic lesion in experimental animal models. A new functional assessment instrument, the dynamic feet distance (DFD) was used to describe the distance between the two feet throughout the gait cycle in normal and affected rodents. The purpose of this investigation was the evaluation and characterization of the DFD during treadmill locomotion in normal and T9 contusion injured rats, using three-dimensional (3D) instrumented gait analysis. Despite that normal and injured rats showed a similar pattern in the fifth metatarsal head joints distance excursion, we found a significantly wider distance between the feet during the entire gait cycle following spinal injury. This is the first study to quantify the distance between the two feet, throughout the gait cycle, and the biomechanical adjustments made between limbs in laboratory rodents after nervous system injury. Copyright © 2017 Elsevier B.V. All rights reserved.

Runoff thresholds and land-to-marine ecosystem connectivity in a dry tropical setting: St. John, US Virgin Islands

NASA Astrophysics Data System (ADS)

Ramos-Scharron, C. E.; LaFevor, M. C.; Roy, J.

2017-12-01

Developing a conceptually sound yet practical understanding of runoff and sediment delivery from human occupied lands to tropical ocean waters still represents a pivotal need of coral reef management worldwide. In the dry tropical and ephemeral streamflow setting that typifies the small watersheds ( 1s km2) draining the US Virgin Islands, changes in hydrologic and sediment delivery dynamics provoked by unsurfaced road networks represent a major threat to coral reefs and other sensitive marine ecosystems. Through a combined empirical and modeling approach, this study evaluates how road building and associated stormflow restoration strategies affect rainfall thresholds for runoff generation at varying spatial scales and their impact on land-to-sea connectivity. Rainfall thresholds and runoff coefficients for precipitation excess on unpaved roads are 2-3 mm and 22-30% (respectively) or a full order of magnitude different from those for undisturbed hillslopes and watersheds. Here we discuss the use of a `volume-to-breakthrough' inspired index to predict the potential of road runoff to reach downslope portions of the watershed and the coastline as runon. The index integrates the effects of storm-by-storm runoff accumulation for every road drainage point with its flow distance to specific locations along the stream network. While large runoff volumes and short flow distances imply a relatively high connectivity potential, small volumes and long distances are associated to low delivery potential. The index has proven able to discern observed runoff responses under a variety of road-stream network scenarios and rainfall conditions. These results enhance our understanding of ephemeral stream hydrology and are serving to improve coral reef management strategies throughout the Northeastern Caribbean.

Potential Overwintering Locations of Soybean Aphid (Hemiptera: Aphididae) Colonizing Soybean in Ohio and Wisconsin.

PubMed

Crossley, Michael S; Hogg, David B

2015-04-01

Soybean aphids, Aphis glycines Matsumura, depend on long-distance, wind-aided dispersal to complete their life cycle. Despite our general understanding of soybean aphid biology, little is explicitly known about dispersal of soybean aphids between winter and summer hosts in North America. This study compared genotypic diversity of soybean aphids sampled from several overwintering locations in the Midwest and soybean fields in Ohio and Wisconsin to test the hypothesis that these overwintering locations are sources of the soybean colonists. In addition, air parcel trajectory analyses were used to demonstrate the potential for long-distance dispersal events to occur to or from these overwintering locations. Results suggest that soybean aphids from overwintering locations along the Illinois-Iowa border and northern Indiana-Ohio are potential colonists of soybean in Ohio and Wisconsin, but that Ohio is also colonized by soybean aphids from other unknown overwintering locations. Soybean aphids in Ohio and Wisconsin exhibit a small degree of population structure that is not associated with the locations of soybean fields in which they occur, but that may be related to specific overwintering environments, multiple introductions to North America, or spatial variation in aphid phenology. There may be a limited range of suitable habitat for soybean aphid overwintering, in which case management of soybean aphids may be more effective at their overwintering sites. Further research efforts should focus on discovering more overwintering locations of soybean aphid in North America, and the relative impact of short- and long-distance dispersal events on soybean aphid population dynamics. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Groundwater similarity across a watershed derived from time-warped and flow-corrected time series

NASA Astrophysics Data System (ADS)

Rinderer, M.; McGlynn, B. L.; van Meerveld, H. J.

2017-05-01

Information about catchment-scale groundwater dynamics is necessary to understand how catchments store and release water and why water quantity and quality varies in streams. However, groundwater level monitoring is often restricted to a limited number of sites. Knowledge of the factors that determine similarity between monitoring sites can be used to predict catchment-scale groundwater storage and connectivity of different runoff source areas. We used distance-based and correlation-based similarity measures to quantify the spatial and temporal differences in shallow groundwater similarity for 51 monitoring sites in a Swiss prealpine catchment. The 41 months long time series were preprocessed using Dynamic Time-Warping and a Flow-corrected Time Transformation to account for small timing differences and bias toward low-flow periods. The mean distance-based groundwater similarity was correlated to topographic indices, such as upslope contributing area, topographic wetness index, and local slope. Correlation-based similarity was less related to landscape position but instead revealed differences between seasons. Analysis of variance and partial Mantel tests showed that landscape position, represented by the topographic wetness index, explained 52% of the variability in mean distance-based groundwater similarity, while spatial distance, represented by the Euclidean distance, explained only 5%. The variability in distance-based similarity and correlation-based similarity between groundwater and streamflow time series was significantly larger for midslope locations than for other landscape positions. This suggests that groundwater dynamics at these midslope sites, which are important to understand runoff source areas and hydrological connectivity at the catchment scale, are most difficult to predict.

Single and multiple vortex rings in three-dimensional Bose-Einstein condensates: Existence, stability, and dynamics

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

Wang, Wenlong; Bisset, R. N.; Ticknor, Christopher

In the present work, we explore the existence, stability, and dynamics of single- and multiple-vortex-ring states that can arise in Bose-Einstein condensates. Earlier works have illustrated the bifurcation of such states in the vicinity of the linear limit for isotropic or anisotropic three-dimensional harmonic traps. Here, we extend these states to the regime of large chemical potentials, the so-called Thomas-Fermi limit, and explore their properties such as equilibrium radii and inter-ring distance for multi-ring states, as well as their vibrational spectra and possible instabilities. In this limit, both the existence and stability characteristics can be partially traced to a particlemore » picture that considers the rings as individual particles oscillating within the trap and interacting pairwise with one another. In conclusion, we examine some representative instability scenarios of the multi-ring dynamics, including breakup and reconnections, as well as the transient formation of vortex lines.« less

Single and multiple vortex rings in three-dimensional Bose-Einstein condensates: Existence, stability, and dynamics

DOE PAGES

Wang, Wenlong; Bisset, R. N.; Ticknor, Christopher; ...

2017-04-27

In the present work, we explore the existence, stability, and dynamics of single- and multiple-vortex-ring states that can arise in Bose-Einstein condensates. Earlier works have illustrated the bifurcation of such states in the vicinity of the linear limit for isotropic or anisotropic three-dimensional harmonic traps. Here, we extend these states to the regime of large chemical potentials, the so-called Thomas-Fermi limit, and explore their properties such as equilibrium radii and inter-ring distance for multi-ring states, as well as their vibrational spectra and possible instabilities. In this limit, both the existence and stability characteristics can be partially traced to a particlemore » picture that considers the rings as individual particles oscillating within the trap and interacting pairwise with one another. In conclusion, we examine some representative instability scenarios of the multi-ring dynamics, including breakup and reconnections, as well as the transient formation of vortex lines.« less

Spatial variability in oviposition damage by periodical cicadas in a fragmented landscape.

PubMed

Cook, William M; Holt, Robert D; Yao, Jin

2001-03-01

Effects of the periodical cicada (Magicicada spp.) on forest dynamics are poorly documented. A 1998 emergence of M. cassini in eastern Kansas led to colonization of a fragmented experimental landscape undergoing secondary succession. We hypothesized that per-tree rates of oviposition damage by cicadas would reflect: (1) distance from the source of the emergence, (2) patch size, and (3) local tree density. Ovipositing females displayed clear preferences for host species and damage incidence showed predictable spatial patterns. Two species (smooth sumac, Rhus glabra, and eastern red cedar, Juniperus virginiana) were rarely attacked, whereas others (rough-leaved dogwood, Cornus drummondii; slippery elm, Ulmus rubra; box elder, Acer negundo, and honey locust, Gleditsia triacanthos) were strongly attacked. The dominant early successional tree, dogwood, received on average the most attacks. As predicted, attacks per stem declined strongly with distance from the emergence source, and with local stem density (a "dilution" effect). Contrary to expectations, there were more attacks per stem on larger patches. Because ovipositing cicadas cut damaging slits in host tree branches, potentially affecting tree growth rate, competitive ability, and capacity to reproduce, cicada damage could potentially influence spatial variation in secondary succession.

Vorticity Dynamics in Single and Multiple Swirling Reacting Jets

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

Incomplete Thermalization from Trap-Induced Integrability Breaking: Lessons from Classical Hard Rods

NASA Astrophysics Data System (ADS)

Cao, Xiangyu; Bulchandani, Vir B.; Moore, Joel E.

2018-04-01

We study a one-dimensional gas of hard rods trapped in a harmonic potential, which breaks integrability of the hard-rod interaction in a nonuniform way. We explore the consequences of such broken integrability for the dynamics of a large number of particles and find three distinct regimes: initial, chaotic, and stationary. The initial regime is captured by an evolution equation for the phase-space distribution function. For any finite number of particles, this hydrodynamics breaks down and the dynamics becomes chaotic after a characteristic timescale determined by the interparticle distance and scattering length. The system fails to thermalize over the timescale studied (1 04 natural units), but the time-averaged ensemble is a stationary state of the hydrodynamic evolution. We close by discussing logical extensions of the results to similar systems of quantum particles.

Model for Spiral Galaxys Rotation Curves

NASA Astrophysics Data System (ADS)

Hodge, John

2003-11-01

A model of spiral galaxy dynamics is proposed. An expression describing the rotation velocity of particles v in a galaxy as a function of the distance from the center r (RC) is developed. The resulting, intrinsic RC of a galaxy is Keplerian in the inner bulge and rising in the disk region without modifying the Newtonian gravitational potential (MOND) and without unknown dark matter. The v^2 is linearly related to r of the galaxy in part of the rapidly rising region of the HI RC (RRRC) and to r^2 in another part of the RRRC. The r to discontinuities in the surface brightness versus r curve is related to the 21 cm line width, the measured mass of the central supermassive black hole (SBH), and the maximum v^2 in the RRRC. The distance to spiral galaxies can be calculated from these relationships that tightly correlates with the distance calculated using Cepheid variables. Differing results in measuring the mass of the SBH from differing measurement procedures are explained. This model is consistent with previously unexplained data, has predicted new relationships, and suggests a new model of the universe. Full text: http://web.infoave.net/ ˜scjh.

Optimal approach to quantum communication using dynamic programming.

PubMed

Jiang, Liang; Taylor, Jacob M; Khaneja, Navin; Lukin, Mikhail D

2007-10-30

Reliable preparation of entanglement between distant systems is an outstanding problem in quantum information science and quantum communication. In practice, this has to be accomplished by noisy channels (such as optical fibers) that generally result in exponential attenuation of quantum signals at large distances. A special class of quantum error correction protocols, quantum repeater protocols, can be used to overcome such losses. In this work, we introduce a method for systematically optimizing existing protocols and developing more efficient protocols. Our approach makes use of a dynamic programming-based searching algorithm, the complexity of which scales only polynomially with the communication distance, letting us efficiently determine near-optimal solutions. We find significant improvements in both the speed and the final-state fidelity for preparing long-distance entangled states.

Improving single-molecule FRET measurements by confining molecules in nanopipettes

NASA Astrophysics Data System (ADS)

Vogelsang, J.; Doose, S.; Sauer, M.; Tinnefeld, P.

2007-07-01

In recent years Fluorescence Resonance Energy Transfer (FRET) has been widely used to determine distances, observe distance dynamics, and monitor molecular binding at the single-molecule level. A basic constraint of single-molecule FRET studies is the limited distance resolution owing to low photon statistics. We demonstrate that by confining molecules in nanopipettes (50-100 nm diameter) smFRET can be measured with improved photon statistics reducing the width of FRET proximity ratio distributions (PRD). This increase in distance resolution makes it possible to reveal subpopulations and dynamics in biomolecular complexes. Our data indicate that the width of PRD is not only determined by photon statistics (shot noise) and distance distributions between the chromophores but that photoinduced dark states of the acceptor also contribute to the PRD width. Furthermore, acceptor dark states such as triplet states influence the accuracy of determined mean FRET values. In this context, we present a strategy for the correction of the shift of the mean PR that is related to triplet induced blinking of the acceptor using reference FCS measurements.

Learning a Mahalanobis Distance-Based Dynamic Time Warping Measure for Multivariate Time Series Classification.

PubMed

Mei, Jiangyuan; Liu, Meizhu; Wang, Yuan-Fang; Gao, Huijun

2016-06-01

Multivariate time series (MTS) datasets broadly exist in numerous fields, including health care, multimedia, finance, and biometrics. How to classify MTS accurately has become a hot research topic since it is an important element in many computer vision and pattern recognition applications. In this paper, we propose a Mahalanobis distance-based dynamic time warping (DTW) measure for MTS classification. The Mahalanobis distance builds an accurate relationship between each variable and its corresponding category. It is utilized to calculate the local distance between vectors in MTS. Then we use DTW to align those MTS which are out of synchronization or with different lengths. After that, how to learn an accurate Mahalanobis distance function becomes another key problem. This paper establishes a LogDet divergence-based metric learning with triplet constraint model which can learn Mahalanobis matrix with high precision and robustness. Furthermore, the proposed method is applied on nine MTS datasets selected from the University of California, Irvine machine learning repository and Robert T. Olszewski's homepage, and the results demonstrate the improved performance of the proposed approach.

Algorithm for removing scalp signals from functional near-infrared spectroscopy signals in real time using multidistance optodes.

PubMed

Kiguchi, Masashi; Funane, Tsukasa

2014-11-01

A real-time algorithm for removing scalp-blood signals from functional near-infrared spectroscopy signals is proposed. Scalp and deep signals have different dependencies on the source-detector distance. These signals were separated using this characteristic. The algorithm was validated through an experiment using a dynamic phantom in which shallow and deep absorptions were independently changed. The algorithm for measurement of oxygenated and deoxygenated hemoglobins using two wavelengths was explicitly obtained. This algorithm is potentially useful for real-time systems, e.g., brain-computer interfaces and neuro-feedback systems.

Formation of 2D nanoparticles with block structure in simultaneous electric explosion of conductors

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

Kryzhevich, Dmitrij S., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Zolnikov, Konstantin P., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Abdrashitov, Andrei V.

2014-11-14

A molecular dynamics simulation of nanoparticle formation in simultaneous electric explosion of conductors is performed. Interatomic interaction is described using potentials calculated in the framework of the embedded atom method. High-rate heating results in failure of the conductors with the formation of nanoparticles. The influence of the heating rate, temperature distribution over the specimen cross-section and the distance between simultaneously exploded conductors on the structure of formed nanoparticles is studied. The calculation results show that the electric explosion of conductors allows the formation of nanoparticles with block structure.

Effect of dispersion forces on the capillary-wave fluctuations of liquid surfaces.

PubMed

Chacón, Enrique; Fernández, Eva M; Tarazona, Pedro

2014-04-01

We present molecular dynamics evidence for the nonanalytic effects of the long-range dispersion forces on the capillary waves fluctuations of a Lennard-Jones liquid surface. The results of the intrinsic sampling method, for the analysis of the instantaneous interfacial shape, are obtained in large systems for several cut-off distances of the potential tail, and they show good agreement with the theoretical prediction by Napiórkowski and Dietrich, based on a density functional analysis. The enhancement of the capillary waves is quantified to be within 1% for a simple liquid near its triple point.

Strategy for a Sustained Quality Delivery Mode of ODL Programmes for Massive Enrollments and E-Learning: The Case for Zimbabwe Open University

ERIC Educational Resources Information Center

Kabanda, Gabriel

2014-01-01

The market dynamics in distance education has precipitated phenomenal growth opportunities in enrollments and e-learning. The purpose of the paper was to develop a strategy for sustained quality delivery mode of distance education progammes that precipitate massive enrollments and e-learning in an open and distance learning (ODL) institution using…

Long-distance dispersal of spruce budworm (Choristoneura fumiferana Clemens) in Minnesota (USA) and Ontario (Canada) via the atmospheric pathway

Treesearch

Brian R. Sturtevant; Gary L. Achtemeier; Joseph J. Charney; Dean P. Anderson; Barry J. Cooke; Phillip A. Townsend

2013-01-01

Dispersal can play an important role in the population dynamics of forest insects, but the role of long-distance immigration and emigration remains unclear due to the difficulty of quantifying dispersal distance and direction. We designed an agent-based spruce budworm flight behavior model that, when interfaced with temperature, wind speed, and precipitation output...

Relativistic impulse dynamics.

PubMed

Swanson, Stanley M

2011-08-01

Classical electrodynamics has some annoying rough edges. The self-energy of charges is infinite without a cutoff. The calculation of relativistic trajectories is difficult because of retardation and an average radiation reaction term. By reconceptuallizing electrodynamics in terms of exchanges of impulses rather than describing it by forces and potentials, we eliminate these problems. A fully relativistic theory using photonlike null impulses is developed. Numerical calculations for a two-body, one-impulse-in-transit model are discussed. A simple relationship between center-of-mass scattering angle and angular momentum was found. It reproduces the Rutherford cross section at low velocities and agrees with the leading term of relativistic distinguishable-particle quantum cross sections (Møller, Mott) when the distance of closest approach is larger than the Compton wavelength of the particle. Magnetism emerges as a consequence of viewing retarded and advanced interactions from the vantage point of an instantaneous radius vector. Radiation reaction becomes the local conservation of energy-momentum between the radiating particle and the emitted impulse. A net action is defined that could be used in developing quantum dynamics without potentials. A reinterpretation of Newton's laws extends them to relativistic motion.

Structural organisation and dynamics in king penguin colonies

NASA Astrophysics Data System (ADS)

Gerum, Richard; Richter, Sebastian; Fabry, Ben; Le Bohec, Céline; Bonadonna, Francesco; Nesterova, Anna; Zitterbart, Daniel P.

2018-04-01

During breeding, king penguins do not build nests, however they show strong territorial behaviour and keep a pecking distance to neighbouring penguins. Penguin positions in breeding colonies are highly stable over weeks and appear regularly spaced, but thus far no quantitative analysis of the structural order inside a colony has been performed. In this study, we use the radial distribution function to analyse the spatial coordinates of penguin positions. Coordinates are obtained from aerial images of two colonies that were observed for several years. Our data demonstrate that the structural order in king penguin colonies resembles a 2D liquid of particles with a Lennard-Jones-type interaction potential. We verify this using a molecular dynamics simulation with thermally driven particles, whereby temperature corresponds to penguin movements, the energy well depth ɛ of the attractive potential corresponds to the strength of the colony-forming behaviour, and the repulsive zone corresponds to the pecking radius. We can recapitulate the liquid disorder of the colony, as measured by the radial distribution function, when the particles have a temperature of several (1.4–10) \

Characterization of Bifunctional Spin Labels for Investigating the Structural and Dynamic Properties of Membrane Proteins Using EPR Spectroscopy.

PubMed

Sahu, Indra D; Craig, Andrew F; Dunagum, Megan M; McCarrick, Robert M; Lorigan, Gary A

2017-10-05

Site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is a very powerful technique to study structural and dynamic properties of membrane proteins. The most widely used spin label is methanthiosulfonate (MTSL). However, the flexibility of this spin label introduces greater uncertainties in EPR measurements obtained for determining structures, side-chain dynamics, and backbone motion of membrane protein systems. Recently, a newer bifunctional spin label (BSL), 3,4-bis(methanethiosulfonylmethyl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxy, has been introduced to overcome the dynamic limitations associated with the MTSL spin label and has been invaluable in determining protein backbone dynamics and inter-residue distances due to its restricted internal motion and fewer size restrictions. While BSL has been successful in providing more accurate information about the structure and dynamics of several proteins, a detailed characterization of the spin label is still lacking. In this study, we characterized BSLs by performing CW-EPR spectral line shape analysis as a function of temperature on spin-labeled sites inside and outside of the membrane for the integral membrane protein KCNE1 in POPC/POPG lipid bilayers and POPC/POPG lipodisq nanoparticles. The experimental data revealed a powder pattern spectral line shape for all of the KCNE1-BSL samples at 296 K, suggesting the motion of BSLs approaches the rigid limit regime for these series of samples. BSLs were further utilized to report for the first time the distance measurement between two BSLs attached on an integral membrane protein KCNE1 in POPC/POPG lipid bilayers at room temperature using dipolar line broadening CW-EPR spectroscopy. The CW dipolar line broadening EPR data revealed a 15 ± 2 Å distance between doubly attached BSLs on KCNE1 (53/57-63/67) which is consistent with molecular dynamics modeling and the solution NMR structure of KCNE1 which yielded a distance of 17 Å. This study demonstrates the utility of investigating the structural and dynamic properties of membrane proteins in physiologically relevant membrane mimetics using BSLs.

Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

DTIC Science & Technology

2011-07-01

Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

High-resolution non-contact measurement of the electrical activity of plants in situ using optical recording

PubMed Central

Zhao, Dong-Jie; Chen, Yang; Wang, Zi-Yang; Xue, Lin; Mao, Tong-Lin; Liu, Yi-Min; Wang, Zhong-Yi; Huang, Lan

2015-01-01

The limitations of conventional extracellular recording and intracellular recording make high-resolution multisite recording of plant bioelectrical activity in situ challenging. By combining a cooled charge-coupled device camera with a voltage-sensitive dye, we recorded the action potentials in the stem of Helianthus annuus and variation potentials at multiple sites simultaneously with high spatial resolution. The method of signal processing using coherence analysis was used to determine the synchronization of the selected signals. Our results provide direct visualization of the phloem, which is the distribution region of the electrical activities in the stem and leaf of H. annuus, and verify that the phloem is the main action potential transmission route in the stems of higher plants. Finally, the method of optical recording offers a unique opportunity to map the dynamic bioelectrical activity and provides an insight into the mechanisms of long-distance electrical signal transmission in higher plants. PMID:26333536

Hydrogen bond asymmetric local potentials in compressed ice.

PubMed

Huang, Yongli; Ma, Zengsheng; Zhang, Xi; Zhou, Guanghui; Zhou, Yichun; Sun, Chang Q

2013-10-31

A combination of the Lagrangian mechanics of oscillators vibration, molecular dynamics decomposition of volume evolution, and Raman spectroscopy of phonon relaxation has enabled us to resolve the asymmetric, local, and short-range potentials pertaining to the hydrogen bond (O:H-O) in compressed ice. Results show that both oxygen atoms in the O:H-O bond shift initially outwardly with respect to the coordination origin (H), lengthening the O-O distance by 0.0136 nm from 0.2597 to 0.2733 nm by Coulomb repulsion between electron pairs on adjacent oxygen atoms. Both oxygen atoms then move toward right along the O:H-O bond by different amounts upon being compressed, approaching identical length of 0.11 nm. The van der Waals potential VL(r) for the O:H noncovalent bond reaches a valley at -0.25 eV, and the lowest exchange VH(r) for the H-O polar-covalent bond is valued at -3.97 eV.

On the theory of Lorentz gases with long range interactions

NASA Astrophysics Data System (ADS)

Nota, Alessia; Simonella, Sergio; Velázquez, Juan J. L.

We construct and study the stochastic force field generated by a Poisson distribution of sources at finite density, x1,x2,…, in ℝ3 each of them yielding a long range potential QiΦ(x - xi) with possibly different charges Qi ∈ ℝ. The potential Φ is assumed to behave typically as |x|-s for large |x|, with s > 1/2. We will denote the resulting random field as “generalized Holtsmark field”. We then consider the dynamics of one tagged particle in such random force fields, in several scaling limits where the mean free path is much larger than the average distance between the scatterers. We estimate the diffusive time scale and identify conditions for the vanishing of correlations. These results are used to obtain appropriate kinetic descriptions in terms of a linear Boltzmann or Landau evolution equation depending on the specific choices of the interaction potential.

Effect of dynamic three-dimensional culture on osteogenic potential of human periodontal ligament-derived mesenchymal stem cells entrapped in alginate microbeads.

PubMed

Vecchiatini, R; Penolazzi, L; Lambertini, E; Angelozzi, M; Morganti, C; Mazzitelli, S; Trombelli, L; Nastruzzi, C; Piva, R

2015-08-01

Bioreactors are devices that efficiently create an environment that enables cell cultures to grow in a three-dimensional (3D) context mimicking in vivo conditions. In this study, we investigate the effect of dynamic fluid flow on the osteogenic potential of human mesenchymal stem cells obtained from periodontal ligament and entrapped in alginate microbeads. After proper immunophenotyping, cells were encapsulated in barium alginate, cultured in 3D static or 3D dynamic conditions represented by a bioreactor system. Calcein-AM/propidium iodide staining was used to assess cellular viability. Quantitative real-time polymerase chain reaction was used to analyze the expression of osteogenic markers (Runx2 and COL1). Alizarin Red S staining and the Fourier transform infrared spectroscopy were used to assess mineral matrix deposition. Optimal encapsulation procedure, in terms of polymer pumping rate, distance from droplet generator to the gelling bath and atomizing airflow was assessed. Cell viability was not affected by encapsulation in alginate microbeads. Bioreactor cell exposure was effective in anticipating osteogenic differentiation and improving mineral matrix deposition. For the first time human mesenchymal stem cells obtained from periodontal ligaments encapsulated in alginate microbeads were cultured in a bioreactor system. This combination could represent a promising strategy to create a cell-based smart system with enhanced osteogenic potential useful for many different dental applications. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The optimal distance between two electrode tips during recording of compound nerve action potentials in the rat median nerve

PubMed Central

Li, Yongping; Lao, Jie; Zhao, Xin; Tian, Dong; Zhu, Yi; Wei, Xiaochun

2014-01-01

The distance between the two electrode tips can greatly influence the parameters used for recording compound nerve action potentials. To investigate the optimal parameters for these recordings in the rat median nerve, we dissociated the nerve using different methods and compound nerve action potentials were orthodromically or antidromically recorded with different electrode spacings. Compound nerve action potentials could be consistently recorded using a method in which the middle part of the median nerve was intact, with both ends dissociated from the surrounding fascia and a ground wire inserted into the muscle close to the intact part. When the distance between two stimulating electrode tips was increased, the threshold and supramaximal stimulating intensity of compound nerve action potentials were gradually decreased, but the amplitude was not changed significantly. When the distance between two recording electrode tips was increased, the amplitude was gradually increased, but the threshold and supramaximal stimulating intensity exhibited no significant change. Different distances between recording and stimulating sites did not produce significant effects on the aforementioned parameters. A distance of 5 mm between recording and stimulating electrodes and a distance of 10 mm between recording and stimulating sites were found to be optimal for compound nerve action potential recording in the rat median nerve. In addition, the orthodromic compound action potential, with a biphasic waveform that was more stable and displayed less interference (however also required a higher threshold and higher supramaximal stimulus), was found to be superior to the antidromic compound action potential. PMID:25206798

The impact of land use change and hydroclimatic variability on landscape connectivity dynamics across surface water networks at subcontinental scale

NASA Astrophysics Data System (ADS)

Tulbure, M. G.; Bishop-Taylor, R.; Broich, M.

2017-12-01

Land use (LU) change and hydroclimatic variability affect spatiotemporal landscape connectivity dynamics, important for species movement and dispersal. Despite the fact that LU change can strongly influence dispersal potential over time, prior research has only focused on the impacts of dynamic changes in the distribution of potential habitats. We used 8 time-steps of historical LU together with a Landsat-derived time-series of surface water habitat dynamics (1986-2011) over the Murray-Darling Basin (MDB), a region with extreme hydroclimatic variability, impacted by LU changes. To assess how changing LU and hydroclimatic variability affect landscape connectivity across time, we compared 4 scenarios, namely one where both climate and LU are dynamic over time, one where climate is kept steady (i.e. a median surface water extent layer), and two scenarios where LU is kept steady (i.e. resistance values associated with the most recent or the first LU layer). We used circuit theory to assign landscape features with `resistance' costs and graph theory network analysis, with surface water habitats as `nodes' connected by dispersal paths or `edges' Findings comparing a dry and an average season show high differences in number of nodes (14581 vs 21544) and resistance distances. The combined effect of LU change and landscape wetness was lower than expected, likely a function of the large, MDB-wide, aggregation scale. Spatially explicit analyses are expected to identify areas where the synergistic effect of LU change and landscape wetness greatly reduce or increase landscape connectivity, as well as areas where the two effects cancel each other out.

Understanding the Spatio-Temporal Dynamics of Denitrification in an Oregon Salt Marsh

NASA Astrophysics Data System (ADS)

Moon, J. B.; Stecher, H. A.; DeWitt, T.; Nahlik, A.; Fennessy, M. S.; Michael, L.; Regutti, R.; Mckane, R.; Marois, D.; Naithani, K. J.

2016-12-01

Salt marshes are highly susceptible to a range of climate change effects (e.g., sea-level rise, salinity changes, storm severity, shifts in vegetation across watershed). It is unclear how these effects will alter the spatial and temporal dynamics of denitrification, a potential pathway of nitrogen interception and removal from adjacent estuaries. Our overall objective is to determine whether salt marshes in the Pacific Northwest act as sources or sinks of nitrogen to estuaries, and to be able to predict changes in these dynamics under future climate scenarios. We have built a probabilistic denitrification model based on observations from a salt marsh in the Yaquina Estuary (Newport, Oregon). We observed a non-linear relationship between denitrification rates and distance to the marsh-upland interface and soil nitrate concentrations, which are indicators of nitrate delivery flow paths from upslope red alder. We also modeled spatial variability in oxygen availability as a function of elevation, which affects inundation period, and distance to channel, which affects the saturation period through the dewatering rate. Simulations suggest denitrification "hot spots" occur in mid-marsh locations, where both nitrate availability and inundation periods are maximized. Once marsh accretion is outpaced, sea level rise will likely reduce salt marsh area due to steep adjacent uplands that limit marsh retreat, and increase inundation duration near the marsh-upland interface. Expansion of red alder cover is concurrently expected to increase nitrate availability to downslope ecosystems. Taking these effects together, our future scenario simulations suggest a movement of "hot-spots" towards the marsh-upland boundary.

Trouble with diffusion: Reassessing hillslope erosion laws with a particle-based model

NASA Astrophysics Data System (ADS)

Tucker, Gregory E.; Bradley, D. Nathan

2010-03-01

Many geomorphic systems involve a broad distribution of grain motion length scales, ranging from a few particle diameters to the length of an entire hillslope or stream. Studies of analogous physical systems have revealed that such broad motion distributions can have a significant impact on macroscale dynamics and can violate the assumptions behind standard, local gradient flux laws. Here, a simple particle-based model of sediment transport on a hillslope is used to study the relationship between grain motion statistics and macroscopic landform evolution. Surface grains are dislodged by random disturbance events with probabilities and distances that depend on local microtopography. Despite its simplicity, the particle model reproduces a surprisingly broad range of slope forms, including asymmetric degrading scarps and cinder cone profiles. At low slope angles the dynamics are diffusion like, with a short-range, thin-tailed hop length distribution, a parabolic, convex upward equilibrium slope form, and a linear relationship between transport rate and gradient. As slope angle steepens, the characteristic grain motion length scale begins to approach the length of the slope, leading to planar equilibrium forms that show a strongly nonlinear correlation between transport rate and gradient. These high-probability, long-distance motions violate the locality assumption embedded in many common gradient-based geomorphic transport laws. The example of a degrading scarp illustrates the potential for grain motion dynamics to vary in space and time as topography evolves. This characteristic renders models based on independent, stationary statistics inapplicable. An accompanying analytical framework based on treating grain motion as a survival process is briefly outlined.

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PubMed Central

Dasgupta, Bhaskar; Kasahara, Kota; Kamiya, Narutoshi; Nakamura, Haruki; Kinjo, Akira R.

2014-01-01

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. PMID:24625758

Intrinsic group behaviour: Dependence of pedestrian dyad dynamics on principal social and personal features

PubMed Central

Yücel, Zeynep; Brščić, Dražen; Kanda, Takayuki; Hagita, Norihiro

2017-01-01

Being determined by human social behaviour, pedestrian group dynamics may depend on “intrinsic properties” such as the purpose of the pedestrians, their personal relation, gender, age, and body size. In this work we investigate the dynamical properties of pedestrian dyads (distance, spatial formation and velocity) by analysing a large data set of automatically tracked pedestrian trajectories in an unconstrained “ecological” setting (a shopping mall), whose apparent physical and social group properties have been analysed by three different human coders. We observed that females walk slower and closer than males, that workers walk faster, at a larger distance and more abreast than leisure oriented people, and that inter-group relation has a strong effect on group structure, with couples walking very close and abreast, colleagues walking at a larger distance, and friends walking more abreast than family members. Pedestrian height (obtained automatically through our tracking system) influences velocity and abreast distance, both growing functions of the average group height. Results regarding pedestrian age show that elderly people walk slowly, while active age adults walk at the maximum velocity. Groups with children have a strong tendency to walk in a non-abreast formation, with a large distance (despite a low abreast distance). A cross-analysis of the interplay between these intrinsic features, taking in account also the effect of an “extrinsic property” such as crowd density, confirms these major results but reveals also a richer structure. An interesting and unexpected result, for example, is that the velocity of groups with children increases with density, at least in the low-medium density range found under normal conditions in shopping malls. Children also appear to behave differently according to the gender of the parent. PMID:29095913

Intrinsic group behaviour: Dependence of pedestrian dyad dynamics on principal social and personal features.

PubMed

Zanlungo, Francesco; Yücel, Zeynep; Brščić, Dražen; Kanda, Takayuki; Hagita, Norihiro

2017-01-01

Being determined by human social behaviour, pedestrian group dynamics may depend on "intrinsic properties" such as the purpose of the pedestrians, their personal relation, gender, age, and body size. In this work we investigate the dynamical properties of pedestrian dyads (distance, spatial formation and velocity) by analysing a large data set of automatically tracked pedestrian trajectories in an unconstrained "ecological" setting (a shopping mall), whose apparent physical and social group properties have been analysed by three different human coders. We observed that females walk slower and closer than males, that workers walk faster, at a larger distance and more abreast than leisure oriented people, and that inter-group relation has a strong effect on group structure, with couples walking very close and abreast, colleagues walking at a larger distance, and friends walking more abreast than family members. Pedestrian height (obtained automatically through our tracking system) influences velocity and abreast distance, both growing functions of the average group height. Results regarding pedestrian age show that elderly people walk slowly, while active age adults walk at the maximum velocity. Groups with children have a strong tendency to walk in a non-abreast formation, with a large distance (despite a low abreast distance). A cross-analysis of the interplay between these intrinsic features, taking in account also the effect of an "extrinsic property" such as crowd density, confirms these major results but reveals also a richer structure. An interesting and unexpected result, for example, is that the velocity of groups with children increases with density, at least in the low-medium density range found under normal conditions in shopping malls. Children also appear to behave differently according to the gender of the parent.

Simple and easy assessment of falling risk in the elderly by functional reach test using elastic stick.

PubMed

Demura, Shin-Ichi; Yamada, Takayoshi

2007-10-01

Dynamic balance ability related to maintaining postural stability during movement is closely tied to fall risk in the elderly. The functional reach (FR) test has been developed to evaluate their dynamic balance. Although a simple and new FR test using an elastic stick has been proposed by modifying the above original FR test, the abilities related to both FR tests are judged to differ because of the large difference in the testing method. This study aimed to compare center of gravity fluctuation, muscle activity and functional reach distance as measured by the original FR test and the elastic stick FR test. First, reach distance, back/forth and right/left moving distance of the center of gravity, and activity of the lower leg muscles (soleus and tibialis anterior) were compared between both tests based on data obtained from 30 young male adults. All parameters except for the right/left moving distance were significantly larger in the elastic stick FR test. Next, the reach distance was examined in both FR tests using 53 elderly subjects; it was significantly longer in the elastic stick FR test, but showed no significant sex difference. The reach distance in both tests was significantly shorter (about 7 cm) in the elderly than in young adults. In conclusion, the elastic stick FR test involves greater leg muscle strength exertion and forward transferring of the center of gravity as compared with the original FR test. Because the elastic stick FR test relates largely to leg muscle function and equilibrium function, it may be more useful for evaluating the dynamic balance ability of the elderly.

Dynamics of quantum correlation between separated nitrogen-vacancy centers embedded in plasmonic waveguide

PubMed Central

Yang, Wan-li; An, Jun-Hong; Zhang, Cheng-jie; Chen, Chang-yong; Oh, C. H.

2015-01-01

We investigate the dynamics of quantum correlation between two separated nitrogen vacancy centers (NVCs) placed near a one-dimensional plasmonic waveguide. As a common medium of the radiation field of NVCs propagating, the plasmonic waveguide can dynamically induce quantum correlation between the two NVCs. It is interesting to find that such dynamically induced quantum correlation can be preserved in the long-time steady state by locally applying individual driving on the two NVCs. In particular, we also show that a large degree of quantum correlation can be established by this scheme even when the distance between the NVCs is much larger than their operating wavelength. This feature may open new perspectives for devising active decoherence-immune solid-state optical devices and long-distance NVC-based quantum networks in the context of plasmonic quantum electrodynamics. PMID:26493045

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

PubMed Central

2015-01-01

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide. PMID:25838811

Zero-temperature directed polymer in random potential in 4+1 dimensions.

PubMed

Kim, Jin Min

2016-12-01

Zero-temperature directed polymer in random potential in 4+1 dimensions is described. The fluctuation ΔE(t) of the lowest energy of the polymer varies as t^{β} with β=0.159±0.007 for polymer length t and ΔE follows ΔE(L)∼L^{α} at saturation with α=0.275±0.009, where L is the system size. The dynamic exponent z≈1.73 is obtained from z=α/β. The estimated values of the exponents satisfy the scaling relation α+z=2 very well. We also monitor the end to end distance of the polymer and obtain z independently. Our results show that the upper critical dimension of the Kardar-Parisi-Zhang equation is higher than d=4+1 dimensions.

Landscape characteristics of Rhizophora mangle forests and propagule deposition in coastal environments of Florida (USA)

USGS Publications Warehouse

Sengupta, R.; Middleton, B.; Yan, C.; Zuro, M.; Hartman, H.

2005-01-01

Field dispersal studies are seldom conducted at regional scales even though reliable information on mid-range dispersal distance is essential for models of colonization. The purpose of this study was to examine the potential distance of dispersal of Rhizophora mangle propagules by comparing deposition density with landscape characteristics of mangrove forests. Propagule density was estimated at various distances to mangrove sources (R. mangle) on beaches in southwestern Florida in both high-and low-energy environments, either facing open gulf waters vs. sheltered, respectively. Remote sensing and Geographic Information Systems were used to identify source forests and to determine their landscape characteristics (forest size and distance to deposition area) for the regression analyses. Our results indicated that increasing density of propagules stranded on beaches was related negatively to the distance of the deposition sites from the nearest stands of R. mangle and that deposition was greatly diminished 2 km or more from the source. Measures of fragmentation such as the area of the R. mangle forests were related to propagule deposition but only in low-energy environments. Our results suggest that geographic models involving the colonization of coastal mangrove systems should include dispersal dynamics at mid-range scales, i.e., for our purposes here, beyond the local scale of the forest and up to 5 km distant. Studies of mangrove propagule deposition at various spatial scales are key to understanding regeneration limitations in natural gaps and restoration areas. Therefore, our study of mid-range propagule dispersal has broad application to plant ecology, restoration, and modeling. ?? Springer 2005.

The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations

PubMed Central

Kirmizialtin, Serdal; Silalahi, Alexander R.J.; Elber, Ron; Fenley, Marcia O.

2012-01-01

The distributions of different cations around A-RNA are computed by Poisson-Boltzmann (PB) equation and replica exchange molecular dynamics (MD). Both the nonlinear PB and size-modified PB theories are considered. The number of ions bound to A-RNA, which can be measured experimentally, is well reproduced in all methods. On the other hand, the radial ion distribution profiles show differences between MD and PB. We showed that PB results are sensitive to ion size and functional form of the solvent dielectric region but not the solvent dielectric boundary definition. Size-modified PB agrees with replica exchange molecular dynamics much better than nonlinear PB when the ion sizes are chosen from atomistic simulations. The distribution of ions 14 Å away from the RNA central axis are reasonably well reproduced by size-modified PB for all ion types with a uniform solvent dielectric model and a sharp dielectric boundary between solvent and RNA. However, this model does not agree with MD for shorter distances from the A-RNA. A distance-dependent solvent dielectric function proposed by another research group improves the agreement for sodium and strontium ions, even for shorter distances from the A-RNA. However, Mg2+ distributions are still at significant variances for shorter distances. PMID:22385854

Vortex dynamics and wall shear stress behaviour associated with an elliptic jet impinging upon a flat plate

NASA Astrophysics Data System (ADS)

Long, J.; New, T. H.

2016-07-01

Vortical structures and dynamics of a Re h = 2100 elliptic jet impinging upon a flat plate were studied at H/ d h = 1, 2 and 4 jet-to-plate separation distances. Flow investigations were conducted along both its major and minor planes using laser-induced fluorescence and digital particle image velocimetry techniques. Results show that the impingement process along the major plane largely consists of primary jet ring-vortex and wall-separated secondary vortex formations, where they subsequently separate from the flat plate at smaller H/ d h = 1 and 2 separation distances. Key vortex formation locations occur closer to the impingement point as the separation distance increases. Interestingly, braid vortices and rib structures begin to take part in the impingement process at H/ d h = 4 and wave instabilities dominate the flow field. In contrast, significantly more coherent primary and secondary vortices with physically larger vortex core sizes and higher vortex strengths are observed along the minor plane, with no signs of braid vortices and rib structures. Lastly, influences of these different flow dynamics on the major and minor plane instantaneous and mean skin friction coefficient levels are investigated to shed light on the effects of separation distance on the wall shear stress distributions.

Frenkel pair recombinations in UO2: Importance of explicit description of polarizability in core-shell molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Devynck, Fabien; Iannuzzi, Marcella; Krack, Matthias

2012-05-01

The oxygen and uranium Frenkel pair (FP) recombination mechanisms are studied in UO2 using an empirical interatomic potential accounting for the polarizability of the ions, namely a dynamical core-shell model. The results are compared to a more conventional rigid-ion model. Both model types have been implemented into the cp2k program package and thoroughly validated. The overall picture indicates that the FP recombination mechanism is a complex process involving several phenomena. The FP recombination can happen instantaneously when the distance between the interstitial and the vacancy is small or can be thermally activated at larger separation distances. However, other criteria can prevail over the interstitial-vacancy distance. The surrounding environment of the FP defect, the mechanical stiffness of the matrix, and the orientation of the migration path are shown to be major factors acting on the FP lifetime. The core-shell and rigid-ion models provide a similar qualitative description of the FP recombination mechanism. However, the FP stabilities determined by both models significantly differ in the lower temperature range considered. Indeed, the recombination time of the oxygen and uranium FPs can be up to an order of magnitude lower in the core-shell model at T=600 K and T=1800 K, respectively. These differences highlight the importance of the explicit description of polarizability on some crucial properties such as the resistance to amorphization. This refined description of the interatomic interactions would certainly affect the description of the recrystallization process following a displacement cascade. In turn, the self-healing phase would be better accounted for in the core-shell model and the misestimate inherent to the lack of polarizability in the rigid-ion model corrected.

Motion data classification on the basis of dynamic time warping with a cloud point distance measure

NASA Astrophysics Data System (ADS)

Switonski, Adam; Josinski, Henryk; Zghidi, Hafedh; Wojciechowski, Konrad

2016-06-01

The paper deals with the problem of classification of model free motion data. The nearest neighbors classifier which is based on comparison performed by Dynamic Time Warping transform with cloud point distance measure is proposed. The classification utilizes both specific gait features reflected by a movements of subsequent skeleton joints and anthropometric data. To validate proposed approach human gait identification challenge problem is taken into consideration. The motion capture database containing data of 30 different humans collected in Human Motion Laboratory of Polish-Japanese Academy of Information Technology is used. The achieved results are satisfactory, the obtained accuracy of human recognition exceeds 90%. What is more, the applied cloud point distance measure does not depend on calibration process of motion capture system which results in reliable validation.

Dynamic Evaluation of Distance Education Courses.

ERIC Educational Resources Information Center

Champagne, Matthew V.

This paper focuses on the Interactive and Distance Education Assessment (IDEA) laboratory, an assessment system developed by psychology students and faculty at Rensselaer Polytechnic Institute (New York) that incorporated learning styles, teaching styles, and other measures of individual difference into the evaluation of interactive and distance…

Scalable parallel distance field construction for large-scale applications

DOE PAGES

Yu, Hongfeng; Xie, Jinrong; Ma, Kwan -Liu; ...

2015-10-01

Computing distance fields is fundamental to many scientific and engineering applications. Distance fields can be used to direct analysis and reduce data. In this paper, we present a highly scalable method for computing 3D distance fields on massively parallel distributed-memory machines. Anew distributed spatial data structure, named parallel distance tree, is introduced to manage the level sets of data and facilitate surface tracking overtime, resulting in significantly reduced computation and communication costs for calculating the distance to the surface of interest from any spatial locations. Our method supports several data types and distance metrics from real-world applications. We demonstrate itsmore » efficiency and scalability on state-of-the-art supercomputers using both large-scale volume datasets and surface models. We also demonstrate in-situ distance field computation on dynamic turbulent flame surfaces for a petascale combustion simulation. In conclusion, our work greatly extends the usability of distance fields for demanding applications.« less

Scalable Parallel Distance Field Construction for Large-Scale Applications.

PubMed

Yu, Hongfeng; Xie, Jinrong; Ma, Kwan-Liu; Kolla, Hemanth; Chen, Jacqueline H

2015-10-01

Computing distance fields is fundamental to many scientific and engineering applications. Distance fields can be used to direct analysis and reduce data. In this paper, we present a highly scalable method for computing 3D distance fields on massively parallel distributed-memory machines. A new distributed spatial data structure, named parallel distance tree, is introduced to manage the level sets of data and facilitate surface tracking over time, resulting in significantly reduced computation and communication costs for calculating the distance to the surface of interest from any spatial locations. Our method supports several data types and distance metrics from real-world applications. We demonstrate its efficiency and scalability on state-of-the-art supercomputers using both large-scale volume datasets and surface models. We also demonstrate in-situ distance field computation on dynamic turbulent flame surfaces for a petascale combustion simulation. Our work greatly extends the usability of distance fields for demanding applications.

The influence of bat echolocation call duration and timing on auditory encoding of predator distance in noctuoid moths.

PubMed

Gordon, Shira D; Ter Hofstede, Hannah M

2018-03-22

Animals co-occur with multiple predators, making sensory systems that can encode information about diverse predators advantageous. Moths in the families Noctuidae and Erebidae have ears with two auditory receptor cells (A1 and A2) used to detect the echolocation calls of predatory bats. Bat communities contain species that vary in echolocation call duration, and the dynamic range of A1 is limited by the duration of sound, suggesting that A1 provides less information about bats with shorter echolocation calls. To test this hypothesis, we obtained intensity-response functions for both receptor cells across many moth species for sound pulse durations representing the range of echolocation call durations produced by bat species in northeastern North America. We found that the threshold and dynamic range of both cells varied with sound pulse duration. The number of A1 action potentials per sound pulse increases linearly with increasing amplitude for long-duration pulses, saturating near the A2 threshold. For short sound pulses, however, A1 saturates with only a few action potentials per pulse at amplitudes far lower than the A2 threshold for both single sound pulses and pulse sequences typical of searching or approaching bats. Neural adaptation was only evident in response to approaching bat sequences at high amplitudes, not search-phase sequences. These results show that, for short echolocation calls, a large range of sound levels cannot be coded by moth auditory receptor activity, resulting in no information about the distance of a bat, although differences in activity between ears might provide information about direction. © 2018. Published by The Company of Biologists Ltd.

A New Distance Metric for Unsupervised Learning of Categorical Data.

PubMed

Jia, Hong; Cheung, Yiu-Ming; Liu, Jiming

2016-05-01

Distance metric is the basis of many learning algorithms, and its effectiveness usually has a significant influence on the learning results. In general, measuring distance for numerical data is a tractable task, but it could be a nontrivial problem for categorical data sets. This paper, therefore, presents a new distance metric for categorical data based on the characteristics of categorical values. In particular, the distance between two values from one attribute measured by this metric is determined by both the frequency probabilities of these two values and the values of other attributes that have high interdependence with the calculated one. Dynamic attribute weight is further designed to adjust the contribution of each attribute-distance to the distance between the whole data objects. Promising experimental results on different real data sets have shown the effectiveness of the proposed distance metric.

The Mammalian Cortex as a Self-Organizing Complex System: Multi-Scale Homeostatic Approaches to Criticality via Dynamical Balance of Inhibition against Excitation

NASA Astrophysics Data System (ADS)

Ng, Tony T.

The mammalian cortex is a highly structured network of densely packed neurons that interact strongly with each other in very specific ways. Loosely speaking, neurons are cells that fire clicks at each other as a means of communication. Common sites of communication, known as synapses, are enabled by transmitter molecules released from presynaptic sender cells, which bind to receptors on postsynaptic receiver cells. There are two major classes of neurons - excitatory ones that prompt their downstream neighbors to fire spikes through depolarization, and inhibitory ones that suppress spike activity of their postsynaptic partners via hyperpolarization. Depolarization and hyperpolarization make membrane potential of a cell more positive and more negative, respectively. A sufficiently depolarized neuron fires a spike, which technically is called an action potential. In this thesis, we focus on the interplay between three of the cortex's most ubiquitous features and examine some of the consequences that their interactions have on cortical dynamics. One of the features, widespread projections between clusters of excitatory neurons, is topological. The two remaining features, homeostasis and balance between the amount of excitatory and inhibitory activity are dynamical. Here, homeostasis refers to the regulatory mechanism of individual cells or collections of cells that maintains constant levels of spike activity over time. Simply by varying the average homeostatic firing rate in clusters of excitatory neurons or by tuning the common homoeostatic rate of individual inhibitory neurons, we show via simulation that cluster-based activity bursts can exhibit critical dynamics and display power-law distributions with exponents that are consistent with those found in in vivo experiments of awake animals. Criticality is an idea that originated in statistical physics. At the critical point, activity levels of sites across an entire system, such as those of different cortical regions across the brain, can dynamically correlate not only over short distances, but also over large distances. The spatial extent of time-varying signal propagation can range from a couple of regions to a dozen regions to hundreds and thousands of regions and beyond. It has been shown in previous studies that size of a network's pattern repertoire, degree of information transmission from stimuli to responses, and potential to respond to a large range of stimulus intensities, are maximized at the critical state. In addition to demonstrating the presence of criticality in our class of networks, we show that (1) another pervasive connectivity motif in the cortex is incapable of supporting criticality, (2) excitation-inhibition balance modulates the distribution of spike-based bursts of various sizes, (3) how critical dynamics at the cluster level emerges from excitation-inhibition balance, and (4) how we can reconcile differences in burst statistics at spike-based and cluster-based levels observed in animal experiments.

Identification of individual coherent sets associated with flow trajectories using coherent structure coloring

NASA Astrophysics Data System (ADS)

Schlueter-Kuck, Kristy L.; Dabiri, John O.

2017-09-01

We present a method for identifying the coherent structures associated with individual Lagrangian flow trajectories even where only sparse particle trajectory data are available. The method, based on techniques in spectral graph theory, uses the Coherent Structure Coloring vector and associated eigenvectors to analyze the distance in higher-dimensional eigenspace between a selected reference trajectory and other tracer trajectories in the flow. By analyzing this distance metric in a hierarchical clustering, the coherent structure of which the reference particle is a member can be identified. This algorithm is proven successful in identifying coherent structures of varying complexities in canonical unsteady flows. Additionally, the method is able to assess the relative coherence of the associated structure in comparison to the surrounding flow. Although the method is demonstrated here in the context of fluid flow kinematics, the generality of the approach allows for its potential application to other unsupervised clustering problems in dynamical systems such as neuronal activity, gene expression, or social networks.

Parameters of Six Selected Galactic Potential Models

NASA Astrophysics Data System (ADS)

Bajkova, Anisa; Bobylev, Vadim

2017-11-01

This paper is devoted to the refinement of the parameters of the six three-component (bulge, disk, halo) axisymmetric Galactic gravitational potential models on the basis of modern data on circular velocities of Galactic objects located at distances up to 200 kpc from the Galactic center. In all models the bulge and disk are described by the Miyamoto-Nagai expressions. To describe the halo, the models of Allen-Santillán (I), Wilkinson-Evans (II), Navarro- Frenk-White (III), Binney (IV), Plummer (V), and Hernquist (VI) are used. The sought-for parameters of potential models are determined by fitting the model rotation curves to the measured velocities, taking into account restrictions on the local dynamical matter density p⊙ - 0.1M⊙ pc-3 and the vertical force |Kz=1.1|/2πG = 77M⊙ pc-2. A comparative analysis of the refined potential models is made and for each of the models the estimates of a number of the Galactic characteristics are presented.

Distance Education for Aboriginal Communities in Canada: Past Experience and Future Potential.

ERIC Educational Resources Information Center

Gruber, Steve; Coldevin, Gary

1995-01-01

Reviews problems with the current educational situation in Canadian aboriginal communities. Notes the potential of distance education to reduce problems associated with cultural assimilation and to enhance multimedia resources. Discusses strengths and weaknesses of two distance education programs for aboriginals and concludes with guidelines for…

Potential of Social Networking Sites for Distance Education Student Engagement

ERIC Educational Resources Information Center

Lester, Jaime; Perini, Michael

2010-01-01

This chapter explores the potential of social networking sites for increasing student engagement for distance education learners. The authors present a modified student engagement model with a focus on the integration of technology, specifically social networking sites for community college distance education learners. The chapter concludes with…

Brownian motion of a circle swimmer in a harmonic trap

NASA Astrophysics Data System (ADS)

Jahanshahi, Soudeh; Löwen, Hartmut; ten Hagen, Borge

2017-02-01

We study the dynamics of a Brownian circle swimmer with a time-dependent self-propulsion velocity in an external temporally varying harmonic potential. For several situations, the noise-free swimming paths, the noise-averaged mean trajectories, and the mean-square displacements are calculated analytically or by computer simulation. Based on our results, we discuss optimal swimming strategies in order to explore a maximum spatial range around the trap center. In particular, we find a resonance situation for the maximum escape distance as a function of the various frequencies in the system. Moreover, the influence of the Brownian noise is analyzed by comparing noise-free trajectories at zero temperature with the corresponding noise-averaged trajectories at finite temperature. The latter reveal various complex self-similar spiral or rosette-like patterns. Our predictions can be tested in experiments on artificial and biological microswimmers under dynamical external confinement.

Dynamically tunable electromagnetically-induced-transparency-like resonances in graphene nanoring and nanodisk hybrid metamaterials

NASA Astrophysics Data System (ADS)

Chen, De-Chao; Li, Hong-Ju; Xia, Sheng-Xuan; Qin, Meng; Zhai, Xiang; Wang, Ling-Ling

2017-08-01

A tunable electromagnetically-induced-transparency-like (EIT-like) device is proposed numerically and theoretically in the mid-infrared region, which is composed of periodically patterned ring and disk graphene. Distinguished from the commonly used three-level system, the hybridization of the plasmon mode is applied to describing and explaining the EIT-like phenomenon in the proposed systems. What is more, further researches have revealed that the spectral position of the transparency window can be tuned not only by geometrically changing the couple distance in graphene nanostructures, but also by dynamically altering the radius of the graphene nanodisk and the chemical potential of the graphene. At the transparency window, there exist large optical delays, which can slow down the speed of light in vacuum. This work may pave the way to the development of applications including tunable sensors, slow-light devices, and optical switches.

Extended Communication Efforts Involved with College Long-Distance Relationships

ERIC Educational Resources Information Center

Firmin, Michael W.; Firmin, Ruth L.; Merical, Kaile Lorenzen

2013-01-01

The present phenomenological, qualitative research study involved in-depth interviews of all 16 female, sophomore students involved in respective distance relationships at a private, selective, comprehensive, Midwest university. Among other results found in the study, the present article focuses on communication dynamics involved with the…

Distance Learning Technology and Applications.

ERIC Educational Resources Information Center

Minoli, Daniel

This book is intended to give technology providers a better understanding of the dynamics of interactive distance learning (DL). For technology consumers it provides an understanding of the basics of available telecommunication technologies and the tradeoffs among available alternatives. Among the topics discussed in the book's 12 chapters are the…

DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles.

PubMed

Tan, Li Huey; Xing, Hang; Lu, Yi

2014-06-17

CONSPECTUS: Several properties of nanomaterials, such as morphologies (e.g., shapes and surface structures) and distance dependent properties (e.g., plasmonic and quantum confinement effects), make nanomaterials uniquely qualified as potential choices for future applications from catalysis to biomedicine. To realize the full potential of these nanomaterials, it is important to demonstrate fine control of the morphology of individual nanoparticles, as well as precise spatial control of the position, orientation, and distances between multiple nanoparticles. In addition, dynamic control of nanomaterial assembly in response to multiple stimuli, with minimal or no error, and the reversibility of the assemblies are also required. In this Account, we summarize recent progress of using DNA as a powerful programmable tool to realize the above goals. First, inspired by the discovery of genetic codes in biology, we have discovered DNA sequence combinations to control different morphologies of nanoparticles during their growth process and have shown that these effects are synergistic or competitive, depending on the sequence combination. The DNA, which guides the growth of the nanomaterial, is stable and retains its biorecognition ability. Second, by taking advantage of different reactivities of phosphorothioate and phosphodiester backbone, we have placed phosphorothioate at selective positions on different DNA nanostructures including DNA tetrahedrons. Bifunctional linkers have been used to conjugate phosphorothioate on one end and bind nanoparticles or proteins on the other end. In doing so, precise control of distances between two or more nanoparticles or proteins with nanometer resolution can be achieved. Furthermore, by developing facile methods to functionalize two hemispheres of Janus nanoparticles with two different DNA sequences regioselectively, we have demonstrated directional control of nanomaterial assembly, where DNA strands with specific hybridization serve as orthogonal linkers. Third, by using functional DNA that includes DNAzyme, aptamer, and aptazyme, dynamic control of assemblies of gold nanoparticles, quantum dots, carbon nanotubes, and iron oxide nanoparticles in response to one or more stimuli cooperatively have been achieved, resulting in colorimetric, fluorescent, electrochemical, and magnetic resonance signals for a wide range of targets, such as metal ions, small molecules, proteins, and intact cells. Fourth, by mimicking biology, we have employed DNAzymes as proofreading units to remove errors in nanoparticle assembly and further used DNAzyme cascade reactions to modify or repair DNA sequences involved in the assembly. Finally, by taking advantage of different affinities of biotin and desthiobiotin toward streptavidin, we have demonstrated reversible assembly of proteins on DNA origami.

Molecular Dynamics Simulations of Ligand-Induced Flap Conformational Changes in Cathepsin-D-A Comparative Study.

PubMed

Arodola, Olayide A; Soliman, Mahmoud E S

2016-11-01

The flap region in aspartic proteases is a unique structural feature to this class of enzymes, and found to have a profound impact on protein overall structure, function, and dynamics. Understanding the structure and dynamic behavior of the flap regions is crucial in the design of selective inhibitors against aspartic proteases. Cathepsin-D, an aspartic protease enzyme, has been implicated in a long list of degenerative diseases as well as breast cancer progression. Presented herein, for the first time, is a comprehensive description of the conformational flap dynamics of cathepsin-D using a comparative 50 ns "multiple" molecular dynamics simulations. Diverse collective metrics were proposed to accurately define flap dynamics. These are distance d1 between the flap tips residues (Gly79 and Met301); dihedral angle ϕ; in addition to TriCα angles Gly79-Asp33-Asp223, θ1 , and Gly79-Asp223-Met301, θ2 . The maximum distance attained throughout the simulation was 17.42 and 11.47 Å for apo and bound cathepsin-D, respectively, while the minimum distance observed was 8.75 and 6.32 Å for apo and bound cathepsin-D, respectively. The movement of the flap as well as the twist of the active pocket can properly be explained by measuring the angle, θ1 , between Gly79-Asp33-Met301 and correlating it with the distance Cα of the flap tip residues. The asymmetrical opening of the binding cavity was best described by the large shift of -6.26° to +20.94° in the dihedral angle, ϕ, corresponding to the full opening of the flap at a range of 31-33 ns. A wide-range of post-dynamic analyses was also applied in this report to supplement our findings. We believe that this report would augment current efforts in designing potent structure-based inhibitors against cathepsin-D in the treatment of breast cancer and other degenerative diseases. J. Cell. Biochem. 117: 2643-2657, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Assessing the role of landscape connectivity on Opisthorchis viverrini transmission dynamics.

PubMed

Wang, Yi-Chen; Yuen, Roy; Feng, Chen-Chieh; Sithithaworn, Paiboon; Kim, Ick-Hoi

2017-08-01

Opisthorchis viverrini (Ov) is one of the most important human parasitic diseases in Southeast Asia. Although the concept of connectivity is widely used to comprehend disease dispersal, knowledge of the influences of landscape connectivity on Ov transmission is still rudimentary. This study aimed to investigate the role of landscape connectivity in Ov transmission between the human and the first intermediate snail hosts. Fieldwork was conducted in three villages respectively in Kamalasai District, Kalasin Province, Phu Wiang District, Khon Kaen Province, and Nong Saeng District, Udon Thani Province. Bithynia snails were collected to examine parasitic infections, water samples were analyzed for fecal contamination, and locations of septic tanks and connections between habitat patches with observable water movement were surveyed. Euclidean distance, topological link and distance, and graph measures were employed to quantify the connectivity between human and snail habitats. The findings showed that snail patches with higher fecal contents were generally located nearer to septic tanks. The statistically significant results for the topological link and distance measures highlighted the importance of water in functionally facilitating Ov transmission. Graph measures revealed differences in landscape connectivity across the sites. The site with the largest landscape component size and the most mutually connected snail patches coincided with the presence of Ov parasite, reinforcing its higher risk for human to snail transmission. The site with the dissected landscape structure potentially limited the transmission. This study underscored the potential effect of landscape connectivity on Ov transmission, contributing to the understanding of the spatial variation of Ov infection risk. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A Systemic Small RNA Signaling System in Plants

PubMed Central

Yoo, Byung-Chun; Kragler, Friedrich; Varkonyi-Gasic, Erika; Haywood, Valerie; Archer-Evans, Sarah; Lee, Young Moo; Lough, Tony J.; Lucas, William J.

2004-01-01

Systemic translocation of RNA exerts non-cell-autonomous control over plant development and defense. Long-distance delivery of mRNA has been proven, but transport of small interfering RNA and microRNA remains to be demonstrated. Analyses performed on phloem sap collected from a range of plants identified populations of small RNA species. The dynamic nature of this population was reflected in its response to growth conditions and viral infection. The authenticity of these phloem small RNA molecules was confirmed by bioinformatic analysis; potential targets for a set of phloem small RNA species were identified. Heterografting studies, using spontaneously silencing coat protein (CP) plant lines, also established that transgene-derived siRNA move in the long-distance phloem and initiate CP gene silencing in the scion. Biochemical analysis of pumpkin (Cucurbita maxima) phloem sap led to the characterization of C. maxima Phloem SMALL RNA BINDING PROTEIN1 (CmPSRP1), a unique component of the protein machinery probably involved in small RNA trafficking. Equivalently sized small RNA binding proteins were detected in phloem sap from cucumber (Cucumis sativus) and lupin (Lupinus albus). PSRP1 binds selectively to 25-nucleotide single-stranded RNA species. Microinjection studies provided direct evidence that PSRP1 could mediate the cell-to-cell trafficking of 25-nucleotide single-stranded, but not double-stranded, RNA molecules. The potential role played by PSRP1 in long-distance transmission of silencing signals is discussed with respect to the pathways and mechanisms used by plants to exert systemic control over developmental and physiological processes. PMID:15258266

The structure, dynamics and movement patterns of the Australian sheep industry.

PubMed

East, I J; Foreman, I

2011-12-01

To describe the structure of Australia's sheep industries and the movement of sheep to enable examination of the potential for animal movements to spread disease between farms. The structure, size, marketing and movement patterns of Australian sheep farms was determined through (i) review of data published by the Australian Bureau of Statistics and Australian Bureau of Agricultural and Resource Economics, (ii) interviews with producers and saleyard managers and (iii) expert opinion. Twelve geographic regions are described, based on the type and extent of sheep farming in each region. Five production sectors were identified within the Australian sheep industry, with the proportion of each varying between the geographic regions. Over the past 20 years, the industry has decreased in size and contracted from the northern and central areas of Australia. Movement of sheep onto the majority (79%) of properties was limited to the introduction of less than 50 stud rams annually, although cross-bred- and wether-based farms introduced up to 2000 sheep annually; 75% of sheep movements occurred over distances less than 200 km, but stud rams moved up to 500 km. An increasing percentage of movements off farms was direct to abattoirs and over 80% of sheep sold through saleyards were purchased by abattoirs. The majority of Australian sheep farms operate as self-replacing enterprises and introduce few stock. In addition, most sheep movements occur over distances of less than 200 km and therefore sheep movements within Australia have only a limited potential to spread disease over larger distances. © 2011 The Authors. Australian Veterinary Journal © 2011 Australian Veterinary Association.

Optimal estimation of recurrence structures from time series

NASA Astrophysics Data System (ADS)

beim Graben, Peter; Sellers, Kristin K.; Fröhlich, Flavio; Hutt, Axel

2016-05-01

Recurrent temporal dynamics is a phenomenon observed frequently in high-dimensional complex systems and its detection is a challenging task. Recurrence quantification analysis utilizing recurrence plots may extract such dynamics, however it still encounters an unsolved pertinent problem: the optimal selection of distance thresholds for estimating the recurrence structure of dynamical systems. The present work proposes a stochastic Markov model for the recurrent dynamics that allows for the analytical derivation of a criterion for the optimal distance threshold. The goodness of fit is assessed by a utility function which assumes a local maximum for that threshold reflecting the optimal estimate of the system's recurrence structure. We validate our approach by means of the nonlinear Lorenz system and its linearized stochastic surrogates. The final application to neurophysiological time series obtained from anesthetized animals illustrates the method and reveals novel dynamic features of the underlying system. We propose the number of optimal recurrence domains as a statistic for classifying an animals' state of consciousness.

Effects of national culture on human failures in container shipping: the moderating role of Confucian dynamism.

PubMed

Lu, Chin-Shan; Lai, Kee-hung; Lun, Y H Venus; Cheng, T C E

2012-11-01

Recent reports on work safety in container shipping operations highlight high frequencies of human failures. In this study, we empirically examine the effects of seafarers' perceptions of national culture on the occurrence of human failures affecting work safety in shipping operations. We develop a model adopting Hofstede's national culture construct, which comprises five dimensions, namely power distance, collectivism/individualism, uncertainty avoidance, masculinity/femininity, and Confucian dynamism. We then formulate research hypotheses from theory and test the hypotheses using survey data collected from 608 seafarers who work on global container carriers. Using a point scale for evaluating seafarers' perception of the five national culture dimensions, we find that Filipino seafarers score highest on collectivism, whereas Chinese and Taiwanese seafarers score highest on Confucian dynamism, followed by collectivism, masculinity, power distance, and uncertainty avoidance. The results also indicate that Taiwanese seafarers have a propensity for uncertainty avoidance and masculinity, whereas Filipino seafarers lean more towards power distance, masculinity, and collectivism, which are consistent with the findings of Hofstede and Bond (1988). The results suggest that there will be fewer human failures in container shipping operations when power distance is low, and collectivism and uncertainty avoidance are high. Specifically, this study finds that Confucian dynamism plays an important moderating role as it affects the strength of associations between some national culture dimensions and human failures. Finally, we discuss our findings' contribution to the development of national culture theory and their managerial implications for reducing the occurrence of human failures in shipping operations. Copyright © 2012 Elsevier Ltd. All rights reserved.

Stay Here, Go Further: The Status of Open and Distance Education in Bangladesh Open University (BOU) in Comparison to Two Other South Asian Countries

ERIC Educational Resources Information Center

Jahan, Monira; Akhter, Selina; Habib, Rakib

2012-01-01

Distance education has emerged out of social compulsion, the dynamics of change and new cultures. It was the failure of traditional systems to be able to meet the demand in countries, where the resources available for tertiary education are limited, which basically gave birth to the new trend of education known as open and distance education. This…

Nitranilic acid hexahydrate, a novel benchmark system of the Zundel cation in an intrinsically asymmetric environment: spectroscopic features and hydrogen bond dynamics characterised by experimental and theoretical methods.

PubMed

Molčanov, Krešimir; Stare, Jernej; Vener, Mikhail V; Kojić-Prodić, Biserka; Mali, Gregor; Grdadolnik, Jože; Mohaček-Grošev, Vlasta

2014-01-21

Nitranilic acid (2,5-dihydroxy-3,6-dinitro-2,5-cyclohexadiene-1,4-dione) as a strong dibasic acid in acidic aqueous media creates the Zundel cation, H5O2(+). The structural unit in a crystal comprises (H5O2)2(+) (2,5-dihydroxy-3,6-dinitro-1,4-benzoquinonate)(2-) dihydrate where the Zundel cation reveals no symmetry, being an ideal case for studying proton dynamics and its stability. The Zundel cation and proton transfer dynamics are studied by variable-temperature X-ray diffraction, IR and solid-state NMR spectroscopy, and various quantum chemical methods, including periodic DFT calculations, ab initio molecular dynamics simulation, and quantization of nuclear motion along three fully coupled internal coordinates. The Zundel cation features a short H-bond with the O···O distance of 2.433(2) Å with an asymmetric placement of hydrogen. The proton potential is of a single well type and, due to the non-symmetric surroundings, of asymmetric shape. The formation of the Zundel cation is facilitated by the electronegative NO2 groups. The employed spectroscopic techniques supported by calculations confirm the presence of a short H-bond with a complex proton dynamics.

Direct construction of mesoscopic models from microscopic simulations

NASA Astrophysics Data System (ADS)

Lei, Huan; Caswell, Bruce; Karniadakis, George Em

2010-02-01

Starting from microscopic molecular-dynamics (MD) simulations of constrained Lennard-Jones (LJ) clusters (with constant radius of gyration Rg ), we construct two mesoscopic models [Langevin dynamics and dissipative particle dynamics (DPD)] by coarse graining the LJ clusters into single particles. Both static and dynamic properties of the coarse-grained models are investigated and compared with the MD results. The effective mean force field is computed as a function of the intercluster distance, and the corresponding potential scales linearly with the number of particles per cluster and the temperature. We verify that the mean force field can reproduce the equation of state of the atomistic systems within a wide density range but the radial distribution function only within the dilute and the semidilute regime. The friction force coefficients for both models are computed directly from the time-correlation function of the random force field of the microscopic system. For high density or a large cluster size the friction force is overestimated and the diffusivity underestimated due to the omission of many-body effects as a result of the assumed pairwise form of the coarse-grained force field. When the many-body effect is not as pronounced (e.g., smaller Rg or semidilute system), the DPD model can reproduce the dynamic properties of the MD system.

Dynamical Classifications of the Kuiper Belt

NASA Astrophysics Data System (ADS)

Maggard, Steven; Ragozzine, Darin

2018-04-01

The Minor Planet Center (MPC) contains a plethora of observational data on thousands of Kuiper Belt Objects (KBOs). Understanding their orbital properties refines our understanding of the formation of the solar system. My analysis pipeline, BUNSHIN, uses Bayesian methods to take the MPC observations and generate 30 statistically weighted orbital clones for each KBO that are propagated backwards along their orbits until the beginning of the solar system. These orbital integrations are saved as REBOUND SimulationArchive files (Rein & Tamayo 2017) which we will make publicly available, allowing many others to perform statistically-robust dynamical classification or complex dynamical investigations of outer solar system small bodies.This database has been used to expand the known collisional family members of the dwarf planet Haumea. Detailed orbital integrations are required to determine the dynamical distances between family members, in the form of "Delta v" as measured from conserved proper orbital elements (Ragozzine & Brown 2007). Our preliminary results have already ~tripled the number of known Haumea family members, allowing us to show that the Haumea family can be identified purely through dynamical clustering.We will discuss the methods associated with BUNSHIN and the database it generates, the refinement of the updated Haumea family, a brief search for other possible clusterings in the outer solar system, and the potential of our research to aid other dynamicists.

Universal quantum uncertainty relations between nonergodicity and loss of information

NASA Astrophysics Data System (ADS)

Awasthi, Natasha; Bhattacharya, Samyadeb; SenDe, Aditi; Sen, Ujjwal

2018-03-01

We establish uncertainty relations between information loss in general open quantum systems and the amount of nonergodicity of the corresponding dynamics. The relations hold for arbitrary quantum systems interacting with an arbitrary quantum environment. The elements of the uncertainty relations are quantified via distance measures on the space of quantum density matrices. The relations hold for arbitrary distance measures satisfying a set of intuitively satisfactory axioms. The relations show that as the nonergodicity of the dynamics increases, the lower bound on information loss decreases, which validates the belief that nonergodicity plays an important role in preserving information of quantum states undergoing lossy evolution. We also consider a model of a central qubit interacting with a fermionic thermal bath and derive its reduced dynamics to subsequently investigate the information loss and nonergodicity in such dynamics. We comment on the "minimal" situations that saturate the uncertainty relations.

Degree-Pruning Dynamic Programming Approaches to Central Time Series Minimizing Dynamic Time Warping Distance.

PubMed

Sun, Tao; Liu, Hongbo; Yu, Hong; Chen, C L Philip

2016-06-28

The central time series crystallizes the common patterns of the set it represents. In this paper, we propose a global constrained degree-pruning dynamic programming (g(dp)²) approach to obtain the central time series through minimizing dynamic time warping (DTW) distance between two time series. The DTW matching path theory with global constraints is proved theoretically for our degree-pruning strategy, which is helpful to reduce the time complexity and computational cost. Our approach can achieve the optimal solution between two time series. An approximate method to the central time series of multiple time series [called as m_g(dp)²] is presented based on DTW barycenter averaging and our g(dp)² approach by considering hierarchically merging strategy. As illustrated by the experimental results, our approaches provide better within-group sum of squares and robustness than other relevant algorithms.

Depth interval estimates from motion parallax and binocular disparity beyond interaction space.

PubMed

Gillam, Barbara; Palmisano, Stephen A; Govan, Donovan G

2011-01-01

Static and dynamic observers provided binocular and monocular estimates of the depths between real objects lying well beyond interaction space. On each trial, pairs of LEDs were presented inside a dark railway tunnel. The nearest LED was always 40 m from the observer, with the depth separation between LED pairs ranging from 0 up to 248 m. Dynamic binocular viewing was found to produce the greatest (ie most veridical) estimates of depth magnitude, followed next by static binocular viewing, and then by dynamic monocular viewing. (No significant depth was seen with static monocular viewing.) We found evidence that both binocular and monocular dynamic estimates of depth were scaled for the observation distance when the ground plane and walls of the tunnel were visible up to the nearest LED. We conclude that both motion parallax and stereopsis provide useful long-distance depth information and that motion-parallax information can enhance the degree of stereoscopic depth seen.

Handheld lasers allow efficient detection of fluorescent marked organisms in the field.

PubMed

Rice, Kevin B; Fleischer, Shelby J; De Moraes, Consuelo M; Mescher, Mark C; Tooker, John F; Gish, Moshe

2015-01-01

Marking organisms with fluorescent dyes and powders is a common technique used in ecological field studies that monitor movement of organisms to examine life history traits, behaviors, and population dynamics. External fluorescent marking is relatively inexpensive and can be readily employed to quickly mark large numbers of individuals; however, the ability to detect marked organisms in the field at night has been hampered by the limited detection distances provided by portable fluorescent ultraviolet lamps. In recent years, significant advances in LED lamp and laser technology have led to development of powerful, low-cost ultraviolet light sources. In this study, we evaluate the potential of these new technologies to improve detection of fluorescent-marked organisms in the field and to create new possibilities for tracking marked organisms in visually challenging environments such as tree canopies and aquatic habitats. Using handheld lasers, we document a method that provides a fivefold increase in detection distance over previously available technologies. This method allows easy scouting of tree canopies (from the ground), as well as shallow aquatic systems. This novel detection method for fluorescent-marked organisms thus promises to significantly enhance the use of fluorescent marking as a non-destructive technique for tracking organisms in natural environments, facilitating field studies that aim to document otherwise inaccessible aspects of the movement, behavior, and population dynamics of study organisms, including species with significant economic impacts or relevance for ecology and human health.

Wettability and impact dynamics of water droplets on rice ( Oryza sativa L.) leaves

NASA Astrophysics Data System (ADS)

Kwon, Dae Hee; Huh, Hyung Kyu; Lee, Sang Joon

2014-03-01

We investigated the wettability and impact dynamics of water droplets on rice leaves at various leaf inclination angles and orientations. Contact angle, contact angle hysteresis (CAH), and roll-off angle ( α roll) of water droplets were measured quantitatively. Results showed that droplet motion exhibited less resistance along the longitudinal direction. Impact dynamic parameters, such as impact behaviors, maximum spreading factor, contact distance, and contact time were also investigated. Three different impact behaviors were categorized based on the normal component of Weber number irrespective of the inclination angle of the rice leaf. The asymmetric impact behavior induced by the tangential Weber number was also identified. Variation in the maximum spreading factor according to the normal Weber number was measured and compared with theoretical value obtained according to scaling law to show the wettability of the rice leaves. The contact distance of the impacting droplets depended on the inclination angle of the leaves. Along the longitudinal direction of rice leaves, contact distance was farther than that along the transverse direction. This result is consistent with the smaller values of CAH and α roll along the longitudinal direction.

Scaling law on formation and rupture of a dynamical liquid bridge

NASA Astrophysics Data System (ADS)

Zhang, Huang; Zhang, Zehao; Liu, Qianfeng; Li, Shuiqing; Department of Thermal Engineering, Tsinghua University Collaboration; Institute of Nuclear Energy; Technology, Tsinghua University Collaboration

2017-11-01

The formation and breakup of a pendular liquid bridge in dynamic state is investigated experimentally. The experimental setup arises from a system to measure the coefficient of restitution (COR) of a glass sphere impacting and bouncing on a wetted surface. We compare the effect of surface tension and gravity on the liquid bridge rupture by the capillary length κ-1. For water and liquid 1 (50% water mixed with 50% glycerol), the gravity is dominant on the liquid bridge breakup. And we find that the rupture distance is in good linear trend with the non-dimensional number G by the scaling law analysis. Further, for liquid 2 (25% water mixed with 75% glycerol) that is relatively high viscous, the linear changing of the rupture distance with the capillary number Ca is found. The relation of the rupture distance with G and Ca would be helpful in understanding the complex behavior of the dynamical liquid bridge. This work was funded by the Major State Basic Research Development Program of China (Grant No. 2016YFC0203705) and the China Postdoctoral Science Foundation (Grant No. 2016M601024).

Decay of aftershock density with distance indicates triggering by dynamic stress

USGS Publications Warehouse

Felzer, K.R.; Brodsky, E.E.

2006-01-01

The majority of earthquakes are aftershocks, yet aftershock physics is not well understood. Many studies suggest that static stress changes trigger aftershocks, but recent work suggests that shaking (dynamic stresses) may also play a role. Here we measure the decay of aftershocks as a function of distance from magnitude 2-6 mainshocks in order to clarify the aftershock triggering process. We find that for short times after the mainshock, when low background seismicity rates allow for good aftershock detection, the decay is well fitted by a single inverse power law over distances of 0.2-50 km. The consistency of the trend indicates that the same triggering mechanism is working over the entire range. As static stress changes at the more distant aftershocks are negligible, this suggests that dynamic stresses may be triggering all of these aftershocks. We infer that the observed aftershock density is consistent with the probability of triggering aftershocks being nearly proportional to seismic wave amplitude. The data are not fitted well by models that combine static stress change with the evolution of frictionally locked faults. ?? 2006 Nature Publishing Group.

Watching from a distance: A robotically controlled laser and real-time subject tracking software for the study of conditioned predator/prey-like interactions.

PubMed

Wilson, James C; Kesler, Mitch; Pelegrin, Sara-Lynn E; Kalvi, LeAnna; Gruber, Aaron; Steenland, Hendrik W

2015-09-30

The physical distance between predator and prey is a primary determinant of behavior, yet few paradigms exist to study this reliably in rodents. The utility of a robotically controlled laser for use in a predator-prey-like (PPL) paradigm was explored for use in rats. This involved the construction of a robotic two-dimensional gimbal to dynamically position a laser beam in a behavioral test chamber. Custom software was used to control the trajectory and final laser position in response to user input on a console. The software also detected the location of the laser beam and the rodent continuously so that the dynamics of the distance between them could be analyzed. When the animal or laser beam came within a fixed distance the animal would either be rewarded with electrical brain stimulation or shocked subcutaneously. Animals that received rewarding electrical brain stimulation could learn to chase the laser beam, while animals that received aversive subcutaneous shock learned to actively avoid the laser beam in the PPL paradigm. Mathematical computations are presented which describe the dynamic interaction of the laser and rodent. The robotic laser offers a neutral stimulus to train rodents in an open field and is the first device to be versatile enough to assess distance between predator and prey in real time. With ongoing behavioral testing this tool will permit the neurobiological investigation of predator/prey-like relationships in rodents, and may have future implications for prosthetic limb development through brain-machine interfaces. Copyright © 2015 Elsevier B.V. All rights reserved.

Predicting punching acceleration from selected strength and power variables in elite karate athletes: a multiple regression analysis.

PubMed

Loturco, Irineu; Artioli, Guilherme Giannini; Kobal, Ronaldo; Gil, Saulo; Franchini, Emerson

2014-07-01

This study investigated the relationship between punching acceleration and selected strength and power variables in 19 professional karate athletes from the Brazilian National Team (9 men and 10 women; age, 23 ± 3 years; height, 1.71 ± 0.09 m; and body mass [BM], 67.34 ± 13.44 kg). Punching acceleration was assessed under 4 different conditions in a randomized order: (a) fixed distance aiming to attain maximum speed (FS), (b) fixed distance aiming to attain maximum impact (FI), (c) self-selected distance aiming to attain maximum speed, and (d) self-selected distance aiming to attain maximum impact. The selected strength and power variables were as follows: maximal dynamic strength in bench press and squat-machine, squat and countermovement jump height, mean propulsive power in bench throw and jump squat, and mean propulsive velocity in jump squat with 40% of BM. Upper- and lower-body power and maximal dynamic strength variables were positively correlated to punch acceleration in all conditions. Multiple regression analysis also revealed predictive variables: relative mean propulsive power in squat jump (W·kg-1), and maximal dynamic strength 1 repetition maximum in both bench press and squat-machine exercises. An impact-oriented instruction and a self-selected distance to start the movement seem to be crucial to reach the highest acceleration during punching execution. This investigation, while demonstrating strong correlations between punching acceleration and strength-power variables, also provides important information for coaches, especially for designing better training strategies to improve punching speed.

Feature Integration across Space, Time, and Orientation

ERIC Educational Resources Information Center

Otto, Thomas U.; Ogmen, Haluk; Herzog, Michael H.

2009-01-01

The perception of a visual target can be strongly influenced by flanking stimuli. In static displays, performance on the target improves when the distance to the flanking elements increases--presumably because feature pooling and integration vanishes with distance. Here, we studied feature integration with dynamic stimuli. We show that features of…

The Online Classroom: A Thorough Depiction of Distance Learning Spaces

ERIC Educational Resources Information Center

McKenna, Kelly

2018-01-01

This study investigated the online higher education learning space of a doctoral program offered at a distance. It explored the learning space, the stakeholders, utilization, and creators of the space. Developing a successful online classroom experience that incorporates an engaging environment and dynamic community setting conducive to learning…

Classification and recognition of dynamical models: the role of phase, independent components, kernels and optimal transport.

PubMed

Bissacco, Alessandro; Chiuso, Alessandro; Soatto, Stefano

2007-11-01

We address the problem of performing decision tasks, and in particular classification and recognition, in the space of dynamical models in order to compare time series of data. Motivated by the application of recognition of human motion in image sequences, we consider a class of models that include linear dynamics, both stable and marginally stable (periodic), both minimum and non-minimum phase, driven by non-Gaussian processes. This requires extending existing learning and system identification algorithms to handle periodic modes and nonminimum phase behavior, while taking into account higher-order statistics of the data. Once a model is identified, we define a kernel-based cord distance between models that includes their dynamics, their initial conditions as well as input distribution. This is made possible by a novel kernel defined between two arbitrary (non-Gaussian) distributions, which is computed by efficiently solving an optimal transport problem. We validate our choice of models, inference algorithm, and distance on the tasks of human motion synthesis (sample paths of the learned models), and recognition (nearest-neighbor classification in the computed distance). However, our work can be applied more broadly where one needs to compare historical data while taking into account periodic trends, non-minimum phase behavior, and non-Gaussian input distributions.

A Segment-Based Trajectory Similarity Measure in the Urban Transportation Systems.

PubMed

Mao, Yingchi; Zhong, Haishi; Xiao, Xianjian; Li, Xiaofang

2017-03-06

With the rapid spread of built-in GPS handheld smart devices, the trajectory data from GPS sensors has grown explosively. Trajectory data has spatio-temporal characteristics and rich information. Using trajectory data processing techniques can mine the patterns of human activities and the moving patterns of vehicles in the intelligent transportation systems. A trajectory similarity measure is one of the most important issues in trajectory data mining (clustering, classification, frequent pattern mining, etc.). Unfortunately, the main similarity measure algorithms with the trajectory data have been found to be inaccurate, highly sensitive of sampling methods, and have low robustness for the noise data. To solve the above problems, three distances and their corresponding computation methods are proposed in this paper. The point-segment distance can decrease the sensitivity of the point sampling methods. The prediction distance optimizes the temporal distance with the features of trajectory data. The segment-segment distance introduces the trajectory shape factor into the similarity measurement to improve the accuracy. The three kinds of distance are integrated with the traditional dynamic time warping algorithm (DTW) algorithm to propose a new segment-based dynamic time warping algorithm (SDTW). The experimental results show that the SDTW algorithm can exhibit about 57%, 86%, and 31% better accuracy than the longest common subsequence algorithm (LCSS), and edit distance on real sequence algorithm (EDR) , and DTW, respectively, and that the sensitivity to the noise data is lower than that those algorithms.

Physical activity of the selected nearly isotropic comets with perihelia at large heliocentric distance

NASA Astrophysics Data System (ADS)

Kulyk, I.; Rousselot, P.; Korsun, P. P.; Afanasiev, V. L.; Sergeev, A. V.; Velichko, S. F.

2018-03-01

Context. The systematic investigation of comets in a wide range of heliocentric distances can contribute to a better understanding of the physical mechanisms that trigger activity at large distances from the Sun and reveals possible differences in the composition of outer solar system bodies belonging to various dynamical groups. Aims: We seek to analyze the dust environment of the selected nearly isotropic comets with a perihelion distance between 4.5 and 9.1 au, where sublimation of water ice is considered to be negligible. Methods: We present results of multicolor broadband photometric observations for 14 distant active objects conducted between 2008 and 2015 with various telescopes. Images obtained with broadband filters were used to investigate optical colors of the cometary comae and to quantify physical activity of the comet nuclei. Results: The activity level was estimated with Afρ parameters ranging between 95 ± 10 cm and 9600 ± 300 cm. Three returning comets were less active than the dynamically new comets. Dust production rates of the comet nuclei were estimated between 1 and 100 kg s-1 based on some assumptions about the physical properties of dust particles populating comae. The measured colors point out reddening of the continuum for all the comets. The mean values of a normalized reflectivity gradient within the group of the comets amount to 14 ± 2% per 1000 Å and 3 ± 2% per 1000 Å in the BV and VR spectral domains, respectively. The comae of the dynamically new comets, which were observed on their inbound legs, may be slightly redder in the blue spectral interval than comae of the comets observed after the perihelion passages. The dynamically new comets observed both pre- and post-perihelion, seem to have higher production rates post-perihelion than pre-perihelion for similar heliocentric distances.

Dark Matter Halos with VIRUS-P

NASA Astrophysics Data System (ADS)

Murphy, Jeremy; Gebhardt, K.

2010-05-01

We present new, two-dimensional stellar kinematic data on several of the most massive galaxies in the local universe. These data were taken with the integral field spectrograph, VIRUS-P, and extend to unprecedented radial distances. Once robust stellar kinematics are in hand, we run orbit-based axisymmetric dynamical models in order to constrain the stellar mass-to-light ratio and dark matter halo parameters. We have run a large set of dynamical models on the second rank galaxy in the Virgo cluster, M87, and find clear evidence for a massive dark matter halo. The two-dimensional stellar kinematics for several of our other targets, all first and second rank galaxies, are also presented. Dark matter halos are known to dominate the mass profile of elliptical galaxies somewhere between one to two effective radii, yet due to the low surface brightness at these radial distances, determining stellar dynamics is technologically challenging. To overcome this, constraints on the dark matter halo are often made with planetary nebulae or globular clusters at large radii. However, as results from different groups have returned contradictory results, it remains unclear whether different dynamical tracers always follow the stellar kinematics. Due to VIRUS-P's large field of view and on-sky fiber diameter, we are able to determine stellar kinematics at radial distances that overlap with other dynamical tracers. Understanding what the dynamics of stars, planetary nebula and globular clusters tell us about both the extent of the dark matter halo profile and the formation histories of the largest elliptical galaxies is a primary science driver for this work.

Effect of ionization on the oxidation kinetics of aluminum nanoparticles

NASA Astrophysics Data System (ADS)

Zheng, Yao-Ting; He, Min; Cheng, Guang-xu; Zhang, Zaoxiao; Xuan, Fu-Zhen; Wang, Zhengdong

2018-03-01

Molecular dynamics simulation (MD) of the observed stepwise oxidation of core-shell structured Al/Al2O3 nanoparticles is presented. Different from the metal ion hopping process in the Cabrera-Mott model, which is assumed to occur only at a certain distance from the oxide layer, the MD simulation shows that Al atoms jump over various interfacial gaps directly under the thermal driving force. The energy barrier for Al ionization is found to be increased along with the enlargement of interfacial gap. A mechanism of competition between thermal driving force and ionization potential barrier is proposed in the interpretation of stepwise oxidation behavior.

The potential of toe flexor muscles to enhance performance.

PubMed

Goldmann, Jan-Peter; Sanno, Maximilian; Willwacher, Steffen; Heinrich, Kai; Brüggemann, Gert-Peter

2013-01-01

The metatarsal phalangeal joint (MPJ) and its crossing toe flexor muscles (TFM) represent the link between the large energy generating leg extensor muscles and the ground. The purpose of this study was to examine the functional adaptability of TFM to increased mechanical stimuli and the effects on walking, running and jumping performance. Fifteen men performed a heavy resistance TFM strength training with 90% of the maximal voluntary isometric contraction (MVIC) for 7 weeks (560 contractions) for the left and right foot. Maximal MPJ and ankle plantar flexion moments during MVICs were measured in dynamometers before and after the intervention. Motion analyses (inverse dynamics) were performed during barefoot walking, running, and vertical and horizontal jumping. Athletic performance was determined by measuring jump height and distance. Left (0.21 to 0.38 Nm · kg(-1); P < 0.001) and right (0.24 to 0.40 Nm · kg(-1); P < 0.001) MPJ plantar flexion moments in the dynamometer, external MPJ dorsiflexion moments (0.69 to 0.75 Nm · kg(-1); P = 0.012) and jump distance (2.25 to 2.31 m; P = 0.006) in horizontal jumping increased significantly. TFM responded highly to increased loading within a few weeks. The increased force potential made a contribution to an athlete's performance enhancement.

Correlations of Platooning Track Test and Wind Tunnel Data

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

Lammert, Michael P.; Kelly, Kenneth J.; Yanowitz, Janet

In this report, the National Renewable Energy Laboratory analyzed results from multiple, independent truck platooning projects to compare and contrast track test results with wind tunnel test results conducted by Lawrence Livermore National Laboratory (LLNL). Some highlights from the report include compiled data, and results from four independent SAE J1321 full-size track test campaigns that were compared to LLNL wind tunnel testing results. All platooning scenarios tested demonstrated significant fuel savings with good correlation relative to following distances, but there are still unanswered questions and clear opportunities for system optimization. NOx emissions showed improvements from NREL tests in 2014 tomore » Auburn tests in 2015 with respect to J1321 platooning track testing of Peloton system. NREL evaluated data from Volpe's Naturalistic Study of Truck Following Behavior, which showed minimal impact of naturalistic background platooning. We found significant correlation between multiple track studies, wind tunnel tests, and computational fluid dynamics, but also showed that there is more to learn regarding close formation and longer-distance effects. We also identified potential areas for further research and development, including development of advanced aerodynamic designs optimized for platooning, measurement of platoon system performance in traffic conditions, impact of vehicle lateral offsets on platooning performance, and characterization of the national potential for platooning based on fleet operational characteristics.« less

The probability of quantal secretion near a single calcium channel of an active zone.

PubMed Central

Bennett, M R; Farnell, L; Gibson, W G

2000-01-01

A Monte Carlo analysis has been made of calcium dynamics and quantal secretion at microdomains in which the calcium reaches very high concentrations over distances of <50 nm from a channel and for which calcium dynamics are dominated by diffusion. The kinetics of calcium ions in microdomains due to either the spontaneous or evoked opening of a calcium channel, both of which are stochastic events, are described in the presence of endogenous fixed and mobile buffers. Fluctuations in the number of calcium ions within 50 nm of a channel are considerable, with the standard deviation about half the mean. Within 10 nm of a channel these numbers of ions can give rise to calcium concentrations of the order of 100 microM. The temporal changes in free calcium and calcium bound to different affinity indicators in the volume of an entire varicosity or bouton following the opening of a single channel are also determined. A Monte Carlo analysis is also presented of how the dynamics of calcium ions at active zones, after the arrival of an action potential and the stochastic opening of a calcium channel, determine the probability of exocytosis from docked vesicles near the channel. The synaptic vesicles in active zones are found docked in a complex with their calcium-sensor associated proteins and a voltage-sensitive calcium channel, forming a secretory unit. The probability of quantal secretion from an isolated secretory unit has been determined for different distances of an open calcium channel from the calcium sensor within an individual unit: a threefold decrease in the probability of secretion of a quantum occurs with a doubling of the distance from 25 to 50 nm. The Monte Carlo analysis also shows that the probability of secretion of a quantum is most sensitive to the size of the single-channel current compared with its sensitivity to either the binding rates of the sites on the calcium-sensor protein or to the number of these sites that must bind a calcium ion to trigger exocytosis of a vesicle. PMID:10777721

Dynamics of surface-migration: Electron-induced reaction of 1,2-dihaloethanes on Si(100)

NASA Astrophysics Data System (ADS)

Huang, Kai; MacLean, Oliver; Guo, Si Yue; McNab, Iain R.; Ning, Zhanyu; Wang, Chen-Guang; Ji, Wei; Polanyi, John C.

2016-10-01

Scanning Tunneling Microscopy was used to investigate the electron-induced reaction of 1,2-dibromoethane (DBE) and 1,2-dichloroethane (DCE) on Si(100).We observed a long-lived physisorbed molecular state of DBE at 75 K and of DCE at 110 K. As a result we were able to characterize by experiment and also by ab initio theory the dynamics of ethylene production in the electron-induced surface-reaction of these physisorbed species. For both DBE and DCE the ethylene product was observed to migrate across the surface. In the case of DBE the recoil of the ethylene favored the silicon rows, migrating by an average distance of 22 Å, and up to 100 Å. Trajectory calculations were performed for this electron-induced reaction, using an 'Impulsive Two-State' model involving an anionic excited state and a neutral ground-potential. The model agreed with experiment in reproducing both migration and desorption of the ethylene product. The computed migration exhibited a 'ballistic' launch and subsequent 'bounces', thereby accounting for the observed long-range migratory dynamics.

Study of the filtration performance of a plain wave fabric filter using response surface methodology.

PubMed

Qian, Fuping; Wang, Haigang

2010-04-15

The gas-solid two-phase flows in the plain wave fabric filter were simulated by computational fluid dynamics (CFD) technology, and the warps and wefts of the fabric filter were made of filaments with different dimensions. The numerical solutions were carried out using commercial computational fluid dynamics (CFD) code Fluent 6.1. The filtration performances of the plain wave fabric filter with different geometry parameters and operating condition, including the horizontal distance, the vertical distance and the face velocity were calculated. The effects of geometry parameters and operating condition on filtration efficiency and pressure drop were studied using response surface methodology (RSM) by means of the statistical software (Minitab V14), and two second-order polynomial models were obtained with regard to the effect of the three factors as stated above. Moreover, the models were modified by dismissing the insignificant terms. The results show that the horizontal distance, vertical distance and the face velocity all play an important role in influencing the filtration efficiency and pressure drop of the plane wave fabric filters. The horizontal distance of 3.8 times the fiber diameter, the vertical distance of 4.0 times the fiber diameter and Reynolds number of 0.98 are found to be the optimal conditions to achieve the highest filtration efficiency at the same face velocity, while maintaining an acceptable pressure drop. 2009 Elsevier B.V. All rights reserved.

Expectation-maximization of the potential of mean force and diffusion coefficient in Langevin dynamics from single molecule FRET data photon by photon.

PubMed

Haas, Kevin R; Yang, Haw; Chu, Jhih-Wei

2013-12-12

The dynamics of a protein along a well-defined coordinate can be formally projected onto the form of an overdamped Lagevin equation. Here, we present a comprehensive statistical-learning framework for simultaneously quantifying the deterministic force (the potential of mean force, PMF) and the stochastic force (characterized by the diffusion coefficient, D) from single-molecule Förster-type resonance energy transfer (smFRET) experiments. The likelihood functional of the Langevin parameters, PMF and D, is expressed by a path integral of the latent smFRET distance that follows Langevin dynamics and realized by the donor and the acceptor photon emissions. The solution is made possible by an eigen decomposition of the time-symmetrized form of the corresponding Fokker-Planck equation coupled with photon statistics. To extract the Langevin parameters from photon arrival time data, we advance the expectation-maximization algorithm in statistical learning, originally developed for and mostly used in discrete-state systems, to a general form in the continuous space that allows for a variational calculus on the continuous PMF function. We also introduce the regularization of the solution space in this Bayesian inference based on a maximum trajectory-entropy principle. We use a highly nontrivial example with realistically simulated smFRET data to illustrate the application of this new method.

Pyroclastic Density Current Hazards in the Auckland Volcanic Field, New Zealand

NASA Astrophysics Data System (ADS)

Brand, B. D.; Gravley, D.; Clarke, A. B.; Bloomberg, S. H.

2012-12-01

The most dangerous phenomena associated with phreatomagmatic eruptions are dilute pyroclastic density currents (PDCs). These are turbulent, ground-hugging sediment gravity currents that travel radially away from the explosive center at up to 100 m/s. The Auckland Volcanic Field (AVF), New Zealand, consists of approximately 50 eruptive centers, at least 39 of which have had explosive phreatomagmatic behaviour. A primary concern for future AVF eruptions is the impact of dilute PDCs in and around the Auckland area. We combine field observations from the Maungataketake tuff ring, which has one of the best exposures of dilute PDC deposits in the AVF, with a quantitative model for flow of and sedimentation from a radially-spreading, steady-state, depth-averaged dilute PDC (modified from Bursik and Woods, 1996 Bull Volcanol 58:175-193). The model allows us to explore the depositional mechanisms, macroscale current dynamics, and potential impact on societal infrastructure of dilute PDCs from a future AVF eruption. The lower portion of the Maungataketake tuff ring pyroclastic deposits contains trunks, limbs and fragments of Podocarp trees (<1 m in diameter) that were blown down by dilute PDCs up to 0.7-0.9 km from the vent. Beyond this trees were encapsulated and buried in growth position up to the total runout distance of 1.6-1.8 km. This observation suggests that the dynamic pressure of the current quickly dropped as it travelled away from source. Using the tree diameter and yield strength of the wood, we calculate that dynamic pressures (Pdyn) of 10-75 kPa are necessary to topple trees of this size and composition. Thus the two main criteria for model success based on the field evidence include (a) Pdyn must be >10 kPa nearer than 0.9 km to the vent, and <10 kPa beyond 0.9 km, and (b) the total run-out distance must be between 1.6 and 1.8 km. Model results suggest the two main forces controlling the runout distance and Pdyn over the extent of the current are sedimentation rate and entrainment of ambient atmosphere, which are a function of the grain size and initial bulk density, thickness and velocity of a given current. Initial velocities of 60 m s-1, initial bulk densities of 35 kg m-3 and initial current thickness of 70 m are the input parameters that reproduce the best fit to our field data. This preliminary validation of the model allows us to estimate the impact of dilute PDCs from future larger phreatomagmatic eruptions. In the case of a dilute PDC traveling 5-7 km from source: Pdyn >35 kPa can be expected within 3 km from source, ensuring complete destruction of the area; Pdyn > 15 kPa up to 5 km from source, resulting in heavy structural damage to most buildings and near destruction of weaker buildings; and Pdyn <10 kPa at ~6 km from source, resulting in severe damage to weaker structures at least up to this distance. This exercise illustrates our ability to combine field measurements with numerical techniques to explore controlling parameters of dilute PDC dynamics. These tools can be used to understand and estimate the damage potential and extent of past and future eruptions in the AVF or other similar volcanically active regions.

Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence

PubMed Central

Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M.

2012-01-01

Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics could greatly contribute to understanding various aspects of functional diversity. PMID:22768346

Scale dependency of fracture energy and estimates thereof via dynamic rupture solutions with strong thermal weakening

NASA Astrophysics Data System (ADS)

Viesca, R. C.; Garagash, D.

2013-12-01

Seismological estimates of fracture energy show a scaling with the total slip of an earthquake [e.g., Abercrombie and Rice, GJI 2005]. Potential sources for this scale dependency are coseismic fault strength reductions that continue with increasing slip or an increasing amount of off-fault inelastic deformation with dynamic rupture propagation [e.g., Andrews, JGR 2005; Rice, JGR 2006]. Here, we investigate the former mechanism by solving for the slip dependence of fracture energy at the crack tip of a dynamically propagating rupture in which weakening takes place by strong reductions of friction via flash heating of asperity contacts and thermal pressurization of pore fluid leading to reductions in effective normal stress. Laboratory measurements of small characteristic slip evolution distances for friction (~10 μm at low slip rates of μm-mm/s, possibly up to 1 mm for slip rates near 0.1 m/s) [e.g., Marone and Kilgore, Nature 1993; Kohli et al., JGR 2011] imply that flash weakening of friction occurs at small slips before any significant thermal pressurization and may thus have a negligible contribution to the total fracture energy [Brantut and Rice, GRL 2011; Garagash, AGU 2011]. The subsequent manner of weakening under thermal pressurization (the dominant contributor to fracture energy) spans a range of behavior from the deformation of a finite-thickness shear zone in which diffusion is negligible (i.e., undrained-adiabatic) to that in which large-scale diffusion obscures the existence of a thin shear zone and thermal pressurization effectively occurs by the heating of slip on a plane. Separating the contribution of flash heating, the dynamic rupture solutions reduce to a problem with a single parameter, which is the ratio of the undrained-adiabatic slip-weakening distance (δc) to the characteristic slip-on-a-plane slip-weakening distance (L*). However, for any value of the parameter, there are two end-member scalings of the fracture energy: for small slip, the undrained-adiabatic behavior expectedly results in fracture energy scaling as G ~ δ^2, and for large slip (where TP approaches slip on a plane) we find that G ~ δ^(2/3). This last result is a slight correction to estimates made assuming a constant, kinematically imposed slip rate and slip-on-a-plane TP resulting in G ~ δ^(1/2) [Rice, JGR 2006]. We compile fracture energy estimates of both continental and subduction zone earthquakes. In doing so, we incorporate independent estimates of fault prestress to distinguish fracture energy G from the parameter G' defined by Abercrombie and Rice [2005], which represents the energetic quantity that is most directly inferred following seismological estimates of radiated energy, seismic moment and source radius. We find that the dynamic rupture solutions (which account for the variable manner of thermal pressurization and result in a self-consistent slip rate history) allow for a close match of the estimated fracture energy over several orders of total event slip, further supporting the proposed explanation that fracture energy scaling may largely be attributed to a fault strength that weakens gradually with slip, and additionally, the potential prevalence of thermal pressurization.

Fit Point-Wise AB Initio Calculation Potential Energies to a Multi-Dimension Long-Range Model

NASA Astrophysics Data System (ADS)

Zhai, Yu; Li, Hui; Le Roy, Robert J.

2016-06-01

A potential energy surface (PES) is a fundamental tool and source of understanding for theoretical spectroscopy and for dynamical simulations. Making correct assignments for high-resolution rovibrational spectra of floppy polyatomic and van der Waals molecules often relies heavily on predictions generated from a high quality ab initio potential energy surface. Moreover, having an effective analytic model to represent such surfaces can be as important as the ab initio results themselves. For the one-dimensional potentials of diatomic molecules, the most successful such model to date is arguably the ``Morse/Long-Range'' (MLR) function developed by R. J. Le Roy and coworkers. It is very flexible, is everywhere differentiable to all orders. It incorporates correct predicted long-range behaviour, extrapolates sensibly at both large and small distances, and two of its defining parameters are always the physically meaningful well depth {D}_e and equilibrium distance r_e. Extensions of this model, called the Multi-Dimension Morse/Long-Range (MD-MLR) function, linear molecule-linear molecule systems and atom-non-linear molecule system. have been applied successfully to atom-plus-linear molecule, linear molecule-linear molecule and atom-non-linear molecule systems. However, there are several technical challenges faced in modelling the interactions of general molecule-molecule systems, such as the absence of radial minima for some relative alignments, difficulties in fitting short-range potential energies, and challenges in determining relative-orientation dependent long-range coefficients. This talk will illustrate some of these challenges and describe our ongoing work in addressing them. Mol. Phys. 105, 663 (2007); J. Chem. Phys. 131, 204309 (2009); Mol. Phys. 109, 435 (2011). Phys. Chem. Chem. Phys. 10, 4128 (2008); J. Chem. Phys. 130, 144305 (2009) J. Chem. Phys. 132, 214309 (2010) J. Chem. Phys. 140, 214309 (2010)

Action-Based Dynamical Modelling For The Milky Way Disk

NASA Astrophysics Data System (ADS)

Trick, Wilma; Rix, Hans-Walter; Bovy, Jo

2016-09-01

We present Road Mapping, a full-likelihood dynamical modelling machinery, that aims to recover the Milky Way's (MW) gravitational potential from large samples of stars in the Galactic disk. Road Mapping models the observed positions and velocities of stars with a parameterized, action-based distribution function (DF) in a parameterized axisymmetric gravitational potential (Binney & McMillan 2011, Binney 2012, Bovy & Rix 2013).In anticipation of the Gaia data release in autumn, we have fully tested Road Mapping and demonstrated its robustness against the breakdown of its assumptions.Using large suites of mock data, we investigated in isolated test cases how the modelling would be affected if the data's true potential or DF was not included in the families of potentials and DFs assumed by Road Mapping, or if we misjudged measurement errors or the spatial selection function (SF) (Trick et al., submitted to ApJ). We found that the potential can be robustly recovered — given the limitations of the assumed potential model—, even for minor misjudgments in DF or SF, or for proper motion errors or distances known to within 10%.We were also able to demonstrate that Road Mapping is still successful if the strong assumption of axisymmetric breaks down (Trick et al., in preparation). Data drawn from a highresolution simulation (D'Onghia et al. 2013) of a MW-like galaxy with pronounced spiral arms does neither follow the assumed simple DF, nor does it come from an axisymmetric potential. We found that as long as the survey volume is large enough, Road Mapping gives good average constraints on the galaxy's potential.We are planning to apply Road Mapping to a real data set — the Tycho-2 catalogue (Hog et al. 2000) —very soon, and might be able to present some preliminary results already at the conference.

Dynamics analysis of microsphere in a dual-beam fiber-optic trap with transverse offset.

PubMed

Chen, Xinlin; Xiao, Guangzong; Luo, Hui; Xiong, Wei; Yang, Kaiyong

2016-04-04

A comprehensive dynamics analysis of microsphere has been presented in a dual-beam fiber-optic trap with transverse offset. As the offset distance between two counterpropagating beams increases, the motion type of the microsphere starts with capture, then spiral motion, then orbital rotation, and ends with escape. We analyze the transformation process and mechanism of the four motion types based on ray optics approximation. Dynamic simulations show that the existence of critical offset distances at which different motion types transform. The result is an important step toward explaining physical phenomena in a dual-beam fiber-optic trap with transverse offset, and is generally applicable to achieving controllable motions of microspheres in integrated systems, such as microfluidic systems and lab-on-a-chip systems.

An Analysis of the Market Potential for Distance Learning Opportunities in Transportation Professional Development.

ERIC Educational Resources Information Center

Durkop, Brooke R.; Jasek, Debbie; Kuhn, Beverly T.

The feasibility and sustainability of a distance learning program at the Texas Transportation Institute, which is part of the Texas A&M University system, was investigated. A literature review and online survey of current transportation professionals were conducted to examine the market potential for a distance learning program and to identify…

Distance-responsive genes found in dancing honey bees.

PubMed

Sen Sarma, M; Rodriguez-Zas, S L; Gernat, T; Nguyen, T; Newman, T; Robinson, G E

2010-10-01

We report that regions of the honey bee brain involved in visual processing and learning and memory show a specific genomic response to distance information. These results were obtained with an established method that separates effects of perceived distance from effects of actual distance flown. Individuals forced to shift from a short to perceived long distance to reach a feeding site showed gene expression differences in the optic lobes and mushroom bodies relative to individuals that continued to perceive a short distance, even though they all flew the same distance. Bioinformatic analyses suggest that the genomic response to distance information involves learning and memory systems associated with well-known signaling pathways, synaptic remodeling, transcription factors and protein metabolism. By showing distance-sensitive brain gene expression, our findings also significantly extend the emerging paradigm of the genome as a dynamic regulator of behavior, that is particularly responsive to stimuli important in social life. © 2010 The Authors. Genes, Brain and Behavior © 2010 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.

Spatial Pattern of Attacks of the Invasive Woodwasp Sirex noctilio, at Landscape and Stand Scales.

PubMed

Lantschner, M Victoria; Corley, Juan C

2015-01-01

Invasive insect pests are responsible for important damage to native and plantation forests, when population outbreaks occur. Understanding the spatial pattern of attacks by forest pest populations is essential to improve our understanding of insect population dynamics and for predicting attack risk by invasives or planning pest management strategies. The woodwasp Sirex noctilio is an invasive woodwasp that has become probably the most important pest of pine plantations in the Southern Hemisphere. Our aim was to study the spatial dynamics of S. noctilio populations in Southern Argentina. Specifically we describe: (1) the spatial patterns of S. noctilio outbreaks and their relation with environmental factors at a landscape scale; and (2) characterize the spatial pattern of attacked trees at the stand scale. We surveyed the spatial distribution of S. noctilio outbreaks in three pine plantation landscapes, and we assessed potential associations with topographic variables, habitat characteristics, and distance to other outbreaks. We also looked at the spatial distribution of attacked trees in 20 stands with different levels of infestation, and assessed the relationship of attacks with stand composition and management. We found that the spatial pattern of pine stands with S. noctilio outbreaks at the landscape scale is influenced mainly by the host species present, slope aspect, and distance to other outbreaks. At a stand scale, there is strong aggregation of attacked trees in stands with intermediate infestation levels, and the degree of attacks is influenced by host species and plantation management. We conclude that the pattern of S. noctilio damage at different spatial scales is influenced by a combination of both inherent population dynamics and the underlying patterns of environmental factors. Our results have important implications for the understanding and management of invasive insect outbreaks in forest systems.

Lab Experiments Probe Interactions Between Dilute Pyroclastic Density Currents and 3D Barriers

NASA Astrophysics Data System (ADS)

Fauria, K.; Andrews, B. J.; Manga, M.

2014-12-01

We conducted scaled laboratory experiments of unconfined dilute pyroclastic density currents (PDCs) to examine interactions between three - dimensional obstacles and dilute PDCs. While it is known that PDCs can surmount barriers by converting kinetic energy into potential energy, the signature of topography on PDC dynamics is unclear. To examine the interplay between PDCs and topography, we turbulently suspended heated and ambient-temperature 20 μm talc powder in air within an 8.5 x 6.1 x 2.6 m tank. Experimental parameters (Froude number, densimetric and thermal Richardson number, particle Stokes and Settling numbers) were scaled such that the experimental currents were dynamically similar to natural PCS. The Reynolds number, however, is much smaller than in natural currents, but still large enough for the flows to be turbulent. We placed cylindrical and ridge-like objects in the path of the currents, illuminated the currents with orthogonal laser sheets, and recorded each experiment with high definition cameras. We observed currents surmounting ridge-like barriers (barrier height = current height). Slanted ridges redirected the currents upward and parallel to the upstream face of the ridges (~45° from horizontal). Down stream of the slanted ridges, ambient-temperature currents reattached to the floor. By comparison, hot currents reversed buoyancy and lifted off. These observations suggest that obstacles enhance air entrainment, a process key to affecting runout distance and the depletion of fine particles in ignimbrites. Moreover, we observed vortex shedding in the wake of cylinders. Our experiments demonstrate that barriers of various shapes affect PDC dynamics and can shorten PDC runout distances. Understanding the effects of topography on PDCs is required for interpreting many deposits because processes such as vortex shedding and topographically-induced changes in turbulent length scales and entrainment likely leave depositional signatures.

A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein

PubMed Central

Sethi, Anurag; Tian, Jianhui; Derdeyn, Cynthia A.; Korber, Bette; Gnanakaran, S.

2013-01-01

The HIV-1 envelope (Env) spike, which consists of a compact, heterodimeric trimer of the glycoproteins gp120 and gp41, is the target of neutralizing antibodies. However, the high mutation rate of HIV-1 and plasticity of Env facilitates viral evasion from neutralizing antibodies through various mechanisms. Mutations that are distant from the antibody binding site can lead to escape, probably by changing the conformation or dynamics of Env; however, these changes are difficult to identify and define mechanistically. Here we describe a network analysis-based approach to identify potential allosteric immune evasion mechanisms using three known HIV-1 Env gp120 protein structures from two different clades, B and C. First, correlation and principal component analyses of molecular dynamics (MD) simulations identified a high degree of long-distance coupled motions that exist between functionally distant regions within the intrinsic dynamics of the gp120 core, supporting the presence of long-distance communication in the protein. Then, by integrating MD simulations with network theory, we identified the optimal and suboptimal communication pathways and modules within the gp120 core. The results unveil both strain-dependent and -independent characteristics of the communication pathways in gp120. We show that within the context of three structurally homologous gp120 cores, the optimal pathway for communication is sequence sensitive, i.e. a suboptimal pathway in one strain becomes the optimal pathway in another strain. Yet the identification of conserved elements within these communication pathways, termed inter-modular hotspots, could present a new opportunity for immunogen design, as this could be an additional mechanism that HIV-1 uses to shield vulnerable antibody targets in Env that induce neutralizing antibody breadth. PMID:23696718

Lower Limb Kinematics and Dynamic Postural Stability in Anterior Cruciate Ligament-Reconstructed Female Athletes

PubMed Central

Delahunt, Eamonn; Chawke, Mark; Kelleher, Judy; Murphy, Katie; Prendiville, Anna; Sweeny, Lauren; Patterson, Matt

2013-01-01

Context: Deficits in lower limb kinematics and postural stability are predisposing factors to the development of knee ligamentous injury. The extent to which these deficits are present after anterior cruciate ligament (ACL) reconstruction is still largely unknown. The primary hypothesis of the present study was that female athletes who have undergone ACL reconstruction and who have returned to sport participation would exhibit deficits in dynamic postural stability as well as deficiencies in hip- and knee-joint kinematics when compared with an age-, activity-, and sex-matched uninjured control group. Objective: To investigate dynamic postural stability as quantified by the Star Excursion Balance Test (SEBT) and simultaneous hip- and knee-joint kinematic profiles in female athletes who have undergone ACL reconstruction. Design: Descriptive laboratory study. Setting: University motion-analysis laboratory. Patients or Other Participants: Fourteen female athletes who had previously undergone ACL reconstruction (ACL-R) and 17 age- and sex-matched uninjured controls. Intervention(s): Each participant performed 3 trials of the anterior, posterior-medial, and posterior-lateral directional components of the SEBT. Main Outcome Measure(s): Reach distances for each directional component were quantified and expressed as a percentage of leg length. Simultaneous hip- and knee-joint kinematic profiles were recorded using a motion-analysis system. Results: The ACL-R group had decreased reach distances on the posterior-medial (P < .01) and posterior-lateral (P < .01) directional components of the SEBT. During performance of the directional components of the SEBT, ACL-R participants demonstrated altered hip-joint frontal-, sagittal-, and transverse-plane kinematic profiles (P < .05), as well as altered knee-joint sagittal-plane kinematic profiles (P < .05). Conclusions: Deficits in dynamic postural stability and concomitant altered hip- and knee-joint kinematics are present after ACL reconstruction and return to competitive activity. The extent to which these deficits influence potential future injury is worthy of investigation. PMID:23672381

A Hierarchical Approach Embedding Hydrologic and Population Modeling for a West Nile Virus Vector Prediction

NASA Astrophysics Data System (ADS)

Jian, Y.; Silvestri, S.; Marani, M.; Saltarin, A.; Chillemi, G.

2012-12-01

We applied a hierarchical state space model to predict the abundance of Cx.pipiens (a West Nile Virus vector) in the Po River Delta Region, Northeastern Italy. The study area has large mosquito abundance, due to a favorable environment and climate as well as dense human population. Mosquito data were collected on a weekly basis at more than 20 sites from May to September in 2010 and 2011. Cx.pipiens was the dominant species in our samples, accounting for about 90% of the more than 300,000 total captures. The hydrological component of the model accounted for evapotranspiration, infiltration and deep percolation to infer, in a 0D context, the local dynamics of soil moisture as a direct exogenous forcing of mosquito dynamics. The population model had a Gompertz structure, which included exogenous meteorological forcings and delayed internal dynamics. The models were coupled within a hierarchical statistical structure to overcome the relatively short length of the samples by exploiting the large number of concurrent observations available. The results indicated that Cx.pipiens abundance had significant density dependence at 1 week lag, which approximately matched its development time from larvae to adult. Among the exogenous controls, temperature, daylight hours, and soil moisture explained most of the dynamics. Longer daylight hours and lower soil moisture values resulted in higher abundance. The negative correlation of soil moisture and mosquito population can be explained with the abundance of water in the region (e.g. due to irrigation) and the preference for eutrophic habitats by Cx.pipien. Variations among sites were explained by land use factors as represented by distance to the nearest rice field and NDVI values: the carrying capacity decreased with increased distance to the nearest rice filed, while the maximum growth rate was positively related with NDVI. The model shows a satisfactory performance in predicting (potentially one week in advance) mosquito abundance and particularly its peak timing and magnitude.

Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

DTIC Science & Technology

2009-01-01

implicit solvents on peptide structure and dynamics , we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two...end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those...to maintain the temperature of the systems. Introduction Molecular dynamics (MD) simulation techniques are widely used to study structure and

Developing an International Distance Education Program: A Blended Learning Approach

ERIC Educational Resources Information Center

Mathur, Ravisha; Oliver, Lisa

2007-01-01

Building a dynamic international distance education program can be a complex operation. The purpose of this paper is to discuss a model for global learning that utilizes a blended learning approach. This paper will describe how a blended learning approach was implemented in an international instructional technology Master's program to the benefit…

Ultrasound monitoring of inter-knee distances during gait.

PubMed

Lai, Daniel T H; Wrigley, Tim V; Palaniswami, M

2009-01-01

Knee osteoarthritis is an extremely common, debilitating disease associated with pain and loss of function. There is considerable interest in monitoring lower limb alignment due to its close association with joint overload leading to disease progression. The effects of gait modifications that can lower joint loading are of particular interest. Here we describe an ultrasound-based system for monitoring an important aspect of dynamic lower limb alignment, the inter-knee distance during walking. Monitoring this gait parameter should facilitate studies in reducing knee loading, a primary risk factor of knee osteoarthritis progression. The portable device is composed of an ultrasound sensor connected to an Intel iMote2 equipped with Bluetooth wireless capability. Static tests and calibration results show that the sensor possesses an effective beam envelope of 120 degrees, with maximum distance errors of 10% at the envelope edges. Dynamic walking trials reveal close correlation of inter-knee distance trends between that measured by an optical system (Optotrak Certus NDI) and the sensor device. The maximum average root mean square error was found to be 1.46 cm. Future work will focus on improving the accuracy of the device.

A feature based comparison of pen and swipe based signature characteristics.

PubMed

Robertson, Joshua; Guest, Richard

2015-10-01

Dynamic Signature Verification (DSV) is a biometric modality that identifies anatomical and behavioral characteristics when an individual signs their name. Conventionally signature data has been captured using pen/tablet apparatus. However, the use of other devices such as the touch-screen tablets has expanded in recent years affording the possibility of assessing biometric interaction on this new technology. To explore the potential of employing DSV techniques when a user signs or swipes with their finger, we report a study to correlate pen and finger generated features. Investigating the stability and correlation between a set of characteristic features recorded in participant's signatures and touch-based swipe gestures, a statistical analysis was conducted to assess consistency between capture scenarios. The results indicate that there is a range of static and dynamic features such as the rate of jerk, size, duration and the distance the pen traveled that can lead to interoperability between these two systems for input methods for use within a potential biometric context. It can be concluded that this data indicates that a general principle is that the same underlying constructional mechanisms are evident. Copyright © 2015 Elsevier B.V. All rights reserved.

Near-infrared spectroscopic assessment of oxygen delivery to free flaps on monkeys following vascular occlusions and inhalation of pure oxygen

NASA Astrophysics Data System (ADS)

Tian, Fenghua; Ding, Haishu; Cai, Zhigang; Wang, Guangzhi; Zhao, Fuyun

2002-04-01

In recent studies, near-infrared spectroscopy (NIRS) has been considered as a potentially ideal noninvasive technique for the postoperative monitoring of plastic surgery. In this study, free flaps were raised on rhesus monkeys' forearms and oxygen delivery to these flaps was monitored following vascular occlusions and inhalation of pure oxygen. Optical fibers were adopted in the probe of the oximeter so that the detection could be performed in reflectance mode. The distance between emitter and detector can be adjusted easily to achieve the best efficacy. Different and repeatable patterns of changes were measured following vascular occlusions (arterial occlusion, venous occlusion and total occlusion) on flaps. It is clear that the near-infrared spectroscopy is capable of postoperatively monitoring vascular problems in flaps. NIRS showed high sensitivity to detect the dynamic changes in flaps induced by inhalation of pure oxygen in this study. The experimental results indicated that it was potential to assess tissue viability utilizing the dynamic changes induced by a noninvasive stimulation. It may be a new assessing method that is rapid, little influenced by other factors and brings less discomfort to patients.

Dynamic protoneural networks in plants

PubMed Central

Debono, Marc-Williams

2013-01-01

Taking as a basis of discussion Kalanchoe’s spontaneous and evoked extracellular activities recorded at the whole plant level, we put the challenging questions: do these low-voltage variations, together with endocellular events, reflect integrative properties and complex behavior in plants? Does it reflect common perceptive systems in animal and plant species? Is the ability of plants to treat short-term variations and information transfer without nervous system relevant? Is a protoneural construction of the world by lower organisms possible? More generally, the aim of this paper is to reevaluate the probably underestimated role of plant surface potentials in the plant relation life, carefully comparing the biogenesis of both animal and plant organisms in the era of plant neurobiology. Knowing that surface potentials participate at least to morphogenesis, cell to cell coupling, long distance transmission and transduction of stimuli, some hypothesis are given indicating that plants have to be studied as environmental biosensors and non linear dynamic systems able to detect transitional states between perception and response to stimuli. This study is conducted in the frame of the “plasticity paradigm,” which gives a theoretical model of evolutionary processes and suggests some hypothesis about the nature of complexity, information and behavior. PMID:23603975

Density and energy relaxation in an open one-dimensional system

NASA Astrophysics Data System (ADS)

Jose, Prasanth P.; Bagchi, Biman

2004-05-01

A new master equation to mimic the dynamics of a collection of interacting random walkers in an open system is proposed and solved numerically. In this model, the random walkers interact through excluded volume interaction (single-file system); and the total number of walkers in the lattice can fluctuate because of exchange with a bath. In addition, the movement of the random walkers is biased by an external perturbation. Two models for the latter are considered: (1) an inverse potential (V∝1/r), where r is the distance between the center of the perturbation and the random walker and (2) an inverse of sixth power potential (V∝1/r6). The calculated density of the walkers and the total energy show interesting dynamics. When the size of the system is comparable to the range of the perturbing field, the energy relaxation is found to be highly nonexponential. In this range, the system can show stretched exponential (e-(t/τs)β) and even logarithmic time dependence of energy relaxation over a limited range of time. Introduction of density exchange in the lattice markedly weakens this nonexponentiality of the relaxation function, irrespective of the nature of perturbation.

Performance Improvement of Raman Distributed Temperature System by Using Noise Suppression

NASA Astrophysics Data System (ADS)

Li, Jian; Li, Yunting; Zhang, Mingjiang; Liu, Yi; Zhang, Jianzhong; Yan, Baoqiang; Wang, Dong; Jin, Baoquan

2018-06-01

In Raman distributed temperature system, the key factor for performance improvement is noise suppression, which seriously affects the sensing distance and temperature accuracy. Therefore, we propose and experimentally demonstrate dynamic noise difference algorithm and wavelet transform modulus maximum (WTMM) to de-noising Raman anti-Stokes signal. Experimental results show that the sensing distance can increase from 3 km to 11.5 km and the temperature accuracy increases to 1.58 °C at the sensing distance of 10.4 km.

Spherically symmetric vacuum solutions arising from trace dynamics modifications to gravitation

NASA Astrophysics Data System (ADS)

Adler, Stephen L.; Ramazanoğlu, Fethi M.

2015-12-01

We derive the equations governing static, spherically symmetric vacuum solutions to the Einstein equations, as modified by the frame-dependent effective action (derived from trace dynamics) that gives an alternative explanation of the origin of "dark energy". We give analytic and numerical results for the solutions of these equations, first in polar coordinates, and then in isotropic coordinates. General features of the static case are that: (i) there is no horizon, since g00 is nonvanishing for finite values of the polar radius, and only vanishes (in isotropic coordinates) at the internal singularity, (ii) the Ricci scalar R vanishes identically, and (iii) there is a physical singularity at cosmological distances. The large distance singularity may be an artifact of the static restriction, since we find that the behavior at large distances is altered in a time-dependent solution using the McVittie Ansatz.

Photonic water dynamically responsive to external stimuli

PubMed Central

Sano, Koki; Kim, Youn Soo; Ishida, Yasuhiro; Ebina, Yasuo; Sasaki, Takayoshi; Hikima, Takaaki; Aida, Takuzo

2016-01-01

Fluids that contain ordered nanostructures with periodic distances in the visible-wavelength range, anomalously exhibit structural colours that can be rapidly modulated by external stimuli. Indeed, some fish can dynamically change colour by modulating the periodic distance of crystalline guanine sheets cofacially oriented in their fluid cytoplasm. Here we report that a dilute aqueous colloidal dispersion of negatively charged titanate nanosheets exhibits structural colours. In this ‘photonic water', the nanosheets spontaneously adopt a cofacial geometry with an ultralong periodic distance of up to 675 nm due to a strong electrostatic repulsion. Consequently, the photonic water can even reflect near-infrared light up to 1,750 nm. The structural colour becomes more vivid in a magnetic flux that induces monodomain structural ordering of the colloidal dispersion. The reflective colour of the photonic water can be modulated over the entire visible region in response to appropriate physical or chemical stimuli. PMID:27572806

Analytical investigation of the dynamics of tethered constellations in Earth orbit, phase 2

NASA Technical Reports Server (NTRS)

Lorenzini, Enrico C.

1987-01-01

A control law was developed to control the elevator during short-distance maneuvers along the tether of a 4-mass tethered system. This control law (called retarded exponential or RE) was analyzed parametrically in order to assess which control parameters provide a good dynamic response and a smooth time history of the acceleration on board the elevator. The short-distance maneuver under investigation consists of a slow crawling of the elevator over the distance of 10 m that represents a typical maneuver for fine tuning the acceleration level on board the elevator. The contribution of aerodynamic and thermal perturbations upon acceleration levels was also evaluated and acceleration levels obtained when such pertubations are taken into account were compared to those obtained by neglecting the thermal and aerodynamic forces. In addition, the preparation of a tether simulation questionnaire is illustrated. Analytic solutions to be compared to numerical cases and simulator test cases are also discussed.

Analysis of Fragmentation During Dynamic Loading: Investigations in the Ries Impact Crater, Germany

NASA Astrophysics Data System (ADS)

Weimer, D.; Hergarten, S.; Kenkmann, T.

2015-09-01

We tested three methods to quantify fragmentation of rocks during dynamic loading and found a trend of decreasing fracture density with increasing distance from crater center. Fragmentation attenuation rates in the near- and far-field are different.

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances.

PubMed

Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P; Daggett, Valerie; Adkins, Joshua N

2014-06-01

Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS(3) ) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine-lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS(3), a distance constraint of 26-30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods. © 2014 The Protein Society.

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances

PubMed Central

Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P; Daggett, Valerie; Adkins, Joshua N

2014-01-01

Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS3) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS3, a distance constraint of 26–30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods. PMID:24639379

Visual perception and regulatory conflict: motivation and physiology influence distance perception.

PubMed

Cole, Shana; Balcetis, Emily; Zhang, Sam

2013-02-01

Regulatory conflict can emerge when people experience a strong motivation to act on goals but a conflicting inclination to withhold action because physical resources available, or physiological potentials, are low. This study demonstrated that distance perception is biased in ways that theory suggests assists in managing this conflict. Participants estimated the distance to a target location. Individual differences in physiological potential measured via waist-to-hip ratio interacted with manipulated motivational states to predict visual perception. Among people low in physiological potential and likely to experience regulatory conflict, the environment appeared easier to traverse when motivation was strong compared with weak. Among people high in potential and less likely to experience conflict, perception was not predicted by motivational strength. The role of motivated distance perception in self-regulation is discussed. 2013 APA, all rights reserved

Graphene: A partially ordered non-periodic solid

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

Wei, Dongshan; Wang, Feng, E-mail: fengwang@uark.edu

2014-10-14

Molecular dynamics simulations were performed to study the structural features of graphene over a wide range of temperatures from 50 to 4000 K using the PPBE-G potential [D. Wei, Y. Song, and F. Wang, J. Chem. Phys. 134, 184704 (2011)]. This potential was developed by force matching the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional and has been validated previously to provide accurate potential energy surface for graphene at temperatures as high as 3000 K. Simulations with the PPBE‑G potential are the best available approximation to a direct Car-Parrinello Molecular Dynamics study of graphene. One advantage of the PBE-G potential is to allowmore » large simulation boxes to be modeled efficiently so that properties showing strong finite size effects can be studied. Our simulation box contains more than 600 000 C atoms and is one of the largest graphene boxes ever modeled. With the PPBE-G potential, the thermal-expansion coefficient is negative up to 4000 K. With a large box and an accurate potential, the critical exponent for the scaling properties associated with the normal-normal and height-height correlation functions was confirmed to be 0.85. This exponent remains constant up to 4000 K suggesting graphene to be in the deeply cooled regime even close to the experimental melting temperature. The reduced peak heights in the radial distribution function of graphene show an inverse power law dependence to distance, which indicates that a macroscopic graphene sheet will lose long-range crystalline order as predicted by the Mermin-Wagner instability. Although graphene loses long-range translational order, it retains long range orientational order as indicated by its orientational correlation function; graphene is thus partially ordered but not periodic.« less

Scaling and Multifractality in Road Accidental Distances

NASA Astrophysics Data System (ADS)

Qiu, Tian; Wan, Chi; Zou, Xiang-Xiang; Wang, Xiao-Fan

Accidental distance dynamics is investigated, based on the road accidental data of the Great Britain. The distance distribution of all the districts as an ensemble presents a power law tail, which is different from that of the individual district. A universal distribution is found for different districts, by rescaling the distribution functions of individual districts, which can be well fitted by the Weibull distribution. The male and female drivers behave similarly in the distance distribution. The multifractal characteristic is further studied for the individual district and all the districts as an ensemble, and different behaviors are also revealed between them. The accidental distances of the individual district show a weak multifractality, whereas of all the districts present a strong multifractality when taking them as an ensemble.

Influences of posterior-located center of gravity on lumbar extension strength, balance, and lumbar lordosis in chronic low back pain.

PubMed

Kim, Dae-Hun; Park, Jin-Kyu; Jeong, Myeong-Kyun

2014-01-01

In patients with chronic low back pain, the center of gravity (COG) is abnormally located posterior to the center in most cases. The purpose of this study was to examine the effects of posterior-located COG on the functions (lumbar extension strength, and static and dynamic balance) and structure (lumbar lordosis angle and lumbosacral angle) of the lumbar spine. In this study, the COG of chronic low back pain patients who complained of only low back pain were examined using dynamic body balance equipment. A total of 164 subjects participated in the study (74 males and 90 females), and they were divided into two groups of 82 patients each. One group (n=82) consisted of patients whose COG was located at the center (C-COG); the other group (n=82) consisted of patients whose COG was located posterior to the center (P-COG). The following measures assessed the lumber functions and structures of the two groups: lumbar extension strength, moving speed of static and dynamic COGs, movement distance of the static and dynamic COGs, lumbar lordosis angle, and lumbosacral angle. The measured values were analyzed using independent t-tests. The group of patients with P-COG showed more decreases in lumbar extension strength, lumbar lordosis angle, and lumbosacral angle compared to the group of patients with C-COG. Also this group showed increases in moving speed and movement distance of the static COG. However, there were no differences in moving speed and movement distance of the dynamic COG between the two groups. These findings suggest that chronic LBP patients with P-COG have some disadvantages to establish lumbar extension strength and static and dynamic balance, which require specific efforts to maintain a neutral position and to control posture.

Patterns, drivers and implications of dissolved oxygen dynamics in tropical mangrove forests

NASA Astrophysics Data System (ADS)

Mattone, Carlo; Sheaves, Marcus

2017-10-01

Estuarine mangrove forests regulate and facilitate many ecological processes, and provide nursery ground for many commercially important species. However, mangroves grow in sediments with high carbon loading and high respiration rates which can potentially influencing the dissolved oxygen (DO) dynamics of tidal water flowing into mangrove forests, as bacteria strip DO from the incoming water to carry out metabolic functions. In turn this is likely to influence the way nekton and other aquatic organisms utilize mangrove forests. Despite these possibilities, previous work has focused on looking at DO dynamics within mangrove creeks, with little research focusing on understanding DO dynamics within the mangrove forests themselves during tidal inundation or of DO levels of pools within the forest remaining once the tide has ebbed. The present study investigates the pattern in DO at various distances within an estuarine Rhizophora stylosa forest in tropical north Queensland. DO levels were recorded at 5 min interval over 2 days and multiple tidal cycles, data were collected between 2013 and 2014 for a total of 32 tidal cycles encompassing multiples seasons and tidal amplitudes. There were substantial fluctuations in DO, often varying from normoxic to hypoxic within the same tidal cycle. A range of factors influenced DO dynamics, in particular: tidal height, amount of sunlight, tidal phase, and distance from the outer edge of the mangrove forest. In fact, spring tides tend to have high DO saturation, particularly during the flooding phase, however as the tide starts ebbing, DO depletes rapidly especially in areas further inside the forest. Moreover during tidal disconnection the remnant pools within the forest quickly became anoxic. These variations in DO suggest that the use of mangrove forests by animals is likely to be constrained by their ability to withstand low DO levels, and provides a plausible explanation for the apparent paucity of benthic organism observed inside similar mangrove forest in previous studies of South Pacific mangroves. Low DO levels coupled with low densities of benthic prey also provides a likely explanation for the limited utilisation of landwards areas of these forests by fish and other nekton.

Visualizing global properties of a molecular dynamics trajectory.

PubMed

Zhou, Hao; Li, Shangyang; Makowski, Lee

2016-01-01

Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule. © 2015 Wiley Periodicals, Inc.

Adaptive Detection and ISI Mitigation for Mobile Molecular Communication.

PubMed

Chang, Ge; Lin, Lin; Yan, Hao

2018-03-01

Current studies on modulation and detection schemes in molecular communication mainly focus on the scenarios with static transmitters and receivers. However, mobile molecular communication is needed in many envisioned applications, such as target tracking and drug delivery. Until now, investigations about mobile molecular communication have been limited. In this paper, a static transmitter and a mobile bacterium-based receiver performing random walk are considered. In this mobile scenario, the channel impulse response changes due to the dynamic change of the distance between the transmitter and the receiver. Detection schemes based on fixed distance fail in signal detection in such a scenario. Furthermore, the intersymbol interference (ISI) effect becomes more complex due to the dynamic character of the signal which makes the estimation and mitigation of the ISI even more difficult. In this paper, an adaptive ISI mitigation method and two adaptive detection schemes are proposed for this mobile scenario. In the proposed scheme, adaptive ISI mitigation, estimation of dynamic distance, and the corresponding impulse response reconstruction are performed in each symbol interval. Based on the dynamic channel impulse response in each interval, two adaptive detection schemes, concentration-based adaptive threshold detection and peak-time-based adaptive detection, are proposed for signal detection. Simulations demonstrate that the ISI effect is significantly reduced and the adaptive detection schemes are reliable and robust for mobile molecular communication.

Contact stiffness and damping of liquid films in dynamic atomic force microscope

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

Xu, Rong-Guang; Leng, Yongsheng, E-mail: leng@gwu.edu

2016-04-21

The mechanical properties and dissipation behaviors of nanometers confined liquid films have been long-standing interests in surface force measurements. The correlation between the contact stiffness and damping of the nanoconfined film is still not well understood. We establish a novel computational framework through molecular dynamics (MD) simulation for the first time to study small-amplitude dynamic atomic force microscopy (dynamic AFM) in a simple nonpolar liquid. Through introducing a tip driven dynamics to mimic the mechanical oscillations of the dynamic AFM tip-cantilever assembly, we find that the contact stiffness and damping of the confined film exhibit distinct oscillations within 6-7 monolayermore » distances, and they are generally out-of-phase. For the solid-like film with integer monolayer thickness, further compression of the film before layering transition leads to higher stiffness and lower damping, while much lower stiffness and higher damping occur at non-integer monolayer distances. These two alternating mechanisms dominate the mechanical properties and dissipation behaviors of simple liquid films under cyclic elastic compression and inelastic squeeze-out. Our MD simulations provide a direct picture of correlations between the structural property, mechanical stiffness, and dissipation behavior of the nanoconfined film.« less

Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K.

2017-11-01

We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the electrodes. The simulated number density and electrostatic potential profiles for reline clearly show the presence of multilayer structures up to a distance of 1.2 nm from the respective electrodes. The observation of positive values of the surface potential at zero charge indicates the presence of significant nonelectrostatic attraction between the choline cation and graphene electrode. The computed differential capacitance (Cd) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of Cd with positive and negative surface potentials.

Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study.

PubMed

Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K

2017-11-21

We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the electrodes. The simulated number density and electrostatic potential profiles for reline clearly show the presence of multilayer structures up to a distance of 1.2 nm from the respective electrodes. The observation of positive values of the surface potential at zero charge indicates the presence of significant nonelectrostatic attraction between the choline cation and graphene electrode. The computed differential capacitance (C d ) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of C d with positive and negative surface potentials.

Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly

NASA Astrophysics Data System (ADS)

Buono, Ronald A.; Kucharczyk, Nathalie; Neuenschwander, Magrit; Kemmink, Johan; Hwang, Lih-Yueh; Fauchère, Jean-Luc; Venanzi, Carol A.

1996-06-01

The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several decades. Recent advances in the computational methodology of restrained molecular dynamics, used in conjunction with data obtained from two-dimensional 1H NMR spectroscopy, make it a promising method to study peptide and protein structure and function. Several issues, however, need to be addressed in order to assess the validity of this method for its explanatory and predictive value. Among the issues addressed in this study are: the accuracy and generizability of the GROMOS peptide molecular mechanics force field; the effect of inclusion of solvent on the simulations; and the effect of different types of restraining algorithms on the computational results. The decapeptide Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly, which corresponds to the sequence of ACTH1-10, has been synthesized, cyclized, and studied by two-dimensional 1H NMR spectroscopy. Restrained molecular dynamics (RMD) and time-averaged restrained molecular dynamics (TARMD) simulations were carried out on four different distance-geometry starting structures in order to determine and contrast the behavior of cyclic ACTH1-10 in vacuum and in solution. For the RMD simulations, the structures did not fit the NOE data well, even at high values of the restraining potential. The TARMD simulation method, however, was able to give structures that fit the NOE data at high values of the restraining potential. In both cases, inclusion of explicit solvent molecules in the simulation had little effect on the quality of the fit, although it was found to dampen the motion of the cyclic peptide. For both simulation techniques, the number and size of the NOE violations increased as the restraining potential approached zero. This is due, presumably, to inadequacies in the force field. Additional TARMD vacuum-phase simulations, run with a larger memory length or with a larger sampling size (16 additional distance-geometry structures), yielded no significantly different results. The computed data were then analyzed to help explain the sparse NOE data and poor chymotryptic activity of the cyclic peptide. Cyclic ACTH1-10, which contains the functional moieties of the catalytic triad of chymotrypsin, was evaluated as a potential mimic of chymotrypsin by measurement of the rate of hydrolysis of esters of L-and d-phenylalanine. The poor rate of hydrolysis is attributed to the flexibility of the decapeptide, the motion of the side chains, which result in the absence of long-range NOEs, the small size of the macrocycle relative to that of the substrate, and the inappropriate orientation of the Gly, His, and Ser residues. The results demonstrate the utility of this method in computer-aided molecular design of cyclic peptides and suggest structural modifications for future work based on a larger and more rigid peptide framework.

Effect of vacancy defects on generalized stacking fault energy of fcc metals.

PubMed

Asadi, Ebrahim; Zaeem, Mohsen Asle; Moitra, Amitava; Tschopp, Mark A

2014-03-19

Molecular dynamics (MD) and density functional theory (DFT) studies were performed to investigate the influence of vacancy defects on generalized stacking fault (GSF) energy of fcc metals. MEAM and EAM potentials were used for MD simulations, and DFT calculations were performed to test the accuracy of different common parameter sets for MEAM and EAM potentials in predicting GSF with different fractions of vacancy defects. Vacancy defects were placed at the stacking fault plane or at nearby atomic layers. The effect of vacancy defects at the stacking fault plane and the plane directly underneath of it was dominant compared to the effect of vacancies at other adjacent planes. The effects of vacancy fraction, the distance between vacancies, and lateral relaxation of atoms on the GSF curves with vacancy defects were investigated. A very similar variation of normalized SFEs with respect to vacancy fractions were observed for Ni and Cu. MEAM potentials qualitatively captured the effect of vacancies on GSF.

Optical Voltage Sensing Using DNA Origami

PubMed Central

2018-01-01

We explore the potential of DNA nanotechnology for developing novel optical voltage sensing nanodevices that convert a local change of electric potential into optical signals. As a proof-of-concept of the sensing mechanism, we assembled voltage responsive DNA origami structures labeled with a single pair of FRET dyes. The DNA structures were reversibly immobilized on a nanocapillary tip and underwent controlled structural changes upon application of an electric field. The applied field was monitored through a change in FRET efficiency. By exchanging the position of a single dye, we could tune the voltage sensitivity of our DNA origami structure, demonstrating the flexibility and versatility of our approach. The experimental studies were complemented by coarse-grained simulations that characterized voltage-dependent elastic deformation of the DNA nanostructures and the associated change in the distance between the FRET pair. Our work opens a novel pathway for determining the mechanical properties of DNA origami structures and highlights potential applications of dynamic DNA nanostructures as voltage sensors. PMID:29430924

Trailing Vortex-Induced Loads During Close Encounters in Cruise

NASA Technical Reports Server (NTRS)

Mendenhall, Michael R.; Lesieutre, Daniel J; Kelly, Michael J.

2015-01-01

The trailing vortex induced aerodynamic loads on a Falcon 20G business jet flying in the wake of a DC-8 are predicted to provide a preflight estimate of safe trail distances during flight test measurements in the wake. Static and dynamic loads on the airframe flying in the near wake are shown at a matrix of locations, and the dynamic motion of the Falcon 20G during traverses of the DC-8 primary trailing vortex is simulated. Safe trailing distances for the test flights are determined, and optimum vortex traverse schemes are identified to moderate the motion of the trailing aircraft during close encounters with the vortex wake.

Molecular Dynamics Simulation of Telomere and TRF1

NASA Astrophysics Data System (ADS)

Kaburagi, Masaaki; Fukuda, Masaki; Yamada, Hironao; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako; Kato, Takamitsu A.; Uesaka, Mitsuru

Telomeres play a central role in determining longevity of a cell. Our study focuses on the interaction between telomeric guanines and TRF1 as a means to observe the telomeric based mechanism of the genome protection. In this research, we performed molecular dynamics simulations of a telomeric DNA and TRF1. Our results show a stable structure with a high affinity for the specific protein. Additionally, we calculated the distance between guanines and the protein in their complex state. From this comparison, we found the calculated values of distance to be very similar, and the angle of guanines in their complex states was larger than that in their single state.

Generalized correlation integral vectors: A distance concept for chaotic dynamical systems

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

Haario, Heikki, E-mail: heikki.haario@lut.fi; Kalachev, Leonid, E-mail: KalachevL@mso.umt.edu; Hakkarainen, Janne

2015-06-15

Several concepts of fractal dimension have been developed to characterise properties of attractors of chaotic dynamical systems. Numerical approximations of them must be calculated by finite samples of simulated trajectories. In principle, the quantities should not depend on the choice of the trajectory, as long as it provides properly distributed samples of the underlying attractor. In practice, however, the trajectories are sensitive with respect to varying initial values, small changes of the model parameters, to the choice of a solver, numeric tolerances, etc. The purpose of this paper is to present a statistically sound approach to quantify this variability. Wemore » modify the concept of correlation integral to produce a vector that summarises the variability at all selected scales. The distribution of this stochastic vector can be estimated, and it provides a statistical distance concept between trajectories. Here, we demonstrate the use of the distance for the purpose of estimating model parameters of a chaotic dynamic model. The methodology is illustrated using computational examples for the Lorenz 63 and Lorenz 95 systems, together with a framework for Markov chain Monte Carlo sampling to produce posterior distributions of model parameters.« less

A New Model for Self-organized Dynamics and Its Flocking Behavior

NASA Astrophysics Data System (ADS)

Motsch, Sebastien; Tadmor, Eitan

2011-09-01

We introduce a model for self-organized dynamics which, we argue, addresses several drawbacks of the celebrated Cucker-Smale (C-S) model. The proposed model does not only take into account the distance between agents, but instead, the influence between agents is scaled in term of their relative distance. Consequently, our model does not involve any explicit dependence on the number of agents; only their geometry in phase space is taken into account. The use of relative distances destroys the symmetry property of the original C-S model, which was the key for the various recent studies of C-S flocking behavior. To this end, we introduce here a new framework to analyze the phenomenon of flocking for a rather general class of dynamical systems, which covers systems with non-symmetric influence matrices. In particular, we analyze the flocking behavior of the proposed model as well as other strongly asymmetric models with "leaders". The methodology presented in this paper, based on the notion of active sets, carries over from the particle to kinetic and hydrodynamic descriptions. In particular, we discuss the hydrodynamic formulation of our proposed model, and prove its unconditional flocking for slowly decaying influence functions.

Atomic Dynamics in Simple Liquid: de Gennes Narrowing Revisited

NASA Astrophysics Data System (ADS)

Wu, Bin; Iwashita, Takuya; Egami, Takeshi

2018-03-01

The de Gennes narrowing phenomenon is frequently observed by neutron or x -ray scattering measurements of the dynamics of complex systems, such as liquids, proteins, colloids, and polymers. The characteristic slowing down of dynamics in the vicinity of the maximum of the total scattering intensity is commonly attributed to enhanced cooperativity. In this Letter, we present an alternative view on its origin through the examination of the time-dependent pair correlation function, the van Hove correlation function, for a model liquid in two, three, and four dimensions. We find that the relaxation time increases monotonically with distance and the dependence on distance varies with dimension. We propose a heuristic explanation of this dependence based on a simple geometrical model. This finding sheds new light on the interpretation of the de Gennes narrowing phenomenon and the α -relaxation time.

Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions.

PubMed

Calligari, Paolo; Gerolin, Marco; Abergel, Daniel; Polimeno, Antonino

2017-01-10

In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed.

Towards Understanding the Successful Learner: A Case Study of IGNOU

ERIC Educational Resources Information Center

Nair, Sindhu P.

2012-01-01

The growth of enrolment in the ODL system has been considerable. However, another parameter of significance in the context of Open and Distance learning is the learner success rate. While enrolment rates have been very encouraging in distance education, the pass-out rates haven't been similar. There is a need to focus on the dynamics involved…

Power Distance and Group Dynamics of an International Project Team: A Case Study

ERIC Educational Resources Information Center

Paulus, Trena M.; Bichelmeyer, Barbara; Malopinsky, Larissa; Pereira, Maura; Rastogi, Polly

2005-01-01

Project-based team activities are commonly used in higher education. Teams comprised of members from different national cultures can be faced with unique challenges during the creative process. Hofstede's (1991) cultural dimension of power distance was used to examine one such design team's intra- and inter-group interactions in a graduate-level…

49 CFR 213.333 - Automated vehicle inspection systems.

Code of Federal Regulations, 2011 CFR

2011-10-01

... hours of the inspection, output reports that— (1) Provide a continuous plot, on a constant-distance axis... instrumented car having dynamic response characteristics that are representative of other equipment assigned to... instrumented car having dynamic response characteristics that are representative of other equipment assigned to...

49 CFR 213.333 - Automated vehicle inspection systems.

Code of Federal Regulations, 2010 CFR

2010-10-01

... hours of the inspection, output reports that— (1) Provide a continuous plot, on a constant-distance axis... instrumented car having dynamic response characteristics that are representative of other equipment assigned to... instrumented car having dynamic response characteristics that are representative of other equipment assigned to...

How interactions between animal movement and landscape processes modify range dynamics and extinction risk

EPA Science Inventory

Range dynamics models now incorporate many of the mechanisms and interactions that drive species distributions. However, connectivity continues to be studied using overly simple distance-based dispersal models with little consideration of how the individual behavior of dispersin...

Initial correlations in open-systems dynamics: The Jaynes-Cummings model

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

Smirne, Andrea; Vacchini, Bassano; INFN, Sezione di Milano, Via Celoria 16, I-20133 Milano

2010-12-15

Employing the trace distance as a measure for the distinguishability of quantum states, we study the influence of initial correlations on the dynamics of open systems. We concentrate on the Jaynes-Cummings model for which the knowledge of the exact joint dynamics of system and reservoir allows the treatment of initial states with arbitrary correlations. As a measure for the correlations in the initial state we consider the trace distance between the system-environment state and the product of its marginal states. In particular, we examine the correlations contained in the thermal equilibrium state for the total system, analyze their dependence onmore » the temperature and on the coupling strength, and demonstrate their connection to the entanglement properties of the eigenstates of the Hamiltonian. A detailed study of the time dependence of the distinguishability of the open system states evolving from the thermal equilibrium state and its corresponding uncorrelated product state shows that the open system dynamically uncovers typical features of the initial correlations.« less

Balancing Dynamic Strength of Spur Gears Operated at Extended Center Distance

NASA Technical Reports Server (NTRS)

Lin, Hsiang Hsi; Liou, Chuen-Huei; Oswald, Fred B.; Townsend, Dennis P.

1996-01-01

This paper presents an analytical study on using hob offset to balance the dynamic tooth strength of spur gears operated at a center distance greater than the standard value. This study is an extension of a static study by Mabie and others. The study was limited to the offset values that assure the pinion and gear teeth will neither be undercut nor become pointed. The analysis presented in this paper was performed using DANST-PC, a new version of the NASA gear dynamics code. The operating speed of the transmission influences the amount of hob offset required to equalize the dynamic stresses in the pinion and gear. The optimum hob offset for the pinion was found to vary within a small range as the speed changes. The optimum value is generally greater than the optimum value found by static procedures. For gears that must operate over a wide range of speeds, an average offset value may be used.

Brain dynamics that correlate with effects of learning on auditory distance perception.

PubMed

Wisniewski, Matthew G; Mercado, Eduardo; Church, Barbara A; Gramann, Klaus; Makeig, Scott

2014-01-01

Accuracy in auditory distance perception can improve with practice and varies for sounds differing in familiarity. Here, listeners were trained to judge the distances of English, Bengali, and backwards speech sources pre-recorded at near (2-m) and far (30-m) distances. Listeners' accuracy was tested before and after training. Improvements from pre-test to post-test were greater for forward speech, demonstrating a learning advantage for forward speech sounds. Independent component (IC) processes identified in electroencephalographic (EEG) data collected during pre- and post-testing revealed three clusters of ICs across subjects with stimulus-locked spectral perturbations related to learning and accuracy. One cluster exhibited a transient stimulus-locked increase in 4-8 Hz power (theta event-related synchronization; ERS) that was smaller after training and largest for backwards speech. For a left temporal cluster, 8-12 Hz decreases in power (alpha event-related desynchronization; ERD) were greatest for English speech and less prominent after training. In contrast, a cluster of IC processes centered at or near anterior portions of the medial frontal cortex showed learning-related enhancement of sustained increases in 10-16 Hz power (upper-alpha/low-beta ERS). The degree of this enhancement was positively correlated with the degree of behavioral improvements. Results suggest that neural dynamics in non-auditory cortical areas support distance judgments. Further, frontal cortical networks associated with attentional and/or working memory processes appear to play a role in perceptual learning for source distance.

Vortex dynamics during blade-vortex interactions

NASA Astrophysics Data System (ADS)

Peng, Di; Gregory, James W.

2015-05-01

Vortex dynamics during parallel blade-vortex interactions (BVIs) were investigated in a subsonic wind tunnel using particle image velocimetry (PIV). Vortices were generated by applying a rapid pitch-up motion to an airfoil through a pneumatic system, and the subsequent interactions with a downstream, unloaded target airfoil were studied. The blade-vortex interactions may be classified into three categories in terms of vortex behavior: close interaction, very close interaction, and collision. For each type of interaction, the vortex trajectory and strength variation were obtained from phase-averaged PIV data. The PIV results revealed the mechanisms of vortex decay and the effects of several key parameters on vortex dynamics, including separation distance (h/c), Reynolds number, and vortex sense. Generally, BVI has two main stages: interaction between vortex and leading edge (vortex-LE interaction) and interaction between vortex and boundary layer (vortex-BL interaction). Vortex-LE interaction, with its small separation distance, is dominated by inviscid decay of vortex strength due to pressure gradients near the leading edge. Therefore, the decay rate is determined by separation distance and vortex strength, but it is relatively insensitive to Reynolds number. Vortex-LE interaction will become a viscous-type interaction if there is enough separation distance. Vortex-BL interaction is inherently dominated by viscous effects, so the decay rate is dependent on Reynolds number. Vortex sense also has great impact on vortex-BL interaction because it changes the velocity field and shear stress near the surface.

Theoretical analysis of degradation mechanisms in the formation of morphogen gradients

NASA Astrophysics Data System (ADS)

Bozorgui, Behnaz; Teimouri, Hamid; Kolomeisky, Anatoly B.

2015-07-01

Fundamental biological processes of development of tissues and organs in multicellular organisms are governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in the concentration profiles of signaling molecules, which are frequently referred as morphogen gradients, lead to a cell differentiation via activating specific genes in a concentration-dependent manner. It is widely accepted that the establishment of the morphogen gradients involves multiple biochemical reactions and diffusion processes. One of the critical elements in the formation of morphogen gradients is a degradation of signaling molecules. We develop a new theoretical approach that provides a comprehensive description of the degradation mechanisms. It is based on the idea that the degradation works as an effective potential that drives the signaling molecules away from the source region. Utilizing the method of first-passage processes, the dynamics of the formation of morphogen gradients for various degradation mechanisms is explicitly evaluated. It is found that linear degradation processes lead to a dynamic behavior specified by times to form the morphogen gradients that depend linearly on the distance from the source. This is because the effective potential due to the degradation is quite strong. At the same time, nonlinear degradation mechanisms yield a quadratic scaling in the morphogen gradients formation times since the effective potentials are much weaker. Physical-chemical explanations of these phenomena are presented.

Propagation of a finite-amplitude elastic pulse in a bar of Berea sandstone: A detailed look at the mechanisms of classical nonlinearity, hysteresis, and nonequilibrium dynamics: Nonlinear propagation of elastic pulse

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

Remillieux, Marcel C.; Ulrich, T. J.; Goodman, Harvey E.

Here, we study the propagation of a finite-amplitude elastic pulse in a long thin bar of Berea sandstone. In previous work, this type of experiment has been conducted to quantify classical nonlinearity, based on the amplitude growth of the second harmonic as a function of propagation distance. To greatly expand on that early work, a non-contact scanning 3D laser Doppler vibrometer was used to track the evolution of the axial component of the particle velocity over the entire surface of the bar as functions of the propagation distance and source amplitude. With these new measurements, the combined effects of classicalmore » nonlinearity, hysteresis, and nonequilibrium dynamics have all been measured simultaneously. We then show that the numerical resolution of the 1D wave equation with terms for classical nonlinearity and attenuation accurately captures the spectral features of the waves up to the second harmonic. But, for higher harmonics the spectral content is shown to be strongly influenced by hysteresis. This work also shows data which not only quantifies classical nonlinearity but also the nonequilibrium dynamics based on the relative change in the arrival time of the elastic pulse as a function of strain and distance from the source. Finally, a comparison is made to a resonant bar measurement, a reference experiment used to quantify nonequilibrium dynamics, based on the relative shift of the resonance frequencies as a function of the maximum dynamic strain in the sample.« less

Propagation of a finite-amplitude elastic pulse in a bar of Berea sandstone: A detailed look at the mechanisms of classical nonlinearity, hysteresis, and nonequilibrium dynamics: Nonlinear propagation of elastic pulse

DOE PAGES

Remillieux, Marcel C.; Ulrich, T. J.; Goodman, Harvey E.; ...

2017-10-18

Here, we study the propagation of a finite-amplitude elastic pulse in a long thin bar of Berea sandstone. In previous work, this type of experiment has been conducted to quantify classical nonlinearity, based on the amplitude growth of the second harmonic as a function of propagation distance. To greatly expand on that early work, a non-contact scanning 3D laser Doppler vibrometer was used to track the evolution of the axial component of the particle velocity over the entire surface of the bar as functions of the propagation distance and source amplitude. With these new measurements, the combined effects of classicalmore » nonlinearity, hysteresis, and nonequilibrium dynamics have all been measured simultaneously. We then show that the numerical resolution of the 1D wave equation with terms for classical nonlinearity and attenuation accurately captures the spectral features of the waves up to the second harmonic. But, for higher harmonics the spectral content is shown to be strongly influenced by hysteresis. This work also shows data which not only quantifies classical nonlinearity but also the nonequilibrium dynamics based on the relative change in the arrival time of the elastic pulse as a function of strain and distance from the source. Finally, a comparison is made to a resonant bar measurement, a reference experiment used to quantify nonequilibrium dynamics, based on the relative shift of the resonance frequencies as a function of the maximum dynamic strain in the sample.« less

Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations.

PubMed

Lu, Haiting; Huang, Xiaoqin; AbdulHameed, Mohamed Diwan M; Zhan, Chang-Guo

2014-04-01

Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been performed to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson-Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2A6-inhibitor binding affinity are two crucial internuclear distances, that is, the distance between the heme iron atom of CYP2A6 and the coordinating atom of the inhibitor, and the hydrogen-bonding distance between the N297 side chain of CYP2A6 and the pyridine nitrogen of the inhibitor. The combined MD simulations and QM/MM-PBSA calculations have led to dynamic CYP2A6-inhibitor binding structures that are consistent with the observed dynamic behaviors and structural features of CYP2A6-inhibitor binding, and led to the binding free energies that are in good agreement with the experimentally-derived binding free energies. The agreement between the calculated binding free energies and the experimentally-derived binding free energies suggests that the combined MD and QM/MM-PBSA approach may be used as a valuable tool to accurately predict the CYP2A6-inhibitor binding affinities in future computational design of new, potent and selective CYP2A6 inhibitors. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach

PubMed Central

Hoefling, Martin; Lima, Nicola; Haenni, Dominik; Seidel, Claus A. M.; Schuler, Benjamin; Grubmüller, Helmut

2011-01-01

Förster Resonance Energy Transfer (FRET) experiments probe molecular distances via distance dependent energy transfer from an excited donor dye to an acceptor dye. Single molecule experiments not only probe average distances, but also distance distributions or even fluctuations, and thus provide a powerful tool to study biomolecular structure and dynamics. However, the measured energy transfer efficiency depends not only on the distance between the dyes, but also on their mutual orientation, which is typically inaccessible to experiments. Thus, assumptions on the orientation distributions and averages are usually made, limiting the accuracy of the distance distributions extracted from FRET experiments. Here, we demonstrate that by combining single molecule FRET experiments with the mutual dye orientation statistics obtained from Molecular Dynamics (MD) simulations, improved estimates of distances and distributions are obtained. From the simulated time-dependent mutual orientations, FRET efficiencies are calculated and the full statistics of individual photon absorption, energy transfer, and photon emission events is obtained from subsequent Monte Carlo (MC) simulations of the FRET kinetics. All recorded emission events are collected to bursts from which efficiency distributions are calculated in close resemblance to the actual FRET experiment, taking shot noise fully into account. Using polyproline chains with attached Alexa 488 and Alexa 594 dyes as a test system, we demonstrate the feasibility of this approach by direct comparison to experimental data. We identified cis-isomers and different static local environments as sources of the experimentally observed heterogeneity. Reconstructions of distance distributions from experimental data at different levels of theory demonstrate how the respective underlying assumptions and approximations affect the obtained accuracy. Our results show that dye fluctuations obtained from MD simulations, combined with MC single photon kinetics, provide a versatile tool to improve the accuracy of distance distributions that can be extracted from measured single molecule FRET efficiencies. PMID:21629703

The data of establishing a three-dimensional culture system for in vitro recapitulation and mechanism exploration of tumor satellite formation during cancer cell transition.

PubMed

Chen, Chun-Nan; Chen, You-Tzung; Yang, Tsung-Lin

2017-12-01

Tumor satellite formation is an indicator of cancer invasiveness and correlates with recurrence, metastasis, and poorer prognosis. By analyzing pathological specimens, tumor satellites formed at the tumor-host interface reflect the phenomena of epithelial-mesenchymal transition. It is impossible to reveal the dynamic processes and the decisive factors of tumor satellite formation using clinicopathological approaches alone. Therefore, establishment of an in vitro system to monitor the phenomena is important to explicitly elucidate underlying mechanisms. In this study, we explored the feasibility of creating an in vitro three-dimensional collagen culture system to recapitulate the process of tumor satellite formation. This data presented here are referred to the research article (Chen et al., 2017) [1]. Using this model, the dynamic process of tumor satellite formation could be recapitulated in different types of human cancer cells. Induced by calcium deprivation, the treated cells increased the incidence and migratory distance of tumor satellites. E-cadherin internalization and invadopodia formation were enhanced by calcium deprivation and were associated with cellular dynamic change during tumor satellite formation. The data confirmed the utility of this culture system to recapitulate dynamic cellular alteration and to explore the potential mechanisms of tumor satellite formation.

Dynamic Evolution Of Off-Fault Medium During An Earthquake: A Micromechanics Based Model

NASA Astrophysics Data System (ADS)

Thomas, Marion Y.; Bhat, Harsha S.

2018-05-01

Geophysical observations show a dramatic drop of seismic wave speeds in the shallow off-fault medium following earthquake ruptures. Seismic ruptures generate, or reactivate, damage around faults that alter the constitutive response of the surrounding medium, which in turn modifies the earthquake itself, the seismic radiation, and the near-fault ground motion. We present a micromechanics based constitutive model that accounts for dynamic evolution of elastic moduli at high-strain rates. We consider 2D in-plane models, with a 1D right lateral fault featuring slip-weakening friction law. The two scenarios studied here assume uniform initial off-fault damage and an observationally motivated exponential decay of initial damage with fault normal distance. Both scenarios produce dynamic damage that is consistent with geological observations. A small difference in initial damage actively impacts the final damage pattern. The second numerical experiment, in particular, highlights the complex feedback that exists between the evolving medium and the seismic event. We show that there is a unique off-fault damage pattern associated with supershear transition of an earthquake rupture that could be potentially seen as a geological signature of this transition. These scenarios presented here underline the importance of incorporating the complex structure of fault zone systems in dynamic models of earthquakes.

Dynamic Evolution Of Off-Fault Medium During An Earthquake: A Micromechanics Based Model

NASA Astrophysics Data System (ADS)

Thomas, M. Y.; Bhat, H. S.

2017-12-01

Geophysical observations show a dramatic drop of seismic wave speeds in the shallow off-fault medium following earthquake ruptures. Seismic ruptures generate, or reactivate, damage around faults that alter the constitutive response of the surrounding medium, which in turn modifies the earthquake itself, the seismic radiation, and the near-fault ground motion. We present a micromechanics based constitutive model that accounts for dynamic evolution of elastic moduli at high-strain rates. We consider 2D in-plane models, with a 1D right lateral fault featuring slip-weakening friction law. The two scenarios studied here assume uniform initial off-fault damage and an observationally motivated exponential decay of initial damage with fault normal distance. Both scenarios produce dynamic damage that is consistent with geological observations. A small difference in initial damage actively impacts the final damage pattern. The second numerical experiment, in particular, highlights the complex feedback that exists between the evolving medium and the seismic event. We show that there is a unique off-fault damage pattern associated with supershear transition of an earthquake rupture that could be potentially seen as a geological signature of this transition. These scenarios presented here underline the importance of incorporating the complex structure of fault zone systems in dynamic models of earthquakes.

Determination of Dynamics of Plant Plasma Membrane Proteins with Fluorescence Recovery and Raster Image Correlation Spectroscopy.

PubMed

Laňková, Martina; Humpolíčková, Jana; Vosolsobě, Stanislav; Cit, Zdeněk; Lacek, Jozef; Čovan, Martin; Čovanová, Milada; Hof, Martin; Petrášek, Jan

2016-04-01

A number of fluorescence microscopy techniques are described to study dynamics of fluorescently labeled proteins, lipids, nucleic acids, and whole organelles. However, for studies of plant plasma membrane (PM) proteins, the number of these techniques is still limited because of the high complexity of processes that determine the dynamics of PM proteins and the existence of cell wall. Here, we report on the usage of raster image correlation spectroscopy (RICS) for studies of integral PM proteins in suspension-cultured tobacco cells and show its potential in comparison with the more widely used fluorescence recovery after photobleaching method. For RICS, a set of microscopy images is obtained by single-photon confocal laser scanning microscopy (CLSM). Fluorescence fluctuations are subsequently correlated between individual pixels and the information on protein mobility are extracted using a model that considers processes generating the fluctuations such as diffusion and chemical binding reactions. As we show here using an example of two integral PM transporters of the plant hormone auxin, RICS uncovered their distinct short-distance lateral mobility within the PM that is dependent on cytoskeleton and sterol composition of the PM. RICS, which is routinely accessible on modern CLSM instruments, thus represents a valuable approach for studies of dynamics of PM proteins in plants.

Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations.

PubMed

Jaeger, Vance W; Pfaendtner, Jim

2016-12-01

Ionic liquid (IL) containing solvents can change the structure, dynamics, function, and stability of proteins. In order to investigate the mechanisms by which ILs induce structural changes in a large multidomain protein, we study the interactions of human serum albumin (HSA) with two different ILs, 1-butyl-3-methylimidazolium tetrafluoroborate and choline dihydrogen phosphate. Root mean square deviation and fluctuation calculations indicate that high concentrations of ILs in mixtures with water lead to protein structures that remain close to their crystallographic structures on time scales of hundreds of nanoseconds. To overcome potential time scale limitations due to the high viscosity of the solvent, we employed enhanced sampling techniques to estimate the free energy of an experimentally determined important transition within the protein structure. Metadynamics simulations show that the free energy landscape of the unfolding of loop 1 of domain I is different in the presence of ILs than it is in water, consistent with previously published experimental evidence. We then apply essential dynamics coarse graining to systematically predict differences in the dynamics of proteins solvated in IL-water mixtures versus pure water systems. We also demonstrate that the presence of ionic liquids changes the distribution of intermolecular distances among several ligands, indicating that the protein structure swells in the presence of certain ILs, consistent with experimental evidence.

Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth

NASA Astrophysics Data System (ADS)

De Martino, Daniele; Masoero, Davide

2016-12-01

We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modeling. In the asymptotic regime of slow diffusion, that coincides with the relevant experimental range, the resulting non-linear Fokker-Planck equation is solved for the steady state in the WKB approximation that maps it into the ground state of a quantum particle in an Airy potential plus a centrifugal term. We retrieve scaling laws for growth rate fluctuations and time response with respect to the distance from the maximum growth rate suggesting that suboptimal populations can have a faster response to perturbations.

Pentacene appended to a TEMPO stable free radical: the effect of magnetic exchange coupling on photoexcited pentacene.

PubMed

Chernick, Erin T; Casillas, Rubén; Zirzlmeier, Johannes; Gardner, Daniel M; Gruber, Marco; Kropp, Henning; Meyer, Karsten; Wasielewski, Michael R; Guldi, Dirk M; Tykwinski, Rik R

2015-01-21

Understanding the fundamental spin dynamics of photoexcited pentacene derivatives is important in order to maximize their potential for optoelectronic applications. Herein, we report on the synthesis of two pentacene derivatives that are functionalized with the [(2,2,6,6-tetramethylpiperidin-1-yl)oxy] (TEMPO) stable free radical. The presence of TEMPO does not quench the pentacene singlet excited state, but does quench the photoexcited triplet excited state as a function of TEMPO-to-pentacene distance. Time-resolved electron paramagnetic resonance experiments confirm that triplet quenching is accompanied by electron spin polarization transfer from the pentacene excited state to the TEMPO doublet state in the weak coupling regime.

Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer

NASA Astrophysics Data System (ADS)

Yang, Haw; Luo, Guobin; Karnchanaphanurach, Pallop; Louie, Tai-Man; Rech, Ivan; Cova, Sergio; Xun, Luying; Xie, X. Sunney

2003-10-01

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.

Fully automated segmentation of the pectoralis muscle boundary in breast MR images

NASA Astrophysics Data System (ADS)

Wang, Lei; Filippatos, Konstantinos; Friman, Ola; Hahn, Horst K.

2011-03-01

Dynamic Contrast Enhanced MRI (DCE-MRI) of the breast is emerging as a novel tool for early tumor detection and diagnosis. The segmentation of the structures in breast DCE-MR images, such as the nipple, the breast-air boundary and the pectoralis muscle, serves as a fundamental step for further computer assisted diagnosis (CAD) applications, e.g. breast density analysis. Moreover, the previous clinical studies show that the distance between the posterior breast lesions and the pectoralis muscle can be used to assess the extent of the disease. To enable automatic quantification of the distance from a breast tumor to the pectoralis muscle, a precise delineation of the pectoralis muscle boundary is required. We present a fully automatic segmentation method based on the second derivative information represented by the Hessian matrix. The voxels proximal to the pectoralis muscle boundary exhibit roughly the same Eigen value patterns as a sheet-like object in 3D, which can be enhanced and segmented by a Hessian-based sheetness filter. A vector-based connected component filter is then utilized such that only the pectoralis muscle is preserved by extracting the largest connected component. The proposed method was evaluated quantitatively with a test data set which includes 30 breast MR images by measuring the average distances between the segmented boundary and the annotated surfaces in two ground truth sets, and the statistics showed that the mean distance was 1.434 mm with the standard deviation of 0.4661 mm, which shows great potential for integration of the approach in the clinical routine.

Handheld Lasers Allow Efficient Detection of Fluorescent Marked Organisms in the Field

PubMed Central

Fleischer, Shelby J.; De Moraes, Consuelo M.; Mescher, Mark C.; Tooker, John F.

2015-01-01

Marking organisms with fluorescent dyes and powders is a common technique used in ecological field studies that monitor movement of organisms to examine life history traits, behaviors, and population dynamics. External fluorescent marking is relatively inexpensive and can be readily employed to quickly mark large numbers of individuals; however, the ability to detect marked organisms in the field at night has been hampered by the limited detection distances provided by portable fluorescent ultraviolet lamps. In recent years, significant advances in LED lamp and laser technology have led to development of powerful, low-cost ultraviolet light sources. In this study, we evaluate the potential of these new technologies to improve detection of fluorescent-marked organisms in the field and to create new possibilities for tracking marked organisms in visually challenging environments such as tree canopies and aquatic habitats. Using handheld lasers, we document a method that provides a fivefold increase in detection distance over previously available technologies. This method allows easy scouting of tree canopies (from the ground), as well as shallow aquatic systems. This novel detection method for fluorescent-marked organisms thus promises to significantly enhance the use of fluorescent marking as a non-destructive technique for tracking organisms in natural environments, facilitating field studies that aim to document otherwise inaccessible aspects of the movement, behavior, and population dynamics of study organisms, including species with significant economic impacts or relevance for ecology and human health. PMID:26035303

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

Vakili, Hajar; Rahvar, Sohrab; Kroupa, Pavel, E-mail: vakili@physics.sharif.edu

Shell galaxies are understood to form through the collision of a dwarf galaxy with an elliptical galaxy. Shell structures and kinematics have been noted to be independent tools to measure the gravitational potential of the shell galaxies. We compare theoretically the formation of shells in Type I shell galaxies in different gravity theories in this work because this is so far missing in the literature. We include Newtonian plus dark halo gravity, and two non-Newtonian gravity models, MOG and MOND, in identical initial systems. We investigate the effect of dynamical friction, which by slowing down the dwarf galaxy in themore » dark halo models limits the range of shell radii to low values. Under the same initial conditions, shells appear on a shorter timescale and over a smaller range of distances in the presence of dark matter than in the corresponding non-Newtonian gravity models. If galaxies are embedded in a dark matter halo, then the merging time may be too rapid to allow multi-generation shell formation as required by observed systems because of the large dynamical friction effect. Starting from the same initial state, the observation of small bright shells in the dark halo model should be accompanied by large faint ones, while for the case of MOG, the next shell generation patterns iterate with a specific time delay. The first shell generation pattern shows a degeneracy with the age of the shells and in different theories, but the relative distance of the shells and the shell expansion velocity can break this degeneracy.« less

Experimental results on the enhanced backscatter phenomenon and its dynamics

NASA Astrophysics Data System (ADS)

Wu, Chensheng; Nelson, William; Ko, Jonathan; Davis, Christopher C.

2014-10-01

Enhanced backscatter effects have long been predicted theoretically and experimentally demonstrated. The reciprocity of a turbulent channel generates a group of paired rays with identical trajectory and phase information that leads to a region in phase space with double intensity and scintillation index. Though simulation work based on phase screen models has demonstrated the existence of the phenomenon, few experimental results have been published describing its characteristics, and possible applications of the enhanced backscatter phenomenon are still unclear. With the development of commercially available high powered lasers and advanced cameras with high frame rates, we have successfully captured the enhanced backscatter effects from different reflection surfaces. In addition to static observations, we have also tilted and pre-distorted the transmitted beam at various frequencies to track the dynamic properties of the enhanced backscatter phenomenon to verify its possible application in guidance and beam and image correction through atmospheric turbulence. In this paper, experimental results will be described, and discussions on the principle and applications of the phenomenon will be included. Enhanced backscatter effects are best observed in certain levels of turbulence (Cn 2≍10-13 m-2/3), and show significant potential for providing self-guidance in beam correction that doesn't introduce additional costs (unlike providing a beacon laser). Possible applications of this phenomenon include tracking fast moving object with lasers, long distance (>1km) alignment, and focusing a high-power corrected laser beam over long distances.

GABAergic excitation of spider mechanoreceptors increases information capacity by increasing entropy rather than decreasing jitter.

PubMed

Pfeiffer, Keram; French, Andrew S

2009-09-02

Neurotransmitter chemicals excite or inhibit a range of sensory afferents and sensory pathways. These changes in firing rate or static sensitivity can also be associated with changes in dynamic sensitivity or membrane noise and thus action potential timing. We measured action potential firing produced by random mechanical stimulation of spider mechanoreceptor neurons during long-duration excitation by the GABAA agonist muscimol. Information capacity was estimated from signal-to-noise ratio by averaging responses to repeated identical stimulation sequences. Information capacity was also estimated from the coherence function between input and output signals. Entropy rate was estimated by a data compression algorithm and maximum entropy rate from the firing rate. Action potential timing variability, or jitter, was measured as normalized interspike interval distance. Muscimol increased firing rate, information capacity, and entropy rate, but jitter was unchanged. We compared these data with the effects of increasing firing rate by current injection. Our results indicate that the major increase in information capacity by neurotransmitter action arose from the increased entropy rate produced by increased firing rate, not from reduction in membrane noise and action potential jitter.

Theoretical studies of potential energy surface and rotational spectra of Xe -H2O van der Waals complex

NASA Astrophysics Data System (ADS)

Wang, Lin; Yang, Minghui

2008-11-01

In this work we report an ab initio intermolecular potential energy surface and theoretical spectroscopic studies for Xe -H2O complex. The ab initio energies are calculated with CCSD(T) method and large basis sets (aug-cc-pVQZ for H and O and aug-cc-pVQZ-PP for Xe) augmented by a {3s3p2d2f1g} set of bond functions. This potential energy surface has a global minimum corresponding to a planar and nearly linear hydrogen bonded configuration with a well depth of 192.5cm-1 at intermolecular distance of 4.0Å, which is consistent with the previous determined potential by Wen and Jäger [J. Phys. Chem. A 110, 7560 (2006)]. The bound state calculations have been performed for the complex by approximating the water molecule as a rigid rotor. The theoretical rotational transition frequencies, isotopic shifts, nuclear quadrupole coupling constants, and structure parameters are in good agreement with the experimental observed values. The wavefunctions are analyzed to understand the dynamics of the ground and the first excited states.

Dynamics of nonlinear Schrödinger breathers in a potential trap

NASA Astrophysics Data System (ADS)

Malomed, B. A.; Rosanov, N. N.; Fedorov, S. V.

2018-05-01

We consider the evolution of the 2-soliton (breather) of the nonlinear Schrödinger equation on a semi-infinite line with the zero boundary condition and a linear potential, which corresponds to the gravity field in the presence of a hard floor. This setting can be implemented in atomic Bose-Einstein condensates, and in a nonlinear planar waveguide in optics. In the absence of the gravity, repulsion of the breather from the floor leads to its splitting into constituent fundamental solitons, if the initial distance from the floor is smaller than a critical value; otherwise, the moving breather persists. In the presence of gravity, the breather always splits into a pair of "co-hopping" fundamental solitons, which may be frequency locked in the form of a quasi-breather, or unlocked, forming an incoherent pseudo-breather. Some essential results are obtained in an analytical form, in addition to the systematic numerical investigation.

Anthropogenic Signatures of Lead in the Northeast Atlantic

NASA Astrophysics Data System (ADS)

Rusiecka, D.; Gledhill, M.; Milne, A.; Achterberg, E. P.; Annett, A. L.; Atkinson, S.; Birchill, A.; Karstensen, J.; Lohan, M.; Mariez, C.; Middag, R.; Rolison, J. M.; Tanhua, T.; Ussher, S.; Connelly, D.

2018-03-01

Anthropogenic activities have resulted in enhanced lead (Pb) emissions to the environment over the past century, mainly through the combustion of leaded gasoline. Here we present the first combined dissolved (DPb), labile (LpPb), and particulate (PPb) Pb data set from the Northeast Atlantic (Celtic Sea) since the phasing out of leaded gasoline in Europe. Concentrations of DPb in surface waters have decreased by fourfold over the last four decades. We demonstrate that anthropogenic Pb is transported from the Mediterranean Sea over long distances (>2,500 km). Benthic DPb fluxes exceeded the atmospheric Pb flux in the region, indicating the importance of sediments as a contemporary Pb source. A strong positive correlation between DPb, PPb, and LpPb indicates a dynamic equilibrium between the phases and the potential for particles to "buffer" the DPb pool. This study provides insights into Pb biogeochemical cycling and demonstrates the potential of Pb in constraining ocean circulation patterns.

Electron dynamics inside a vacuum tube diode through linear differential equations

NASA Astrophysics Data System (ADS)

González, Gabriel; Orozco, Fco. Javier González; Orozco

2014-04-01

In this paper we analyze the motion of charged particles in a vacuum tube diode by solving linear differential equations. Our analysis is based on expressing the volume charge density as a function of the current density and coordinates only, i.e. ρ=ρ(J,z), while in the usual scheme the volume charge density is expressed as a function of the current density and electrostatic potential, i.e. ρ=ρ(J,V). We show that, in the case of slow varying charge density, the space-charge-limited current is reduced up to 50%. Our approach gives the well-known behavior of the classical current density proportional to the three-halves power of the bias potential and inversely proportional to the square of the gap distance between electrodes, and does not require the solution of the nonlinear differential equation normally associated with the Child-Langmuir formulation.

Social Network Analysis Reveals Potential Fission-Fusion Behavior in a Shark

NASA Astrophysics Data System (ADS)

Haulsee, Danielle E.; Fox, Dewayne A.; Breece, Matthew W.; Brown, Lori M.; Kneebone, Jeff; Skomal, Gregory B.; Oliver, Matthew J.

2016-09-01

Complex social networks and behaviors are difficult to observe for free-living marine species, especially those that move great distances. Using implanted acoustic transceivers to study the inter- and intraspecific interactions of sand tiger sharks Carcharias taurus, we observed group behavior that has historically been associated with higher order mammals. We found evidence strongly suggestive of fission-fusion behavior, or changes in group size and composition of sand tigers, related to five behavioral modes (summering, south migration, community bottleneck, dispersal, north migration). Our study shows sexually dimorphic behavior during migration, in addition to presenting evidence of a potential solitary phase for these typically gregarious sharks. Sand tigers spent up to 95 consecutive and 335 cumulative hours together, with the strongest relationships occurring between males. Species that exhibit fission-fusion group dynamics pose a particularly challenging issue for conservation and management because changes in group size and composition affect population estimates and amplify anthropogenic impacts.

Online Business Education in the Twenty-First Century: An Analysis of Potential Target Markets.

ERIC Educational Resources Information Center

Evans, Joel R.; Haase, Ilene M.

2001-01-01

Discusses the potential for online business education. Highlights include a background of distance education for higher education; the interest of corporate America in distance education; and results of a survey of Internet users that focused on potential customers for online business education and considered demographics, service expectations,…

The Seasonal Dynamics of Artificial Nest Predation Rates along Edges in a Mosaic Managed Reedbed.

PubMed

Malzer, Iain; Helm, Barbara

2015-01-01

Boundaries between different habitats can be responsible for changes in species interactions, including modified rates of encounter between predators and prey. Such 'edge effects' have been reported in nesting birds, where nest predation rates can be increased at habitat edges. The literature concerning edge effects on nest predation rates reveals a wide variation in results, even within single habitats, suggesting edge effects are not fixed, but dynamic throughout space and time. This study demonstrates the importance of considering dynamic mechanisms underlying edge effects and their relevance when undertaking habitat management. In reedbed habitats, management in the form of mosaic winter reed cutting can create extensive edges which change rapidly with reed regrowth during spring. We investigate the seasonal dynamics of reedbed edges using an artificial nest experiment based on the breeding biology of a reedbed specialist. We first demonstrate that nest predation decreases with increasing distance from the edge of cut reed blocks, suggesting edge effects have a pivotal role in this system. Using repeats throughout the breeding season we then confirm that nest predation rates are temporally dynamic and decline with the regrowth of reed. However, effects of edges on nest predation were consistent throughout the season. These results are of practical importance when considering appropriate habitat management, suggesting that reed cutting may heighten nest predation, especially before new growth matures. They also contribute directly to an overall understanding of the dynamic processes underlying edge effects and their potential role as drivers of time-dependent habitat use.

Compact normalisations in the elliptic restricted three body problem

NASA Astrophysics Data System (ADS)

Palacián, Jesús F.; Vanegas, Jasson; Yanguas, Patricia

2017-11-01

This paper considers the spatial elliptic restricted three body problem in the case that the particle with negligible mass is revolving around one of the primaries. The system is modelled in an inertial frame through a Hamiltonian function representing a non-autonomous dynamical system with three degrees of freedom that depends periodically on time. Three Lie transformations are applied at first order to eliminate successively the mean anomaly of the infinitesimal particle's motion, the time dependence of the system and the argument of the node of the particle with negligible mass. All the transformations are implemented in a compact way, that is, carrying out the computations by means of infinite series. This approach can be very useful to deal with certain artificial satellite problems or, in general, with systems such that the ratio between the distance of the infinitesimal particle to the body around it orbits and the distance between the two primaries is smaller than one but close to it. In this case the Legendre expansion of the potential converges slowly and many terms of the series must be taken into consideration.

The Pedestrian Evacuation Analyst: geographic information systems software for modeling hazard evacuation potential

USGS Publications Warehouse

Jones, Jeanne M.; Ng, Peter; Wood, Nathan J.

2014-01-01

Recent disasters such as the 2011 Tohoku, Japan, earthquake and tsunami; the 2013 Colorado floods; and the 2014 Oso, Washington, mudslide have raised awareness of catastrophic, sudden-onset hazards that arrive within minutes of the events that trigger them, such as local earthquakes or landslides. Due to the limited amount of time between generation and arrival of sudden-onset hazards, evacuations are typically self-initiated, on foot, and across the landscape (Wood and Schmidtlein, 2012). Although evacuation to naturally occurring high ground may be feasible in some vulnerable communities, evacuation modeling has demonstrated that other communities may require vertical-evacuation structures within a hazard zone, such as berms or buildings, if at-risk individuals are to survive some types of sudden-onset hazards (Wood and Schmidtlein, 2013). Researchers use both static least-cost-distance (LCD) and dynamic agent-based models to assess the pedestrian evacuation potential of vulnerable communities. Although both types of models help to understand the evacuation landscape, LCD models provide a more general overview that is independent of population distributions, which may be difficult to quantify given the dynamic spatial and temporal nature of populations (Wood and Schmidtlein, 2012). Recent LCD efforts related to local tsunami threats have focused on an anisotropic (directionally dependent) path distance modeling approach that incorporates travel directionality, multiple travel speed assumptions, and cost surfaces that reflect variations in slope and land cover (Wood and Schmidtlein, 2012, 2013). The Pedestrian Evacuation Analyst software implements this anisotropic path-distance approach for pedestrian evacuation from sudden-onset hazards, with a particular focus at this time on local tsunami threats. The model estimates evacuation potential based on elevation, direction of movement, land cover, and travel speed and creates a map showing travel times to safety (a time map) throughout a hazard zone. Model results provide a general, static view of the evacuation landscape at different pedestrian travel speeds and can be used to identify areas outside the reach of naturally occurring high ground. In addition, data on the size and location of different populations within the hazard zone can be integrated with travel-time maps to create tables and graphs of at-risk population counts as a function of travel time to safety. As a decision-support tool, the Pedestrian Evacuation Analyst provides the capability to evaluate the effectiveness of various vertical-evacuation structures within a study area, both through time maps of the modeled travel-time landscape with a potential structure in place and through comparisons of population counts within reach of safety. The Pedestrian Evacuation Analyst is designed for use by researchers examining the pedestrian-evacuation potential of an at-risk community. In communities where modeled evacuation times exceed the event (for example, tsunami wave) arrival time, researchers can use the software with emergency managers to assess the area and population served by potential vertical-evacuation options. By automating and managing the modeling process, the software allows researchers to concentrate efforts on providing crucial and timely information on community vulnerability to sudden-onset hazards.

Word spotting for handwritten documents using Chamfer Distance and Dynamic Time Warping

NASA Astrophysics Data System (ADS)

Saabni, Raid M.; El-Sana, Jihad A.

2011-01-01

A large amount of handwritten historical documents are located in libraries around the world. The desire to access, search, and explore these documents paves the way for a new age of knowledge sharing and promotes collaboration and understanding between human societies. Currently, the indexes for these documents are generated manually, which is very tedious and time consuming. Results produced by state of the art techniques, for converting complete images of handwritten documents into textual representations, are not yet sufficient. Therefore, word-spotting methods have been developed to archive and index images of handwritten documents in order to enable efficient searching within documents. In this paper, we present a new matching algorithm to be used in word-spotting tasks for historical Arabic documents. We present a novel algorithm based on the Chamfer Distance to compute the similarity between shapes of word-parts. Matching results are used to cluster images of Arabic word-parts into different classes using the Nearest Neighbor rule. To compute the distance between two word-part images, the algorithm subdivides each image into equal-sized slices (windows). A modified version of the Chamfer Distance, incorporating geometric gradient features and distance transform data, is used as a similarity distance between the different slices. Finally, the Dynamic Time Warping (DTW) algorithm is used to measure the distance between two images of word-parts. By using the DTW we enabled our system to cluster similar word-parts, even though they are transformed non-linearly due to the nature of handwriting. We tested our implementation of the presented methods using various documents in different writing styles, taken from Juma'a Al Majid Center - Dubai, and obtained encouraging results.

Changes in the limb kinematics and walking-distance estimation after shank elongation: evidence for a locomotor body schema?

PubMed

Dominici, Nadia; Daprati, Elena; Nico, Daniele; Cappellini, Germana; Ivanenko, Yuri P; Lacquaniti, Francesco

2009-03-01

When walking, step length provides critical information on traveled distance along the ongoing path [corrected] Little is known on the role that knowledge about body dimensions plays within this process. Here we directly addressed this question by evaluating whether changes in body proportions interfere with computation of traveled distance for targets located outside the reaching space. We studied locomotion and distance estimation in an achondroplastic child (ACH, 11 yr) before and after surgical elongation of the shank segments of both lower limbs and in healthy adults walking on stilts, designed to mimic shank-segment elongation. Kinematic analysis of gait revealed that dynamic coupling of the thigh, shank, and foot segments changed substantially as a result of elongation. Step length remained unvaried, in spite of the significant increase in total limb length ( approximately 1.5-fold). These relatively shorter strides resulted from smaller oscillations of the shank segment, as would be predicted by proportional increments in limb size and not by asymmetrical segmental increment as in the present case (length of thighs was not modified). Distance estimation was measured by walking with eyes closed toward a memorized target. Before surgery, the behavior of ACH was comparable to that of typically developing participants. In contrast, following shank elongation, the ACH walked significantly shorter distances when aiming at the same targets. Comparable changes in limb kinematics, stride length, and estimation of traveled distance were found in adults wearing on stilts, suggesting that path integration errors in both cases were related to alterations in the intersegmental coordination of the walking limbs. The results are consistent with a dynamic locomotor body schema used for controlling step length and path estimation, based on inherent relationships between gait parameters and body proportions.

Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations.

PubMed

Chowdhury, Rezaul; Beglov, Dmitri; Moghadasi, Mohammad; Paschalidis, Ioannis Ch; Vakili, Pirooz; Vajda, Sandor; Bajaj, Chandrajit; Kozakov, Dima

2014-10-14

Molecular mechanics and dynamics simulations use distance based cutoff approximations for faster computation of pairwise van der Waals and electrostatic energy terms. These approximations traditionally use a precalculated and periodically updated list of interacting atom pairs, known as the "nonbonded neighborhood lists" or nblists, in order to reduce the overhead of finding atom pairs that are within distance cutoff. The size of nblists grows linearly with the number of atoms in the system and superlinearly with the distance cutoff, and as a result, they require significant amount of memory for large molecular systems. The high space usage leads to poor cache performance, which slows computation for large distance cutoffs. Also, the high cost of updates means that one cannot afford to keep the data structure always synchronized with the configuration of the molecules when efficiency is at stake. We propose a dynamic octree data structure for implicit maintenance of nblists using space linear in the number of atoms but independent of the distance cutoff. The list can be updated very efficiently as the coordinates of atoms change during the simulation. Unlike explicit nblists, a single octree works for all distance cutoffs. In addition, octree is a cache-friendly data structure, and hence, it is less prone to cache miss slowdowns on modern memory hierarchies than nblists. Octrees use almost 2 orders of magnitude less memory, which is crucial for simulation of large systems, and while they are comparable in performance to nblists when the distance cutoff is small, they outperform nblists for larger systems and large cutoffs. Our tests show that octree implementation is approximately 1.5 times faster in practical use case scenarios as compared to nblists.

Reflection on the "New Dynamics" of Distance Education: An Interview with Sir John Daniel

ERIC Educational Resources Information Center

Latchem, Colin

2012-01-01

This article presents an interview with Sir John Daniel outgoing President and CEO of the Commonwealth of Learning. Sir John Daniel's term as President and Chief Executive Officer of the Commonwealth of Learning (COL) ended on May 31, 2012. Readers of "Distance Education" will know of Sir John's work at the Tele-universite (Directeur des…

Towards a Better Understanding of the Dynamic Role of the Distance Language Learner: Learner Perceptions of Personality, Motivation, Roles, and Approaches

ERIC Educational Resources Information Center

Hurd, Stella

2006-01-01

This study investigated the experience of learners enrolled on an Open University (UK) French course, and included personality factors, motivation, and tutor and student roles. The data gathered via multiple elicitation methods gave useful insights into issues of special relevance to distance language education, in particular the lack of fit…

An open-population hierarchical distance sampling model

USGS Publications Warehouse

Sollmann, Rachel; Beth Gardner,; Richard B Chandler,; Royle, J. Andrew; T Scott Sillett,

2015-01-01

Modeling population dynamics while accounting for imperfect detection is essential to monitoring programs. Distance sampling allows estimating population size while accounting for imperfect detection, but existing methods do not allow for direct estimation of demographic parameters. We develop a model that uses temporal correlation in abundance arising from underlying population dynamics to estimate demographic parameters from repeated distance sampling surveys. Using a simulation study motivated by designing a monitoring program for island scrub-jays (Aphelocoma insularis), we investigated the power of this model to detect population trends. We generated temporally autocorrelated abundance and distance sampling data over six surveys, using population rates of change of 0.95 and 0.90. We fit the data generating Markovian model and a mis-specified model with a log-linear time effect on abundance, and derived post hoc trend estimates from a model estimating abundance for each survey separately. We performed these analyses for varying number of survey points. Power to detect population changes was consistently greater under the Markov model than under the alternatives, particularly for reduced numbers of survey points. The model can readily be extended to more complex demographic processes than considered in our simulations. This novel framework can be widely adopted for wildlife population monitoring.

An open-population hierarchical distance sampling model.

PubMed

Sollmann, Rahel; Gardner, Beth; Chandler, Richard B; Royle, J Andrew; Sillett, T Scott

2015-02-01

Modeling population dynamics while accounting for imperfect detection is essential to monitoring programs. Distance sampling allows estimating population size while accounting for imperfect detection, but existing methods do not allow for estimation of demographic parameters. We develop a model that uses temporal correlation in abundance arising from underlying population dynamics to estimate demographic parameters from repeated distance sampling surveys. Using a simulation study motivated by designing a monitoring program for Island Scrub-Jays (Aphelocoma insularis), we investigated the power of this model to detect population trends. We generated temporally autocorrelated abundance and distance sampling data over six surveys, using population rates of change of 0.95 and 0.90. We fit the data generating Markovian model and a mis-specified model with a log-linear time effect on abundance, and derived post hoc trend estimates from a model estimating abundance for each survey separately. We performed these analyses for varying numbers of survey points. Power to detect population changes was consistently greater under the Markov model than under the alternatives, particularly for reduced numbers of survey points. The model can readily be extended to more complex demographic processes than considered in our simulations. This novel framework can be widely adopted for wildlife population monitoring.

Emergent properties of gene evolution: Species as attractors in phenotypic space

NASA Astrophysics Data System (ADS)

Reuveni, Eli; Giuliani, Alessandro

2012-02-01

The question how the observed discrete character of the phenotype emerges from a continuous genetic distance metrics is the core argument of two contrasted evolutionary theories: punctuated equilibrium (stable evolution scattered with saltations in the phenotype) and phyletic gradualism (smooth and linear evolution of the phenotype). Identifying phenotypic saltation on the molecular levels is critical to support the first model of evolution. We have used DNA sequences of ∼1300 genes from 6 isolated populations of the budding yeast Saccharomyces cerevisiae. We demonstrate that while the equivalent measure of the genetic distance show a continuum between lineage distance with no evidence of discrete states, the phenotypic space illustrates only two (discrete) possible states that can be associated with a saltation of the species phenotype. The fact that such saltation spans large fraction of the genome and follows by continuous genetic distance is a proof of the concept that the genotype-phenotype relation is not univocal and may have severe implication when looking for disease related genes and mutations. We used this finding with analogy to attractor-like dynamics and show that punctuated equilibrium could be explained in the framework of non-linear dynamics systems.

Flap Conformations in HIV-1 Protease are Altered by Mutations

NASA Astrophysics Data System (ADS)

Fanucci, Gail; Blackburn, Mandy; Veloro, Angelo; Galiano, Luis; Fangu, Ding; Simmerling, Carlos

2009-03-01

HIV-1 protease (PR) is an enzyme that is a major drug target in the treatment of AIDS. Although the structure and function of HIV-1 PR have been studied for over 20 years, questions remain regarding the conformations and dynamics of the β-hairpin turns (flaps) that cover the active site cavity. Distance measurements with pulsed EPR spectroscopy of spin labeled constructs of HIV-1 PR have been used to characterize the flap conformations in the apo and inhibitor bound states. From the most probably distances and the breadth of the distance distribution profiles from analysis of the EPR data, insights regarding the flap conformations and flexibility are gained. The EPR results clearly show how drug pressure selected mutations alter the average conformation of the flaps and the degree of opening of the flaps. Molecular dynamics simulations successfully regenerate the experimentally determined distance distribution profiles, and more importantly, provide structural models for full interpretation of the EPR results. By combining experiment and theory to understand the role that altered flap flexibility/conformations play in the mechanism of drug resistance, key insights are gained toward the rational development of new inhibitors of this important enzyme.

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

PubMed Central

Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin-ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; Galler, Andreas; Gawelda, Wojciech; Gosztola, David; Haldrup, Kristoffer; Harlang, Tobias; Liu, Yizhu; Møller, Klaus B.; Németh, Zoltán; Nozawa, Shunsuke; Pápai, Mátyás; Sato, Tokushi; Sato, Takahiro; Suarez-Alcantara, Karina; Togashi, Tadashi; Tono, Kensuke; Uhlig, Jens; Vithanage, Dimali A.; Wärnmark, Kenneth; Yabashi, Makina; Zhang, Jianxin; Sundström, Villy; Nielsen, Martin M.

2015-01-01

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined. PMID:25727920

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

DOE PAGES

Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; ...

2015-03-02

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances.more » Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.« less

Zoom microscope objective using electrowetting lenses.

PubMed

Li, Lei; Wang, Di; Liu, Chao; Wang, Qiong-Hua

2016-02-08

We report a zoom microscope objective which can achieve continuous zoom change and correct the aberrations dynamically. The objective consists of three electrowetting liquid lenses and two glass lenses. The magnification is changed by applying voltages on the three electrowetting lenses. Besides, the three electrowetting liquid lenses can play a role to correct the aberrations. A digital microscope based on the proposed objective is demonstrated. We analyzed the properties of the proposed objective. In contrast to the conventional objectives, the proposed objective can be tuned from ~7.8 × to ~13.2 × continuously. For our objective, the working distance is fixed, which means no movement parts are needed to refocus or change its magnification. Moreover, the zoom objective can be dynamically optimized for a wide range of wavelength. Using such an objective, the fabrication tolerance of the optical system is larger than that of a conventional system, which can decrease the fabrication cost. The proposed zoom microscope objective cannot only take place of the conventional objective, but also has potential application in the 3D microscopy.

Optimization of a mirror-based neutron source using differential evolution algorithm

NASA Astrophysics Data System (ADS)

Yurov, D. V.; Prikhodko, V. V.

2016-12-01

This study is dedicated to the assessment of capabilities of gas-dynamic trap (GDT) and gas-dynamic multiple-mirror trap (GDMT) as potential neutron sources for subcritical hybrids. In mathematical terms the problem of the study has been formulated as determining the global maximum of fusion gain (Q pl), the latter represented as a function of trap parameters. A differential evolution method has been applied to perform the search. Considered in all calculations has been a configuration of the neutron source with 20 m long distance between the mirrors and 100 MW heating power. It is important to mention that the numerical study has also taken into account a number of constraints on plasma characteristics so as to provide physical credibility of searched-for trap configurations. According to the results obtained the traps considered have demonstrated fusion gain up to 0.2, depending on the constraints applied. This enables them to be used either as neutron sources within subcritical reactors for minor actinides incineration or as material-testing facilities.

A single particle model to simulate the dynamics of entangled polymer melts.

PubMed

Kindt, P; Briels, W J

2007-10-07

We present a computer simulation model of polymer melts representing each chain as one single particle. Besides the position coordinate of each particle, we introduce a parameter n(ij) for each pair of particles i and j within a specified distance from each other. These numbers, called entanglement numbers, describe the deviation of the system of ignored coordinates from its equilibrium state for the given configuration of the centers of mass of the polymers. The deviations of the entanglement numbers from their equilibrium values give rise to transient forces, which, together with the conservative forces derived from the potential of mean force, govern the displacements of the particles. We have applied our model to a melt of C(800)H(1602) chains at 450 K and have found good agreement with experiments and more detailed simulations. Properties addressed in this paper are radial distribution functions, dynamic structure factors, and linear as well as nonlinear rheological properties.

Dynamically controlled electromagnetically induced transparency in terahertz graphene metamaterial for modulation and slow light applications

NASA Astrophysics Data System (ADS)

He, Xunjun; Yao, Yuan; Yang, Xingyu; Lu, Guangjun; Yang, Wenlong; Yang, Yuqiang; Wu, Fengmin; Yu, Zhigang; Jiang, Jiuxing

2018-03-01

By patterning two graphene resonators on a SiO2/Si substrate, a dynamically controlled electromagnetically induced transparency (EIT) in the terahertz graphene metamaterial was numerically studied through tuning the structural parameter and Fermi energy of graphene. The calculated surface current distributions demonstrate that the distinct EIT window in the graphene metamaterial results from the near-field coupling of two graphene resonators. Moreover, the EIT window can be actively controlled by tuning Fermi energy combined states of two resonators. When the Fermi energy combined state of two resonators changes from (0.21 and 0.16 eV) to (0.4 and 0.11 eV), the amplitude modulation depth of the EIT peak is 97.8% at 0.45 THz, and the corresponding enhanced factor of group delay with 6 times is obtained. This study offers an alternative tuning method to existing optical, thermal, and relative distance tuning, delivering a promising potential for designing active and miniaturized THz devices.

Modeling birds on wires.

PubMed

Aydoğdu, A; Frasca, P; D'Apice, C; Manzo, R; Thornton, J M; Gachomo, B; Wilson, T; Cheung, B; Tariq, U; Saidel, W; Piccoli, B

2017-02-21

In this paper we introduce a mathematical model to study the group dynamics of birds resting on wires. The model is agent-based and postulates attraction-repulsion forces between the interacting birds: the interactions are "topological", in the sense that they involve a given number of neighbors irrespective of their distance. The model is first mathematically analyzed and then simulated to study its main properties: we observe that the model predicts birds to be more widely spaced near the borders of each group. We compare the results from the model with experimental data, derived from the analysis of pictures of pigeons and starlings taken in New Jersey: two different image elaboration protocols allow us to establish a good agreement with the model and to quantify its main parameters. We also discuss the potential handedness of the birds, by analyzing the group organization features and the group dynamics at the arrival of new birds. Finally, we propose a more refined mathematical model that describes landing and departing birds by suitable stochastic processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Stochastic formation of magnetic vortex structures in asymmetric disks triggered by chaotic dynamics

DOE PAGES

Im, Mi-Young; Lee, Ki-Suk; Vogel, Andreas; ...

2014-12-17

The non-trivial spin configuration in a magnetic vortex is a prototype for fundamental studies of nanoscale spin behaviour with potential applications in magnetic information technologies. Arrays of magnetic vortices interfacing with perpendicular thin films have recently been proposed as enabler for skyrmionic structures at room temperature, which has opened exciting perspectives on practical applications of skyrmions. An important milestone for achieving not only such skyrmion materials but also general applications of magnetic vortices is a reliable control of vortex structures. However, controlling magnetic processes is hampered by stochastic behaviour, which is associated with thermal fluctuations in general. Here we showmore » that the dynamics in the initial stages of vortex formation on an ultrafast timescale plays a dominating role for the stochastic behaviour observed at steady state. Our results show that the intrinsic stochastic nature of vortex creation can be controlled by adjusting the interdisk distance in asymmetric disk arrays.« less

Transmission of biology and culture among post-contact Native Americans on the western Great Plains.

PubMed

Lycett, Stephen J; von Cramon-Taubadel, Noreen

2016-08-12

The transmission of genes and culture between human populations has major implications for understanding potential correlations between history, biological, and cultural variation. Understanding such dynamics in 19th century, post-contact Native Americans on the western Great Plains is especially challenging given passage of time, complexity of known dynamics, and difficulties of determining genetic patterns in historical populations for whom, even today, genetic data for their descendants are rare. Here, biometric data collected under the direction of Franz Boas from communities penecontemporaneous with the classic bison-hunting societies, were used as a proxy for genetic variation and analyzed together with cultural data. We show that both gene flow and "culture flow" among populations on the High Plains were mediated by geography, fitting a model of isolation-by-distance. Moreover, demographic and cultural exchange among these communities largely overrode the visible signal of the prior millennia of cultural and genetic histories of these populations.

Distributional dynamics of a vulnerable species in response to past and future climate change: a window for conservation prospects

PubMed Central

Bai, Yunjun; Wei, Xueping

2018-01-01

Background The ongoing change in climate is predicted to exert unprecedented effects on Earth’s biodiversity at all levels of organization. Biological conservation is important to prevent biodiversity loss, especially for species facing a high risk of extinction. Understanding the past responses of species to climate change is helpful for revealing response mechanisms, which will contribute to the development of effective conservation strategies in the future. Methods In this study, we modelled the distributional dynamics of a ‘Vulnerable’ species, Pseudolarix amabilis, in response to late Quaternary glacial-interglacial cycles and future 2080 climate change using an ecological niche model (MaxEnt). We also performed migration vector analysis to reveal the potential migration of the population over time. Results Historical modelling indicates that the range dynamics of P. amabilis is highly sensitive to climate change and that its long-distance dispersal ability and potential for evolutionary adaption are limited. Compared to the current climatically suitable areas for this species, future modelling showed significant migration northward towards future potential climatically suitable areas. Discussion In combination with the predicted future distribution, the mechanism revealed by the historical response suggests that this species will not be able to fully occupy the future expanded areas of suitable climate or adapt to the unsuitable climate across the future contraction regions. As a result, we suggest assisted migration as an effective supplementary means of conserving this vulnerable species in the face of the unprecedentedly rapid climate change of the 21st century. As a study case, this work highlights the significance of introducing historical perspectives while researching species conservation, especially for currently vulnerable or endangered taxa that once had a wider distribution in geological time. PMID:29362700

Distributional dynamics of a vulnerable species in response to past and future climate change: a window for conservation prospects.

PubMed

Bai, Yunjun; Wei, Xueping; Li, Xiaoqiang

2018-01-01

The ongoing change in climate is predicted to exert unprecedented effects on Earth's biodiversity at all levels of organization. Biological conservation is important to prevent biodiversity loss, especially for species facing a high risk of extinction. Understanding the past responses of species to climate change is helpful for revealing response mechanisms, which will contribute to the development of effective conservation strategies in the future. In this study, we modelled the distributional dynamics of a 'Vulnerable' species, Pseudolarix amabilis , in response to late Quaternary glacial-interglacial cycles and future 2080 climate change using an ecological niche model (MaxEnt). We also performed migration vector analysis to reveal the potential migration of the population over time. Historical modelling indicates that the range dynamics of P. amabilis is highly sensitive to climate change and that its long-distance dispersal ability and potential for evolutionary adaption are limited. Compared to the current climatically suitable areas for this species, future modelling showed significant migration northward towards future potential climatically suitable areas. In combination with the predicted future distribution, the mechanism revealed by the historical response suggests that this species will not be able to fully occupy the future expanded areas of suitable climate or adapt to the unsuitable climate across the future contraction regions. As a result, we suggest assisted migration as an effective supplementary means of conserving this vulnerable species in the face of the unprecedentedly rapid climate change of the 21st century. As a study case, this work highlights the significance of introducing historical perspectives while researching species conservation, especially for currently vulnerable or endangered taxa that once had a wider distribution in geological time.

Long-term consistency in spatial patterns of primate seed dispersal.

PubMed

Heymann, Eckhard W; Culot, Laurence; Knogge, Christoph; Noriega Piña, Tony Enrique; Tirado Herrera, Emérita R; Klapproth, Matthias; Zinner, Dietmar

2017-03-01

Seed dispersal is a key ecological process in tropical forests, with effects on various levels ranging from plant reproductive success to the carbon storage potential of tropical rainforests. On a local and landscape scale, spatial patterns of seed dispersal create the template for the recruitment process and thus influence the population dynamics of plant species. The strength of this influence will depend on the long-term consistency of spatial patterns of seed dispersal. We examined the long-term consistency of spatial patterns of seed dispersal with spatially explicit data on seed dispersal by two neotropical primate species, Leontocebus nigrifrons and Saguinus mystax (Callitrichidae), collected during four independent studies between 1994 and 2013. Using distributions of dispersal probability over distances independent of plant species, cumulative dispersal distances, and kernel density estimates, we show that spatial patterns of seed dispersal are highly consistent over time. For a specific plant species, the legume Parkia panurensis , the convergence of cumulative distributions at a distance of 300 m, and the high probability of dispersal within 100 m from source trees coincide with the dimension of the spatial-genetic structure on the embryo/juvenile (300 m) and adult stage (100 m), respectively, of this plant species. Our results are the first demonstration of long-term consistency of spatial patterns of seed dispersal created by tropical frugivores. Such consistency may translate into idiosyncratic patterns of regeneration.

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

NASA Astrophysics Data System (ADS)

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.; Jin, Wencan; Dadap, Jerry I.; Hybertsen, Mark S.; Osgood, Richard M.

2018-04-01

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n =1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energy and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. This opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.

Love as a Battlefield: Attachment and Relationship Dynamics in Couples Identified for Male Partner Violence

ERIC Educational Resources Information Center

Allison, Colleen J.; Bartholomew, Kim; Mayseless, Ofra; Dutton, Donald G.

2008-01-01

The authors explored the attachment dynamics of heterosexual couples identified for male partner violence. Based on semistructured interviews, participants were assessed for attachment orientations. Based on a thematic analysis of the interviews, two strategies for regulating distance within these relationships were identified: pursuit and…

Dynamic Assessment, Tutor Mediation and Academic Writing Development

ERIC Educational Resources Information Center

Shrestha, Prithvi; Coffin, Caroline

2012-01-01

Supporting undergraduate students with their academic literacies has recently been a major focus in higher education in the UK. This paper explores the value of tutor mediation in the context of academic writing development among undergraduate business studies students in open and distance learning, following the dynamic assessment (DA) approach…

Role of Distance-Based Routing in Traffic Dynamics on Mobile Networks

NASA Astrophysics Data System (ADS)

Yang, Han-Xin; Wang, Wen-Xu

2013-06-01

Despite of intensive investigations on transportation dynamics taking place on complex networks with fixed structures, a deep understanding of networks consisting of mobile nodes is challenging yet, especially the lacking of insight into the effects of routing strategies on transmission efficiency. We introduce a distance-based routing strategy for networks of mobile agents toward enhancing the network throughput and the transmission efficiency. We study the transportation capacity and delivering time of data packets associated with mobility and communication ability. Interestingly, we find that the transportation capacity is optimized at moderate moving speed, which is quite different from random routing strategy. In addition, both continuous and discontinuous transitions from free flow to congestions are observed. Degree distributions are explored in order to explain the enhancement of network throughput and other observations. Our work is valuable toward understanding complex transportation dynamics and designing effective routing protocols.

Dynamics of copper-phthalocyanine molecules on Au/Ge(001).

PubMed

Sotthewes, K; Heimbuch, R; Zandvliet, H J W

2015-10-07

Spatially resolved current-time scanning tunneling spectroscopy combined with current-distance spectroscopy has been used to characterize the dynamic behavior of copper-phthalocyanine (CuPc) molecules adsorbed on a Au-modified Ge(001) surface. The analyzed CuPc molecules are adsorbed in a "molecular bridge" configuration, where two benzopyrrole groups (lobes) are connected to a Au-induced nanowire, whereas the other two lobes are connected to the adjacent nanowire. Three types of lobe configurations are found: a bright lobe, a dim lobe, and a fuzzy lobe. The dim and fuzzy lobes exhibit a well-defined switching behavior between two discrete levels, while the bright lobe shows a broad oscillation band. The observed dynamic behavior is induced by electrons that are injected into the LUMO+1 orbital of the CuPc molecule. By precisely adjusting the tip-molecule distance, the switching frequency of the lobes can be tuned accurately.

Dynamics of copper-phthalocyanine molecules on Au/Ge(001)

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

Sotthewes, K.; Heimbuch, R.; Zandvliet, H. J. W.

2015-10-07

Spatially resolved current-time scanning tunneling spectroscopy combined with current-distance spectroscopy has been used to characterize the dynamic behavior of copper-phthalocyanine (CuPc) molecules adsorbed on a Au-modified Ge(001) surface. The analyzed CuPc molecules are adsorbed in a “molecular bridge” configuration, where two benzopyrrole groups (lobes) are connected to a Au-induced nanowire, whereas the other two lobes are connected to the adjacent nanowire. Three types of lobe configurations are found: a bright lobe, a dim lobe, and a fuzzy lobe. The dim and fuzzy lobes exhibit a well-defined switching behavior between two discrete levels, while the bright lobe shows a broad oscillationmore » band. The observed dynamic behavior is induced by electrons that are injected into the LUMO+1 orbital of the CuPc molecule. By precisely adjusting the tip-molecule distance, the switching frequency of the lobes can be tuned accurately.« less

VMD DisRg: New User-Friendly Implement for calculation distance and radius of gyration in VMD program

PubMed Central

Falsafi-Zadeh, Sajad; Karimi, Zahra; Galehdari, Hamid

2012-01-01

Molecular dynamic simulation is a practical and powerful technique for analysis of protein structure. Several programs have been developed to facilitate the mentioned investigation, under them the visual molecular dynamic or VMD is the most frequently used programs. One of the beneficial properties of the VMD is its ability to be extendable by designing new plug-in. We introduce here a new facility of the VMD for distance analysis and radius of gyration of biopolymers such as protein and DNA. Availability The database is available for free at http://trc.ajums.ac.ir/HomePage.aspx/?TabID/=12618/&Site/=trc.ajums.ac/&Lang/=fa-IR PMID:22553393

Principal component analysis on a torus: Theory and application to protein dynamics.

PubMed

Sittel, Florian; Filk, Thomas; Stock, Gerhard

2017-12-28

A dimensionality reduction method for high-dimensional circular data is developed, which is based on a principal component analysis (PCA) of data points on a torus. Adopting a geometrical view of PCA, various distance measures on a torus are introduced and the associated problem of projecting data onto the principal subspaces is discussed. The main idea is that the (periodicity-induced) projection error can be minimized by transforming the data such that the maximal gap of the sampling is shifted to the periodic boundary. In a second step, the covariance matrix and its eigendecomposition can be computed in a standard manner. Adopting molecular dynamics simulations of two well-established biomolecular systems (Aib 9 and villin headpiece), the potential of the method to analyze the dynamics of backbone dihedral angles is demonstrated. The new approach allows for a robust and well-defined construction of metastable states and provides low-dimensional reaction coordinates that accurately describe the free energy landscape. Moreover, it offers a direct interpretation of covariances and principal components in terms of the angular variables. Apart from its application to PCA, the method of maximal gap shifting is general and can be applied to any other dimensionality reduction method for circular data.

Principal component analysis on a torus: Theory and application to protein dynamics

NASA Astrophysics Data System (ADS)

Sittel, Florian; Filk, Thomas; Stock, Gerhard

2017-12-01

A dimensionality reduction method for high-dimensional circular data is developed, which is based on a principal component analysis (PCA) of data points on a torus. Adopting a geometrical view of PCA, various distance measures on a torus are introduced and the associated problem of projecting data onto the principal subspaces is discussed. The main idea is that the (periodicity-induced) projection error can be minimized by transforming the data such that the maximal gap of the sampling is shifted to the periodic boundary. In a second step, the covariance matrix and its eigendecomposition can be computed in a standard manner. Adopting molecular dynamics simulations of two well-established biomolecular systems (Aib9 and villin headpiece), the potential of the method to analyze the dynamics of backbone dihedral angles is demonstrated. The new approach allows for a robust and well-defined construction of metastable states and provides low-dimensional reaction coordinates that accurately describe the free energy landscape. Moreover, it offers a direct interpretation of covariances and principal components in terms of the angular variables. Apart from its application to PCA, the method of maximal gap shifting is general and can be applied to any other dimensionality reduction method for circular data.

Pattern does not equal process: what does patch occupancy really tell us about metapopulation dynamics?

PubMed

Clinchy, Michael; Haydon, Daniel T; Smith, Andrew T

2002-04-01

Patch occupancy surveys are commonly used to parameterize metapopulation models. If isolation predicts patch occupancy, this is generally attributed to a balance between distance-dependent recolonization and spatially independent extinctions. We investigated whether similar patterns could also be generated by a process of spatially correlated extinctions following a unique colonization event (analogous to nonequilibrium processes in island biogeography). We simulated effects of spatially correlated extinctions on patterns of patch occupancy among pikas (Ochotona princeps) at Bodie, California, using randomly located extinction disks to represent the likely effects of predation. Our simulations produced similar patterns to those cited as evidence of balanced metapopulation dynamics. Simulations using a variety of disk sizes and patch configurations confirmed that our results are potentially applicable to a broad range of species and sites. Analyses of the observed patterns of patch occupancy at Bodie revealed little evidence of rescue effects and strong evidence that most recolonizations are ephemeral in nature. Persistence will be overestimated if static or declining patterns of patch occupancy are mistakenly attributed to dynamically stable metapopulation processes. Consequently, simple patch occupancy surveys should not be considered as substitutes for detailed experimental tests of hypothesized population processes, particularly when conservation concerns are involved.

A new approach of the Star Excursion Balance Test to assess dynamic postural control in people complaining from chronic ankle instability.

PubMed

Pionnier, Raphaël; Découfour, Nicolas; Barbier, Franck; Popineau, Christophe; Simoneau-Buessinger, Emilie

2016-03-01

The purpose of this study was to quantitatively and qualitatively assess dynamic balance with accuracy in individuals with chronic ankle instability (CAI). To this aim, a motion capture system was used while participants performed the Star Excursion Balance Test (SEBT). Reached distances for the 8 points of the star were automatically computed, thereby excluding any dependence to the experimenter. In addition, new relevant variables were also computed, such as absolute time needed to reach each distance, lower limb ranges of motion during unipodal stance, as well as absolute error of pointing. Velocity of the center of pressure and range of variation of ground reaction forces have also been assessed during the unipodal phase of the SEBT thanks to force plates. CAI group exhibited smaller reached distances and greater absolute error of pointing than the control group (p<0.05). Moreover, the ranges of motion of lower limbs joints, the velocity of the center of pressure and the range of variation of the ground reaction forces were all significantly smaller in the CAI group (p<0.05). These reduced quantitative and qualitative performances highlighted a lower dynamic postural control. The limited body movements and accelerations during the unipodal stance in the CAI group could highlight a protective strategy. The present findings could help clinicians to better understand the motor strategies used by CAI patients during dynamic balance and may guide the rehabilitation process. Copyright © 2016 Elsevier B.V. All rights reserved.

Non-equilibrium steady-state distributions of colloids in a tilted periodic potential

NASA Astrophysics Data System (ADS)

Ma, Xiaoguang; Lai, Pik-Yin; Ackerson, Bruce; Tong, Penger

A two-layer colloidal system is constructed to study the effects of the external force F on the non-equilibrium steady-state (NESS) dynamics of the diffusing particles over a tilted periodic potential, in which detailed balance is broken due to the presence of a steady particle flux. The periodic potential is provided by the bottom layer colloidal spheres forming a fixed crystalline pattern on a glass substrate. The corrugated surface of the bottom colloidal crystal provides a gravitational potential field for the top layer diffusing particles. By tilting the sample with respect to gravity, a tangential component F is applied to the diffusing particles. The measured NESS probability density function Pss (x , y) of the particles is found to deviate from the equilibrium distribution depending on the driving or distance from equilibrium. The experimental results are compared with the exact solution of the 1D Smoluchowski equation and the numerical results of the 2D Smoluchowski equation. Moreover, from the obtained exact 1D solution, we develop an analytical method to accurately extract the 1D potential U0 (x) from the measured Pss (x) . Work supported in part by the Research Grants Council of Hong Kong SAR.

Online SAXS investigations of polymeric hollow fibre membranes.

PubMed

Pranzas, P Klaus; Knöchel, Arndt; Kneifel, Klemens; Kamusewitz, Helmut; Weigel, Thomas; Gehrke, Rainer; Funari, Sérgio S; Willumeit, Regine

2003-07-01

Polymeric membranes are used in industrial and analytical separation techniques. In this study small-angle X-ray scattering (SAXS) with synchrotron radiation has been applied for in-situ characterisation during formation of polymeric membranes. The spinning of a polyetherimide (PEI) hollow fibre membrane was chosen for investigation of dynamic aggregation processes during membrane formation, because it allows the measurement of the dynamic equilibrium at different distances from the spinning nozzle. With this system it is possible to resolve structural changes in the nm-size range which occur during membrane formation on the time-scale of milliseconds. Integral structural parameters, like radius of gyration and pair-distance distribution, were determined. Depending on the chosen spinning parameters, e.g. the flow ratio between polymer solution and coagulant water, significant changes in the scattering curves have been observed. The data are correlated with the distance from the spinning nozzle in order to get information about the kinetics of membrane formation which has fundamental influence on structure and properties of the membrane.

Local Elastic Constants for Epoxy-Nanotube Composites from Molecular Dynamics Simulation

NASA Technical Reports Server (NTRS)

Frankland, S. J. V.; Gates, T. S.

2007-01-01

A method from molecular dynamics simulation is developed for determining local elastic constants of an epoxy/nanotube composite. The local values of C11, C33, K12, and K13 elastic constants are calculated for an epoxy/nanotube composite as a function of radial distance from the nanotube. While the results possess a significant amount of statistical uncertainty resulting from both the numerical analysis and the molecular fluctuations during the simulation, the following observations can be made. If the size of the region around the nanotube is increased from shells of 1 to 6 in thickness, then the scatter in the data reduces enough to observe trends. All the elastic constants determined are at a minimum 20 from the center of the nanotube. The C11, C33, and K12 follow similar trends as a function of radial distance from the nanotube. The K13 decreases greater distances from the nanotube and becomes negative which may be a symptom of the statistical averaging.

Planar Steering of a Single Ferrofluid Drop by Optimal Minimum Power Dynamic Feedback Control of Four Electromagnets at a Distance

PubMed Central

Probst, R.; Lin, J.; Komaee, A.; Nacev, A.; Cummins, Z.

2010-01-01

Any single permanent or electro magnet will always attract a magnetic fluid. For this reason it is difficult to precisely position and manipulate ferrofluid at a distance from magnets. We develop and experimentally demonstrate optimal (minimum electrical power) 2-dimensional manipulation of a single droplet of ferrofluid by feedback control of 4 external electromagnets. The control algorithm we have developed takes into account, and is explicitly designed for, the nonlinear (fast decay in space, quadratic in magnet strength) nature of how the magnets actuate the ferrofluid, and it also corrects for electro-magnet charging time delays. With this control, we show that dynamic actuation of electro-magnets held outside a domain can be used to position a droplet of ferrofluid to any desired location and steer it along any desired path within that domain – an example of precision control of a ferrofluid by magnets acting at a distance. PMID:21218157

Television monitor field shifter and an opto-electronic method for obtaining a stereo image of optimal depth resolution and reduced depth distortion on a single screen

NASA Technical Reports Server (NTRS)

Diner, Daniel B. (Inventor)

1989-01-01

A method and apparatus is developed for obtaining a stereo image with reduced depth distortion and optimum depth resolution. Static and dynamic depth distortion and depth resolution tradeoff is provided. Cameras obtaining the images for a stereo view are converged at a convergence point behind the object to be presented in the image, and the collection-surface-to-object distance, the camera separation distance, and the focal lengths of zoom lenses for the cameras are all increased. Doubling the distances cuts the static depth distortion in half while maintaining image size and depth resolution. Dynamic depth distortion is minimized by panning a stereo view-collecting camera system about a circle which passes through the convergence point and the camera's first nodal points. Horizontal field shifting of the television fields on a television monitor brings both the monitor and the stereo views within the viewer's limit of binocular fusion.

Psychophysical evidence for auditory motion parallax.

PubMed

Genzel, Daria; Schutte, Michael; Brimijoin, W Owen; MacNeilage, Paul R; Wiegrebe, Lutz

2018-04-17

Distance is important: From an ecological perspective, knowledge about the distance to either prey or predator is vital. However, the distance of an unknown sound source is particularly difficult to assess, especially in anechoic environments. In vision, changes in perspective resulting from observer motion produce a reliable, consistent, and unambiguous impression of depth known as motion parallax. Here we demonstrate with formal psychophysics that humans can exploit auditory motion parallax, i.e., the change in the dynamic binaural cues elicited by self-motion, to assess the relative depths of two sound sources. Our data show that sensitivity to relative depth is best when subjects move actively; performance deteriorates when subjects are moved by a motion platform or when the sound sources themselves move. This is true even though the dynamic binaural cues elicited by these three types of motion are identical. Our data demonstrate a perceptual strategy to segregate intermittent sound sources in depth and highlight the tight interaction between self-motion and binaural processing that allows assessment of the spatial layout of complex acoustic scenes.

Complex network description of the ionosphere

NASA Astrophysics Data System (ADS)

Lu, Shikun; Zhang, Hao; Li, Xihai; Li, Yihong; Niu, Chao; Yang, Xiaoyun; Liu, Daizhi

2018-03-01

Complex networks have emerged as an essential approach of geoscience to generate novel insights into the nature of geophysical systems. To investigate the dynamic processes in the ionosphere, a directed complex network is constructed, based on a probabilistic graph of the vertical total electron content (VTEC) from 2012. The results of the power-law hypothesis test show that both the out-degree and in-degree distribution of the ionospheric network are not scale-free. Thus, the distribution of the interactions in the ionosphere is homogenous. None of the geospatial positions play an eminently important role in the propagation of the dynamic ionospheric processes. The spatial analysis of the ionospheric network shows that the interconnections principally exist between adjacent geographical locations, indicating that the propagation of the dynamic processes primarily depends on the geospatial distance in the ionosphere. Moreover, the joint distribution of the edge distances with respect to longitude and latitude directions shows that the dynamic processes travel further along the longitude than along the latitude in the ionosphere. The analysis of small-world-ness indicates that the ionospheric network possesses the small-world property, which can make the ionosphere stable and efficient in the propagation of dynamic processes.

Seismic Study of the Dynamics of the Solar Subsurface from SoHO Observations

NASA Technical Reports Server (NTRS)

Korzennik, Sylvain G.; Wagner, William J. (Technical Monitor)

2001-01-01

In collaboration with Dr. Baudin, we have developed and refined the new observational methodology for local helioseismology known as time-distance analysis. Global helioseismology study the solar oscillations as a superposition of resonant modes, whose properties (mode frequencies) reflect the global structure of the sun (sound speed stratification, rotation rate, etc). In contrast, local helioseismology look at the solar oscillations as wave packets whose propagation will be affected by perturbations of the media sampled. These local perturbations (sound speed or velocity flows) will modify the propagation time, that in turn can be used as a diagnostic tool for a given region. From a data reduction perspective, the processing of solar dopplergrams that result in time-distance maps, i.e. propagation times as a function of distance between bounces at the surface, is radically different from the methodology used for global mode analysis. We have, in a first step, further develop the programs needed to carry out such analysis. We have then applied them to NMI data set, and explore the trade-off between various averaging and filtering approaches - steps required to improve the signal-to-noise ratio of correlation maps - and the resulting stability and precision of the fitted propagation times. While excessive averaging (whether over space, propagation distance, or time) will reduce the diagnostic potential of the method, insufficient averaging lead to unstable fits, or uncertainties so large as to hide the information we seek. In a second phase, we have developed the analysis methodology required to infer local properties from perturbation in time propagation. Namely, we have developed time-distance inversion techniques, with an emphasis on inferences of velocity flows from time anomalies. Note also that during the period covered by this grant, all the investigators on this proposal (i.e., Drs. Baudin, Eff-Darwich, Korzennik, and Noyes) took part in the organization of the SOHO 6 /GONG 99 Workshop: Structure and Dynamics of the Interior of the Sun and Sunlike Stars, held on June 1-4 1999 at the Boston Park Plaza Hotel in Boston, Massachusetts, USA. it was very well attended by more than 160 participants from 26 countries from all over the world. The proceedings were published in two volumes as ESA SP-418, with Sessions I-III in Volume 1, and Sessions IV-VI in Volume 2 (1,000 pages in total). The complete contents are also included in digital form on a CD-ROM included with Volume 1. This CD-ROM also contains additional multi-media material that complements some of the contributions.

Simulation-Based Design for Wearable Robotic Systems: An Optimization Framework for Enhancing a Standing Long Jump.

PubMed

Ong, Carmichael F; Hicks, Jennifer L; Delp, Scott L

2016-05-01

Technologies that augment human performance are the focus of intensive research and development, driven by advances in wearable robotic systems. Success has been limited by the challenge of understanding human-robot interaction. To address this challenge, we developed an optimization framework to synthesize a realistic human standing long jump and used the framework to explore how simulated wearable robotic devices might enhance jump performance. A planar, five-segment, seven-degree-of-freedom model with physiological torque actuators, which have variable torque capacity depending on joint position and velocity, was used to represent human musculoskeletal dynamics. An active augmentation device was modeled as a torque actuator that could apply a single pulse of up to 100 Nm of extension torque. A passive design was modeled as rotational springs about each lower limb joint. Dynamic optimization searched for physiological and device actuation patterns to maximize jump distance. Optimization of the nominal case yielded a 2.27 m jump that captured salient kinematic and kinetic features of human jumps. When the active device was added to the ankle, knee, or hip, jump distance increased to between 2.49 and 2.52 m. Active augmentation of all three joints increased the jump distance to 3.10 m. The passive design increased jump distance to 3.32 m by adding torques of 135, 365, and 297 Nm to the ankle, knee, and hip, respectively. Dynamic optimization can be used to simulate a standing long jump and investigate human-robot interaction. Simulation can aid in the design of performance-enhancing technologies.

Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase.

PubMed

Sharma, Reetu; Sastry, G Narahari

2015-01-01

Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant's functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies.

Assessment of stability during gait in patients with spinal deformity-A preliminary analysis using the dynamic stability margin.

PubMed

Simon, Anne-Laure; Lugade, Vipul; Bernhardt, Kathie; Larson, A Noelle; Kaufman, Kenton

2017-06-01

Daily living activities are dynamic, requiring spinal motion through space. Current assessment of spinal deformities is based on static measurements from full-spine standing radiographs. Tools to assess dynamic stability during gait might be useful to enhance the standard evaluation. The aim of this study was to evaluate gait dynamic imbalance in patients with spinal deformity using the dynamic stability margin (DSM). Twelve normal subjects and 17 patients with spinal deformity were prospectively recruited. A kinematic 3D gait analysis was performed for the control group (CG) and the spinal deformity group (SDG). The DSM (distance between the extrapolated center of mass and the base of support) and time-distance parameters were calculated for the right and left side during gait. The relationship between DSM and step length was assessed using three variables: gait stability, symmetry, and consistency. Variables' accuracy was validated by a discriminant analysis. Patients with spinal deformity exhibited gait instability according to the DSM (0.25m versus 0.31m) with decreased velocity (1.1ms -1 versus 1.3ms -1 ) and decreased step length (0.32m versus 0.38m). According to the discriminant analysis, gait stability was the more accurate variable (area under the curve AUC=0.98) followed by gait symmetry and consistency. However, gait consistency showed 100% of specificity, sensitivity, and accuracy of precision. The DSM showed that patients with spinal malalignment exhibit decreased gait stability, symmetry, and consistency besides gait time-distance parameter changes. Additional work is required to determine how to apply the DSM for preoperative and postoperative spinal deformity management. Copyright © 2017. Published by Elsevier B.V.

Lifelong Learning & Distance Higher Education. Perspectives on Distance Education

ERIC Educational Resources Information Center

McIntosh, Christopher, Ed.

2005-01-01

Reflecting a common objective of ensuring quality Education for All, this book is a joint initiative of UNESCO and COL and jointly published. Lifelong Learning in Distance Higher Education brings together a diverse group of experts from many countries. The book provides a clear picture of the challenges, problems and potential of distance higher…

Problems and Prospects of Open and Distance Education in Nigeria

ERIC Educational Resources Information Center

Yusuf, Mudasiru Olalere

2006-01-01

Distance education as a mean of providing access to education, particularly tertiary level education, has gained great prominence in the world. Nigeria has taken giant steps of recent to introduce open and distance education programme. This paper explores the major terms inherent in open and distance education, its potentials, possible factors…

Implications of Online Learning for the Conceptual Development and Practice of Distance Education

ERIC Educational Resources Information Center

Garrison, Randy

2009-01-01

The purpose of this article is to examine the foundational principles and practices of distance education for the purpose of understanding recent developments in the areas of online and blended learning. It is argued that mainstream distance education has not embraced the full collaborative potential of online learning. Distance education…

Closing the Gap: Opportunities for Distance Education to Benefit Adult Learners in Higher Education

ERIC Educational Resources Information Center

Carlsen, A.; Holmberg, C.; Neghina, C.; Owusu-Boampong, A.

2016-01-01

Distance education in higher education is a fast-growing and widespread phenomenon. As many adults are unable to participate in on-campus education, distance education offers flexible learning paths that greatly enhance accessibility to higher education. Exploring distance education's potential to increase the participation of adult learners in…

A Combined Experimental and Numerical Modeling Study of the Deformation and Rupture of Axisymmetric Liquid Bridges under Coaxial Stretching.

PubMed

Zhuang, Jinda; Ju, Y Sungtaek

2015-09-22

The deformation and rupture of axisymmetric liquid bridges being stretched between two fully wetted coaxial disks are studied experimentally and theoretically. We numerically solve the time-dependent Navier-Stokes equations while tracking the deformation of the liquid-air interface using the arbitrary Lagrangian-Eulerian (ALE) moving mesh method to fully account for the effects of inertia and viscous forces on bridge dynamics. The effects of the stretching velocity, liquid properties, and liquid volume on the dynamics of liquid bridges are systematically investigated to provide direct experimental validation of our numerical model for stretching velocities as high as 3 m/s. The Ohnesorge number (Oh) of liquid bridges is a primary factor governing the dynamics of liquid bridge rupture, especially the dependence of the rupture distance on the stretching velocity. The rupture distance generally increases with the stretching velocity, far in excess of the static stability limit. For bridges with low Ohnesorge numbers, however, the rupture distance stay nearly constant or decreases with the stretching velocity within certain velocity windows due to the relative rupture position switching and the thread shape change. Our work provides an experimentally validated modeling approach and experimental data to help establish foundation for systematic further studies and applications of liquid bridges.

Conceptual Design and Dynamics Testing and Modeling of a Mars Tumbleweed Rover

NASA Technical Reports Server (NTRS)

Calhoun Philip C.; Harris, Steven B.; Raiszadeh, Behzad; Zaleski, Kristina D.

2005-01-01

The NASA Langley Research Center has been developing a novel concept for a Mars planetary rover called the Mars Tumbleweed. This concept utilizes the wind to propel the rover along the Mars surface, bringing it the potential to cover vast distances not possible with current Mars rover technology. This vehicle, in its deployed configuration, must be large and lightweight to provide the ratio of drag force to rolling resistance necessary to initiate motion from rest on the Mars surface. One Tumbleweed design concept that satisfies these considerations is called the Eggbeater-Dandelion. This paper describes the basic design considerations and a proposed dynamics model of the concept for use in simulation studies. It includes a summary of rolling/bouncing dynamics tests that used videogrammetry to better understand, characterize, and validate the dynamics model assumptions, especially the effective rolling resistance in bouncing/rolling dynamic conditions. The dynamics test used cameras to capture the motion of 32 targets affixed to a test article s outer structure. Proper placement of the cameras and alignment of their respective fields of view provided adequate image resolution of multiple targets along the trajectory as the test article proceeded down the ramp. Image processing of the frames from multiple cameras was used to determine the target positions. Position data from a set of these test runs was compared with results of a three dimensional, flexible dynamics model. Model input parameters were adjusted to match the test data for runs conducted. This process presented herein provided the means to characterize the dynamics and validate the simulation of the Eggbeater-Dandelion concept. The simulation model was used to demonstrate full scale Tumbleweed motion from a stationary condition on a flat-sloped terrain using representative Mars environment parameters.

Distance Reached in the Anteromedial Reach Test as a Function of Learning and Leg Length

ERIC Educational Resources Information Center

Bent, Nicholas P.; Rushton, Alison B.; Wright, Chris C.; Batt, Mark E.

2012-01-01

The Anteromedial Reach Test (ART) is a new outcome measure for assessing dynamic knee stability in anterior cruciate ligament-injured patients. The effect of learning and leg length on distance reached in the ART was examined. Thirty-two healthy volunteers performed 15 trials of the ART on each leg. There was a moderate correlation (r = 0.44-0.50)…

A New Tool for Managing Students' Self-Evaluations in Traditional and Distance Education Courses.

ERIC Educational Resources Information Center

Contreras-Castillo, Juan; Block, Arthur Edwards

This paper describes a Web-based question-answering system called E-teacher that can be used in both traditional and distance learning courses to review academic contents. E-teacher is a self-editing template-based system that consists of a set of PHP scripts that generate the HTML code dynamically, or "on the fly." The entire E-teacher…

Distance estimation and collision prediction for on-line robotic motion planning

NASA Technical Reports Server (NTRS)

Kyriakopoulos, K. J.; Saridis, G. N.

1992-01-01

An efficient method for computing the minimum distance and predicting collisions between moving objects is presented. This problem is incorporated into the framework of an in-line motion-planning algorithm to satisfy collision avoidance between a robot and moving objects modeled as convex polyhedra. In the beginning, the deterministic problem where the information about the objects is assumed to be certain is examined. L(1) or L(infinity) norms are used to represent distance and the problem becomes a linear programming problem. The stochastic problem is formulated where the uncertainty is induced by sensing and the unknown dynamics of the moving obstacles. Two problems are considered: First, filtering of the distance between the robot and the moving object at the present time. Second, prediction of the minimum distance in the future in order to predict the collision time.

Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials

PubMed Central

Shirota, Matsuyuki; Ishida, Takashi; Kinoshita, Kengo

2009-01-01

Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all-atom distance-dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT-TS score, but decreased the Z-score of the native structure. The attractiveness of potential improved both the correlation and Z-score for template-based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states. PMID:19588493

Edge effects, not connectivity, determine the incidence and development of a foliar fungal plant disease.

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

Johnson, Brenda, L.; Haddad, Nick, M.

2011-08-01

Using a model plant-pathogen system in a large-scale habitat corridor experiment, we found that corridors do not facilitate the movement of wind-dispersed plant pathogens, that connectivity of patches does not enhance levels of foliar fungal plant disease, and that edge effects are the key drivers of plant disease dynamics. Increased spread of infectious disease is often cited as a potential negative effect of habitat corridors used in conservation, but the impacts of corridors on pathogen movement have never been tested empirically. Using sweet corn (Zea mays) and southern corn leaf blight (Cochliobolus heterostrophus) as a model plant-pathogen system, we testedmore » the impacts of connectivity and habitat fragmentation on pathogen movement and disease development at the Savannah River Site, South Carolina, USA. Over time, less edgy patches had higher proportions of diseased plants, and distance of host plants to habitat edges was the greatest determinant of disease development. Variation in average daytime temperatures provided a possible mechanism for these disease patterns. Our results show that worries over the potentially harmful effects of conservation corridors on disease dynamics are misplaced, and that, in a conservation context, many diseases can be better managed by mitigating edge effects.« less

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

PubMed Central

Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology. PMID:25414723

Dose to the contralateral breast: a comparison of two techniques using the enhanced dynamic wedge versus a standard wedge.

PubMed

Warlick, W B; O'Rear, J H; Earley, L; Moeller, J H; Gaffney, D K; Leavitt, D D

1997-01-01

The dose to the contralateral breast has been associated with an increased risk of developing a second breast malignancy. Varying techniques have been devised and described in the literature to minimize this dose. Metal beam modifiers such as standard wedges are used to improve the dose distribution in the treated breast, but unfortunately introduce an increased scatter dose outside the treatment field, in particular to the contralateral breast. The enhanced dynamic wedge is a means of remote wedging created by independently moving one collimator jaw through the treatment field during dose delivery. This study is an analysis of differing doses to the contralateral breast using two common clinical set-up techniques with the enhanced dynamic wedge versus the standard metal wedge. A tissue equivalent block (solid water), modeled to represent a typical breast outline, was designed as an insert in a Rando phantom to simulate a standard patient being treated for breast conservation. Tissue equivalent material was then used to complete the natural contour of the breast and to reproduce appropriate build-up and internal scatter. Thermoluminescent dosimeter (TLD) rods were placed at predetermined distances from the geometric beam's edge to measure the dose to the contralateral breast. A total of 35 locations were used with five TLDs in each location to verify the accuracy of the measured dose. The radiation techniques used were an isocentric set-up with co-planar, non divergent posterior borders and an isocentric set-up with a half beam block technique utilizing the asymmetric collimator jaw. Each technique used compensating wedges to optimize the dose distribution. A comparison of the dose to the contralateral breast was then made with the enhanced dynamic wedge vs. the standard metal wedge. The measurements revealed a significant reduction in the contralateral breast dose with the enhanced dynamic wedge compared to the standard metal wedge in both set-up techniques. The dose was measured at varying distances from the geometric field edge, ranging from 2 to 8 cm. The average dose with the enhanced dynamic wedge was 2.7-2.8%. The average dose with the standard wedge was 4.0-4.7%. Thermoluminescent dosimeter measurements suggest an increase in both scattered electrons and photons with metal wedges. The enhanced dynamic wedge is a practical clinical advance which improves the dose distribution in patients undergoing breast conservation while at the same time minimizing dose to the contralateral breast, thereby reducing the potential carcinogenic effects.

Coronal Magnetic Field Measurement from EUV Images Made by the Solar Dynamics Observatory

NASA Technical Reports Server (NTRS)

Gopalswamy, Natchimuthuk; Nitta, Nariaki; Akiyama, Sachiko; Makela, Pertti; Yashiro, Seiji

2012-01-01

By measuring the geometrical properties of the coronal mass ejection (CME) flux rope and the leading shock observed on 2010 June 13 by the Solar Dynamics Observatory (SDO) mission's Atmospheric Imaging Assembly we determine the Alfven speed and the magnetic field strength in the inner corona at a heliocentric distance of approx. 1.4 Rs The basic measurements are the shock standoff distance (Delta R) ahead of the CME flux rope, the radius of curvature of the flux rope (R(sub c)), and the shock speed. We first derive the Alfvenic Mach number (M) using the relationship, Delta R/R(sub c) = 0.81[(gamma-1) M(exp 2) + 2] / [(gamma +1)(M2 - 1)], where gamma is the only parameter that needed to be assumed. For gamma = 4/3, the Mach number declined from 3.7 to 1.5 indicating shock weakening within the field of view of the imager. The shock formation coincided with the appearance of a type II radio burst at a frequency of approx. 300 MHz (harmonic component), providing an independent confirmation of the shock. The shock compression ratio derived from the radio dynamic spectrum was found to be consistent with that derived from the theory of fast-mode MHD shocks. From the measured shock speed and the derived Mach number, we found the Alfven speed to increase from approx 140 km/s to 460 km/s over the distance range 1.2-1.5 Rs. By deriving the upstream plasma density from the emission frequency of the associated type II radio burst, we determined the coronal magnetic field to be in the range 1.3-1.5 G. The derived magnetic field values are consistent with other estimates in a similar distance range. This work demonstrates that the EUV imagers, in the presence of radio dynamic spectra, can be used as coronal magnetometers

Mechanistic understanding of human-wildlife conflict through a novel application of dynamic occupancy models.

PubMed

Goswami, Varun R; Medhi, Kamal; Nichols, James D; Oli, Madan K

2015-08-01

Crop and livestock depredation by wildlife is a primary driver of human-wildlife conflict, a problem that threatens the coexistence of people and wildlife globally. Understanding mechanisms that underlie depredation patterns holds the key to mitigating conflicts across time and space. However, most studies do not consider imperfect detection and reporting of conflicts, which may lead to incorrect inference regarding its spatiotemporal drivers. We applied dynamic occupancy models to elephant crop depredation data from India between 2005 and 2011 to estimate crop depredation occurrence and model its underlying dynamics as a function of spatiotemporal covariates while accounting for imperfect detection of conflicts. The probability of detecting conflicts was consistently <1.0 and was negatively influenced by distance to roads and elevation gradient, averaging 0.08-0.56 across primary periods (distinct agricultural seasons within each year). The probability of crop depredation occurrence ranged from 0.29 (SE 0.09) to 0.96 (SE 0.04). The probability that sites raided by elephants in primary period t would not be raided in primary period t + 1 varied with elevation gradient in different seasons and was influenced negatively by mean rainfall and village density and positively by distance to forests. Negative effects of rainfall variation and distance to forests best explained variation in the probability that sites not raided by elephants in primary period t would be raided in primary period t + 1. With our novel application of occupancy models, we teased apart the spatiotemporal drivers of conflicts from factors that influence how they are observed, thereby allowing more reliable inference on mechanisms underlying observed conflict patterns. We found that factors associated with increased crop accessibility and availability (e.g., distance to forests and rainfall patterns) were key drivers of elephant crop depredation dynamics. Such an understanding is essential for rigorous prediction of future conflicts, a critical requirement for effective conflict management in the context of increasing human-wildlife interactions. © 2015 Society for Conservation Biology.

On the asymmetric evolution of the perihelion distances of near-Earth Jupiter family comets around the discovery time

NASA Astrophysics Data System (ADS)

Sosa, A.; Fernández, J. A.; Pais, P.

2012-12-01

We study the dynamical evolution of the near-Earth Jupiter family comets (NEJFCs) that came close to or crossed the Earth's orbit at the epoch of their discovery (perihelion distances qdisc < 1.3 AU). We found a minimum in the time evolution of the mean perihelion distance bar{q} of the NEJFCs at the discovery time of each comet (taken as t = 0) and a past-future asymmetry of bar{q} in an interval -1000 yr, +1000 yr centred on t = 0, confirming previous results. The asymmetry indicates that there are more comets with greater q in the past than in the future. For comparison purposes, we also analysed the population of near-Earth asteroids in cometary orbits (defined as those with aphelion distances Q > 4.5 AU) and with absolute magnitudes H < 18. We found some remarkable differences in the dynamical evolution of both populations that argue against a common origin. To further analyse the dynamical evolution of NEJFCs, we integrated in time a large sample of fictitious comets, cloned from the observed NEJFCs, over a 20 000 yr time interval and started the integration before the comet's discovery time, when it had a perihelion distance q > 2 AU. By assuming that NEJFCs are mostly discovered when they decrease their perihelion distances below a certain threshold qthre = 1.05 AU for the first time during their evolution, we were able to reproduce the main features of the observed bar{q} evolution in the interval [-1000, 1000] yr with respect to the discovery time. Our best fits indicate that 40% of the population of NEJFCs would be composed of young, fresh comets that entered the region q < 2 AU a few hundred years before decreasing their perihelion distances below qthre, while 60% would be composed of older, more evolved comets, discovered after spending at least 3000 yr in the q < 2 AU region before their perihelion distances drop below qthre. As a byproduct, we put some constraints on the physical lifetime τphys of NEJFCs in the q < 2 AU region. We found a lower limit of a few hundreds of revolutions and an upper limit of about 10 000-12 000 yr, or about 1600-2000 revolutions, somewhat longer than some previous estimates. These constraints are consistent with other estimates of τphys, based either on mass loss (sublimation, outbursts, splittings) or on the extinction rate of Jupiter family comets (JFCs).

Repulsive Casimir-Polder potential by a negative reflecting surface

NASA Astrophysics Data System (ADS)

Yuan, Qi-Zhang

2015-07-01

We present a scheme to generate an all-range long repulsive Casimir-Polder potential between a perfect negative reflecting surface and a ground-state atom. The repulsive potential is stable and does not decay with time. The Casimir-Polder potential is proportional to z-2 at short atom-surface distances and to z-4 at long atom-surface distances. Because of these advantages, this potential can help in building quantum reflectors, quantum levitating devices, and waveguides for matter waves.

DYNAMICS OF WATER TRANSPORT AND STORAGE IN CONIFERS STUDIED WITH DEUTERIUM AND HEAT TRACING TECHNIQUES

EPA Science Inventory

The volume and complexity of their vascular systems make the dynamics of long-distance water transport difficult to study. We used heat and deuterated water (D2O) as tracers to characterize whole-tree water transport and storage properties in individual trees belonging to the co...

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...

The effects of five-order nonlinear on the dynamics of dark solitons in optical fiber.

PubMed

He, Feng-Tao; Wang, Xiao-Lin; Duan, Zuo-Liang

2013-01-01

We study the influence of five-order nonlinear on the dynamic of dark soliton. Starting from the cubic-quintic nonlinear Schrodinger equation with the quadratic phase chirp term, by using a similarity transformation technique, we give the exact solution of dark soliton and calculate the precise expressions of dark soliton's width, amplitude, wave central position, and wave velocity which can describe the dynamic behavior of soliton's evolution. From two different kinds of quadratic phase chirps, we mainly analyze the effect on dark soliton's dynamics which different fiver-order nonlinear term generates. The results show the following two points with quintic nonlinearities coefficient increasing: (1) if the coefficients of the quadratic phase chirp term relate to the propagation distance, the solitary wave displays a periodic change and the soliton's width increases, while its amplitude and wave velocity reduce. (2) If the coefficients of the quadratic phase chirp term do not depend on propagation distance, the wave function only emerges in a fixed area. The soliton's width increases, while its amplitude and the wave velocity reduce.

The Effects of Five-Order Nonlinear on the Dynamics of Dark Solitons in Optical Fiber

PubMed Central

Wang, Xiao-Lin; Duan, Zuo-Liang

2013-01-01

We study the influence of five-order nonlinear on the dynamic of dark soliton. Starting from the cubic-quintic nonlinear Schrodinger equation with the quadratic phase chirp term, by using a similarity transformation technique, we give the exact solution of dark soliton and calculate the precise expressions of dark soliton's width, amplitude, wave central position, and wave velocity which can describe the dynamic behavior of soliton's evolution. From two different kinds of quadratic phase chirps, we mainly analyze the effect on dark soliton's dynamics which different fiver-order nonlinear term generates. The results show the following two points with quintic nonlinearities coefficient increasing: (1) if the coefficients of the quadratic phase chirp term relate to the propagation distance, the solitary wave displays a periodic change and the soliton's width increases, while its amplitude and wave velocity reduce. (2) If the coefficients of the quadratic phase chirp term do not depend on propagation distance, the wave function only emerges in a fixed area. The soliton's width increases, while its amplitude and the wave velocity reduce. PMID:23818814

Galaxy distances and deviations from universal expansion; Proceedings of the NATO Advanced Research Workshop, Kona, HI, Jan. 13-17, 1986

NASA Astrophysics Data System (ADS)

Madore, Barry F.; Tully, R. Brent

A collection of papers on galaxy distances and deviations from universal expansion is presented. Individual topics addressed include: new results on the distance scale and the Hubble constant, Magellanic Clouds and the distance scale, CCD observations of Cepheids in nearby galaxies, distances using A supergiant stars, infrared calibration of the Cepheid distance scale, two stepping stones to the Hubble constant, physical models of supernovae and the distance scale, 21 cm line widths and distances of spiral galaxies, infrared color-luminosity relations for field galaxies, minimizing the scatter in the Tully-Fisher relation, photometry of galaxies and the local peculiar motion, elliptical galaxies and nonuniformities in the Hubble flow, and large-scale anisotropy in the Hubble flow. Also discussed are: improved distance indicator for elliptical galaxies, anisotropy of galaxies detected by IRAS, the local gravitational field, measurements of the CBR, measure of cosmological times, ages from nuclear cosmochronology, extragalactic gas at high redshift, supercluster infall models, Virgo infall and the mass density of the universe, dynamics of superclusters and Omega(0), distribution of galaxies versus dark matter, peculiar velocities and galaxy formation, cosmological shells and blast waves.

Trapping of quantum particles and light beams by switchable potential wells

NASA Astrophysics Data System (ADS)

Sonkin, Eduard; Malomed, Boris A.; Granot, Er'El; Marchewka, Avi

2010-09-01

We consider basic dynamical effects in settings based on a pair of local potential traps that may be effectively switched on and off, or suddenly displaced, by means of appropriate control mechanisms, such as scanning tunneling microscopy or photo-switchable quantum dots. The same models, based on the linear Schrödinger equation with time-dependent trapping potentials, apply to the description of optical planar systems designed for the switching of trapped light beams. The analysis is carried out in the analytical form, using exact solutions of the Schrödinger equation. The first dynamical problem considered in this work is the retention of a particle released from a trap which was suddenly turned off, while another local trap was switched on at a distance—immediately or with a delay. In this case, we demonstrate that the maximum of the retention rate is achieved at a specific finite value of the strength of the new trap, and at a finite value of the temporal delay, depending on the distance between the two traps. Another problem is retrapping of the bound particle when the addition of the second trap transforms the single-well setting into a double-well potential (DWP). In that case, we find probabilities for the retrapping into the ground or first excited state of the DWP. We also analyze effects entailed by the application of a kick to a bound particle, the most interesting one being a kick-induced transition between the DWP’s ground and excited states. In the latter case, the largest transition probability is achieved at a particular strength of the kick.

Exploration of the region near the sun-earth collinear libration points for the control of large formations

NASA Astrophysics Data System (ADS)

Heritier, Aurelie

Spacecraft formations possess many applications in the future of space exploration. During the last decade, due to the detection of a large number of extrasolar planets, new studies on formation flying in multi-body regimes have emerged to support searches for Earth-like planets in other solar systems. The L2 Sun-Earth libration point region has been a popular destination in creating an architecture for astronomical missions. It is a relatively cold environment, far from the disturbances of the Sun and, therefore, ideal for astronomical instruments. However, controlling multiple spacecraft in a multi-body environment is challenging and a good understanding of the natural dynamics in this regime is essential. The current investigation explores the dynamical environment near the L2 Sun-Earth libration point to aid in the control of formations of spacecraft. By exploiting the natural dynamics in the circular restricted three-body model (CR3BP), natural regions are determined that are particularly suitable for maintaining formations of spacecraft. The natural dynamics at small distances from a given reference trajectory are initially investigated for the placement of small formations of spacecraft. Some regions with low relative drift represent suitable locations to maintain small formations and are derived analytically using variational equations. Spacecraft located in such regions avoid large variations in their mutual distances while maintaining the orientation of the formation. These regions represent quadric surfaces, and the type of quadric surfaces, either ellipsoids or elliptic cylinders, depends on the eigenstructure reflecting the phase space along the given reference trajectory. The natural flow at large distances from a given reference trajectory is explored next to characterize regions that are suitable to maintain large formations, i.e., when the mutual distances between the spacecraft reaches tens of thousands of kilometers. Spheres of points at various locations along the reference orbit are constructed to classify the space, and regions of low natural drift on the spheres are numerically identified when the distance between two vehicles is large. These low drift regions are examined in detail, and a correspondance with the quadric surfaces that are derived for small formations is established. In particular, the orientation of these low drift zones along a given reference orbit are investigated as some parameters vary, such as the size of the formation as well as the reference orbit. Using the low natural drift regions, control strategies are then developed for large formations. Traditional controllers, such as impulsive maneuvers and linear quadratic regulators (LQR), are employed to quantify the level of control that is required to maintain large formations along specific directions in the CR3BP. Designs of new controllers are also investigated to produce some set of desired relative motions between two spacecraft placed at large mutual distances. In a potential formation option investigated in this analysis, a deputy vehicle maintains a fixed circular motion in a plane relative to a chief spacecraft moving along its reference trajectory. Finally, the effectiveness of using the low natural drift regions as derived for large formations is tested for the New Worlds Observer mission concept. This scenario involves a large telescope-occulter formation for star observations, to detect and characterize habitable terrestrial exoplanets. The low drift zones are employed to reduce the control effort to maintain a large telescope-occulter formation during the observation of inertially-fixed target stars. In particular, the occulter is maintained via a linear quadratic regulator during star observations. Given a set of inertially-fixed target stars, an automatic star sequence design process is proposed with observation and reconfiguration phases using the low drift regions. This design creates star sequences that lead to relatively small overall maneuver costs for this particular mission concept.

Ab initio Potential Energy Surface for H-H2

NASA Technical Reports Server (NTRS)

Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

1993-01-01

Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

Three-dimensional modeling and animation of two carpal bones: a technique.

PubMed

Green, Jason K; Werner, Frederick W; Wang, Haoyu; Weiner, Marsha M; Sacks, Jonathan M; Short, Walter H

2004-05-01

The objectives of this study were to (a). create 3D reconstructions of two carpal bones from single CT data sets and animate these bones with experimental in vitro motion data collected during dynamic loading of the wrist joint, (b). develop a technique to calculate the minimum interbone distance between the two carpal bones, and (c). validate the interbone distance calculation process. This method utilized commercial software to create the animations and an in-house program to interface with three-dimensional CAD software to calculate the minimum distance between the irregular geometries of the bones. This interbone minimum distance provides quantitative information regarding the motion of the bones studied and may help to understand and quantify the effects of ligamentous injury.

Replication of Cancellation Orders Using First-Passage Time Theory in Foreign Currency Market

NASA Astrophysics Data System (ADS)

Boilard, Jean-François; Kanazawa, Kiyoshi; Takayasu, Hideki; Takayasu, Misako

Our research focuses on the annihilation dynamics of limit orders in a spot foreign currency market for various currency pairs. We analyze the cancellation order distribution conditioned on the normalized distance from the mid-price; where the normalized distance is defined as the final distance divided by the initial distance. To reproduce real data, we introduce two simple models that assume the market price moves randomly and cancellation occurs either after fixed time t or following the Poisson process. Results of our model qualitatively reproduce basic statistical properties of cancellation orders of the data when limit orders are cancelled according to the Poisson process. We briefly discuss implication of our findings in the construction of more detailed microscopic models.

Modeling dilute pyroclastic density currents on Earth and Mars

NASA Astrophysics Data System (ADS)

Clarke, A. B.; Brand, B. D.; De'Michieli Vitturi, M.

2013-12-01

The surface of Mars has been shaped extensively by volcanic activity, including explosive eruptions that may have been heavily influenced by water- or ice-magma interaction. However, the dynamics of associated pyroclastic density currents (PDCs) under Martian atmospheric conditions and controls on deposition and runout from such currents are poorly understood. This work combines numerical modeling with terrestrial field measurements to explore the dynamics of dilute PDC dynamics on Earth and Mars, especially as they relate to deposit characteristics. We employ two numerical approaches. Model (1) consists of simulation of axi-symmetric flow and sedimentation from a steady-state, depth-averaged density current. Equations for conservation of mass, momentum, and energy are solved simultaneously, and the effects of atmospheric entrainment, particle sedimentation, basal friction, temperature changes, and variations in current thickness and density are explored. The Rouse number and Brunt-Väisälä frequency are used to estimate the wavelength of internal gravity waves in a density-stratified current, which allows us to predict deposit dune wavelengths. The model predicts realistic runout distances and bedform wavelengths for several well-documented field cases on Earth. The model results also suggest that dilute PDCs on Mars would have runout distances up to three times that of equivalent currents on Earth and would produce longer-wavelength bedforms. In both cases results are heavily dependent on source conditions, grain-size characteristics, and entrainment and friction parameters. Model (2) relaxes several key simplifications, resulting in a fully 3D, multiphase, unsteady model that captures more details of propagation, including density stratification, and depositional processes. Using this more complex approach, we focus on the role of unsteady or pulsatory vent conditions typically associated with phreatomagmatic eruptions. Runout distances from Model (2) agree reasonably well with Model (1) results, but details of deposit distribution vary between the two models. Model (2) shows that the Earth case initially outpaces the Mars case due to faster propagation velocities associated with higher gravitational acceleration. However, the Mars currents ultimately out-distance the Earth currents due to slower particle settling rates, which also largely explain the longer wavelength bedforms. Model (2) also predicts a peak in the streamwise distribution of deposits farther from the source compared to equivalent results from Model (1), and produces more complex patterns of vertical distribution of particles in the moving current, which varies significantly in time and space. This combination of modeling and deposit data results in a powerful tool for testing hypotheses related to PDCs on Mars, potentially improving our capacity to interpret Martian features on both the outcrop (e.g., Home Plate) and regional scale (e.g., Apollinaris Mons).

Vapor plume oscillation mechanisms in transient keyhole during tandem dual beam fiber laser welding

NASA Astrophysics Data System (ADS)

Chen, Xin; Zhang, Xiaosi; Pang, Shengyong; Hu, Renzhi; Xiao, Jianzhong

2018-01-01

Vapor plume oscillations are common physical phenomena that have an important influence on the welding process in dual beam laser welding. However, until now, the oscillation mechanisms of vapor plumes remain unclear. This is primarily because mesoscale vapor plume dynamics inside a millimeter-scale, invisible, and time-dependent keyhole are difficult to quantitatively observe. In this paper, based on a developed three-dimensional (3D) comprehensive model, the vapor plume evolutions in a dynamical keyhole are directly simulated in tandem dual beam, short-wavelength laser welding. Combined with the vapor plume behaviors outside the keyhole observed by high-speed imaging, the vapor plume oscillations in dynamical keyholes at different inter-beam distances are the first, to our knowledge, to be quantitatively analyzed. It is found that vapor plume oscillations outside the keyhole mainly result from vapor plume instabilities inside the keyhole. The ejection velocity at the keyhole opening and dynamical behaviors outside the keyhole of a vapor plume both violently oscillate with the same order of magnitude of high frequency (several kHz). Furthermore, the ejection speed at the keyhole opening and ejection area outside the keyhole both decrease as the beam distance increases, while the degree of vapor plume instability first decreases and then increases with increasing beam distance from 0.6 to 1.0 mm. Moreover, the oscillation mechanisms of a vapor plume inside the dynamical keyhole irradiated by dual laser beams are investigated by thoroughly analyzing the vapor plume occurrence and flow process. The vapor plume oscillations in the dynamical keyhole are found to mainly result from violent local evaporations and severe keyhole geometry variations. In short, the quantitative method and these findings can serve as a reference for further understanding of the physical mechanisms in dual beam laser welding and of processing optimizations in industrial applications.

The geography of malaria genetics in the Democratic Republic of Congo: A complex and fragmented landscape

PubMed Central

Carrel, Margaret; Patel, Jaymin; Taylor, Steve M.; Janko, Mark; Mwandagalirwa, Melchior Kashamuka; Tshefu, Antoinette K.; Escalante, Ananias A.; McCollum, Andrea; Alam, Md Tauqeer; Udhayakumar, Venkatachalam; Meshnick, Steven; Emch, Michael

2014-01-01

Understanding how malaria parasites move between populations is important, particularly given the potential for malaria to be reintroduced into areas where it was previously eliminated. We examine the distribution of malaria genetics across seven sites within the Democratic Republic of Congo (DRC) and two nearby countries, Ghana and Kenya, in order to understand how the relatedness of malaria parasites varies across space, and whether there are barriers to the flow of malaria parasites within the DRC or across borders. Parasite DNA was retrieved from dried blood spots from 7 Demographic and Health Survey sample clusters in the DRC. Malaria genetic characteristics of parasites from Ghana and Kenya were also obtained. For each of 9 geographic sites (7 DRC, 1 Ghana and 1 Kenya), a pair-wise RST statistic was calculated, indicating the genetic distance between malaria parasites found in those locations. Mapping genetics across the spatial extent of the study area indicates a complex genetic landscape, where relatedness between two proximal sites may be relatively high (RST > 0.64) or low (RST < 0.05), and where distal sites also exhibit both high and low genetic similarity. Mantel’s tests suggest that malaria genetics differ as geographic distances increase. Principal Coordinate Analysis suggests that genetically related samples are not co-located. Barrier analysis reveals no significant barriers to gene flow between locations. Malaria genetics in the DRC have a complex and fragmented landscape. Limited exchange of genes across space is reflected in greater genetic distance between malaria parasites isolated at greater geographic distances. There is, however, evidence for close genetic ties between distally located sample locations, indicating that movement of malaria parasites and flow of genes is being driven by factors other than distance decay. This research demonstrates the contributions that spatial disease ecology and landscape genetics can make to understanding the evolutionary dynamics of infectious diseases. PMID:25459204

Impaired Long Distance Functional Connectivity and Weighted Network Architecture in Alzheimer's Disease

PubMed Central

Liu, Yong; Yu, Chunshui; Zhang, Xinqing; Liu, Jieqiong; Duan, Yunyun; Alexander-Bloch, Aaron F.; Liu, Bing; Jiang, Tianzi; Bullmore, Ed

2014-01-01

Alzheimer's disease (AD) is increasingly recognized as a disconnection syndrome, which leads to cognitive impairment due to the disruption of functional activity across large networks or systems of interconnected brain regions. We explored abnormal functional magnetic resonance imaging (fMRI) resting-state dynamics, functional connectivity, and weighted functional networks, in a sample of patients with severe AD (N = 18) and age-matched healthy volunteers (N = 21). We found that patients had reduced amplitude and regional homogeneity of low-frequency fMRI oscillations, and reduced the strength of functional connectivity, in several regions previously described as components of the default mode network, for example, medial posterior parietal cortex and dorsal medial prefrontal cortex. In patients with severe AD, functional connectivity was particularly attenuated between regions that were separated by a greater physical distance; and loss of long distance connectivity was associated with less efficient global and nodal network topology. This profile of functional abnormality in severe AD was consistent with the results of a comparable analysis of data on 2 additional groups of patients with mild AD (N = 17) and amnestic mild cognitive impairment (MCI; N = 18). A greater degree of cognitive impairment, measured by the mini-mental state examination across all patient groups, was correlated with greater attenuation of functional connectivity, particularly over long connection distances, for example, between anterior and posterior components of the default mode network, and greater reduction of global and nodal network efficiency. These results indicate that neurodegenerative disruption of fMRI oscillations and connectivity in AD affects long-distance connections to hub nodes, with the consequent loss of network efficiency. This profile was evident also to a lesser degree in the patients with less severe cognitive impairment, indicating that the potential of resting-state fMRI measures as biomarkers or predictors of disease progression in AD. PMID:23314940

A multilevel-skin neighbor list algorithm for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Chenglong; Zhao, Mingcan; Hou, Chaofeng; Ge, Wei

2018-01-01

Searching of the interaction pairs and organization of the interaction processes are important steps in molecular dynamics (MD) algorithms and are critical to the overall efficiency of the simulation. Neighbor lists are widely used for these steps, where thicker skin can reduce the frequency of list updating but is discounted by more computation in distance check for the particle pairs. In this paper, we propose a new neighbor-list-based algorithm with a precisely designed multilevel skin which can reduce unnecessary computation on inter-particle distances. The performance advantages over traditional methods are then analyzed against the main simulation parameters on Intel CPUs and MICs (many integrated cores), and are clearly demonstrated. The algorithm can be generalized for various discrete simulations using neighbor lists.

The Seasonal Dynamics of Artificial Nest Predation Rates along Edges in a Mosaic Managed Reedbed

PubMed Central

Malzer, Iain; Helm, Barbara

2015-01-01

Boundaries between different habitats can be responsible for changes in species interactions, including modified rates of encounter between predators and prey. Such ‘edge effects’ have been reported in nesting birds, where nest predation rates can be increased at habitat edges. The literature concerning edge effects on nest predation rates reveals a wide variation in results, even within single habitats, suggesting edge effects are not fixed, but dynamic throughout space and time. This study demonstrates the importance of considering dynamic mechanisms underlying edge effects and their relevance when undertaking habitat management. In reedbed habitats, management in the form of mosaic winter reed cutting can create extensive edges which change rapidly with reed regrowth during spring. We investigate the seasonal dynamics of reedbed edges using an artificial nest experiment based on the breeding biology of a reedbed specialist. We first demonstrate that nest predation decreases with increasing distance from the edge of cut reed blocks, suggesting edge effects have a pivotal role in this system. Using repeats throughout the breeding season we then confirm that nest predation rates are temporally dynamic and decline with the regrowth of reed. However, effects of edges on nest predation were consistent throughout the season. These results are of practical importance when considering appropriate habitat management, suggesting that reed cutting may heighten nest predation, especially before new growth matures. They also contribute directly to an overall understanding of the dynamic processes underlying edge effects and their potential role as drivers of time-dependent habitat use. PMID:26448338

Ecological Succession Pattern of Fungal Community in Soil along a Retreating Glacier

PubMed Central

Tian, Jianqing; Qiao, Yuchen; Wu, Bing; Chen, Huai; Li, Wei; Jiang, Na; Zhang, Xiaoling; Liu, Xingzhong

2017-01-01

Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2–188 years of deglaciation. Shannon diversity and evenness peaked at a distance of 370 m and declined afterwards. The response of fungal diversity to distance varied in different phyla. Basidiomycota Shannon diversity significantly decreased with distance, while the pattern of Rozellomycota Shannon diversity was unimodal. Abundance of most frequencies OTU2 (Cryptococcus terricola) increased with successional distance, whereas that of OTU65 (Tolypocladium tundrense) decreased. Based on null deviation analyses, composition of the fungal community was initially governed by deterministic processes strongly but later less deterministic processes. Our results revealed that distance, altitude, soil microbial biomass carbon, soil microbial biomass nitrogen and NH4+–N significantly correlated with fungal community composition along the chronosequence. These results suggest that the drivers of fungal community are dynamics in a glacier chronosequence, that may relate to fungal ecophysiological traits and adaptation in an evolving ecosystem. The information will provide understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession under different scales and scenario. PMID:28649234

Ecological Succession Pattern of Fungal Community in Soil along a Retreating Glacier.

PubMed

Tian, Jianqing; Qiao, Yuchen; Wu, Bing; Chen, Huai; Li, Wei; Jiang, Na; Zhang, Xiaoling; Liu, Xingzhong

2017-01-01

Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2-188 years of deglaciation. Shannon diversity and evenness peaked at a distance of 370 m and declined afterwards. The response of fungal diversity to distance varied in different phyla. Basidiomycota Shannon diversity significantly decreased with distance, while the pattern of Rozellomycota Shannon diversity was unimodal. Abundance of most frequencies OTU2 ( Cryptococcus terricola ) increased with successional distance, whereas that of OTU65 ( Tolypocladium tundrense ) decreased. Based on null deviation analyses, composition of the fungal community was initially governed by deterministic processes strongly but later less deterministic processes. Our results revealed that distance, altitude, soil microbial biomass carbon, soil microbial biomass nitrogen and [Formula: see text]-N significantly correlated with fungal community composition along the chronosequence. These results suggest that the drivers of fungal community are dynamics in a glacier chronosequence, that may relate to fungal ecophysiological traits and adaptation in an evolving ecosystem. The information will provide understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession under different scales and scenario.

Research on structures, mechanical properties, and mechanical responses of TKX-50 and TKX-50 based PBX with molecular dynamics.

PubMed

Ma, Song; Li, Yajin; Li, Yang; Luo, Yunjun

2016-02-01

To improve the practicality and safety of a novel explosive dihydroxylamm onium 5,5'-bis (tetrazole)-1,1'-diolate (TKX-50), polyvinylidene difluoride (PVDF) and polychlorotrifluoroe-thylene (PCTFE) were respectively added to the TKX-50, forming the polymer-bonded explosives (PBX). Interfacial and mechanical properties of PBX were investigated through molecular dynamics (MD) method, desensitizing mechanisms of fluorine-polymers for TKX-50 were researched by compression and bulk shear simulations. Results show that the binding energies (E bind ) between polymers (PVDF or PCTFE) and TKX-50 surfaces all rank in order of (011) > (100) > (010), shorter interatomic distance and the resulted higher potentials lead to higher E bind on TKX-50/PVDF interfaces than that on PCTFE/TKX-50 interfaces. Compared with TKX-50, the ductility of PBX is improved due to the isotropic mechanical property and flexibility of fluorine-polymers especially the PCTFE. Desensitizing effect of fluorine-polymers for TKX-50 is found under loading condition, which is attributed to the enhanced compressibility and buffer capacity against external pressure in compression, as well as the improved lubricity to reduce the sliding potentials in bulk shear process. Graphical Abstract Comparisons of the internal stress and slide potentials of the novel explosive,TKX-50 and its based PBX. Desensitizing effects can be found by the adding of fluorine-polymers, it owes to their better flexibility and lubricity as well as the amorphous nature.

Robust Dynamic Multi-objective Vehicle Routing Optimization Method.

PubMed

Guo, Yi-Nan; Cheng, Jian; Luo, Sha; Gong, Dun-Wei

2017-03-21

For dynamic multi-objective vehicle routing problems, the waiting time of vehicle, the number of serving vehicles, the total distance of routes were normally considered as the optimization objectives. Except for above objectives, fuel consumption that leads to the environmental pollution and energy consumption was focused on in this paper. Considering the vehicles' load and the driving distance, corresponding carbon emission model was built and set as an optimization objective. Dynamic multi-objective vehicle routing problems with hard time windows and randomly appeared dynamic customers, subsequently, were modeled. In existing planning methods, when the new service demand came up, global vehicle routing optimization method was triggered to find the optimal routes for non-served customers, which was time-consuming. Therefore, robust dynamic multi-objective vehicle routing method with two-phase is proposed. Three highlights of the novel method are: (i) After finding optimal robust virtual routes for all customers by adopting multi-objective particle swarm optimization in the first phase, static vehicle routes for static customers are formed by removing all dynamic customers from robust virtual routes in next phase. (ii)The dynamically appeared customers append to be served according to their service time and the vehicles' statues. Global vehicle routing optimization is triggered only when no suitable locations can be found for dynamic customers. (iii)A metric measuring the algorithms' robustness is given. The statistical results indicated that the routes obtained by the proposed method have better stability and robustness, but may be sub-optimum. Moreover, time-consuming global vehicle routing optimization is avoided as dynamic customers appear.

Army Distance Learning: Potential for Reducing Shortages in Army Enlisted Occupations.

ERIC Educational Resources Information Center

Shanley, Michael G.; Leonard, Henry A.; Winkler, John D.

The potential of distance learning (DL) to expedite the U.S. Army's efforts to redress personnel shortages in Army enlisted occupations was studied by evaluating how DL-based training strategies might affect skill shortages in the following occupations: helicopter repairer; electronic switching system operator; microwave systems…

Crossing Cultures and Borders in International Online Distance Higher Education

ERIC Educational Resources Information Center

Sadykova, Gulnara; Dautermann, Jennie

2009-01-01

The growing demand for higher education worldwide, along with global expansion of telecommunication technologies, give online distance education a potential world-wide reach for institutions in many countries. Given the persistent international digital divide and the potential for the host institutions and languages to be those of wealthy,…

Eliciting Naturalistic Cortical Responses with a Sensory Prosthesis via Optimized Microstimulation

DTIC Science & Technology

2016-08-12

error and correlation as metrics amenable to highly efficient convex optimization. This study concentrates on characterizing the neural responses to both...spiking signal. For LFP, distance measures such as the traditional mean-squared error and cross- correlation can be used, whereas distances between spike...with parameters that describe their associated temporal dynamics and relations to the observed output. A description of the model follows, but we

Impact of Underwater Explosions on Concrete Bridge Foundations

DTIC Science & Technology

2016-06-01

www.theconstructioncivil.org/ [16] M. Aggour, A. Hachichi and M. Mayer, “Nondestructive evaluation of timber bridge piles,” in Proceedings of a Session a Structure Congress...detonation must be executed a safe distance from any critical infrastructure to ensure the survivability of the structure . This thesis implements...be executed a safe distance from any critical infrastructure to ensure the survivability of the structure . This thesis implements the Dynamic System

Long Distance Modulation of Disorder-to-Order Transitions in Protein Allostery.

PubMed

Wang, Jingheng; Custer, Gregory; Beckett, Dorothy; Matysiak, Silvina

2017-08-29

Elucidation of the molecular details of allosteric communication between distant sites in a protein is key to understanding and manipulating many biological regulatory processes. Although protein disorder is acknowledged to play an important thermodynamic role in allostery, the molecular mechanisms by which this disorder is harnessed for long distance communication are known for a limited number of systems. Transcription repression by the Escherichia coli biotin repressor, BirA, is allosterically activated by binding of the small molecule effector biotinoyl-5'-AMP. The effector acts by promoting BirA dimerization, which is a prerequisite for sequence-specific binding to the biotin biosynthetic operon operator sequence. A 30 Å distance separates the effector binding and dimerization surfaces in BirA, and previous studies indicate that allostery is mediated, in part, by disorder-to-order transitions on the two coupled sites. In this work, combined experimental and computational methods have been applied to investigate the molecular basis of allosteric communication in BirA. Double-mutant cycle analysis coupled with thermodynamic measurements indicates functional coupling between residues in disordered loops on the two distant surfaces. All atom molecular dynamics simulations reveal that this coupling occurs through long distance reciprocal modulation of the structure and dynamics of disorder-to-order transitions on the two surfaces.

Heterodyne laser Doppler distance sensor with phase coding measuring stationary as well as laterally and axially moving objects

NASA Astrophysics Data System (ADS)

Pfister, T.; Günther, P.; Nöthen, M.; Czarske, J.

2010-02-01

Both in production engineering and process control, multidirectional displacements, deformations and vibrations of moving or rotating components have to be measured dynamically, contactlessly and with high precision. Optical sensors would be predestined for this task, but their measurement rate is often fundamentally limited. Furthermore, almost all conventional sensors measure only one measurand, i.e. either out-of-plane or in-plane distance or velocity. To solve this problem, we present a novel phase coded heterodyne laser Doppler distance sensor (PH-LDDS), which is able to determine out-of-plane (axial) position and in-plane (lateral) velocity of rough solid-state objects simultaneously and independently with a single sensor. Due to the applied heterodyne technique, stationary or purely axially moving objects can also be measured. In addition, it is shown theoretically as well as experimentally that this sensor offers concurrently high temporal resolution and high position resolution since its position uncertainty is in principle independent of the lateral object velocity in contrast to conventional distance sensors. This is a unique feature of the PH-LDDS enabling precise and dynamic position and shape measurements also of fast moving objects. With an optimized sensor setup, an average position resolution of 240 nm was obtained.

Dynamic visual acuity using "far" and "near" targets

NASA Technical Reports Server (NTRS)

Peters, Brian T.; Bloomberg, Jacob J.

2005-01-01

CONCLUSIONS: DVA may be useful for assessing the functional consequences of an impaired gaze stabilization mechanism or for testing the effectiveness of a rehabilitation paradigm. Because target distance influences the relative contributions of canal and otolith inputs, the ability to measure DVA at near and far viewing distances may also lead to tests that will independently assess canal and otolith function. OBJECTIVE: To present and test a methodology that uses dynamic visual acuity (DVA) to assess the efficacy of compensatory gaze mechanisms during a functionally relevant activity that differentially measures canal and otolith function. MATERIAL AND METHODS: The effect of treadmill walking at a velocity of 1.79 m/s on subjects' visual acuity was assessed at each of two viewing distances. A custom-written threshold determination program was used to display Landolt C optotypes on a laptop computer screen during a "far" (4 m) target condition and on a micro-display for a "near" (50 cm) target condition. The walking acuity scores for each target distance were normalized by subtracting a corresponding acuity measure obtained while standing still on the treadmill belt. RESULTS: As predicted by subjective reports of relative target motion, the decrease in visual acuity was significantly greater (p < 0.00001) for the near compared to the far condition.

During running in place, grid cells integrate elapsed time and distance run

PubMed Central

Kraus, Benjamin J.; Brandon, Mark P.; Robinson, Robert J.; Connerney, Michael A.; Hasselmo, Michael E.; Eichenbaum, Howard

2015-01-01

Summary The spatial scale of grid cells may be provided by self-generated motion information or by external sensory information from environmental cues. To determine whether grid cell activity reflects distance traveled or elapsed time independent of external information, we recorded grid cells as animals ran in place on a treadmill. Grid cell activity was only weakly influenced by location but most grid cells and other neurons recorded from the same electrodes strongly signaled a combination of distance and time, with some signaling only distance or time. Grid cells were more sharply tuned to time and distance than non-grid cells. Many grid cells exhibited multiple firing fields during treadmill running, parallel to the periodic firing fields observed in open fields, suggesting a common mode of information processing. These observations indicate that, in the absence of external dynamic cues, grid cells integrate self-generated distance and time information to encode a representation of experience. PMID:26539893

Correlation of the Y-Balance Test with Lower-limb Strength of Adult Women

PubMed Central

Lee, Dong-Kyu; Kim, Gyoung-Mo; Ha, Sung-Min; Oh, Jae-Seop

2014-01-01

[Purpose] The purpose of this study was to elucidate the relationship between Y-balance test (YBT) distance and the lower-limb strength of adult women. [Subjects] Forty women aged 45 to 80 years volunteered for this study. [Methods] The participants were tested for maximal muscle strength of the lower limbs (hip extensors, hip flexors, hip abductors, knee extensors, knee flexors, and ankle dorsiflexors) and YBT distances in the anterior, posteromedial, and posterolateral directions. Pearson’s correlation coefficient was used to quantify the linear relationships between YBT distances and lower-limb strength. [Results] Hip extensor and knee flexor strength were positively correlated with YBT anterior distance. Hip extensor, hip abductor, and knee flexor strength were positively correlated with the YBT posteromedial distance. Hip extensor and knee flexor strength were positively correlated with YBT posterolateral distance. [Conclusion] There was a weak correlation between lower-limb strength (hip extensors, hip abductors, and knee flexors) and dynamic postural control as measured by the YBT. PMID:24926122

Clast comminution during pyroclastic density current transport: Mt St Helens

NASA Astrophysics Data System (ADS)

Dawson, B.; Brand, B. D.; Dufek, J.

2011-12-01

Volcanic clasts within pyroclastic density currents (PDCs) tend to be more rounded than those in fall deposits. This rounding reflects degrees of comminution during transport, which produces an increase in fine-grained ash with distance from source (Manga, M., Patel, A., Dufek., J. 2011. Bull Volcanol 73: 321-333). The amount of ash produced due to comminution can potentially affect runout distance, deposit sorting, the volume of ash lofted into the upper atmosphere, and increase internal pore pressure (e.g., Wohletz, K., Sheridan, M. F., Brown, W.K. 1989. J Geophy Res, 94, 15703-15721). For example, increased pore pressure has been shown to produce longer runout distances than non-comminuted PDC flows (e.g., Dufek, J., and M. Manga, 2008. J. Geophy Res, 113). We build on the work of Manga et al., (2011) by completing a pumice abrasion study for two well-exposed flow units from the May 18th, 1980 eruption of Mt St Helens (MSH). To quantify differences in comminution from source, sampling and the image analysis technique developed in Manga et al., 2010 was completed at distances proximal, medial, and distal from source. Within the units observed, data was taken from the base, middle, and pumice lobes within the outcrops. Our study is unique in that in addition to quantifying the degree of pumice rounding with distance from source, we also determine the possible range of ash sizes produced during comminution by analyzing bubble wall thickness of the pumice through petrographic and SEM analysis. The proportion of this ash size is then measured relative to the grain size of larger ash with distance from source. This allows us to correlate ash production with degree of rounding with distance from source, and determine the fraction of the fine ash produced due to comminution versus vent-fragmentation mechanisms. In addition we test the error in 2D analysis by completing a 3D image analysis of selected pumice samples using a Camsizer. We find that the roundness of PDC pumice at MSH increases with distance from source, as does the quantity of fine-grained ash. In addition, we have made the first steps towards determining the proportion of fine ash produced by comminution with distance from source. These results are being tested by numerical methods to understand the effect of an increase in fine ash on overall flow dynamics of the PDCs in which they were produced.

Off-fault heterogeneities promote supershear transition of dynamic mode II cracks

NASA Astrophysics Data System (ADS)

Albertini, Gabriele; Kammer, David S.

2017-08-01

The transition from sub-Rayleigh to supershear propagation of mode II cracks is a fundamental problem of fracture mechanics. It has extensively been studied in homogeneous uniform setups. When the applied shear load exceeds a critical value, transition occurs through the Burridge-Andrews mechanism at a well-defined crack length. However, velocity structures in geophysical conditions can be complex and affect the transition. Damage induced by previous earthquakes causes low-velocity zones surrounding mature faults and inclusions with contrasting material properties can be present at seismogenic depth. We relax the assumption of homogeneous media and investigate dynamic shear fracture in heterogeneous media using two-dimensional finite element simulations and a linear slip-weakening law. We analyze the role of heterogeneities in the elastic media, while keeping the frictional interface properties uniform. We show that supershear transition is possible due to the sole presence of favorable off-fault heterogeneities. Subcritical shear loads, for which propagation would remain permanently sub-Rayleigh in an equivalent homogeneous setup, will transition to supershear as a result of reflected waves. P wave reflected as S waves, followed by further reflections, affect the amplitude of the shear stress peak in front of the propagating crack, leading to supershear transition. A wave reflection model allows to uniquely describe the effect of off-fault inclusions on the shear stress peak. A competing mechanism of modified released potential energy affects transition and becomes predominant with decreasing distance between fault and inclusions. For inclusions at far distances, the wave reflection is the predominant mechanism.

The interacting effects of food, spring temperature, and global climate cycles on population dynamics of a migratory songbird.

PubMed

Townsend, Andrea K; Cooch, Evan G; Sillett, T Scott; Rodenhouse, Nicholas L; Holmes, Richard T; Webster, Michael S

2016-02-01

Although long-distance migratory songbirds are widely believed to be at risk from warming temperature trends, species capable of attempting more than one brood in a breeding season could benefit from extended breeding seasons in warmer springs. To evaluate local and global factors affecting population dynamics of the black-throated blue warbler (Setophaga caerulescens), a double-brooded long-distance migrant, we used Pradel models to analyze 25 years of mark-recapture data collected in New Hampshire, USA. We assessed the effects of spring temperature (local weather) and the El Niño Southern Oscillation index (a global climate cycle), as well as predator abundance, insect biomass, and local conspecific density on population growth in the subsequent year. Local and global climatic conditions affected warbler populations in different ways. We found that warbler population growth was lower following El Niño years (which have been linked to poor survival in the wintering grounds and low fledging weights in the breeding grounds) than La Niña years. At a local scale, populations increased following years with warm springs and abundant late-season food, but were unaffected by spring temperature following years when food was scarce. These results indicate that the warming temperature trends might have a positive effect on recruitment and population growth of black-throated blue warblers if food abundance is sustained in breeding areas. In contrast, potential intensification of future El Niño events could negatively impact vital rates and populations of this species. © 2015 John Wiley & Sons Ltd.

Forest cover influences dispersal distance of white-tailed deer

USGS Publications Warehouse

Long, E.S.; Diefenbach, D.R.; Rosenberry, C.S.; Wallingford, B.D.; Grund, M.D.

2005-01-01

Animal dispersal patterns influence gene flow, disease spread, population dynamics, spread of invasive species, and establishment of rare or endangered species. Although differences in dispersal distances among taxa have been reported, few studies have described plasticity of dispersal distance among populations of a single species. In 2002-2003, we radiomarked 308 juvenile (7- to 10-month-old), male white-tailed deer (Odocoileus virginianus) in 2 study areas in Pennsylvania. By using a meta-analysis approach, we compared dispersal rates and distances from these populations together with published reports of 10 other nonmigratory populations of white-tailed deer. Population density did not influence dispersal rate or dispersal distance, nor did forest cover influence dispersal rate. However, average (r2 = 0.94, P < 0.001, d.f. = 9) and maximum (r2 = 0.86, P = 0.001, d.f. = 7) dispersal distances of juvenile male deer were greater in habitats with less forest cover. Hence, dispersal behavior of this habitat generalist varies, and use of landscape data to predict population-specific dispersal distances may aid efforts to model population spread, gene flow, or disease transmission. ?? 2005 American Society of Mammalogists.

Distance estimation and collision prediction for on-line robotic motion planning

NASA Technical Reports Server (NTRS)

Kyriakopoulos, K. J.; Saridis, G. N.

1991-01-01

An efficient method for computing the minimum distance and predicting collisions between moving objects is presented. This problem has been incorporated in the framework of an in-line motion planning algorithm to satisfy collision avoidance between a robot and moving objects modeled as convex polyhedra. In the beginning the deterministic problem, where the information about the objects is assumed to be certain is examined. If instead of the Euclidean norm, L(sub 1) or L(sub infinity) norms are used to represent distance, the problem becomes a linear programming problem. The stochastic problem is formulated, where the uncertainty is induced by sensing and the unknown dynamics of the moving obstacles. Two problems are considered: (1) filtering of the minimum distance between the robot and the moving object, at the present time; and (2) prediction of the minimum distance in the future, in order to predict possible collisions with the moving obstacles and estimate the collision time.

Florida long-distance travel characteristics and their potential impacts on the transportation system.

DOT National Transportation Integrated Search

2013-03-01

The overall goal of this project is to enhance the fundamental understanding of Florida long-distance travel characteristics, and to provide policy implications for long-distance transportation planning in the future. To achieve the research goal, th...

Telecommunications, Internationalism, and Distance Education.

ERIC Educational Resources Information Center

Moore, Michael G.

1988-01-01

Discussion of the role of telecommunications in distance education focuses on teleconference networks and international cooperation. Highlights include the TELECON VII Distance Learning Conference, the use of teleconferencing by corporations for continuing education and training, and questions to be addressed concerning the future potential of…

Proximity to the US-Mexico border: a key to explaining geographic variation in US methamphetamine, cocaine and heroin purity.

PubMed

Cunningham, James K; Maxwell, Jane Carlisle; Campollo, Octavio; Cunningham, Kathryn I; Liu, Lon-Mu; Lin, Hui-Lin

2010-10-01

Although illicit drug purity is a widely discussed health risk, research explaining its geographic variation within a country is rare. This study examines whether proximity to the US-Mexico border, the United States' primary drug import portal, is associated with geographic variation in US methamphetamine, heroin and cocaine purity. Distances (proximity) between the US-Mexico border and locations of methamphetamine, cocaine and heroin seizures/acquisitions (n = 239,070) recorded in STRIDE (System to Retrieve Information from Drug Evidence) were calculated for the period of 1990-2004. The association of drug purity with these distances and other variables, including time and seizure/acquisition size, was examined using hierarchical multivariate linear modeling (HMLM). Coterminous United States. Methamphetamine, cocaine and heroin purity generally decreased with distance from the US-Mexico border. Heroin purity, however, after initially declining with distance, turned upwards-a U-shaped association. During 2000-04, methamphetamine purity also had a U-shaped association with distance. For each of the three drugs, temporal changes in the purity of small acquisitions (<10 g) were typically more dynamic in areas closer to the US-Mexico border. Geographic variance in methamphetamine, cocaine and heroin purity throughout the coterminous United States was associated with US-Mexico border proximity. The U-shaped associations between border-distance and purity for heroin and methamphetamine may be due to imports of those drugs via the eastern United States and southeast Canada, respectively. That said, areas closer to the US-Mexico border generally had relatively high illicit drug purity, as well as more dynamic change in the purity of small ('retail level') drug amounts. © 2010 The Authors, Addiction © 2010 Society for the Study of Addiction.

Neural Correlates of the Use of Psychological Distancing to Regulate Responses to Negative Social Cues: A Study of Patients with Borderline Personality Disorder

PubMed Central

Koenigsberg, Harold W.; Fan, Jin; Ochsner, Kevin; Liu, Xun; Guise, Kevin G.; Pizzarello, Scott; Dorantes, Christine; Guerreri, Stephanie; Tecuta, Lucia; Goodman, Marianne; New, Antonia; Siever, Larry J

2009-01-01

Background Emotional instability is a defining feature of borderline personality disorder (BPD), yet little is understood about its underlying neural correlates. One possible contributing factor to emotional instability is a failure to adequately employ adaptive cognitive regulatory strategies such as psychological distancing. Method To determine whether there are differences in neural dynamics underlying this control strategy, between BPD patients and healthy volunteers (HC’s), BOLD fMRI signals were acquired as 18 BPD and 16 HC subjects distanced from or simply looked at negative and neutral pictures depicting social interactions. Contrasts in signal between distance and look condition were compared between groups to identify commonalities and differences in regional activation. Results BPD patients show a different pattern of activation compared to HC subjects when looking at negative vs. neutral pictures. When distancing vs. looking at negative pictures, both groups showed decreased negative affect in rating and increased activation of the dorsolateral prefrontal cortex, areas near/along the intraparietal sulcus (IPS), ventrolateral prefrontal cortex and posterior cingulate/precuneus regions. However, the BPD group showed less BOLD signal change in dorsal anterior cingulate cortex and IPS, less deactivation in the amygdala and greater activation in the superior temporal sulcus and superior frontal gyrus. Conclusion BPD and HC subjects display different neural dynamics while passively viewing social emotional stimuli. In addition, BPD patients do not engage the cognitive control regions to the extent that HC’s do when employing a distancing strategy to regulate emotional reactions, which may be a factor contributing to the affective instability of BPD. PMID:19651401

Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example

NASA Astrophysics Data System (ADS)

Lerner, Eitan; Ingargiola, Antonino; Weiss, Shimon

2018-03-01

Bio-macromolecules carry out complicated functions through structural changes. To understand their mechanism of action, the structure of each step has to be characterized. While classical structural biology techniques allow the characterization of a few "structural snapshots" along the enzymatic cycle (usually of stable conformations), they do not cover all (and often fast interconverting) structures in the ensemble, where each may play an important functional role. Recently, several groups have demonstrated that structures of different conformations in solution could be solved by measuring multiple distances between different pairs of residues using single-molecule Förster resonance energy transfer (smFRET) and using them as constrains for hybrid/integrative structural modeling. However, this approach is limited in cases where the conformational dynamics is faster than the technique's temporal resolution. In this study, we combine existing tools that elucidate sub-millisecond conformational dynamics together with hybrid/integrative structural modeling to study the conformational states of the transcription bubble in the bacterial RNA polymerase-promoter open complex (RPo). We measured microsecond alternating laser excitation-smFRET of differently labeled lacCONS promoter dsDNA constructs. We used a combination of burst variance analysis, photon-by-photon hidden Markov modeling, and the FRET-restrained positioning and screening approach to identify two conformational states for RPo. The experimentally derived distances of one conformational state match the known crystal structure of bacterial RPo. The experimentally derived distances of the other conformational state have characteristics of a scrunched RPo. These findings support the hypothesis that sub-millisecond dynamics in the transcription bubble are responsible for transcription start site selection.

Flexible kinesthetic distance perception: when do your arms tell you how far you have walked?

PubMed

Harrison, Steven J; Kuznetsov, Nikita; Breheim, Samuel

2013-01-01

Given the flexible organization of locomotion evidenced in the many ways the limbs can be coordinated, the authors explored the potentially correspondingly flexible organization of nonvisual (kinesthetic) distance perception. As kinesthetic distance perception is known to be affected by how the limbs are coordinated, the authors probed the potential perceptual contribution of the arms during locomotion by manipulating arm-leg coordination patterns in blind-walked distance-matching tasks. Whereas manipulation of arm-leg coordination for walking with free-swinging arms had no observable perceptual consequences, comparable manipulation for walking with hiking poles did affect distance matching. These results suggest that under conditions in which the arms act to propel the body (e.g., crawling or stair-climbing) a person's nonvisual sense of movement is conveyed in the coordinated actions of all four limbs.

Signal Cloaking by Electric Fish

PubMed Central

STODDARD, PHILIP K.; MARKHAM, MICHAEL R.

2010-01-01

Electric fish produce weak electric fields to image their world in darkness and to communicate with potential mates and rivals. Eavesdropping by electroreceptive predators exerts selective pressure on electric fish to shift their signals into less-detectable high-frequency spectral ranges. Hypopomid electric fish evolved a signal-cloaking strategy that reduces their detectability by predators in the lab (and thus presumably their risk of predation in the field). These fish produce broad-frequency electric fields close to the body, but the heterogeneous local fields merge over space to cancel the low-frequency spectrum at a distance. Mature males dynamically regulate this cloaking mechanism to enhance or suppress low-frequency energy. The mechanism underlying electric-field cloaking involves electrogenic cells that produce two independent action potentials. In a unique twist, these cells orient sodium and potassium currents in the same direction, potentially boosting their capabilities for current generation. Exploration of such evolutionary inventions could aid the design of biogenerators to power implantable medical devices, an ambition that would benefit from the complete genome sequence of a gymnotiform fish. PMID:20209064

Dynamics and Melting of Finite Plasma Crystals

NASA Astrophysics Data System (ADS)

Ludwig, Patrick; K"Ahlert, Hanno; Baumgartner, Henning; Thomsen, Hauke; Bonitz, Michael

2009-11-01

Interacting few-particle systems in external trapping potentials are of strong current interest since they allow to realize and control strong correlation and quantum effects [1]. Here, we present our recent results on the structural and thermodynamic properties of the crystal-like Wigner phase of complex plasma confined in a 3D harmonic potential. We discuss the linear response of the strongly correlated system to external excitations, which can be described in terms of normal modes [2]. By means of first-principle simulations the details of the melting phase transitions of these mesoscopic systems are systematically analysed with the melting temperatures being determined by a modified Lindemann parameter for the pair distance fluctuations [3]. The critical temperatures turn out to be utmost sensitive to finite size effects (i.e., the exact particle number), and form of the (screened) interaction potential.[4pt] [1] PhD Thesis, P. Ludwig, U Rostock (2008)[0pt] [2] C. Henning et al., J. Phys. A 42, 214023 (2009)[0pt] [3] B"oning et al., Phys. Rev. Lett. 100, 113401 (2008)

Dynamics of water transport and storage in conifers studied with deuterium and heat tracing techniques.

Treesearch

F.C. Meinzer; J.R. Brooks; J.-C. Domec; B.L. Gartner; J.M. Warren; D.R. Woodruff; K. Bible; D.C. Shaw

2006-01-01

The volume and complexity of their vascular systems make the dynamics of tong-distance water transport in large trees difficult to study. We used heat and deuterated water (D20) as tracers to characterize whole-tree water transport and storage properties in individual trees belonging to the coniferous species Pseudotsuga menziesii...

How Reflected Wave Fronts Dynamically Establish Hooke's Law in a Spring

ERIC Educational Resources Information Center

Fahy, Stephen; O'Riordan, John; O'Sullivan, Colm; Twomey, Patrick

2012-01-01

A simple benchtop experiment in which a moving cart collides with a fixed spring is described. Force-time and force-distance data recorded during the collision display the transit of compression wave fronts through the spring following impact. These data can be used by students to develop a computational model of the dynamics of this simple…

Catching Galactic open clusters in advanced stages of dynamical evolution

NASA Astrophysics Data System (ADS)

Angelo, M. S.; Piatti, A. E.; Dias, W. S.; Maia, F. F. S.

2018-04-01

During their dynamical evolution, Galactic open clusters (OCs) gradually lose their stellar content mainly because of internal relaxation and tidal forces. In this context, the study of dynamically evolved OCs is necessary to properly understand such processes. We present a comprehensive Washington CT1 photometric analysis of six sparse OCs, namely: ESO 518-3, Ruprecht 121, ESO 134-12, NGC 6573, ESO 260-7 and ESO 065-7. We employed Markov chain Monte-Carlo simulations to robustly determine the central coordinates and the structural parameters and T1 × (C - T1) colour-magnitude diagrams (CMDs) cleaned from field contamination were used to derive the fundamental parameters. ESO 518-03, Ruprecht 121, ESO 134-12 and NGC 6573 resulted to be of nearly the same young age (8.2 ≤log(t yr-1) ≤ 8.3); ESO 260-7 and ESO065-7 are of intermediate age (9.2 ≤log(t yr-1) ≤ 9.4). All studied OCs are located at similar Galactocentric distances (RG ˜ 6 - 6.9 kpc), considering uncertainties, except for ESO 260-7 (RG = 8.9 kpc). These OCs are in a tidally filled regime and are dynamically evolved, since they are much older than their half-mass relaxation times (t/trh ≳ 30) and present signals of low-mass star depletion. We distinguished two groups: those dynamically evolving towards final disruptions and those in an advanced dynamical evolutionary stage. Although we do not rule out that the Milky Way potential could have made differentially faster their dynamical evolutions, we speculate here with the possibility that they have been mainly driven by initial formation conditions.

Catching Galactic open clusters in advanced stages of dynamical evolution

NASA Astrophysics Data System (ADS)

Angelo, M. S.; Piatti, A. E.; Dias, W. S.; Maia, F. F. S.

2018-07-01

During their dynamical evolution, Galactic open clusters (OCs) gradually lose their stellar content mainly because of internal relaxation and tidal forces. In this context, the study of dynamically evolved OCs is necessary to properly understand such processes. We present a comprehensive Washington CT1 photometric analysis of six sparse OCs, namely ESO 518-3, Ruprecht 121, ESO 134-12, NGC 6573, ESO 260-7, and ESO 065-7. We employed Markov chain Monte Carlo simulations to robustly determine the central coordinates and the structural parameters and T1 × (C - T1) colour-magnitude diagrams cleaned from field contamination were used to derive the fundamental parameters. ESO 518-03, Ruprecht 121, ESO 134-12, and NGC 6573 resulted to be of nearly the same young age [8.2 ≤log(t yr-1) ≤ 8.3]; ESO 260-7 and ESO065-7 are of intermediate age [9.2 ≤log(t yr-1) ≤ 9.4]. All studied OCs are located at similar Galactocentric distances (RG ˜6-6.9 kpc), considering uncertainties, except for ESO 260-7 (RG = 8.9 kpc). These OCs are in a tidally filled regime and are dynamically evolved, since they are much older than their half-mass relaxation times (t/trh ≳ 30) and present signals of low-mass star depletion. We distinguished two groups: those dynamically evolving towards final disruptions and those in an advanced dynamical evolutionary stage. Although we do not rule out that the Milky Way potential could have made differentially faster their dynamical evolutions, we speculate here with the possibility that they have been mainly driven by initial formation conditions.

Molecular simulations and density functional theory calculations of bromine in clathrate hydrate phases

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

Dureckova, Hana, E-mail: houci059@uottawa.ca; Woo, Tom K., E-mail: tom.woo@uottawa.ca; Alavi, Saman, E-mail: saman.alavi@nrc-cnrc.gc.ca

Bromine forms a tetragonal clathrate hydrate structure (TS-I) very rarely observed in clathrate hydrates of other guest substances. The detailed structure, energetics, and dynamics of Br{sub 2} and Cl{sub 2} in TS-I and cubic structure I (CS-I) clathrate hydrates are studied in this work using molecular dynamics and quantum chemical calculations. X-ray diffraction studies show that the halogen-water–oxygen distances in the cages of these structures are shorter than the sum of the van der Waals radii of halogen and oxygen atoms. This suggests that the stabilizing effects of halogen bonding or other non-covalent interactions (NCIs) may contribute to the formationmore » of the unique tetragonal bromine hydrate structure. We performed molecular dynamics simulations of Br{sub 2} and Cl{sub 2} clathrate hydrates using our previously developed five-site charge models for the dihalogen molecules [Dureckova et al. Can. J. Chem. 93, 864 (2015)] which reproduce the computed electrostatic potentials of the dihalogens and account for the electropositive σ-hole of the halogen bond donor (the dihalogen). Analysis of the radial distribution functions, enthalpies of encapsulation, velocity and orientation autocorrelation functions, and polar angle distributions are carried out for Br{sub 2} and Cl{sub 2} guests in various cages to contrast the properties of these guests in the TS-I and CS-I phases. Quantum chemical partial geometry optimizations of Br{sub 2} and Cl{sub 2} guests in the hydrate cages using the M06-2X functional give short halogen-water distances compatible with values observed in X-ray diffraction experiments. NCI plots of guest-cage structures are generated to qualitatively show the relative strength of the non-bonding interactions between dihalogens and water molecules. The differences between behaviors of Br{sub 2} and Cl{sub 2} guests in the hydrate cages may explain why bromine forms the unique TS-I phase.« less

Variability in rainfall at monitoring stations and derivation of a long-term rainfall intensity record in the Grand Canyon Region, Arizona, USA

USGS Publications Warehouse

Caster, Joshua J.; Sankey, Joel B.

2016-04-11

In this study, we examine rainfall datasets of varying temporal length, resolution, and spatial distribution to characterize rainfall depth, intensity, and seasonality for monitoring stations along the Colorado River within Marble and Grand Canyons. We identify maximum separation distances between stations at which rainfall measurements might be most useful for inferring rainfall characteristics at other locations. We demonstrate a method for applying relations between daily rainfall depth and intensity, from short-term high-resolution data to lower-resolution longer-term data, to synthesize a long-term record of daily rainfall intensity from 1950–2012. We consider the implications of our spatio-temporal characterization of rainfall for understanding local landscape change in sedimentary deposits and archaeological sites, and for better characterizing past and present rainfall and its potential role in overland flow erosion within the canyons. We find that rainfall measured at stations within the river corridor is spatially correlated at separation distances of tens of kilometers, and is not correlated at the large elevation differences that separate stations along the Colorado River from stations above the canyon rim. These results provide guidance for reasonable separation distances at which rainfall measurements at stations within the Grand Canyon region might be used to infer rainfall at other nearby locations along the river. Like other rugged landscapes, spatial variability between rainfall measured at monitoring stations appears to be influenced by canyon and rim physiography and elevation, with preliminary results suggesting the highest elevation landform in the region, the Kaibab Plateau, may function as an important orographic influence. Stations at specific locations within the canyons and along the river, such as in southern (lower) Marble Canyon and eastern (upper) Grand Canyon, appear to have strong potential to receive high-intensity rainfall that can generate runoff which may erode alluvium. The characterization of past and present rainfall variability in this study will be useful for future studies that evaluate more spatially continuous datasets in order to better understand the rainfall dynamics within this, and potentially other, deep canyons.

Three-body problem in d-dimensional space: Ground state, (quasi)-exact-solvability

NASA Astrophysics Data System (ADS)

Turbiner, Alexander V.; Miller, Willard; Escobar-Ruiz, M. A.

2018-02-01

As a straightforward generalization and extension of our previous paper [A. V. Turbiner et al., "Three-body problem in 3D space: Ground state, (quasi)-exact-solvability," J. Phys. A: Math. Theor. 50, 215201 (2017)], we study the aspects of the quantum and classical dynamics of a 3-body system with equal masses, each body with d degrees of freedom, with interaction depending only on mutual (relative) distances. The study is restricted to solutions in the space of relative motion which are functions of mutual (relative) distances only. It is shown that the ground state (and some other states) in the quantum case and the planar trajectories (which are in the interaction plane) in the classical case are of this type. The quantum (and classical) Hamiltonian for which these states are eigenfunctions is derived. It corresponds to a three-dimensional quantum particle moving in a curved space with special d-dimension-independent metric in a certain d-dependent singular potential, while at d = 1, it elegantly degenerates to a two-dimensional particle moving in flat space. It admits a description in terms of pure geometrical characteristics of the interaction triangle which is defined by the three relative distances. The kinetic energy of the system is d-independent; it has a hidden sl(4, R) Lie (Poisson) algebra structure, alternatively, the hidden algebra h(3) typical for the H3 Calogero model as in the d = 3 case. We find an exactly solvable three-body S3-permutationally invariant, generalized harmonic oscillator-type potential as well as a quasi-exactly solvable three-body sextic polynomial type potential with singular terms. For both models, an extra first order integral exists. For d = 1, the whole family of 3-body (two-dimensional) Calogero-Moser-Sutherland systems as well as the Tremblay-Turbiner-Winternitz model is reproduced. It is shown that a straightforward generalization of the 3-body (rational) Calogero model to d > 1 leads to two primitive quasi-exactly solvable problems. The extension to the case of non-equal masses is straightforward and is briefly discussed.

Testing spatial theories of plant coexistence: no consistent differences in intra- and interspecific interaction distances.

PubMed

Vogt, Deborah R; Murrell, David J; Stoll, Peter

2010-01-01

Plants stand still and interact with their immediate neighbors. Theory has shown that the distances over which these interactions occur may have important consequences for population and community dynamics. In particular, if intraspecific competition occurs over longer distances than interspecific competition (heteromyopia), coexistence can be promoted. We examined how intraspecific and interspecific competition scales with neighbor distance in a target-neighbor greenhouse competition experiment. Individuals from co-occurring forbs from calcareous grasslands were grown in isolation and with single conspecific or heterospecific neighbors at distances of 5, 10, or 15 cm (Plantago lanceolata vs. Plantago media and Hieracium pilosella vs. Prunella grandiflora). Neighbor effects were strong and declined with distance. Interaction distances varied greatly within and between species, but we found no evidence for heteromyopia. Instead, neighbor identity effects were mostly explained by relative size differences between target and neighbor. We found a complex interaction between final neighbor size and identity such that neighbor identity may become important only as the neighbor becomes very large compared with the target individual. Our results suggest that species-specific size differences between neighboring individuals determine both the strength of competitive interactions and the distance over which these interactions occur.

Facet Joint Osteoarthritis Affects Spinal Segmental Motion in Degenerative Spondylolisthesis.

PubMed

Kitanaka, Shigeyuki; Takatori, Ryota; Arai, Yuji; Nagae, Masateru; Tonomura, Hitoshi; Mikami, Yasuo; Inoue, Nozomu; Ogura, Taku; Fujiwara, Hiroyoshi; Kubo, Toshikazu

2018-06-15

This is a retrospective clinical case series (case-control study). To clarify the influence of facet joint osteoarthritis (FJOA) on the pathology of degenerative spondylolisthesis (DS) using in vivo 3-dimensional image analysis. There are no radical treatments to prevent progression of DS in patients with lumbar spinal canal stenosis associated with DS. Therefore, an effective treatment method based on the pathology of DS should be developed. In total, 50 patients with lumbar spinal canal stenosis involving L4/5 who underwent dynamic computed tomography were divided into 2 groups: with DS [spondylolisthesis (Sp) group; 12 male, 14 female; mean age, 74 y]; and without DS (non-Sp group; 15 male, 9 female; mean age, 70 y). Degeneration of the intervertebral disk and FJOA at L4/5 were evaluated using magnetic resonance imaging. Disk and intervertebral foramen heights, the distance between the craniocaudal edges of the facet joint, and the interspinous distance were measured on dynamic computed tomographic images. Also, in vivo 3-dimensional segmental motion was evaluated using the volume merge method. There were no significant differences in degenerative findings for the intervertebral disk; however, progressive FJOA was detected in the Sp group. Dynamic changes in the distance between the craniocaudal edges of the facet joints were significantly larger in the Sp group. In this study, progressive FJOA and larger segmental motion in the distance between the craniocaudal edges of the facet joints were found in the Sp group. We clarified for the first time that DS involves ligament laxity due to FJOA that affects spinal segmental motion in vivo. We consider that a treatment method based on FJOA would be useful for treating patients with DS. Level IV.

Simulation-Based Design for Wearable Robotic Systems: An Optimization Framework for Enhancing a Standing Long Jump

PubMed Central

Ong, Carmichael F.; Hicks, Jennifer L.; Delp, Scott L.

2017-01-01

Goal Technologies that augment human performance are the focus of intensive research and development, driven by advances in wearable robotic systems. Success has been limited by the challenge of understanding human–robot interaction. To address this challenge, we developed an optimization framework to synthesize a realistic human standing long jump and used the framework to explore how simulated wearable robotic devices might enhance jump performance. Methods A planar, five-segment, seven-degree-of-freedom model with physiological torque actuators, which have variable torque capacity depending on joint position and velocity, was used to represent human musculoskeletal dynamics. An active augmentation device was modeled as a torque actuator that could apply a single pulse of up to 100 Nm of extension torque. A passive design was modeled as rotational springs about each lower limb joint. Dynamic optimization searched for physiological and device actuation patterns to maximize jump distance. Results Optimization of the nominal case yielded a 2.27 m jump that captured salient kinematic and kinetic features of human jumps. When the active device was added to the ankle, knee, or hip, jump distance increased to between 2.49 and 2.52 m. Active augmentation of all three joints increased the jump distance to 3.10 m. The passive design increased jump distance to 3.32 m by adding torques of 135 Nm, 365 Nm, and 297 Nm to the ankle, knee, and hip, respectively. Conclusion Dynamic optimization can be used to simulate a standing long jump and investigate human-robot interaction. Significance Simulation can aid in the design of performance-enhancing technologies. PMID:26258930

DTFP-Growth: Dynamic Threshold-Based FP-Growth Rule Mining Algorithm Through Integrating Gene Expression, Methylation, and Protein-Protein Interaction Profiles.

PubMed

Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan; Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan; Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan

2018-04-01

Association rule mining is an important technique for identifying interesting relationships between gene pairs in a biological data set. Earlier methods basically work for a single biological data set, and, in maximum cases, a single minimum support cutoff can be applied globally, i.e., across all genesets/itemsets. To overcome this limitation, in this paper, we propose dynamic threshold-based FP-growth rule mining algorithm that integrates gene expression, methylation and protein-protein interaction profiles based on weighted shortest distance to find the novel associations among different pairs of genes in multi-view data sets. For this purpose, we introduce three new thresholds, namely, Distance-based Variable/Dynamic Supports (DVS), Distance-based Variable Confidences (DVC), and Distance-based Variable Lifts (DVL) for each rule by integrating co-expression, co-methylation, and protein-protein interactions existed in the multi-omics data set. We develop the proposed algorithm utilizing these three novel multiple threshold measures. In the proposed algorithm, the values of , , and are computed for each rule separately, and subsequently it is verified whether the support, confidence, and lift of each evolved rule are greater than or equal to the corresponding individual , , and values, respectively, or not. If all these three conditions for a rule are found to be true, the rule is treated as a resultant rule. One of the major advantages of the proposed method compared with other related state-of-the-art methods is that it considers both the quantitative and interactive significance among all pairwise genes belonging to each rule. Moreover, the proposed method generates fewer rules, takes less running time, and provides greater biological significance for the resultant top-ranking rules compared to previous methods.

Accurate classical short-range forces for the study of collision cascades in Fe–Ni–Cr

DOE PAGES

Béland, Laurent Karim; Tamm, Artur; Mu, Sai; ...

2017-05-10

The predictive power of a classical molecular dynamics simulation is largely determined by the physical validity of its underlying empirical potential. In the case of high-energy collision cascades, it was recently shown that correctly modeling interactions at short distances is necessary to accurately predict primary damage production. An ab initio based framework is introduced for modifying an existing embedded-atom method FeNiCr potential to handle these short-range interactions. Density functional theory is used to calculate the energetics of two atoms approaching each other, embedded in the alloy, and to calculate the equation of state of the alloy as it is compressed.more » The pairwise terms and the embedding terms of the potential are modi ed in accordance with the ab initio results. Using this reparametrized potential, collision cascades are performed in Ni 50Fe 50, Ni 80Cr 20 and Ni 33Fe 33Cr 33. The simulations reveal that alloying Ni and NiCr to Fe reduces primary damage production, in agreement with some previous calculations. Alloying Ni and NiFe to Cr does not reduce primary damage production, in contradiction with previous calculations.« less

Is Time the Best Metric to Measure Carbon-Related Climate Change Potential and Tune the Economy Toward Reduced Fossil Carbon Extraction?

NASA Astrophysics Data System (ADS)

DeGroff, F. A.

2016-12-01

Anthropogenic changes to non-anthropogenic carbon fluxes are a primary driver of climate change. There currently exists no comprehensive metric to measure and value anthropogenic changes in carbon flux between all states of carbon. Focusing on atmospheric carbon emissions as a measure of anthropogenic activity on the environment ignores the fungible characteristics of carbon that are crucial in both the biosphere and the worldwide economy. Focusing on a single form of inorganic carbon as a proxy metric for the plethora of anthropogenic activity and carbon compounds will prove inadequate, convoluted, and unmanageable. A broader, more basic metric is needed to capture the entirety of carbon activity, particularly in an economic, profit-driven environment. We propose a new metric to measure changes in the temporal distance of any form or state of carbon from one state to another. Such a metric would be especially useful to measure the temporal distance of carbon from sinks such as the atmosphere or oceans. The effect of changes in carbon flux as a result of any human activity can be measured by the difference between the anthropogenic and non-anthropogenic temporal distance. The change in the temporal distance is a measure of the climate change potential much like voltage is a measure of electrical potential. The integral of the climate change potential is proportional to the anthropogenic climate change. We also propose a logarithmic vector scale for carbon quality, cq, as a measure of anthropogenic changes in carbon flux. The distance between the cq vector starting and ending temporal distances represents the change in cq. A base-10 logarithmic scale would allow the addition and subtraction of exponents to calculate changes in cq. As anthropogenic activity changes the temporal distance of carbon, the change in cq is measured as: cq = ß ( log10 [mean carbon temporal distance] ) where ß represents the carbon price coefficient for a particular country. For any country, cq measures the climate change potential for any domestic anthropogenic activity that results in a change in temporal distance of any carbon. The greater the carbon fees for a country, the larger the ß coefficient would be, and the greater the import fees would be to achieve carbon parity on imports from countries with lower carbon fees.

HIV Transmission Dynamics Among Foreign-Born Persons in the United States.

PubMed

Valverde, Eduardo E; Oster, Alexandra M; Xu, Songli; Wertheim, Joel O; Hernandez, Angela L

2017-12-15

In the United States (US), foreign-born persons are disproportionately affected by HIV and differ epidemiologically from US-born persons with diagnosed HIV infection. Understanding HIV transmission dynamics among foreign-born persons is important to guide HIV prevention efforts for these populations. We conducted molecular transmission network analysis to describe HIV transmission dynamics among foreign-born persons with diagnosed HIV. Using HIV-1 polymerase nucleotide sequences reported to the US National HIV Surveillance System for persons with diagnosed HIV infection during 2001-2013, we constructed a genetic distance-based transmission network using HIV-TRACE and examined the birth region of potential transmission partners in this network. Of 77,686 people, 12,064 (16%) were foreign born. Overall, 28% of foreign-born persons linked to at least one other person in the transmission network. Of potential transmission partners, 62% were born in the United States, 31% were born in the same region as the foreign-born person, and 7% were born in another region of the world. Most transmission partners of male foreign-born persons (63%) were born in the United States, whereas most transmission partners of female foreign-borns (57%) were born in their same world region. These finding suggests that a majority of HIV infections among foreign-born persons in our network occurred after immigrating to the United States. Efforts to prevent HIV infection among foreign-born persons in the United States should include information of the transmission networks in which these individuals acquire or transmit HIV to develop more targeted HIV prevention interventions.

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

NASA Astrophysics Data System (ADS)

Ono, Junichi; Takada, Shoji; Saito, Shinji

2015-06-01

An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchical conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

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

Ono, Junichi; Takada, Shoji; Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502

2015-06-07

An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchicalmore » conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.« less

Modified Mason number for charged paramagnetic colloidal suspensions

NASA Astrophysics Data System (ADS)

Du, Di; Hilou, Elaa; Biswal, Sibani Lisa

2016-06-01

The dynamics of magnetorheological fluids have typically been described by the Mason number, a governing parameter defined as the ratio between viscous and magnetic forces in the fluid. For most experimental suspensions of magnetic particles, surface forces, such as steric and electrostatic interactions, can significantly influence the dynamics. Here we propose a theory of a modified Mason number that accounts for surface forces and show that this modified Mason number is a function of interparticle distance. We demonstrate that this modified Mason number is accurate in describing the dynamics of a rotating pair of paramagnetic colloids of identical or mismatched sizes in either high or low salt solutions. The modified Mason number is confirmed to be pseudoconstant for particle pairs and particle chains undergoing a stable-metastable transition during rotation. The interparticle distance term can be calculated using theory or can be measured experimentally. This modified Mason number is more applicable to magnetorheological systems where surface forces are not negligible.

Dynamic representation of 3D auditory space in the midbrain of the free-flying echolocating bat

PubMed Central

2018-01-01

Essential to spatial orientation in the natural environment is a dynamic representation of direction and distance to objects. Despite the importance of 3D spatial localization to parse objects in the environment and to guide movement, most neurophysiological investigations of sensory mapping have been limited to studies of restrained subjects, tested with 2D, artificial stimuli. Here, we show for the first time that sensory neurons in the midbrain superior colliculus (SC) of the free-flying echolocating bat encode 3D egocentric space, and that the bat’s inspection of objects in the physical environment sharpens tuning of single neurons, and shifts peak responses to represent closer distances. These findings emerged from wireless neural recordings in free-flying bats, in combination with an echo model that computes the animal’s instantaneous stimulus space. Our research reveals dynamic 3D space coding in a freely moving mammal engaged in a real-world navigation task. PMID:29633711

Modeling Zone-3 Protection with Generic Relay Models for Dynamic Contingency Analysis

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

Huang, Qiuhua; Vyakaranam, Bharat GNVSR; Diao, Ruisheng

This paper presents a cohesive approach for calculating and coordinating the settings of multiple zone-3 protections for dynamic contingency analysis. The zone-3 protections are represented by generic distance relay models. A two-step approach for determining zone-3 relay settings is proposed. The first step is to calculate settings, particularly, the reach, of each zone-3 relay individually by iteratively running line open-end fault short circuit analysis; the blinder is also employed and properly set to meet the industry standard under extreme loading conditions. The second step is to systematically coordinate the protection settings of the zone-3 relays. The main objective of thismore » coordination step is to address the over-reaching issues. We have developed a tool to automate the proposed approach and generate the settings of all distance relays in a PSS/E dyr format file. The calculated zone-3 settings have been tested on a modified IEEE 300 system using a dynamic contingency analysis tool (DCAT).« less

Proton-driven spin diffusion in rotating solids via reversible and irreversible quantum dynamics

PubMed Central

Veshtort, Mikhail; Griffin, Robert G.

2011-01-01

Proton-driven spin diffusion (PDSD) experiments in rotating solids have received a great deal of attention as a potential source of distance constraints in large biomolecules. However, the quantitative relationship between the molecular structure and observed spin diffusion has remained obscure due to the lack of an accurate theoretical description of the spin dynamics in these experiments. We start with presenting a detailed relaxation theory of PDSD in rotating solids that provides such a description. The theory applies to both conventional and radio-frequency-assisted PDSD experiments and extends to the non-Markovian regime to include such phenomena as rotational resonance (R2). The basic kinetic equation of the theory in the non-Markovian regime has the form of a memory function equation, with the role of the memory function played by the correlation function. The key assumption used in the derivation of this equation expresses the intuitive notion of the irreversible dissipation of coherences in macroscopic systems. Accurate expressions for the correlation functions and for the spin diffusion constants are given. The theory predicts that the spin diffusion constants governing the multi-site PDSD can be approximated by the constants observed in the two-site diffusion. Direct numerical simulations of PDSD dynamics via reversible Liouville-von Neumann equation are presented to support and compliment the theory. Remarkably, an exponential decay of the difference magnetization can be observed in such simulations in systems consisting of only 12 spins. This is a unique example of a real physical system whose typically macroscopic and apparently irreversible behavior can be traced via reversible microscopic dynamics. An accurate value for the spin diffusion constant can be usually obtained through direct simulations of PDSD in systems consisting of two 13C nuclei and about ten 1H nuclei from their nearest environment. Spin diffusion constants computed by this method are in excellent agreement with the spin diffusion constants obtained through equations given by the relaxation theory of PDSD. The constants resulting from these two approaches were also in excellent agreement with the results of 2D rotary resonance recoupling proton-driven spin diffusion (R3-PDSD) experiments performed in three model compounds, where magnetization exchange occurred over distances up to 4.9 Å. With the methodology presented, highly accurate internuclear distances can be extracted from such data. Relayed transfer of magnetization between distant nuclei appears to be the main (and apparently resolvable) source of uncertainty in such measurements. The non-Markovian kinetic equation was applied to the analysis of the R2 spin dynamics. The conventional semi-phenomenological treatment of relxation in R2 has been shown to be equivalent to the assumption of the Lorentzian spectral density function in the relaxatoin theory of PDSD. As this assumption is a poor approximation in real physical systems, the conventional R2 treatment is likely to carry a significant model error that has not been recognized previously. The relaxation theory of PDSD appears to provide an accurate, parameter-free alternative. Predictions of this theory agreed well with the full quantum mechanical simulations of the R2 dynamics in the few simple model systems we considered. PMID:21992326

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

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

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n = 1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energymore » and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. Finally, this opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.« less

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

DOE PAGES

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.; ...

2018-04-09

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n = 1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energymore » and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. Finally, this opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.« less

Understanding original antigenic sin in influenza with a dynamical system.

PubMed

Pan, Keyao

2011-01-01

Original antigenic sin is the phenomenon in which prior exposure to an antigen leads to a subsequent suboptimal immune response to a related antigen. Immune memory normally allows for an improved and rapid response to antigens previously seen and is the mechanism by which vaccination works. I here develop a dynamical system model of the mechanism of original antigenic sin in influenza, clarifying and explaining the detailed spin-glass treatment of original antigenic sin. The dynamical system describes the viral load, the quantities of healthy and infected epithelial cells, the concentrations of naïve and memory antibodies, and the affinities of naïve and memory antibodies. I give explicit correspondences between the microscopic variables of the spin-glass model and those of the present dynamical system model. The dynamical system model reproduces the phenomenon of original antigenic sin and describes how a competition between different types of B cells compromises the overall effect of immune response. I illustrate the competition between the naïve and the memory antibodies as a function of the antigenic distance between the initial and subsequent antigens. The suboptimal immune response caused by original antigenic sin is observed when the host is exposed to an antigen which has intermediate antigenic distance to a second antigen previously recognized by the host's immune system.

From static electric images to electric flow: towards dynamic perceptual cues in active electroreception.

PubMed

Hofmann, Volker; Sanguinetti-Scheck, Juan I; Gómez-Sena, Leonel; Engelmann, Jacob

2013-01-01

Active electroreception is an ancestral trait found in many aquatic vertebrates and has evolved independently in two teleost lineages, the Gymnotiformes and the Mormyriformes. Unique to these so-called weakly electric fish is their ability to actively generate electrical currents in the water and sense the electrical properties of the environment. How natural behavior contributes to this sensory system has been of interest to neuroethologists since the pioneering works of Lissmann. Here we report on a mutual modeling and experimental study of the stimuli available during active electrolocation of Gnathonemus petersii (Mormyridae). We show the validity of the model (I) by demonstrating that localized spatial patterns of object induced modulations in the electric field (electric images) are comparable to experimentally mapped 2-dimensional electric images and (II) by replicating earlier key findings showing that a normalized metric of electric image width provides an unambiguous cue for distance estimation. We then show that electric images and the distance metric vary systematically when an object is moved along the trunk. These potential ambiguities with regard to localization lead us to a spatiotemporal analysis of electric images. We introduce a new temporal metric for distance estimation that is based on the normalized spatial properties of electrical images. Finally, based on a survey of exploratory behavior, we show how objects situated at the tail, a region previously neglected, cast global electric images that extend over the whole sensory epithelium of the animals. Copyright © 2012 Elsevier Ltd. All rights reserved.

Net degradation of methyl mercury in alder swamps.

PubMed

Kronberg, Rose-Marie; Tjerngren, Ida; Drott, Andreas; Björn, Erik; Skyllberg, Ulf

2012-12-18

Wetlands are generally considered to be sources of methyl mercury (MeHg) in northern temperate landscapes. However, a recent input-output mass balance study during 2007-2010 revealed a black alder (Alnus glutinosa) swamp in southern Sweden to be a consistent and significant MeHg sink, with a 30-60% loss of MeHg. The soil pool of MeHg varied substantially between years, but it always decreased with distance from the stream inlet to the swamp. The soil MeHg pool was significantly lower in the downstream as compared to the upstream half of the swamp (0.66 and 1.34 ng MeHg g⁻¹ SOC⁻¹ annual average⁻¹, respectively, one-way ANOVA, p = 0.0006). In 2008 a significant decrease of %MeHg in soil was paralleled by a significant increase in potential demethylation rate constant (k(d), p < 0.02 and p < 0.004, respectively). In contrast, the potential methylation rate constant (k(m)) was unrelated to distance (p = 0.3). Our results suggest that MeHg was net degraded in the Alnus swamp, and that it had a rapid and dynamic internal turnover of MeHg. Snapshot stream input-output measurements at eight additional Alnus glutinosa swamps in southern Sweden indicate that Alnus swamps in general are sinks for MeHg. Our findings have implications for forestry practices and landscape planning, and suggest that restored or preserved Alnus swamps may be used to mitigate MeHg produced in northern temperate landscapes.

Telidon: Its Potential and Problems for Traditional and Distance Education.

ERIC Educational Resources Information Center

Moore, G. A. B.

1985-01-01

Reports on University of Guelph field trials with Telidon, a videotex system, as the medium for an agricultural information service for Ontario farmers and as an instructional medium for testing and feedback in classrooms. From these experiences, conclusions are drawn about the potential of videotex for traditional and distance education. (MBR)

Remote Live Invigilation: A Pilot Study

ERIC Educational Resources Information Center

Lilley, Mariana; Meere, Jonathan; Barker, Trevor

2016-01-01

There has been a growth in online distance learning programmes in Higher Education. This has led to an increased interest in different approaches to the assessment of online distance learners, including how to enhance student authentication and reduce the potential for cheating in online tests. One potential solution for this is the use of remote…

Study on miss distance based on projectile shock wave sensor

NASA Astrophysics Data System (ADS)

Gu, Guohua; Cheng, Gang; Zhang, Chenjun; Zhou, Lei

2017-05-01

The paper establishes miss distance models based on physical characteristic of shock-wave. The aerodynamic theory shows that the shock-wave of flying super-sonic projectile is generated for the projectile compressing and expending its ambient atmosphere. It advances getting miss distance according to interval of the first sensors, which first catches shock-wave, to solve the problem such as noise filtering on severe background, and signals of amplifier vibration dynamic disposal and electromagnetism compatibility, in order to improves the precision and reliability of gathering wave N signals. For the first time, it can identify the kinds of pills and firing units automatically, measure miss distance and azimuth when pills are firing. Application shows that the tactics and technique index is advanced all of the world.