Direct Perturbation Research Articles

Direct perturbation analysis on the localized waves of the modified nonlinear Schrödinger equation under nonvanishing boundary condition

In this paper, the modified nonlinear Schrödinger equation is investigated via the direct perturbation method, which can describe the femtosecond optical pulse propagation in a monomodal optical fiber. Considering the quintic nonlinear perturbation, we obtain the approximate solution with the first-order correction, which can be expressed by the solution and symmetry of the derivative nonlinear Schrödinger equation. Under the nonvanishing boundary conditions, the approximate dark and anti-dark soliton solutions are derived and the existence conditions are also given. The effects of the perturbation on the propagations and interactions of the solitons on the nonzero background are discussed by comparing the physical quantities of solitons with the unperturbed case. It is found that the quintic nonlinear perturbation can lead to the change of the velocity as well as the pulse compression, but has no influence on the dynamics of the elastic interactions. Finally, numerical simulations are performed to support the theoretical results.

Direct perturbation of neural integrator by bilateral galvanic vestibular stimulation.

Caloric vestibular stimulation (CVS) and galvanic vestibular stimulation (GVS) act primarily on the peripheral vestibular system. Although the electrical current applied during GVS is thought to flow through peripheral vestibular organs, some current may spread into areas within the central nervous system, particularly when the bilateral galvanic vestibular stimulation (bGVS) method is used. According to Alexander's law, the magnitude of nystagmus increases with eccentric gaze movement, due to the function of the neural integrator (NI); thus, if the information for vestibular stimulation corresponds to Alexander's law, the peripheral vestibular organ is stimulated. Therefore, it would appear that if CVS results comply with Alexander's law, and bGVS results do not, the sites stimulated by bGVS are not perfectly located in the peripheral vestibular area. In our experiments on normal human subjects, the magnitude of nystagmus under CVS increased with rising gaze eccentricity in the direction that the magnitude of the nystagmus increases, and this change was found to follow Alexander's law. However, in the case of nystagmus under bGVS, results did not follow Alexander's law. In addition, study of the influences of bGVS at different current intensities on nystagmus magnitude showed that bGVS at 5mA distorted nystagmus magnitude more than at 3mA, which suggests bGVS acts not only on the peripheral vestibular nerves, but also on some areas of the central nervous system, particularly the NI. According to our experiments, bGVS directly affects neural integrator function.

Nuclear data uncertainty propagation analysis for depletion calculation in PWR and FR pin-cells

In order to assess the nuclear data uncertainty propagation in the depletion calculation, a computational code named SUNDEW has been developed based on the home-developed lattice code NECP-CACTI. In the SUNDEW, Generalized Perturbation Theory (GPT) is applied to calculate sensitivity coefficients of response function with respect to the nuclear cross sections. Method of Characteristics (MOC) is employed to solve the transport equation, adjoint and generalized adjoint transport equations. Chebyshev Rational Approximation Method (CRAM) is implemented to solve the depletion equation and adjoint depletion equation. The sensitivity coefficients of Keff and nuclide density with respect to the nuclear cross sections are verified by comparing with the results of direct perturbation calculation. The uncertainties on Keff and the nuclide density at different depletions, which are induced by the nuclear cross sections uncertainties, are analyzed based on ENDF/B-VII.1 covariance data for LWR and fast reactor pin-cells. The numerical results show that there are significant differences between LWR and fast reactor pin-cells. The differences are mainly caused by the differences of the sensitivity coefficients between the LWR and fast reactor pin-cells. In addition, to identify the cross section improvement priority for nuclides, reactions and energy ranges, the dominant contributors to Keff and nuclide density uncertainties are analyzed at different depletions.

Auxin response under osmotic stress.

The phytohormone auxin (indole-3-acetic acid, IAA) is a small organic molecule that coordinates many of the key processes in plant development and adaptive growth. Plants regulate the auxin response pathways at multiple levels including biosynthesis, metabolism, transport and perception. One of the most striking aspects of plant plasticity is the modulation of development in response to changing growth environments. In this review, we explore recent findings correlating auxin response-dependent growth and development with osmotic stresses. Studies of water deficit, dehydration, salt, and other osmotic stresses point towards direct and indirect molecular perturbations in the auxin pathway. Osmotic stress stimuli modulate auxin responses by affecting auxin biosynthesis (YUC, TAA1), transport (PIN), perception (TIR/AFB, Aux/IAA), and inactivation/conjugation (GH3, miR167, IAR3) to coordinate growth and patterning. In turn, stress-modulated auxin gradients drive physiological and developmental mechanisms such as stomata aperture, aquaporin and lateral root positioning. We conclude by arguing that auxin-mediated growth inhibition under abiotic stress conditions is one of the developmental and physiological strategies to acclimate to the changing environment.

Structural optimization under uncertainty in loading directions: Benchmark results

In this paper, using a recently developed unified approach, benchmark results are presented for structural optimization when the only source of uncertainty is the variability of the applied load directions. The worst-load-direction oriented framework can be applied to a broad class of engineering optimization problems. In each case, the central element of the solution searching algorithm is a standard multi-load structure optimization problem, which using an appropriate method, can be solved within reasonable time. The varying load directions are handled by additional linear or nonlinear relations, which describe the allowable perturbations of the nominal load directions. The result of the optimization is a performance measure minimal design which is invariant to the investigated uncertainty type and satisfies the response constraints. In order to illustrate the viability and efficiency of the approach, problem-specific models, algorithms and detailed benchmark results are presented for volume minimization of 2D continuum structures with compliance constraints and weight minimization of 2D truss structures with displacement and stress constraints. In each case, the computational cost of the proposed approach is comparable with its fixed load direction oriented equivalent because the worst-load-direction identification process is searching on the space of allowable direction perturbations, which generally means an easier and smaller computational problem than the standard multi-load structure optimization.

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

Development of a Generalized Perturbation Theory Method for Sensitivity Analysis Using Continuous-Energy Monte Carlo Methods

The sensitivity and uncertainty analysis tools of the Oak Ridge National Laboratory SCALE nuclear modeling and simulation code system that have been developed over the last decade have proven indispensable for numerous application and design studies for nuclear criticality safety and reactor physics. SCALE contains tools for analyzing the uncertainty in the eigenvalue of critical systems with realistic three-dimensional Monte Carlo simulations but currently can only quantify the uncertainty in important neutronic parameters such as multigroup cross sections, fuel fission rates, activation rates, and neutron fluence rates with one- or two-dimensional models. A more complete understanding of the sources of uncertainty in these design-limiting parameters using high-fidelity models could lead to improvements in process optimization and reactor safety and help inform regulators when setting operational safety margins. A novel approach for calculating eigenvalue sensitivity coefficients, known as the CLUTCH (Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Track length importance CHaracterization) method, was recently explored as academic research and has been found to accurately and rapidly calculate sensitivity coefficients in criticality safety applications. The work presented here describes an extension of the CLUTCH method, known as the GEneralized Adjoint Responses in Monte Carlo (GEARMC) method, that enables the calculation of sensitivity coefficients and uncertainty analysis for a generalized set of neutronic responses using high-fidelity continuous-energy Monte Carlo calculations. Several criticality safety systems were examined to demonstrate proof of principle for the GEAR-MC method, and GEAR-MC produced response sensitivity coefficients that agreed well with reference direct perturbation sensitivity coefficients.

Transcriptome dynamics of the microRNA inhibition response.

We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cellline––the first such dynamic study of the microRNA inhibition response––revealing both general and specific aspects of the physiological response. We show miR-9 inhibition inducing a multiphasic transcriptome response, with a direct target perturbation before 4 h, earlier than previously reported, amplified by a downstream peak at ∼32 h consistent with an indirect response due to secondary coherent regulation. Predictive modelling indicates a major role for miR-9 in post-transcriptional control of RNA processing and RNA binding protein regulation. Cluster analysis identifies multiple co-regulated gene regulatory modules. Functionally, we observe a shift over time from mRNA processing at early time points to translation at later time points. We validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies.

Pathogens, disease, and the social-ecological resilience of protected areas

De Vos, A., G. S. Cumming, D. Cumming, J. M. Ament, J. Baum, H. Clements, J. Grewar, K. Maciejewski, and C. Moore. 2016. Pathogens, disease, and the social-ecological resilience of protected areas. Ecology and Society 21(1):20.http://dx.doi.org/10.5751/ES-07984-210120

Changes in motor synergies for tracking movement and responses to perturbations depend on task-irrelevant dimension constraints

We investigated the changes in the motor synergies of target-tracking movements of hands and the responses to perturbation when the dimensionalities of target positions were changed. We used uncontrolled manifold (UCM) analyses to quantify the motor synergies. The target was changed from one to two dimensions, and the direction orthogonal to the movement direction was switched from task-irrelevant directions to task-relevant directions. The movement direction was task-relevant in both task conditions. Hence, we evaluated the effects of constraints on the redundant dimensions on movement tracking. Moreover, we could compare the two types of responses to the same directional perturbations in one- and two-dimensional target tasks. In the one-dimensional target task, the perturbation along the movement direction and the orthogonal direction were task-relevant and -irrelevant perturbations, respectively. In the two-dimensional target task, the both perturbations were task-relevant perturbations. The results of the experiments showed that the variabilities of the hand positions in the two-dimensional target-tracking task decreased, but the variances of the joint angles did not significantly change. For the task-irrelevant perturbations, the variances of the joint angles within the UCM that did not affect hand position (UCM component) increased. For the task-relevant perturbations, the UCM component tended to increase when the available UCM was large. These results suggest that humans discriminate whether the perturbations were task-relevant or -irrelevant and then adjust the responses of the joints by utilizing the available UCM.

Direct perturbation theory for dark-bright solitons: Application to Bose-Einstein condensates

We develop a direct perturbation theory for dark-bright solitons and derive evolution equations for the soliton parameters. In particular, first the linearization equation around the solitons is solved by expanding its solution into a set of complete eigenfunctions of the linearization operator. Then, suppression of secular growth in the linearized solution leads to the evolution equations of soliton parameters. The results are applied to a number of case examples motivated by the physics of atomic Bose-Einstein condensates, where dark-bright solitons have recently been studied both in theory and in experiments. We thus consider perturbations corresponding to (a) finite temperature-induced thermal losses, and (b) the presence of localized (δ-function) impurities. In these cases, relevant equations of motion for the dark-bright soliton center are in agreement with ones previously obtained via alternative methods, including energy-based methods, as well as numerical linear stability analysis and direct simulations.

Characterization of Compensatory Stepping in People With Multiple Sclerosis

ObjectiveTo characterize postural responses to forward and backward external perturbations in people with multiple sclerosis (PwMS), and to relate performance to commonly used clinical outcomes. DesignCross-sectional study. Postural responses were tested during large stepping and smaller feet-in-place perturbations in forward and backward directions. SettingUniversity research laboratory. ParticipantsPwMS (n=54) and age-matched controls (n=21) (N=75). InterventionsNot applicable. Main Outcome MeasuresCenter of mass displacement and step latency after external perturbations. ResultsPwMS exhibited larger center of mass displacements and step latencies than control participants in response to stepping perturbations (P=.003 and P=.028, respectively). Stepping deficits were more pronounced during backward stepping and were significantly correlated to increased severity on clinical measures (European Database for Multiple Sclerosis disability score and Timed 25-Foot Walk). ConclusionsCompensatory stepping is impaired in PwMS and correlates with clinical disability. Measurement of backward compensatory stepping may be more effective at identifying postural dysfunction in PwMS than forward compensatory steps. Prolonged step latencies, large anticipatory postural adjustments, and multiple compensatory steps are especially altered in PwMS, suggesting possible targets for neurorehabilitation.

Multidecadal change in streamflow associated with anthropogenic disturbances in the tropical Andes

Abstract. Andean headwater catchments are an important source of freshwater for downstream water users. However, few long-term studies exist on the relative importance of climate change and direct anthropogenic perturbations on flow regimes in these catchments. In this paper, we assess change in streamflow based on long time series of hydrometeorological data (1974–2008) and land cover reconstructions (1963–2009) in the Pangor catchment (282 km2) located in the tropical Andes. Three main land cover change trajectories can be distinguished during the period 1963–2009: (1) expansion of agricultural land by an area equal to 14 % of the catchment area (or 39 km2) in 46 years' time, (2) deforestation of native forests by 11 % (or −31 km2) corresponding to a mean rate of 67 ha yr−1, and (3) afforestation with exotic species in recent years by about 5 % (or 15 km2). Over the time period 1963–2009, about 50 % of the 64 km2 of native forests was cleared and converted to agricultural land. Given the strong temporal variability of precipitation and streamflow data related to El Niño–Southern Oscillation, we use empirical mode decomposition techniques to detrend the time series. The long-term increasing trend in rainfall is remarkably different from the observed changes in streamflow, which exhibit a decreasing trend. Hence, observed changes in streamflow are not the result of long-term change in precipitation but very likely result from anthropogenic disturbances associated with land cover change.

Differences in co-contraction level between cp and td children during a functional and isometric strength assessment

Accurate coordination of mediolateral foot placement, relative to the center of mass kinematic state, is one of the mechanisms which ensures mediolateral stability during human walking. Previously, we found that shoes constraining ankle moments decreased the degree of foot placement control with respect to the center of mass kinematic state. As such, ankle moment constraints can be seen as a perturbation of foot placement. Direct mechanical perturbations of the swing leg trajectory can improve the degree of foot placement control as an after-effect. Here, we asked whether constrained ankle moments could have a similar effect. If confirmed, this would offer a simple training tool for individuals with impaired foot placement control. Participants walked in three conditions; normal (baseline) while wearing shoes constraining ankle moments (training) and normal again (after-effects). The degree of foot placement control was calculated as the percentage of variance in foot placement that could be predicted based on the center of mass kinematic state in the preceding swing phase. During training, the degree of foot placement control decreased initially compared to baseline, but it gradually improved over time. In the after-effect condition, it was higher than during baseline, yet not significantly so. During training, we observed increased step width, decreased stride time and reduced local dynamic stability. In conclusion, constraining ankle moment control deteriorates the degree of foot placement control. A non-significant trend towards an improved degree of foot placement control after prolonged exposure to constrained ankle moments, allows for speculation on a training potential.

Global distribution of mineral dust and its impact on radiative fluxes as simulated by WRF-Chem

Dust aerosols make a considerable contribution to the climate system and atmospheric hydrological cycle through their radiative and ice nuclei effects. This underlines the need for investigating the sources of dust aerosols, their transport pathways, and radiative forcing. Seasonal distribution of mineral dust around the globe and its impact on radiation fluxes is estimated using two simulations: a model setup that did not include dust aerosols; and an interactive experiment that included dust aerosols and their feedback to the atmosphere. Simulations were performed by the Weather Research and Forecasting with Chemistry (WRF-Chem) model for a 1-year period. The global annual mean dust optical depth (DOD) at 0.55 $$\upmu$$ m is estimated to be 0.057, with a spring peak value of 0.081 and an autumn minimum value of 0.039. Seasonal variation of atmospheric dust loading is shown to be associated with similar significant variation in shortwave and longwave direct radiation perturbation by dust, both at the surface and top of the atmosphere (TOA). The presence of mineral dust in the interactive simulation is estimated to exert a maximum net direct radiation perturbation in summer with values of $$-$$ 2.85 and $$-$$ 1.63 W m $$^{-2}$$ in clear-sky conditions at the surface and TOA, respectively. It also exerts a global annual net direct radiation perturbation of $$-$$ 1.86 and $$-$$ 1.09 W m $$^{-2}$$ at the surface and TOA, respectively. The surface cooling is attributed to the extinction of incoming solar radiation by dust aerosols, while negative perturbation at the TOA (which demonstrates cooling of the Earth-atmosphere system) is predominantly attributed to an increase in outgoing shortwave radiation.

Code development for eigenvalue total sensitivity analysis and total uncertainty analysis

The uncertainties of multigroup cross sections notably impact eigenvalue of neutron-transport equation. We report on a total sensitivity analysis and total uncertainty analysis code named UNICORN that has been developed by applying the direct numerical perturbation method and statistical sampling method. In order to consider the contributions of various basic cross sections and the implicit effects which are indirect results of multigroup cross sections through resonance self-shielding calculation, an improved multigroup cross-section perturbation model is developed. The DRAGON 4.0 code, with application of WIMSD-4 format library, is used by UNICORN to carry out the resonance self-shielding and neutron-transport calculations. In addition, the bootstrap technique has been applied to the statistical sampling method in UNICORN to obtain much steadier and more reliable uncertainty results. The UNICORN code has been verified against TSUNAMI-1D by analyzing the case of TMI-1 pin-cell. The numerical results show that the total uncertainty of eigenvalue caused by cross sections can reach up to be about 0.72%. Therefore the contributions of the basic cross sections and their implicit effects are not negligible.

Post-Newtonian direct and mixed orbital effects due to the oblateness of the central body

The orbital dynamics of a test particle moving in the nonspherically symmetric field of a rotating oblate primary is impacted also by certain indirect, mixed effects arising from the interplay of the different Newtonian and post-Newtonian accelerations which induce known direct perturbations. We systematically calculate the indirect gravitoelectromagnetic shifts per orbit of the Keplerian orbital elements of the test particle arising from the crossing among the first even zonal harmonic J2 of the central body and the post-Newtonian static and stationary components of its gravitational field. We also work out the Newtonian shifts per orbit of order [Formula: see text], and the direct post-Newtonian gravitoelectric effects of order J2c-2 arising from the equations of motion. In the case of both the indirect and direct gravitoelectric J2c-2 shifts, our calculation holds for an arbitrary orientation of the symmetry axis of the central body. We yield numerical estimates of their relative magnitudes for systems ranging from Earth's artificial satellites to stars orbiting supermassive black holes. As far as their measurability is concerned, highly elliptical orbital configuration are desirable.

A generalized analysis of perturbation patterns for the Poiseuille flow in a tube

A linearized problem of stability with respect to a three-dimensional pattern of perturbations in a steady flow of a viscous Newtonian fluid in a tube (the Poiseuille flow) is analyzed. The time evolution of individual harmonics of perturbations in angular and axial directions is studied. The transition to quadratic functionals constructed on the squares of the moduli of perturbation velocity components and their radius derivatives is performed. An upper estimate is obtained for the stability parameter and is used to derive lower estimates for the critical Reynolds numbers in the cases of axisymmetric perturbations as well as in the cases of two-dimensional axisymmetric and nonaxisymmetric rz perturbations.

Transcriptome dynamics of the microRNA inhibition response.

We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line—the first such dynamic study of the microRNA inhibition response—revealing both general and specific aspects of the physiological response. We show miR-9 inhibition inducing a multiphasic transcriptome response, with a direct target perturbation before 4 h, earlier than previously reported, amplified by a downstream peak at ∼32 h consistent with an indirect response due to secondary coherent regulation. Predictive modelling indicates a major role for miR-9 in post-transcriptional control of RNA processing and RNA binding protein regulation. Cluster analysis identifies multiple co-regulated gene regulatory modules. Functionally, we observe a shift over time from mRNA processing at early time points to translation at later time points. We validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies.

Biological assessment of water quality and biodiversity in Rwandan rivers draining into Lake Kivu

This study aimed at assessing the biological water quality and biodiversity of Rwandan rivers draining into Lake Kivu using benthic macroinvertebrates as indicator organisms. We tested the hypothesis that biological water quality and biodiversity are negatively affected by direct human perturbations and land-use changes in the surrounding habitat. Fifty-three rivers from 29 catchment areas were investigated using the ‘Average Score Per Taxon’ and the ‘Baur Biotic Score’ as indices for assessing water quality. The Shannon index and the Pielou’s evenness index were used to measure biodiversity and evenness, respectively. Multiple linear regressions were applied to test the impact of hydromorphology, physical parameters, direct human perturbations and land-use change in the surrounding habitat on water quality and biodiversity. Baur Biotic Score and Average Score per Taxon indicated strong variation in the water quality of the investigated rivers. Best biological water quality was found in the rivers south of Kibuye/Karongi. Diversity was found to be moderate, but slightly increased south of Kibuye/Karongi. Evenness was also lowest south of Kibuye/Karongi. Multiple linear regression analyses indicated that the biodiversity estimations might be affected by the sampling time, but that the assessment of water quality was not. Water velocity significantly influenced water quality as well as biodiversity. Together with pH, it has also the strongest effect on the composition of macrozoobenthos assemblages. We showed that discharge of industrial waste water in the Burehe River resulted in an alarming deterioration of water quality that demonstrates the necessity of effective wastewater treatment for a sustainable usage of water resources. Long-term water quality monitoring is highly recommended to be established in Rwanda using a combination of physicochemical, bacteriological and biomonitoring data.