Portion Of Trajectory Research Articles

Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis.

In a two-state molecular system, transition paths comprise the portions of trajectories during which the system transits from one stable state to the other. Because of their low population, it is essentially impossible to obtain information on transition paths from experiments on a large sample of molecules. However, single-molecule experiments such as laser optical tweezers or Förster resonance energy transfer (FRET) spectroscopy have allowed transition-path durations to be estimated. Here, we use molecular simulations to test the methodology for obtaining information on transition paths in single-molecule FRET by generating photon trajectories from the distance trajectories obtained in the simulation. Encouragingly, we find that this maximum likelihood analysis yields transition-path times within a factor of 2-4 of the values estimated using a good coordinate for folding, but tends to systematically underestimate them. The underestimation can be attributed partly to the fact that the large changes in the end-end distance occur mostly early in a folding trajectory. However, even if the transfer efficiency is a good reaction coordinate for folding, the assumption that the transition-path shape is a step function still leads to an underestimation of the transition-path time as defined here. We find that allowing more flexibility in the form of the transition path model allows more accurate transition-path times to be extracted and points the way toward further improvements in methods for estimating transition-path time and transition-path shape.

Distributed Subtrajectory Join on Massive Datasets

Joining trajectory datasets is a significant operation in mobility data analytics and the cornerstone of various methods that aim to extract knowledge out of them. In the era of Big Data, the production of mobility data has become massive and, consequently, performing such an operation in a centralized way is not feasible. In this article, we address the problem of Distributed Subtrajectory Join processing by utilizing the MapReduce programming model. Compared to traditional trajectory join queries, this problem is even more challenging since the goal is to retrieve all the “maximal” portions of trajectories that are “similar.” We propose three solutions: (i) a well-designed basic solution, coined DTJb ; (ii) a solution that uses a preprocessing step that repartitions the data, labeled DTJr ; and (iii) a solution that, additionally, employs an indexing scheme, named DTJi . In our experimental study, we utilize a 56GB dataset of real trajectories from the maritime domain, which, to the best of our knowledge, is the largest real dataset used for experimentation in the literature of trajectory data management. The results show that DTJi performs up to 16× faster compared with DTJb , 10× faster than DTJr , and 3× faster than the closest related state-of-the-art algorithm.

Ion Pressure at the Auroral Precipitation Boundaries and Its Relationship with the Solar Wind Dynamic Pressure

The data from the DMSP F7 satellite for 1986 are used to study the behavior of ion pressure at the boundaries of auroral precipitation. The study is based on 7489 satellite passages in the nightside sector of the auroral zone, including over 5000 passages in the 2100–2400 MLT sector. Ion pressure is determined as the average for 5 s of observations, which corresponds to a distance of ~40 km in the satellite trajectory portions adjacent to the precipitation boundaries. It is shown that the plasma pressure at the boundaries of auroral precipitation almost linearly increases at all levels of magnetic activity with an increase in the solar wind dynamic pressure (Psw). The pressure distribution as a function of MLT indicates that the precipitation boundaries, including the isotropy boundary, are not isobars, even at a low level of geomagnetic activity. The plasma pressure is maximal in the 22–24 MLT sector and decreases both in the morning and evening sides. The latitudinal position of the precipitation boundaries and the plasma pressure at the boundaries are found during all the phases of a typical substorm with an intensity of AL = –410 nT at its maximum. The latitudinal profile of ion pressure is constructed with respect to the isotropy boundary (IB) at the beginning of substorm. It is shown that, with an increase in dynamic pressure, there is not only a substantial increase in plasma pressure at the auroral precipitation boundaries but also a change in the latitudinal position of the boundaries themselves. As Psw grows, the latitude of the polarward boundary of the oval increases, while that of the equatorward boundary decreases. Despite the considerable expansion of the precipitation region, the latitudinal pressure gradient between the oval boundaries increases, even during quiet periods (average AL = –18 nT, IMF Bz = +1.4 nT) without any disturbances in the auroral zone, by approximately a factor of 2, from 0.06 to 0.12 nPa/deg.

Time-Optimal Trajectory Planning Based on Dynamics for Differential-Wheeled Mobile Robots With a Geometric Corridor

We propose an efficient time-optimal trajectory planning algorithm for an environment with multiple static circular obstacles, which is based on dynamics for differential-wheeled mobile robots (DWMRs) including actuators. This problem is known to be complex particularly if obstacles are present and if full dynamics including actuators is considered. Given a geometric corridor, the proposed technique defines a portion of trajectory between obstacles as a section which is constituted of an arc, out-curve, and in-curve, each with constant control input satisfying bang–bang principle for time-optimization. Then, it designs time-optimal trajectory composed of multiple sections using common tangent between two tangent circles, in which it handles multiple consecutive obstacles without arcs. This method helps to treat complex environment considering dynamics with DWMR's actuators. Simulation results are shown to validate the efficiency of the proposed algorithm.

In situ data analytics and indexing of protein trajectories.

The transition toward exascale computing will be accompanied by a performance dichotomy. Computational peak performance will rapidly increase; I/O performance will either grow slowly or be completely stagnant. Essentially, the rate at which data are generated will grow much faster than the rate at which data can be read from and written to the disk. MD simulations will soon face the I/O problem of efficiently writing to and reading from disk on the next generation of supercomputers. This article targets MD simulations at the exascale and proposes a novel technique for in situ data analysis and indexing of MD trajectories. Our technique maps individual trajectories' substructures (i.e., α-helices, β-strands) to metadata frame by frame. The metadata captures the conformational properties of the substructures. The ensemble of metadata can be used for automatic, strategic analysis within a trajectory or across trajectories, without manually identify those portions of trajectories in which critical changes take place. We demonstrate our technique's effectiveness by applying it to 26.3k helices and 31.2k strands from 9917 PDB proteins and by providing three empirical case studies. © 2017 Wiley Periodicals, Inc.

Long-range atmospheric transport Beryllium-7 to region the Sea of Japan

Concentrations of cosmogenic beryllium-7(7Be) and atmospheric aerosols were measured in the atmosphere of the coastal zone of Vladivostok in 2013–2014. The 7Be concentrations ranged from 0.5 to 4.1 mBq/m3, with the lowest values in summer and the highest in spring and autumn; the mean value was 2.2 mBq/m3. Analysis of meteorological data in the synoptic scale showed an inverse correlation with wet deposition rates R = −0.55 (p = 0.0001) and H2O mixing ratio R = −0.49 (p = 0.0001) and a positive with an average maximum height of 120-h backward trajectories of air masses R = 0.65 (p = 0.0001). Angular cluster analysis showed the 7Be concentration to be dependent on the north-western (R = 0.53, p = 0.001) and eastern winds (R = −0.7, p = 0.0001 for 2013 and R = −0.49, p = 0.002 for 2014). The multiple regression analysis identified five factors in 7Be concentration: altitudes (b = 0.44), air temperature (b = 0.36), a portion of trajectories in the pacific (North-East direction) cluster (b = −0.32), aerosol concentrations (b = 0.28) and wet precipitation rates (b = −0.24). The model has a good correlation with the data (adjusted R2 = 0.55). It was found that the direction and height of the air masses trajectories in the lower troposphere strongly influence the concentration of 7Be.

English

This paper presents an implementation of the modified Newton method for the aerodynamic analysis of Planetary Reentry Capsules. A straightforward method is employed, such that a CATIA model and its hybrid surface mesh are used as input. Reference capsules are analyzed and results are compared to other similar codes. Future improvements of the code consider the Busemann correction of the wall pressure, heat flux evaluation and unsteadiness in order to enable the analysis of the hypersonic portion of trajectory and to assess the vehicle's stability.

A new geometrical and mechanical relation in the respiratory system with airflow limitation—From the perspective of analytical respiratory mechanics

Classic respiratory mechanics is a branch of vectorial mechanics, which aims to recognize all forces acting on the respiratory system. Another branch of mechanics, analytical mechanics, has been used for analyzing the motions of complicated systems with constraints through equilibrium among scalar quantities such as kinetic energy and potential energy. However, until now, there have not been any studies concerning about analytical respiratory mechanics. In this paper, the author has obtained two types of motion equations (linear and nonlinear) for the airflow limitation from formulation of the analytical respiratory mechanics. Reconstructed flow-volume trajectories of the linear equation revealed a new relationship among the slope of the linear portion of trajectory, the coefficient of the dissipation function and the coefficient of the potential function. Reconstructed trajectories of the nonlinear equation suggested that a curved flow-volume trajectory would be caused by the emergence of regional hypoventilated clusters with airtrapped lobules. In conclusion, analytical respiratory mechanics will provide the basis for analyzing the mechanical properties of the respiratory system con cerning pulmonary functional images made by newly developed technologies.

Classification of Weather Patterns and Associated Trajectories of High-Ozone Episodes in the Houston–Galveston–Brazoria Area during the 2005/06 TexAQS-II

Abstract The 850-hPa synoptic flow patterns over eastern Texas and adjacent states during the 2005/06 Second Texas Air Quality Studies (TexAQS-II) period were classified into six groups using a two-stage clustering method. This study identifies synoptic weather patterns that are conducive to creating high-ozone events and reveals potential emission source regions leading to ozone exceedances through backward trajectory analysis. Clusters with dominant southerly synoptic flows and higher average wind speeds (C1 and C2 clusters) were related to low mean daytime ozone levels. Easterly (C3) and northerly (C5) clusters showed a higher probability to exceed the 8-h ozone standard than the other clusters. The dry and sunny postfrontal days with weak northerly or easterly weather patterns were often associated with ozone exceedances in the Houston–Galveston–Brazoria (HGB) area during September 2006. The majority of backward trajectories on ozone episode days were from the east, which brought polluted air from the Houston Ship Channel resulting in high ozone in the southwestern part of the metropolitan area. The shifting trajectories of the C3 and C5 weather patterns were associated with surface wind turning from weak northerly to southeasterly/southerly because of the development of bay/sea breeze. Pollutants were shifting inside the metropolitan area and high ozone built up in the afternoon or early evening. A small portion of trajectories of C3 and C5 that caused high ozone passed over a short distance from the south of Houston, picking up emissions from the industries along the coast.

Non-equilibrium trajectory dynamics and the kinematics of gliding in a flying snake

Given sufficient space, it is possible for gliding animals to reach an equilibrium state with no net forces acting on the body. In contrast, every gliding trajectory must begin with a non-steady component, and the relative importance of this phase is not well understood. Of any terrestrial animal glider, snakes exhibit the greatest active movements, which may affect their trajectory dynamics. Our primary aim was to determine the characteristics of snake gliding during the transition to equilibrium, quantifying changes in velocity, acceleration, and body orientation in the late phase of a glide sequence. We launched ‘flying’ snakes (Chrysopelea paradisi) from a 15 m tower and recorded the mid-to-end portion of trajectories with four videocameras to reconstruct the snake's body position with mm to cm accuracy. Additionally, we developed a simple analytical model of gliding assuming only steady-state forces of lift, drag and weight acting on the body and used it to explore effects of wing loading, lift-to-drag ratio, and initial velocity on trajectory dynamics. Despite the vertical space provided to transition to steady-state gliding, snakes did not exhibit equilibrium gliding and in fact displayed a net positive acceleration in the vertical axis, an effect also predicted by the analytical model.

Clustering uncertain trajectories

Knowledge discovery in Trajectory Databases (TD) is an emerging field which has recently gained great interest. On the other hand, the inherent presence of uncertainty in TD (e.g., due to GPS errors) has not been taken yet into account during the mining process. In this paper, we study the effect of uncertainty in TD clustering and introduce a three-step approach to deal with it. First, we propose an intuitionistic point vector representation of trajectories that encompasses the underlying uncertainty and introduce an effective distance metric to cope with uncertainty. Second, we devise CenTra, a novel algorithm which tackles the problem of discovering the Centroid Trajectory of a group of movements taking into advantage the local similarity between portions of trajectories. Third, we propose a variant of the Fuzzy C-Means (FCM) clustering algorithm, which embodies CenTra at its update procedure. Finally, we relax the vector representation of the Centroid Trajectories by introducing an algorithm that post-processes them, as such providing these mobility patterns to the analyst with a more intuitive representation. The experimental evaluation over synthetic and real world TD demonstrates the efficiency and effectiveness of our approach.

Quasi-Minimum Time Trajectory Planning and Experiments for Prototype Direct-Drive Robot Arm Driven by Stepping Motors Using GA

In this paper, a quasi-minimum time trajectory planning of three-link direct-drive robot arm driven with stepping motors using a genetic algorithm (GA) was proposed. The prototype direct-drive robot arm was newly manufactured in this study. The trajectory for a semiconductor wafer transfer work consists of three trajectory portions: a straight line, a curved line, and a straight line. In the trajectory planning, three trajectory portions are expressed by polynomials of time. Using the boundary and continuous conditions concerning joint angle, joint angular velocity and joint angular acceleration, the whole trajectory is described by a chromosome consisting of five genes. Then, the fitness function of the genetic algorithm for the quasi-minimum time control was defined, under the constraint condition that the stepping motor torques should not exceed pull-out torques. Furthermore, the numerical calculations and experiments have been carried out, and it is confirmed that the quasi-minimum time trajectory planning can be executed successfully, and the trajectory tracking control can be well performed.

遺伝的アルゴリズムを用いたステッピングモータ駆動方式半導体ウエハ搬送ロボットアームの軌道計画と実験

In this paper, the trajectory planning method of a semiconductor wafer transfer three-joint robot arm driven with stepping motors by use of the genetic algorithm is proposed, and the experimental results are demonstrated to confirm the usefulness of the present trajectory planning method. The whole trajectory consists of three trajectory portions; a straight line trajectory portion to take out the semiconductor wafer, a curved line trajectory portion under PTP action, and a straight line trajectory portion to set the semiconductor wafer. In the trajectory planning, the three trajectory portions are expressed by polynomials, and, by using the continuous conditions concerning joint angles, joint angular velocities and joint angular accelerations, the whole trajectory is described by a chromosome consisting of five genes. Then, the fitness function of the genetic algorithm for the quasi minimum time control under the constraint condition that the stepping motor torques should not exceed pull-out torques is defined, and the trajectory planning algorithm is constructed. Furthermore, the numerical calculations have been carried out, and it is confirmed that the trajectory planning can be successfully executed. Additionally, from the experimental results, it is ascertained that the trajectory tracking control of the trajectory of the semiconductor wafer transfer robot can be exactly implemented.

Investigating Heterogeneity in Pneumococcal Transmission

The analysis of communicable agent transmission from field data is typically hampered by missing data, dependence between individual trajectories, and sometimes by heterogeneity among competing pathogens. Methods based on data augmentation and Markov chain Monte Carlo sampling have been used to analyze such data in small communities (typically households), with little diversity in pathogens. In this article the approach is extended to analyze the transmission of 15 Streptococcus pneumoniae serotypes in schoolchildren, where hundreds of individual trajectories interact and a substantial portion of trajectories are unobserved. For each child, the data were augmented to describe the detailed time course of S. pneumoniae carriage. The Bayesian hierarchical model ensured consistency between observed and augmented data; described the latent dynamics of S. pneumoniae acquisition and clearance; and specified priors. To investigate heterogeneity among serotypes, a clustering step was introduced to select a parsimonious description of transmission characteristics. The joint posterior distribution of parameters, augmented data, and clusters of serotypes was explored by reversible-jump MCMC sampling. The approach made it possible to make inferences simultaneously on the number of clusters of serotypes and on the transmission characteristics of each cluster.

Target velocity effects on manual interception kinematics

Participants generated manual interception movements toward a target cursor that moved across a computer screen. The target reached its peak velocity either during the first third, at the midpoint, or during the last third of the movement. In Experiment 1 the view of the target was available for either the first 316, 633, 950, or 1267 ms, after which it disappeared. Results showed that for all viewing conditions, the timing of the interception velocity was related to the temporal properties of the target’s trajectory. In Experiment 2, when the portion of the target trajectory that was viewed was reversed (such that participants did not see the first 316, 633, 950, or 1267 ms of the trajectory, but instead saw only the later portions of the trajectory), there was no clear relationship between the target trajectory and the timing of the aiming trajectory. These results suggest that participants use visual information early in the target’s trajectory to form a representation of the target motion that is used to facilitate manual interception.

A molecular dynamics simulation study of segment B1 of protein G.

The immunoglobulin binding protein, segment B1 of protein G, has been studied experimentally as a paradigm for protein folding. This protein consists of 56 residues, includes both beta sheet and alpha helix and contains neither disulfide bonds nor proline residues. We report an all-atom molecular dynamics study of the native manifold of the protein in explicit solvent. A 2-ns simulation starting from the nuclear magnetic resonance (NMR) structure and a 1-ns control simulation starting from the x-ray structure were performed. The difference between average structures calculated over the equilibrium portion of trajectories is smaller than the difference between their starting conformations. These simulation averages are structurally similar to the x-ray structure and differ in systematic ways from the NMR-determined structure. Partitioning of the fluctuations into fast (< 20 ps) and slow (> 20 ps) components indicates that the beta sheet displays greater long-time mobility than does the alpha helix. Clore and Gronenborn [J. Mol. Biol. 223:853-856, 1992] detected two long-residence water molecules by NMR in a solution structure of segment B1 of protein G. Both molecules were found in the fully exposed regions and were proposed to be stabilized by bifurcated hydrogen bonds to the protein backbone. One of these long-residence water molecules, found near an exposed loop region, is identified in both of our simulations, and is seen to be involved in the formation of a stable water-mediated hydrogen bond bridge. The second water molecule, located near the middle of the alpha helix, is not seen with an exceptional residence time in either as a result of the conformation being closer to the x-ray structure in this region of the protein.

Approximate construction of phase-plane trajectories using isocentric curves

A method is described for constructing phase-plane trajectories, based on setting bounds to the location of that portion of trajectory through a given point which is contained between two isocentric curves.

Control of a remote maneuvering unit during satellite inspection.

Operator performance in flying a simulated remote maneuvering unit (RMU) on a coplanar satellite in-pection mission was evaluated under two conditions of RMU attitude control and two condiitons of cockpit instrumentation. The maneuver was repeatedly performed successfully using either an on-off acceleration-command attitude control system or an on-off rate-command attitude control system, each with either a full panel of cockpit instruments (six) or only one cockpit instrument. The rate-command system was found to be superior for pitch control during station keeping and for roll control in general. The acceleration-command system was superior for pitch control during the trajectory portions of the mission. Because both control systems had disadvantages, investigation of a variable rate-control system is recommended. More economical and precise RMU control was obtained under the full-panel cockpit instrumentation condition irrespective of the control system used. The instruments of most value were found to be those which provided X (longitudinal) and Z (vertical) distance information. The limitations of the simulation and the advantages and disadvantages of an “inside-out“ versus an “outside-in“ television display of the target and its surrounds are also discussed.