Optimal estimation of diffusion coefficients from single-particle trajectories

NASA Astrophysics Data System (ADS)

Vestergaard, Christian L.; Blainey, Paul C.; Flyvbjerg, Henrik

2014-02-01

How does one optimally determine the diffusion coefficient of a diffusing particle from a single-time-lapse recorded trajectory of the particle? We answer this question with an explicit, unbiased, and practically optimal covariance-based estimator (CVE). This estimator is regression-free and is far superior to commonly used methods based on measured mean squared displacements. In experimentally relevant parameter ranges, it also outperforms the analytically intractable and computationally more demanding maximum likelihood estimator (MLE). For the case of diffusion on a flexible and fluctuating substrate, the CVE is biased by substrate motion. However, given some long time series and a substrate under some tension, an extended MLE can separate particle diffusion on the substrate from substrate motion in the laboratory frame. This provides benchmarks that allow removal of bias caused by substrate fluctuations in CVE. The resulting unbiased CVE is optimal also for short time series on a fluctuating substrate. We have applied our estimators to human 8-oxoguanine DNA glycolase proteins diffusing on flow-stretched DNA, a fluctuating substrate, and found that diffusion coefficients are severely overestimated if substrate fluctuations are not accounted for.

Importance sampling large deviations in nonequilibrium steady states. I.

PubMed

Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T

2018-03-28

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

Importance sampling large deviations in nonequilibrium steady states. I

NASA Astrophysics Data System (ADS)

Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.

2018-03-01

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

Glycosylases utilize ``stop and go'' motion to locate DNA damage

NASA Astrophysics Data System (ADS)

Nelson, Shane

2015-03-01

Oxidative damage to DNA results in alterations that are mutagenic or even cytotoxic. Base excision repair is a mechanism that functions to identify and correct these lesions, and is present in organisms ranging from bacteria to humans. DNA glycosylases are the first enzymes in this pathway and function to locate and remove oxidatively damaged bases, and do so utilizing only thermal energy. However, the question remains of how these enzymes locate and recognize a damaged base among millions of undamaged bases. Utilizing fluorescence video microscopy with high spatial and temporal resolution, we have observed a number of different fluorescently labeled glycosylases (including bacterial FPG, NEI, and NTH as well as mammalian MutyH and OGG). These enzymes diffuse along DNA tightropes at approximately 0.01 +/- 0.005 μm2/s with binding lifetimes ranging from one second to several minutes. Chemically induced damage to the DNA substrate causes a ~ 50% reduction in diffusion coefficients and a ~ 400% increase in binding lifetimes, while mutation of the key ``wedge residue'' - which has been shown to be responsible for damage detection - results in a 200% increase in the diffusion coefficient. Utilizing a sliding window approach to measure diffusion coefficients within individual trajectories, we observe that distributions of diffusion coefficients are bimodal, consistent with periods of diffusive motion interspersed with immobile periods. Utilizing a unique chemo-mechanical simulation approach, we demonstrate that the motion of these glycosylases can be explained as free diffusion along the helical pitch of the DNA, punctuated with two different types of pauses: 1) rapid, short-lived pauses as the enzyme rapidly probes DNA bases to interrogate for damage and, 2) less frequent, longer lived pauses that reflect the enzyme bound to and catalytically removing a damaged base. These simulations also indicate that the wedge residue is critical for interrogation and recognition of damage, and thus enzymes missing this residue diffuse faster. Similarly, chemically induced damage increases the frequency with which the enzymes encounter damaged bases, resulting in slower diffusion.

Optimal estimates of the diffusion coefficient of a single Brownian trajectory.

PubMed

Boyer, Denis; Dean, David S; Mejía-Monasterio, Carlos; Oshanin, Gleb

2012-03-01

Modern developments in microscopy and image processing are revolutionizing areas of physics, chemistry, and biology as nanoscale objects can be tracked with unprecedented accuracy. The goal of single-particle tracking is to determine the interaction between the particle and its environment. The price paid for having a direct visualization of a single particle is a consequent lack of statistics. Here we address the optimal way to extract diffusion constants from single trajectories for pure Brownian motion. It is shown that the maximum likelihood estimator is much more efficient than the commonly used least-squares estimate. Furthermore, we investigate the effect of disorder on the distribution of estimated diffusion constants and show that it increases the probability of observing estimates much smaller than the true (average) value.

White matter fiber tracking computation based on diffusion tensor imaging for clinical applications.

PubMed

Dellani, Paulo R; Glaser, Martin; Wille, Paulo R; Vucurevic, Goran; Stadie, Axel; Bauermann, Thomas; Tropine, Andrei; Perneczky, Axel; von Wangenheim, Aldo; Stoeter, Peter

2007-03-01

Fiber tracking allows the in vivo reconstruction of human brain white matter fiber trajectories based on magnetic resonance diffusion tensor imaging (MR-DTI), but its application in the clinical routine is still in its infancy. In this study, we present a new software for fiber tracking, developed on top of a general-purpose DICOM (digital imaging and communications in medicine) framework, which can be easily integrated into existing picture archiving and communication system (PACS) of radiological institutions. Images combining anatomical information and the localization of different fiber tract trajectories can be encoded and exported in DICOM and Analyze formats, which are valuable resources in the clinical applications of this method. Fiber tracking was implemented based on existing line propagation algorithms, but it includes a heuristic for fiber crossings in the case of disk-shaped diffusion tensors. We successfully performed fiber tracking on MR-DTI data sets from 26 patients with different types of brain lesions affecting the corticospinal tracts. In all cases, the trajectories of the central spinal tract (pyramidal tract) were reconstructed and could be applied at the planning phase of the surgery as well as in intraoperative neuronavigation.

Manipulating freely diffusing single 20-nm particles in an Anti-Brownian Electrokinetic Trap (ABELtrap)

NASA Astrophysics Data System (ADS)

Zarrabi, Nawid; Clausen, Caterina; Düser, Monika G.; Börsch, Michael

2013-02-01

Conformational changes of individual fluorescently labeled proteins can be followed in solution using a confocal microscope. Two fluorophores attached to selected domains of the protein report fluctuating conformations. Based on Förster resonance energy transfer (FRET) between these fluorophores on a single protein, sequential distance changes between the dyes provide the real time trajectories of protein conformations. However, observation times are limited for freely diffusing biomolecules by Brownian motion through the confocal detection volume. A. E. Cohen and W. E. Moerner have invented and built microfluidic devices with 4 electrodes for an Anti-Brownian Electrokinetic Trap (ABELtrap). Here we present an ABELtrap based on a laser focus pattern generated by a pair of acousto-optical beam deflectors and controlled by a programmable FPGA chip. Fluorescent 20-nm beads in solution were used to mimic freely diffusing large proteins like solubilized FoF1-ATP synthase. The ABELtrap could hold these nanobeads for about 10 seconds at the given position. Thereby, observation times of a single particle were increased by a factor of 1000.

Revealing nonergodic dynamics in living cells from a single particle trajectory

NASA Astrophysics Data System (ADS)

Lanoiselée, Yann; Grebenkov, Denis S.

2016-05-01

We propose the improved ergodicity and mixing estimators to identify nonergodic dynamics from a single particle trajectory. The estimators are based on the time-averaged characteristic function of the increments and can thus capture additional information on the process as compared to the conventional time-averaged mean-square displacement. The estimators are first investigated and validated for several models of anomalous diffusion, such as ergodic fractional Brownian motion and diffusion on percolating clusters, and nonergodic continuous-time random walks and scaled Brownian motion. The estimators are then applied to two sets of earlier published trajectories of mRNA molecules inside live Escherichia coli cells and of Kv2.1 potassium channels in the plasma membrane. These statistical tests did not reveal nonergodic features in the former set, while some trajectories of the latter set could be classified as nonergodic. Time averages along such trajectories are thus not representative and may be strongly misleading. Since the estimators do not rely on ensemble averages, the nonergodic features can be revealed separately for each trajectory, providing a more flexible and reliable analysis of single-particle tracking experiments in microbiology.

Nonparametric estimates of drift and diffusion profiles via Fokker-Planck algebra.

PubMed

Lund, Steven P; Hubbard, Joseph B; Halter, Michael

2014-11-06

Diffusion processes superimposed upon deterministic motion play a key role in understanding and controlling the transport of matter, energy, momentum, and even information in physics, chemistry, material science, biology, and communications technology. Given functions defining these random and deterministic components, the Fokker-Planck (FP) equation is often used to model these diffusive systems. Many methods exist for estimating the drift and diffusion profiles from one or more identifiable diffusive trajectories; however, when many identical entities diffuse simultaneously, it may not be possible to identify individual trajectories. Here we present a method capable of simultaneously providing nonparametric estimates for both drift and diffusion profiles from evolving density profiles, requiring only the validity of Langevin/FP dynamics. This algebraic FP manipulation provides a flexible and robust framework for estimating stationary drift and diffusion coefficient profiles, is not based on fluctuation theory or solved diffusion equations, and may facilitate predictions for many experimental systems. We illustrate this approach on experimental data obtained from a model lipid bilayer system exhibiting free diffusion and electric field induced drift. The wide range over which this approach provides accurate estimates for drift and diffusion profiles is demonstrated through simulation.

Kinetics of the initial steps of G protein-coupled receptor-mediated cellular signaling revealed by single-molecule imaging.

PubMed

Lill, Yoriko; Martinez, Karen L; Lill, Markus A; Meyer, Bruno H; Vogel, Horst; Hecht, Bert

2005-08-12

We report on an in vivo single-molecule study of the signaling kinetics of G protein-coupled receptors (GPCR) performed using the neurokinin 1 receptor (NK1R) as a representative member. The NK1R signaling cascade is triggered by the specific binding of a fluorescently labeled agonist, substance P (SP). The diffusion of single receptor-ligand complexes in plasma membrane of living HEK 293 cells is imaged using fast single-molecule wide-field fluorescence microscopy at 100 ms time resolution. Diffusion trajectories are obtained which show intra- and intertrace heterogeneity in the diffusion mode. To investigate universal patterns in the diffusion trajectories we take the ligand-binding event as the common starting point. This synchronization allows us to observe changes in the character of the ligand-receptor-complex diffusion. Specifically, we find that the diffusion of ligand-receptor complexes is slowed down significantly and becomes more constrained as a function of time during the first 1000 ms. The decelerated and more constrained diffusion is attributed to an increasing interaction of the GPCR with cellular structures after the ligand-receptor complex is formed.

Novel optical-based methods and analyses for elucidating cellular mechanics and dynamics

NASA Astrophysics Data System (ADS)

Koo, Peter K.

Resolving distinct biochemical interaction states by analyzing the diffusive behaviors of individual protein trajectories is challenging due to the limited statistics provided by short trajectories and experimental noise sources, which are intimately coupled into each proteins localization. In the first part of this thesis, we introduce a novel, a machine-learning based classification methodology, called perturbation expectation-maximization (pEM), which simultaneously analyzes a population of protein trajectories to uncover the system of short-time diffusive behaviors which collectively result from distinct biochemical interactions. We then discuss an experimental application of pEM to Rho GTPase, an integral regulator of cytoskeletal dynamics and cellular homeostasis, inside live cells. We also derive the maximum likelihood estimator (MLE) for driven diffusion, confined diffusion, and fractional Brownian motion. We demonstrate that MLE yields improved estimates in comparison with traditional diffusion analysis, namely mean squared displacement analysis. In addition, we also introduce mleBayes, which is an empirical Bayesian model selection scheme to classify an individual protein trajectory to a given diffusion mode. By employing mleBayes on simulated data, we demonstrate that accurate determination of the underlying diffusive properties, beyond normal diffusion, remains challenging when analyzing particle trajectories on an individual basis. To improve upon the statistical limitations of classification from analyzing trajectories on an individual basis, we extend pEM with a new version (pEMv2) to simultaneously analyzing a collection of particle trajectories to uncover the system of interactions which give rise to unique normal or non-normal diffusive states. We test the performance of pEMv2 on various sets of simulated particle trajectories which transition between various modes of normal and non-normal diffusive states to highlight considerations when employing pEMv2 analysis. We envision the presented methodologies will be applicable to a wide range of single protein tracking data where different interactions result in distinct diffusive behaviors. More generally, this study brings us an important step closer to the possibility of monitoring the endogenous biochemistry of diffusing proteins within live cells with single molecule resolution. In the second part of this thesis, the role of chromatin association to the nuclear envelope in nuclear mechanics is explored. Changes in the mechanical properties of the nucleus are increasingly found to be critical for development and disease. However, relatively little is known about the variables that cells modulate to define nuclear mechanics. The best understood player is lamin A, a protein linked to a diverse set of genetic diseases termed laminopathies. The properties of lamin A that are compromised in these diseases (and therefore underlie their pathology) remains poorly understood. One model focuses on a mechanical role for a polymeric network of lamins associated with the nuclear envelope (NE), which supports nuclear integrity. However, because heterochromatin is strongly associated with lamina, it remains unclear whether it is the lamin polymer, the associated chromatin, or both that allow the lamina to mechanically stabilize nuclei. Decoupling the impact of the lamin polymer itself from that of the associated chromatin has proven very challenging. Here, we take advantage of the model organism, S pombe, which does not express lamies, as an experimental framework in which to address the impact of chromatin and its association with the nuclear periphery on nuclear mechanics. Using a combination of new image analysis tools for in vivo imaging of nuclear dynamics and a novel optical tweezers assay capable of directly probing nuclear mechanics, we find that the association of chromatin with the NE through integral membrane proteins plays a critical role in supporting nuclear integrity. When chromatin is decoupled from the NE, nuclei are softer, undergo much larger nuclear fluctuations in vivo in response to microtubule forces, and are defective at resolving nuclear deformations. Our data further suggest that association of chromatin with the NE attenuates the flow of chromatin into nuclear fluctuations thereby preventing permanent changes in nuclear shape.

Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.

PubMed

Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei

2018-06-05

The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.

Statistical analysis of particle trajectories in living cells

NASA Astrophysics Data System (ADS)

Briane, Vincent; Kervrann, Charles; Vimond, Myriam

2018-06-01

Recent advances in molecular biology and fluorescence microscopy imaging have made possible the inference of the dynamics of molecules in living cells. Such inference allows us to understand and determine the organization and function of the cell. The trajectories of particles (e.g., biomolecules) in living cells, computed with the help of object tracking methods, can be modeled with diffusion processes. Three types of diffusion are considered: (i) free diffusion, (ii) subdiffusion, and (iii) superdiffusion. The mean-square displacement (MSD) is generally used to discriminate the three types of particle dynamics. We propose here a nonparametric three-decision test as an alternative to the MSD method. The rejection of the null hypothesis, i.e., free diffusion, is accompanied by claims of the direction of the alternative (subdiffusion or superdiffusion). We study the asymptotic behavior of the test statistic under the null hypothesis and under parametric alternatives which are currently considered in the biophysics literature. In addition, we adapt the multiple-testing procedure of Benjamini and Hochberg to fit with the three-decision-test setting, in order to apply the test procedure to a collection of independent trajectories. The performance of our procedure is much better than the MSD method as confirmed by Monte Carlo experiments. The method is demonstrated on real data sets corresponding to protein dynamics observed in fluorescence microscopy.

Theoretical limit of spatial resolution in diffuse optical tomography using a perturbation model

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

Konovalov, A B; Vlasov, V V

2014-03-28

We have assessed the limit of spatial resolution of timedomain diffuse optical tomography (DOT) based on a perturbation reconstruction model. From the viewpoint of the structure reconstruction accuracy, three different approaches to solving the inverse DOT problem are compared. The first approach involves reconstruction of diffuse tomograms from straight lines, the second – from average curvilinear trajectories of photons and the third – from total banana-shaped distributions of photon trajectories. In order to obtain estimates of resolution, we have derived analytical expressions for the point spread function and modulation transfer function, as well as have performed a numerical experiment onmore » reconstruction of rectangular scattering objects with circular absorbing inhomogeneities. It is shown that in passing from reconstruction from straight lines to reconstruction using distributions of photon trajectories we can improve resolution by almost an order of magnitude and exceed the accuracy of reconstruction of multi-step algorithms used in DOT. (optical tomography)« less

Invariance property of wave scattering through disordered media

PubMed Central

Pierrat, Romain; Ambichl, Philipp; Gigan, Sylvain; Haber, Alexander; Carminati, Rémi; Rotter, Stefan

2014-01-01

A fundamental insight in the theory of diffusive random walks is that the mean length of trajectories traversing a finite open system is independent of the details of the diffusion process. Instead, the mean trajectory length depends only on the system's boundary geometry and is thus unaffected by the value of the mean free path. Here we show that this result is rooted on a much deeper level than that of a random walk, which allows us to extend the reach of this universal invariance property beyond the diffusion approximation. Specifically, we demonstrate that an equivalent invariance relation also holds for the scattering of waves in resonant structures as well as in ballistic, chaotic or in Anderson localized systems. Our work unifies a number of specific observations made in quite diverse fields of science ranging from the movement of ants to nuclear scattering theory. Potential experimental realizations using light fields in disordered media are discussed. PMID:25425671

Fiberprint: A subject fingerprint based on sparse code pooling for white matter fiber analysis.

PubMed

Kumar, Kuldeep; Desrosiers, Christian; Siddiqi, Kaleem; Colliot, Olivier; Toews, Matthew

2017-09-01

White matter characterization studies use the information provided by diffusion magnetic resonance imaging (dMRI) to draw cross-population inferences. However, the structure, function, and white matter geometry vary across individuals. Here, we propose a subject fingerprint, called Fiberprint, to quantify the individual uniqueness in white matter geometry using fiber trajectories. We learn a sparse coding representation for fiber trajectories by mapping them to a common space defined by a dictionary. A subject fingerprint is then generated by applying a pooling function for each bundle, thus providing a vector of bundle-wise features describing a particular subject's white matter geometry. These features encode unique properties of fiber trajectories, such as their density along prominent bundles. An analysis of data from 861 Human Connectome Project subjects reveals that a fingerprint based on approximately 3000 fiber trajectories can uniquely identify exemplars from the same individual. We also use fingerprints for twin/sibling identification, our observations consistent with the twin data studies of white matter integrity. Our results demonstrate that the proposed Fiberprint can effectively capture the variability in white matter fiber geometry across individuals, using a compact feature vector (dimension of 50), making this framework particularly attractive for handling large datasets. Copyright © 2017 Elsevier Inc. All rights reserved.

Corrected simulations for one-dimensional diffusion processes with naturally occurring boundaries.

PubMed

Shafiey, Hassan; Gan, Xinjun; Waxman, David

2017-11-01

To simulate a diffusion process, a usual approach is to discretize the time in the associated stochastic differential equation. This is the approach used in the Euler method. In the present work we consider a one-dimensional diffusion process where the terms occurring, within the stochastic differential equation, prevent the process entering a region. The outcome is a naturally occurring boundary (which may be absorbing or reflecting). A complication occurs in a simulation of this situation. The term involving a random variable, within the discretized stochastic differential equation, may take a trajectory across the boundary into a "forbidden region." The naive way of dealing with this problem, which we refer to as the "standard" approach, is simply to reset the trajectory to the boundary, based on the argument that crossing the boundary actually signifies achieving the boundary. In this work we show, within the framework of the Euler method, that such resetting introduces a spurious force into the original diffusion process. This force may have a significant influence on trajectories that come close to a boundary. We propose a corrected numerical scheme, for simulating one-dimensional diffusion processes with naturally occurring boundaries. This involves correcting the standard approach, so that an exact property of the diffusion process is precisely respected. As a consequence, the proposed scheme does not introduce a spurious force into the dynamics. We present numerical test cases, based on exactly soluble one-dimensional problems with one or two boundaries, which suggest that, for a given value of the discrete time step, the proposed scheme leads to substantially more accurate results than the standard approach. Alternatively, the standard approach needs considerably more computation time to obtain a comparable level of accuracy to the proposed scheme, because the standard approach requires a significantly smaller time step.

Corrected simulations for one-dimensional diffusion processes with naturally occurring boundaries

NASA Astrophysics Data System (ADS)

Shafiey, Hassan; Gan, Xinjun; Waxman, David

2017-11-01

To simulate a diffusion process, a usual approach is to discretize the time in the associated stochastic differential equation. This is the approach used in the Euler method. In the present work we consider a one-dimensional diffusion process where the terms occurring, within the stochastic differential equation, prevent the process entering a region. The outcome is a naturally occurring boundary (which may be absorbing or reflecting). A complication occurs in a simulation of this situation. The term involving a random variable, within the discretized stochastic differential equation, may take a trajectory across the boundary into a "forbidden region." The naive way of dealing with this problem, which we refer to as the "standard" approach, is simply to reset the trajectory to the boundary, based on the argument that crossing the boundary actually signifies achieving the boundary. In this work we show, within the framework of the Euler method, that such resetting introduces a spurious force into the original diffusion process. This force may have a significant influence on trajectories that come close to a boundary. We propose a corrected numerical scheme, for simulating one-dimensional diffusion processes with naturally occurring boundaries. This involves correcting the standard approach, so that an exact property of the diffusion process is precisely respected. As a consequence, the proposed scheme does not introduce a spurious force into the dynamics. We present numerical test cases, based on exactly soluble one-dimensional problems with one or two boundaries, which suggest that, for a given value of the discrete time step, the proposed scheme leads to substantially more accurate results than the standard approach. Alternatively, the standard approach needs considerably more computation time to obtain a comparable level of accuracy to the proposed scheme, because the standard approach requires a significantly smaller time step.

Slowdown of surface diffusion during early stages of bacterial colonization

NASA Astrophysics Data System (ADS)

Vourc'h, T.; Peerhossaini, H.; Léopoldès, J.; Méjean, A.; Chauvat, F.; Cassier-Chauvat, C.

2018-03-01

We study the surface diffusion of the model cyanobacterium Synechocystis sp. PCC6803 during the incipient stages of cell contact with a glass surface in the dilute regime. We observe a twitching motility with alternating immobile tumble and mobile run periods, resulting in a normal diffusion described by a continuous-time random walk with a coefficient of diffusion D . Surprisingly, D is found to decrease with time down to a plateau. This is observed only when the cyanobacterial cells are able to produce released extracellular polysaccharides, as shown by a comparative study between the wild-type strain and various polysaccharides-depleted mutants. The analysis of the trajectories taken by the bacterial cells shows that the temporal characteristics of their intermittent motion depend on the instantaneous fraction of visited sites during diffusion. This describes quantitatively the time dependence of D , related to the progressive surface coverage by the polysaccharides. The observed slowdown of the surface diffusion may constitute a basic precursor mechanism for microcolony formation and provides clues for controlling biofilm formation.

Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations.

PubMed

Linke, Max; Köfinger, Jürgen; Hummer, Gerhard

2018-05-31

We present a method to calculate the fully anisotropic rotational diffusion tensor from molecular dynamics simulations. Our approach is based on fitting the time-dependent covariance matrix of the quaternions that describe the rigid-body rotational dynamics. Explicit analytical expressions have been derived for the covariances by Favro, which are valid irrespective of the degree of anisotropy. We use these expressions to determine an optimal rotational diffusion tensor from trajectory data. The molecular structures are aligned against a reference by optimal rigid-body superposition. The quaternion covariances can then be obtained directly from the rotation matrices used in the alignment. The rotational diffusion tensor is determined by a fit to the time-dependent quaternion covariances, or directly by Laplace transformation and matrix diagonalization. To quantify uncertainties in the fit, we derive analytical expressions and compare them with the results of Brownian dynamics simulations of anisotropic rotational diffusion. We apply the method to microsecond long trajectories of the Dickerson-Drew B-DNA dodecamer and of horse heart myoglobin. The anisotropic rotational diffusion tensors calculated from simulations agree well with predictions from hydrodynamics.

Measuring a diffusion coefficient by single-particle tracking: statistical analysis of experimental mean squared displacement curves.

PubMed

Ernst, Dominique; Köhler, Jürgen

2013-01-21

We provide experimental results on the accuracy of diffusion coefficients obtained by a mean squared displacement (MSD) analysis of single-particle trajectories. We have recorded very long trajectories comprising more than 1.5 × 10(5) data points and decomposed these long trajectories into shorter segments providing us with ensembles of trajectories of variable lengths. This enabled a statistical analysis of the resulting MSD curves as a function of the lengths of the segments. We find that the relative error of the diffusion coefficient can be minimized by taking an optimum number of points into account for fitting the MSD curves, and that this optimum does not depend on the segment length. Yet, the magnitude of the relative error for the diffusion coefficient does, and achieving an accuracy in the order of 10% requires the recording of trajectories with about 1000 data points. Finally, we compare our results with theoretical predictions and find very good qualitative and quantitative agreement between experiment and theory.

Equilibration and analysis of first-principles molecular dynamics simulations of water

NASA Astrophysics Data System (ADS)

Dawson, William; Gygi, François

2018-03-01

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

PubMed

Dawson, William; Gygi, François

2018-03-28

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Innovation Becoming Trajectories: Leveraging Lateral and Vertical Moves for Collaborative Diffusion of Twenty-First Century Learning Practices

ERIC Educational Resources Information Center

Hung, David; Toh, Yancy; Jamaludin, Azilawati; So, Hyo-Jeong

2017-01-01

This paper argues for innovation diffusion as a "becoming" process in the context of lateral and vertical moves. The context of these innovations involves technology-mediated innovations and their diffusion trajectories in the Singapore education system. Embedded in a centralized-decentralized dialectics, this paper traces particular…

Analysis of single quantum-dot mobility inside 1D nanochannel devices

NASA Astrophysics Data System (ADS)

Hoang, H. T.; Segers-Nolten, I. M.; Tas, N. R.; van Honschoten, J. W.; Subramaniam, V.; Elwenspoek, M. C.

2011-07-01

We visualized individual quantum dots using a combination of a confining nanochannel and an ultra-sensitive microscope system, equipped with a high numerical aperture lens and a highly sensitive camera. The diffusion coefficients of the confined quantum dots were determined from the experimentally recorded trajectories according to the classical diffusion theory for Brownian motion in two dimensions. The calculated diffusion coefficients were three times smaller than those in bulk solution. These observations confirm and extend the results of Eichmann et al (2008 Langmuir 24 714-21) to smaller particle diameters and more narrow confinement. A detailed analysis shows that the observed reduction in mobility cannot be explained by conventional hydrodynamic theory.

The power of a single trajectory

NASA Astrophysics Data System (ADS)

Schnellbächer, Nikolas D.; Schwarz, Ulrich S.

2018-03-01

Random walks are often evaluated in terms of their mean squared displacements, either for a large number of trajectories or for one very long trajectory. An alternative evaluation is based on the power spectral density, but here it is less clear which information can be extracted from a single trajectory. For continuous-time Brownian motion, Krapf et al now have mathematically proven that the one property that can be reliably extracted from a single trajectory is the frequency dependence of the ensemble-averaged power spectral density (Krapf et al 2018 New J. Phys. 20 023029). Their mathematical analysis also identifies the appropriate frequency window for this procedure and shows that the diffusion coefficient can be extracted by averaging over a small number of trajectories. The authors have verified their analytical results both by computer simulations and experiments.

Bayesian Decision Tree for the Classification of the Mode of Motion in Single-Molecule Trajectories

PubMed Central

Türkcan, Silvan; Masson, Jean-Baptiste

2013-01-01

Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to improve our knowledge of the membrane architecture and to understand the nature of interactions between membrane proteins and their environments. Here, we present an analysis technique for single molecule tracking (SMT) trajectories that can determine the preferred model of motion that best matches observed trajectories. The method is based on Bayesian inference to calculate the posteriori probability of an observed trajectory according to a certain model. Information theory criteria, such as the Bayesian information criterion (BIC), the Akaike information criterion (AIC), and modified AIC (AICc), are used to select the preferred model. The considered group of models includes free Brownian motion, and confined motion in 2nd or 4th order potentials. We determine the best information criteria for classifying trajectories. We tested its limits through simulations matching large sets of experimental conditions and we built a decision tree. This decision tree first uses the BIC to distinguish between free Brownian motion and confined motion. In a second step, it classifies the confining potential further using the AIC. We apply the method to experimental Clostridium Perfingens -toxin (CPT) receptor trajectories to show that these receptors are confined by a spring-like potential. An adaptation of this technique was applied on a sliding window in the temporal dimension along the trajectory. We applied this adaptation to experimental CPT trajectories that lose confinement due to disaggregation of confining domains. This new technique adds another dimension to the discussion of SMT data. The mode of motion of a receptor might hold more biologically relevant information than the diffusion coefficient or domain size and may be a better tool to classify and compare different SMT experiments. PMID:24376584

Tracking single Kv2.1 channels in live cells reveals anomalous subdiffusion and ergodicity breaking

NASA Astrophysics Data System (ADS)

Weigel, Aubrey; Simon, Blair; Tamkun, Michael; Krapf, Diego

2011-03-01

The dynamic organization of the plasma membrane is responsible for essential cellular processes, such as receptor trafficking and signaling. By studying the dynamics of transmembrane proteins a greater understanding of these processes as a whole can be achieved. It is broadly observed that the diffusion pattern of membrane protein displays anomalous subdiffusion. However, the mechanisms responsible for this behavior are not yet established. We explore the dynamics of the voltage gated potassium channel Kv2.1 by using single-particle tracking. We analyze Kv2.1 channel trajectories in terms of the time and ensemble distributions of square displacements. Our results reveal that all Kv2.1 channels experience anomalous subdiffusion and we observe that the Kv2.1 diffusion pattern is non-ergodic. We further investigated the role of the actin cytoskeleton in these channel dynamics by applying actin depolymerizing drugs. It is seen that with the breakdown of the actin cytoskeleton the Kv2.1 channel trajectories recover ergodicity.

Extending Bell's beables to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories

NASA Astrophysics Data System (ADS)

Lorenzen, F.; de Ponte, M. A.; Moussa, M. H. Y.

2009-09-01

In this paper, employing the Itô stochastic Schrödinger equation, we extend Bell’s beable interpretation of quantum mechanics to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories. For a particular choice of the source of stochasticity, the one leading to a dissipative Lindblad-type correction to the Hamiltonian dynamics, we find that the diffusive terms in Nelsons stochastic trajectories are naturally incorporated into Bohm’s causal dynamics, yielding a unified Bohm-Nelson theory. In particular, by analyzing the interference between quantum trajectories, we clearly identify the decoherence time, as estimated from the quantum formalism. We also observe the quantum-to-classical transition in the convergence of the infinite ensemble of quantum trajectories to their classical counterparts. Finally, we show that our extended beables circumvent the problems in Bohm’s causal dynamics regarding stationary states in quantum mechanics.

Three-year changes in leisure activities are associated with concurrent changes in white matter microstructure and perceptual speed in individuals aged 80 years and older.

PubMed

Köhncke, Ylva; Laukka, Erika J; Brehmer, Yvonne; Kalpouzos, Grégoria; Li, Tie-Qiang; Fratiglioni, Laura; Bäckman, Lars; Lövdén, Martin

2016-05-01

Accumulating evidence suggests that engagement in leisure activities is associated with favorable trajectories of cognitive aging, but little is known about brain changes related to both activities and cognition. White matter microstructure shows experience-dependent plasticity and declines in aging. Therefore, we investigated the role of change in white matter microstructure in the activities-cognition link. We used repeated assessments of engagement, perceptual speed, and white matter microstructure (probed with diffusion tensor imaging) in a population-based sample of individuals over 80 years without dementia (n = 442, Mage = 85.1; n = 70 for diffusion tensor imaging; 2 occasions 3 years apart). Using multivariate latent change modeling, we observed positive correlations among changes in predominantly social activities, white matter microstructure, and perceptual speed. Interindividual differences in change in white matter microstructure statistically accounted for the association between change in leisure activities and change in perceptual speed. However, as analyses are based on observational data from 2 measurement occasions, causality remains unclear. Copyright © 2016 Elsevier Inc. All rights reserved.

Steepest Ascent Low/Non-Low-Frequency Ratio in Empirical Mode Decomposition to Separate Deterministic and Stochastic Velocities From a Single Lagrangian Drifter

NASA Astrophysics Data System (ADS)

Chu, Peter C.

2018-03-01

SOund Fixing And Ranging (RAFOS) floats deployed by the Naval Postgraduate School (NPS) in the California Current system from 1992 to 2001 at depth between 150 and 600 m (http://www.oc.nps.edu/npsRAFOS/) are used to study 2-D turbulent characteristics. Each drifter trajectory is adaptively decomposed using the empirical mode decomposition (EMD) into a series of intrinsic mode functions (IMFs) with corresponding specific scale for each IMF. A new steepest ascent low/non-low-frequency ratio is proposed in this paper to separate a Lagrangian trajectory into low-frequency (nondiffusive, i.e., deterministic) and high-frequency (diffusive, i.e., stochastic) components. The 2-D turbulent (or called eddy) diffusion coefficients are calculated on the base of the classical turbulent diffusion with mixing length theory from stochastic component of a single drifter. Statistical characteristics of the calculated 2-D turbulence length scale, strength, and diffusion coefficients from the NPS RAFOS data are presented with the mean values (over the whole drifters) of the 2-D diffusion coefficients comparable to the commonly used diffusivity tensor method.

Intrinsic trapping of stochastic sheared magnetic field lines

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

Negrea, M.; Petrisor, I.; Balescu, R.

2004-10-01

The decorrelation trajectory method is applied to the diffusion of magnetic field lines in a perturbed sheared slab magnetic configuration. Some interesting decorrelation trajectories for several values of the magnetic Kubo number and of the shear parameter are exhibited. The asymmetry of the decorrelation trajectories appears in comparison with those obtained in the purely electrostatic case studied in earlier work. The running and asymptotic diffusion tensor components are calculated and displayed.

TRAJECTORY AND INCINERATION OF ROGUE DROPLETS IN A TURBULENT DIFFUSION FLAME

EPA Science Inventory

The trajectory and incineration efficiency of individual droplet streams of a fuel mixture injected into a swirling gas turbulent diffusion flame were measured as a function of droplet size, droplet velocity, interdroplet spacing, and droplet injection angle. Additional experimen...

An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping.

PubMed

Koh, Wonryull; Blackwell, Kim T

2011-04-21

Stochastic simulation of reaction-diffusion systems enables the investigation of stochastic events arising from the small numbers and heterogeneous distribution of molecular species in biological cells. Stochastic variations in intracellular microdomains and in diffusional gradients play a significant part in the spatiotemporal activity and behavior of cells. Although an exact stochastic simulation that simulates every individual reaction and diffusion event gives a most accurate trajectory of the system's state over time, it can be too slow for many practical applications. We present an accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems designed to improve the speed of simulation by reducing the number of time-steps required to complete a simulation run. This method is unique in that it employs two strategies that have not been incorporated in existing spatial stochastic simulation algorithms. First, diffusive transfers between neighboring subvolumes are based on concentration gradients. This treatment necessitates sampling of only the net or observed diffusion events from higher to lower concentration gradients rather than sampling all diffusion events regardless of local concentration gradients. Second, we extend the non-negative Poisson tau-leaping method that was originally developed for speeding up nonspatial or homogeneous stochastic simulation algorithms. This method calculates each leap time in a unified step for both reaction and diffusion processes while satisfying the leap condition that the propensities do not change appreciably during the leap and ensuring that leaping does not cause molecular populations to become negative. Numerical results are presented that illustrate the improvement in simulation speed achieved by incorporating these two new strategies.

Versatile Analysis of Single-Molecule Tracking Data by Comprehensive Testing against Monte Carlo Simulations

PubMed Central

Wieser, Stefan; Axmann, Markus; Schütz, Gerhard J.

2008-01-01

We propose here an approach for the analysis of single-molecule trajectories which is based on a comprehensive comparison of an experimental data set with multiple Monte Carlo simulations of the diffusion process. It allows quantitative data analysis, particularly whenever analytical treatment of a model is infeasible. Simulations are performed on a discrete parameter space and compared with the experimental results by a nonparametric statistical test. The method provides a matrix of p-values that assess the probability for having observed the experimental data at each setting of the model parameters. We show the testing approach for three typical situations observed in the cellular plasma membrane: i), free Brownian motion of the tracer, ii), hop diffusion of the tracer in a periodic meshwork of squares, and iii), transient binding of the tracer to slowly diffusing structures. By plotting the p-value as a function of the model parameters, one can easily identify the most consistent parameter settings but also recover mutual dependencies and ambiguities which are difficult to determine by standard fitting routines. Finally, we used the test to reanalyze previous data obtained on the diffusion of the glycosylphosphatidylinositol-protein CD59 in the plasma membrane of the human T24 cell line. PMID:18805933

Brain microstructural development at near-term age in very-low-birth-weight preterm infants: An atlas-based diffusion imaging study

PubMed Central

Rose, Jessica; Vassar, Rachel; Cahill-Rowley, Katelyn; Guzman, Ximena Stecher; Stevenson, David K.; Barnea-Goraly, Naama

2014-01-01

At near-term age the brain undergoes rapid growth and development. Abnormalities identified during this period have been recognized as potential predictors of neurodevelopment in children born preterm. This study used diffusion tensor imaging (DTI) to examine white matter (WM) microstructure in very-low-birth-weight (VLBW) preterm infants to better understand regional WM developmental trajectories at near-term age. DTI scans were analyzed in a cross-sectional sample of 45 VLBW preterm infants (BW ≤ 1500 g, GA ≤ 32 weeks) within a cohort of 102 neonates admitted to the NICU and recruited to participate prior to standard-of-care MRI, from 2010 to 2011, 66/102 also had DTI. For inclusion in this analysis, 45 infants had DTI, no evidence of brain abnormality on MRI, and were scanned at PMA ≤40 weeks (34.7–38.6). White matter microstructure was analyzed in 19 subcortical regions defined by DiffeoMap neonatal brain atlas, using threshold values of trace b0.006 mm2 s−1 and FA >0.15. Regional fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were calculated and temporal–spatial trajectories of development were examined in relation to PMA and brain region location. Posterior regions within the corona radiata (CR), corpus callosum (CC), and internal capsule (IC) demonstrated significantly higher mean FA values compared to anterior regions. Posterior regions of the CR and IC demonstrated significantly lower RD values compared to anterior regions. Centrally located projection fibers demonstrated higher mean FA and lower RD values than peripheral regions including the posterior limb of the internal capsule (PLIC), cerebral peduncle, retrolenticular part of the IC, posterior thalamic radiation, and sagittal stratum. Centrally located association fibers of the external capsule had higher FA and lower RD than the more peripherally-located superior longitudinal fasciculus (SLF). A significant relationship between PMA-at-scan and FA, MD, and RD was demonstrated by a majority of regions, the strongest correlations were observed in the anterior limb of the internal capsule, a region undergoing early stages of myelination at near-term age, in which FA increased (r = .433, p = .003) and MD (r = –.545, p = .000) and RD (r = –.540, p = .000) decreased with PMA-at-scan. No correlation with PMA-at-scan was observed in the CC or SLF, regions that myelinate later in infancy. Regional patterns of higher FA and lower RD were observed at this near-term age, suggestive of more advanced microstructural development in posterior compared to anterior regions within the CR, CC, and IC and in central compared to peripheral WM structures. Evidence of region-specific rates of microstructural development was observed. Temporal–spatial patterns of WM microstructure development at near-term age have important implications for interpretation of near-term DTI and for identification of aberrations in typical developmental trajectories that may signal future impairment. PMID:24091089

Brain microstructural development at near-term age in very-low-birth-weight preterm infants: an atlas-based diffusion imaging study.

PubMed

Rose, Jessica; Vassar, Rachel; Cahill-Rowley, Katelyn; Guzman, Ximena Stecher; Stevenson, David K; Barnea-Goraly, Naama

2014-02-01

At near-term age the brain undergoes rapid growth and development. Abnormalities identified during this period have been recognized as potential predictors of neurodevelopment in children born preterm. This study used diffusion tensor imaging (DTI) to examine white matter (WM) microstructure in very-low-birth-weight (VLBW) preterm infants to better understand regional WM developmental trajectories at near-term age. DTI scans were analyzed in a cross-sectional sample of 45 VLBW preterm infants (BW≤1500g, GA≤32weeks) within a cohort of 102 neonates admitted to the NICU and recruited to participate prior to standard-of-care MRI, from 2010 to 2011, 66/102 also had DTI. For inclusion in this analysis, 45 infants had DTI, no evidence of brain abnormality on MRI, and were scanned at PMA ≤40weeks (34.7-38.6). White matter microstructure was analyzed in 19 subcortical regions defined by DiffeoMap neonatal brain atlas, using threshold values of trace <0.006mm(2)s(-1) and FA >0.15. Regional fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were calculated and temporal-spatial trajectories of development were examined in relation to PMA and brain region location. Posterior regions within the corona radiata (CR), corpus callosum (CC), and internal capsule (IC) demonstrated significantly higher mean FA values compared to anterior regions. Posterior regions of the CR and IC demonstrated significantly lower RD values compared to anterior regions. Centrally located projection fibers demonstrated higher mean FA and lower RD values than peripheral regions including the posterior limb of the internal capsule (PLIC), cerebral peduncle, retrolenticular part of the IC, posterior thalamic radiation, and sagittal stratum. Centrally located association fibers of the external capsule had higher FA and lower RD than the more peripherally-located superior longitudinal fasciculus (SLF). A significant relationship between PMA-at-scan and FA, MD, and RD was demonstrated by a majority of regions, the strongest correlations were observed in the anterior limb of the internal capsule, a region undergoing early stages of myelination at near-term age, in which FA increased (r=.433, p=.003) and MD (r=-.545, p=.000) and RD (r=-.540, p=.000) decreased with PMA-at-scan. No correlation with PMA-at-scan was observed in the CC or SLF, regions that myelinate later in infancy. Regional patterns of higher FA and lower RD were observed at this near-term age, suggestive of more advanced microstructural development in posterior compared to anterior regions within the CR, CC, and IC and in central compared to peripheral WM structures. Evidence of region-specific rates of microstructural development was observed. Temporal-spatial patterns of WM microstructure development at near-term age have important implications for interpretation of near-term DTI and for identification of aberrations in typical developmental trajectories that may signal future impairment. © 2013.

Geometric diffusion of quantum trajectories

PubMed Central

Yang, Fan; Liu, Ren-Bao

2015-01-01

A quantum object can acquire a geometric phase (such as Berry phases and Aharonov–Bohm phases) when evolving along a path in a parameter space with non-trivial gauge structures. Inherent to quantum evolutions of wavepackets, quantum diffusion occurs along quantum trajectories. Here we show that quantum diffusion can also be geometric as characterized by the imaginary part of a geometric phase. The geometric quantum diffusion results from interference between different instantaneous eigenstate pathways which have different geometric phases during the adiabatic evolution. As a specific example, we study the quantum trajectories of optically excited electron-hole pairs in time-reversal symmetric insulators, driven by an elliptically polarized terahertz field. The imaginary geometric phase manifests itself as elliptical polarization in the terahertz sideband generation. The geometric quantum diffusion adds a new dimension to geometric phases and may have applications in many fields of physics, e.g., transport in topological insulators and novel electro-optical effects. PMID:26178745

Janus Colloids Actively Rotating on the Surface of Water.

PubMed

Wang, Xiaolu; In, Martin; Blanc, Christophe; Würger, Alois; Nobili, Maurizio; Stocco, Antonio

2017-12-05

Biological or artificial microswimmers move performing trajectories of different kinds such as rectilinear, circular, or spiral ones. Here, we report on circular trajectories observed for active Janus colloids trapped at the air-water interface. Circular motion is due to asymmetric and nonuniform surface properties of the particles caused by fabrication. Motion persistence is enhanced by the partial wetted state of the Janus particles actively moving in two dimensions at the air-water interface. The slowing down of in-plane and out-of-plane rotational diffusions is described and discussed.

Robust model-based analysis of single-particle tracking experiments with Spot-On

PubMed Central

Grimm, Jonathan B; Lavis, Luke D

2018-01-01

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce ‘Spot-On’, an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants. PMID:29300163

Robust model-based analysis of single-particle tracking experiments with Spot-On.

PubMed

Hansen, Anders S; Woringer, Maxime; Grimm, Jonathan B; Lavis, Luke D; Tjian, Robert; Darzacq, Xavier

2018-01-04

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce 'Spot-On', an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants. © 2018, Hansen et al.

Non-Gaussian diffusion in static disordered media

NASA Astrophysics Data System (ADS)

Luo, Liang; Yi, Ming

2018-04-01

Non-Gaussian diffusion is commonly considered as a result of fluctuating diffusivity, which is correlated in time or in space or both. In this work, we investigate the non-Gaussian diffusion in static disordered media via a quenched trap model, where the diffusivity is spatially correlated. Several unique effects due to quenched disorder are reported. We analytically estimate the diffusion coefficient Ddis and its fluctuation over samples of finite size. We show a mechanism of population splitting in the non-Gaussian diffusion. It results in a sharp peak in the distribution of displacement P (x ,t ) around x =0 , that has frequently been observed in experiments. We examine the fidelity of the coarse-grained diffusion map, which is reconstructed from particle trajectories. Finally, we propose a procedure to estimate the correlation length in static disordered environments, where the information stored in the sample-to-sample fluctuation has been utilized.

Uphill diffusion in multicomponent mixtures.

PubMed

Krishna, Rajamani

2015-05-21

Molecular diffusion is an omnipresent phenomena that is important in a wide variety of contexts in chemical, physical, and biological processes. In the majority of cases, the diffusion process can be adequately described by Fick's law that postulates a linear relationship between the flux of any species and its own concentration gradient. Most commonly, a component diffuses down the concentration gradient. The major objective of this review is to highlight a very wide variety of situations that cause the uphill transport of one constituent in the mixture. Uphill diffusion may occur in multicomponent mixtures in which the diffusion flux of any species is strongly coupled to that of its partner species. Such coupling effects often arise from strong thermodynamic non-idealities. For a quantitative description we need to use chemical potential gradients as driving forces. The transport of ionic species in aqueous solutions is coupled with its partner ions because of the electro-neutrality constraints; such constraints may accelerate or decelerate a specific ion. When uphill diffusion occurs, we observe transient overshoots during equilibration; the equilibration process follows serpentine trajectories in composition space. For mixtures of liquids, alloys, ceramics and glasses the serpentine trajectories could cause entry into meta-stable composition zones; such entry could result in phenomena such as spinodal decomposition, spontaneous emulsification, and the Ouzo effect. For distillation of multicomponent mixtures that form azeotropes, uphill diffusion may allow crossing of distillation boundaries that are normally forbidden. For mixture separations with microporous adsorbents, uphill diffusion can cause supra-equilibrium loadings to be achieved during transient uptake within crystals; this allows the possibility of over-riding adsorption equilibrium for achieving difficult separations.

Impact of rheology on probabilistic forecasts of sea ice trajectories: application for search and rescue operations in the Arctic

NASA Astrophysics Data System (ADS)

Rabatel, Matthias; Rampal, Pierre; Carrassi, Alberto; Bertino, Laurent; Jones, Christopher K. R. T.

2018-03-01

We present a sensitivity analysis and discuss the probabilistic forecast capabilities of the novel sea ice model neXtSIM used in hindcast mode. The study pertains to the response of the model to the uncertainty on winds using probabilistic forecasts of ice trajectories. neXtSIM is a continuous Lagrangian numerical model that uses an elasto-brittle rheology to simulate the ice response to external forces. The sensitivity analysis is based on a Monte Carlo sampling of 12 members. The response of the model to the uncertainties is evaluated in terms of simulated ice drift distances from their initial positions, and from the mean position of the ensemble, over the mid-term forecast horizon of 10 days. The simulated ice drift is decomposed into advective and diffusive parts that are characterised separately both spatially and temporally and compared to what is obtained with a free-drift model, that is, when the ice rheology does not play any role in the modelled physics of the ice. The seasonal variability of the model sensitivity is presented and shows the role of the ice compactness and rheology in the ice drift response at both local and regional scales in the Arctic. Indeed, the ice drift simulated by neXtSIM in summer is close to the one obtained with the free-drift model, while the more compact and solid ice pack shows a significantly different mechanical and drift behaviour in winter. For the winter period analysed in this study, we also show that, in contrast to the free-drift model, neXtSIM reproduces the sea ice Lagrangian diffusion regimes as found from observed trajectories. The forecast capability of neXtSIM is also evaluated using a large set of real buoy's trajectories and compared to the capability of the free-drift model. We found that neXtSIM performs significantly better in simulating sea ice drift, both in terms of forecast error and as a tool to assist search and rescue operations, although the sources of uncertainties assumed for the present experiment are not sufficient for complete coverage of the observed IABP positions.

Cell biochemistry studied by single-molecule imaging.

PubMed

Mashanov, G I; Nenasheva, T A; Peckham, M; Molloy, J E

2006-11-01

Over the last decade, there have been remarkable developments in live-cell imaging. We can now readily observe individual protein molecules within living cells and this should contribute to a systems level understanding of biological pathways. Direct observation of single fluorophores enables several types of molecular information to be gathered. Temporal and spatial trajectories enable diffusion constants and binding kinetics to be deduced, while analyses of fluorescence lifetime, intensity, polarization or spectra give chemical and conformational information about molecules in their cellular context. By recording the spatial trajectories of pairs of interacting molecules, formation of larger molecular complexes can be studied. In the future, multicolour and multiparameter imaging of single molecules in live cells will be a powerful analytical tool for systems biology. Here, we discuss measurements of single-molecule mobility and residency at the plasma membrane of live cells. Analysis of diffusional paths at the plasma membrane gives information about its physical properties and measurement of temporal trajectories enables rates of binding and dissociation to be derived. Meanwhile, close scrutiny of individual fluorophore trajectories enables ideas about molecular dimerization and oligomerization related to function to be tested directly.

Analysis of Molecular Diffusion by First-Passage Time Variance Identifies the Size of Confinement Zones

PubMed Central

Rajani, Vishaal; Carrero, Gustavo; Golan, David E.; de Vries, Gerda; Cairo, Christopher W.

2011-01-01

The diffusion of receptors within the two-dimensional environment of the plasma membrane is a complex process. Although certain components diffuse according to a random walk model (Brownian diffusion), an overwhelming body of work has found that membrane diffusion is nonideal (anomalous diffusion). One of the most powerful methods for studying membrane diffusion is single particle tracking (SPT), which records the trajectory of a label attached to a membrane component of interest. One of the outstanding problems in SPT is the analysis of data to identify the presence of heterogeneity. We have adapted a first-passage time (FPT) algorithm, originally developed for the interpretation of animal movement, for the analysis of SPT data. We discuss the general application of the FPT analysis to molecular diffusion, and use simulations to test the method against data containing known regions of confinement. We conclude that FPT can be used to identify the presence and size of confinement within trajectories of the receptor LFA-1, and these results are consistent with previous reports on the size of LFA-1 clusters. The analysis of trajectory data for cell surface receptors by FPT provides a robust method to determine the presence and size of confined regions of diffusion. PMID:21402028

A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton

PubMed Central

Das, Raibatak; Cairo, Christopher W.; Coombs, Daniel

2009-01-01

The extraction of hidden information from complex trajectories is a continuing problem in single-particle and single-molecule experiments. Particle trajectories are the result of multiple phenomena, and new methods for revealing changes in molecular processes are needed. We have developed a practical technique that is capable of identifying multiple states of diffusion within experimental trajectories. We model single particle tracks for a membrane-associated protein interacting with a homogeneously distributed binding partner and show that, with certain simplifying assumptions, particle trajectories can be regarded as the outcome of a two-state hidden Markov model. Using simulated trajectories, we demonstrate that this model can be used to identify the key biophysical parameters for such a system, namely the diffusion coefficients of the underlying states, and the rates of transition between them. We use a stochastic optimization scheme to compute maximum likelihood estimates of these parameters. We have applied this analysis to single-particle trajectories of the integrin receptor lymphocyte function-associated antigen-1 (LFA-1) on live T cells. Our analysis reveals that the diffusion of LFA-1 is indeed approximately two-state, and is characterized by large changes in cytoskeletal interactions upon cellular activation. PMID:19893741

Statistics of actin-propelled trajectories in noisy environments

NASA Astrophysics Data System (ADS)

Wen, Fu-Lai; Chen, Hsuan-Yi; Leung, Kwan-tai

2016-06-01

Actin polymerization is ubiquitously utilized to power the locomotion of eukaryotic cells and pathogenic bacteria in living systems. Inevitably, actin polymerization and depolymerization proceed in a fluctuating environment that renders the locomotion stochastic. Previously, we have introduced a deterministic model that manages to reproduce actin-propelled trajectories in experiments, but not to address fluctuations around them. To remedy this, here we supplement the deterministic model with noise terms. It enables us to compute the effects of fluctuating actin density and forces on the trajectories. Specifically, the mean-squared displacement (MSD) of the trajectories is computed and found to show a super-ballistic scaling with an exponent 3 in the early stage, followed by a crossover to a normal, diffusive scaling of exponent 1 in the late stage. For open-end trajectories such as straights and S-shaped curves, the time of crossover matches the decay time of orientational order of the velocities along trajectories, suggesting that it is the spreading of velocities that leads to the crossover. We show that the super-ballistic scaling of MSD arises from the initial, linearly increasing correlation of velocities, before time translational symmetry is established. When the spreading of velocities reaches a steady state in the long-time limit, short-range correlation then yields a diffusive scaling in MSD. In contrast, close-loop trajectories like circles exhibit localized periodic motion, which inhibits spreading. The initial super-ballistic scaling of MSD arises from velocity correlation that both linearly increases and oscillates in time. Finally, we find that the above statistical features of the trajectories transcend the nature of noises, be it additive or multiplicative, and generalize to other self-propelled systems that are not necessarily actin based.

Memoryless control of boundary concentrations of diffusing particles.

PubMed

Singer, A; Schuss, Z; Nadler, B; Eisenberg, R S

2004-12-01

Flux between regions of different concentration occurs in nearly every device involving diffusion, whether an electrochemical cell, a bipolar transistor, or a protein channel in a biological membrane. Diffusion theory has calculated that flux since the time of Fick (1855), and the flux has been known to arise from the stochastic behavior of Brownian trajectories since the time of Einstein (1905), yet the mathematical description of the behavior of trajectories corresponding to different types of boundaries is not complete. We consider the trajectories of noninteracting particles diffusing in a finite region connecting two baths of fixed concentrations. Inside the region, the trajectories of diffusing particles are governed by the Langevin equation. To maintain average concentrations at the boundaries of the region at their values in the baths, a control mechanism is needed to set the boundary dynamics of the trajectories. Different control mechanisms are used in Langevin and Brownian simulations of such systems. We analyze models of controllers and derive equations for the time evolution and spatial distribution of particles inside the domain. Our analysis shows a distinct difference between the time evolution and the steady state concentrations. While the time evolution of the density is governed by an integral operator, the spatial distribution is governed by the familiar Fokker-Planck operator. The boundary conditions for the time dependent density depend on the model of the controller; however, this dependence disappears in the steady state, if the controller is of a renewal type. Renewal-type controllers, however, produce spurious boundary layers that can be catastrophic in simulations of charged particles, because even a tiny net charge can have global effects. The design of a nonrenewal controller that maintains concentrations of noninteracting particles without creating spurious boundary layers at the interface requires the solution of the time-dependent Fokker-Planck equation with absorption of outgoing trajectories and a source of ingoing trajectories on the boundary (the so called albedo problem).

Connection between encounter volume and diffusivity in geophysical flows

NASA Astrophysics Data System (ADS)

Rypina, Irina I.; Smith, Stefan G. Llewellyn; Pratt, Larry J.

2018-04-01

Trajectory encounter volume - the volume of fluid that passes close to a reference fluid parcel over some time interval - has been recently introduced as a measure of mixing potential of a flow. Diffusivity is the most commonly used characteristic of turbulent diffusion. We derive the analytical relationship between the encounter volume and diffusivity under the assumption of an isotropic random walk, i.e., diffusive motion, in one and two dimensions. We apply the derived formulas to produce maps of encounter volume and the corresponding diffusivity in the Gulf Stream region of the North Atlantic based on satellite altimetry, and discuss the mixing properties of Gulf Stream rings. Advantages offered by the derived formula for estimating diffusivity from oceanographic data are discussed, as well as applications to other disciplines.

Imaging carbon nanotube interactions, diffusion, and stability in nanopores.

PubMed

Eichmann, Shannon L; Smith, Billy; Meric, Gulsum; Fairbrother, D Howard; Bevan, Michael A

2011-07-26

We report optical microscopy measurements of three-dimensional trajectories of individual multiwalled carbon nanotubes (MWCNTs) in nanoscale silica slit pores. Trajectories are analyzed to nonintrusively measure MWCNT interactions, diffusion, and stability as a function of pH and ionic strength. Evanescent wave scattering is used to track MWCNT positions normal to pore walls with nanometer-scale resolution, and video microscopy is used to track lateral positions with spatial resolution comparable to the diffraction limit. Analysis of MWCNT excursions normal to pore walls yields particle-wall potentials that agree with theoretical electrostatic and van der Waals potentials assuming a rotationally averaged potential of mean force. MWCNT lateral mean square displacements are used to quantify translational diffusivities, which are comparable to predictions based on the best available theories. Finally, measured MWCNT pH and ionic strength dependent stabilities are in excellent agreement with predictions. Our findings demonstrate novel measurement and modeling tools to understand the behavior of confined MWCNTs relevant to a broad range of applications.

Anomalous Diffusion of Single Particles in Cytoplasm

PubMed Central

Regner, Benjamin M.; Vučinić, Dejan; Domnisoru, Cristina; Bartol, Thomas M.; Hetzer, Martin W.; Tartakovsky, Daniel M.; Sejnowski, Terrence J.

2013-01-01

The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM. PMID:23601312

Numerical Simulations of Vortex Generator Vanes and Jets on a Flat Plate

NASA Technical Reports Server (NTRS)

Allan, Brian G.; Yao, Chung-Sheng; Lin, John C.

2002-01-01

Numerical simulations of a single low-profile vortex generator vane, which is only a small fraction of the boundary-layer thickness, and a vortex generating jet have been performed for flows over a flat plate. The numerical simulations were computed by solving the steady-state solution to the Reynolds-averaged Navier-Stokes equations. The vortex generating vane results were evaluated by comparing the strength and trajectory of the streamwise vortex to experimental particle image velocimetry measurements. From the numerical simulations of the vane case, it was observed that the Shear-Stress Transport (SST) turbulence model resulted in a better prediction of the streamwise peak vorticity and trajectory when compared to the Spalart-Allmaras (SA) turbulence model. It is shown in this investigation that the estimation of the turbulent eddy viscosity near the vortex core, for both the vane and jet simulations, was higher for the SA model when compared to the SST model. Even though the numerical simulations of the vortex generating vane were able to predict the trajectory of the stream-wise vortex, the initial magnitude and decay of the peak streamwise vorticity were significantly under predicted. A comparison of the positive circulation associated with the streamwise vortex showed that while the numerical simulations produced a more diffused vortex, the vortex strength compared very well to the experimental observations. A grid resolution study for the vortex generating vane was also performed showing that the diffusion of the vortex was not a result of insufficient grid resolution. Comparisons were also made between a fully modeled trapezoidal vane with finite thickness to a simply modeled rectangular thin vane. The comparisons showed that the simply modeled rectangular vane produced a streamwise vortex which had a strength and trajectory very similar to the fully modeled trapezoidal vane.

Brownian dynamics simulation of rigid particles of arbitrary shape in external fields.

PubMed

Fernandes, Miguel X; de la Torre, José García

2002-12-01

We have developed a Brownian dynamics simulation algorithm to generate Brownian trajectories of an isolated, rigid particle of arbitrary shape in the presence of electric fields or any other external agents. Starting from the generalized diffusion tensor, which can be calculated with the existing HYDRO software, the new program BROWNRIG (including a case-specific subprogram for the external agent) carries out a simulation that is analyzed later to extract the observable dynamic properties. We provide a variety of examples of utilization of this method, which serve as tests of its performance, and also illustrate its applicability. Examples include free diffusion, transport in an electric field, and diffusion in a restricting environment.

More insights into early brain development through statistical analyses of eigen-structural elements of diffusion tensor imaging using multivariate adaptive regression splines

PubMed Central

Chen, Yasheng; Zhu, Hongtu; An, Hongyu; Armao, Diane; Shen, Dinggang; Gilmore, John H.; Lin, Weili

2013-01-01

The aim of this study was to characterize the maturational changes of the three eigenvalues (λ1 ≥ λ2 ≥ λ3) of diffusion tensor imaging (DTI) during early postnatal life for more insights into early brain development. In order to overcome the limitations of using presumed growth trajectories for regression analysis, we employed Multivariate Adaptive Regression Splines (MARS) to derive data-driven growth trajectories for the three eigenvalues. We further employed Generalized Estimating Equations (GEE) to carry out statistical inferences on the growth trajectories obtained with MARS. With a total of 71 longitudinal datasets acquired from 29 healthy, full-term pediatric subjects, we found that the growth velocities of the three eigenvalues were highly correlated, but significantly different from each other. This paradox suggested the existence of mechanisms coordinating the maturations of the three eigenvalues even though different physiological origins may be responsible for their temporal evolutions. Furthermore, our results revealed the limitations of using the average of λ2 and λ3 as the radial diffusivity in interpreting DTI findings during early brain development because these two eigenvalues had significantly different growth velocities even in central white matter. In addition, based upon the three eigenvalues, we have documented the growth trajectory differences between central and peripheral white matter, between anterior and posterior limbs of internal capsule, and between inferior and superior longitudinal fasciculus. Taken together, we have demonstrated that more insights into early brain maturation can be gained through analyzing eigen-structural elements of DTI. PMID:23455648

Identifying mechanisms for superdiffusive dynamics in cell trajectories

NASA Astrophysics Data System (ADS)

Passucci, Giuseppe; Brasch, Megan; Henderson, James; Manning, M. Lisa

Self-propelled particle (SPP) models have been used to explore features of active matter such as motility-induced phase separation, jamming, and flocking, and are often used to model biological cells. However, many cells exhibit super-diffusive trajectories, where displacements scale faster than t 1 / 2 in all directions, and these are not captured by traditional SPP models. We extract cell trajectories from image stacks of mouse fibroblast cells moving on 2D substrates and find super-diffusive mean-squared displacements in all directions across varying densities. Two SPP model modifications have been proposed to capture super-diffusive dynamics: Levy walks and heterogeneous motility parameters. In mouse fibroblast cells displacement probability distributions collapse when time is rescaled by a power greater than 1/2, which is consistent with Levy walks. We show that a simple SPP model with heterogeneous rotational noise can also generate a similar collapse. Furthermore, a close examination of statistics extracted directly from cell trajectories is consistent with a heterogeneous mobility SPP model and inconsistent with a Levy walk model. Our work demonstrates that a simple set of analyses can distinguish between mechanisms for anomalous diffusion in active matter.

Spiral diffusion of rotating self-propellers with stochastic perturbation

NASA Astrophysics Data System (ADS)

Nourhani, Amir; Ebbens, Stephen J.; Gibbs, John G.; Lammert, Paul E.

2016-09-01

Translationally diffusive behavior arising from the combination of orientational diffusion and powered motion at microscopic scales is a known phenomenon, but the peculiarities of the evolution of expected position conditioned on initial position and orientation have been neglected. A theory is given of the spiral motion of the mean trajectory depending upon propulsion speed, angular velocity, orientational diffusion, and rate of random chirality reversal. We demonstrate the experimental accessibility of this effect using both tadpole-like and Janus sphere dimer rotating motors. Sensitivity of the mean trajectory to the kinematic parameters suggest that it may be a useful way to determine those parameters.

A Skill Score of Trajectory Model Evaluation Using Reinitialized Series of Normalized Cumulative Lagrangian Separation

NASA Astrophysics Data System (ADS)

Liu, Y.; Weisberg, R. H.

2017-12-01

The Lagrangian separation distance between the endpoints of simulated and observed drifter trajectories is often used to assess the performance of numerical particle trajectory models. However, the separation distance fails to indicate relative model performance in weak and strong current regions, such as a continental shelf and its adjacent deep ocean. A skill score is proposed based on the cumulative Lagrangian separation distances normalized by the associated cumulative trajectory lengths. The new metrics correctly indicates the relative performance of the Global HYCOM in simulating the strong currents of the Gulf of Mexico Loop Current and the weaker currents of the West Florida Shelf in the eastern Gulf of Mexico. In contrast, the Lagrangian separation distance alone gives a misleading result. Also, the observed drifter position series can be used to reinitialize the trajectory model and evaluate its performance along the observed trajectory, not just at the drifter end position. The proposed dimensionless skill score is particularly useful when the number of drifter trajectories is limited and neither a conventional Eulerian-based velocity nor a Lagrangian-based probability density function may be estimated.

Lifespan Trajectories of White Matter Changes in Rhesus Monkeys.

PubMed

Kubicki, M; Baxi, M; Pasternak, O; Tang, Y; Karmacharya, S; Chunga, N; Lyall, A E; Rathi, Y; Eckbo, R; Bouix, S; Mortazavi, F; Papadimitriou, G; Shenton, M E; Westin, C F; Killiany, R; Makris, N; Rosene, D L

2018-04-26

Progress in neurodevelopmental brain research has been achieved through the use of animal models. Such models not only help understanding biological changes that govern brain development, maturation and aging, but are also essential for identifying possible mechanisms of neurodevelopmental and age-related chronic disorders, and to evaluate possible interventions with potential relevance to human disease. Genetic relationship of rhesus monkeys to humans makes those animals a great candidate for such models. With the typical lifespan of 25 years, they undergo cognitive maturation and aging that is similar to this observed in humans. Quantitative structural neuroimaging has been proposed as one of the candidate in vivo biomarkers for tracking white matter brain maturation and aging. While lifespan trajectories of white matter changes have been mapped in humans, such knowledge is not available for nonhuman primates. Here, we analyze and model lifespan trajectories of white matter microstructure using in vivo diffusion imaging in a sample of 44 rhesus monkeys. We report quantitative parameters (including slopes and peaks) of lifespan trajectories for 8 individual white matter tracts. We show different trajectories for cellular and extracellular microstructural imaging components that are associated with white matter maturation and aging, and discuss similarities and differences between those in humans and rhesus monkeys, the importance of our findings, and future directions for the field.Significance Statement: Quantitative structural neuroimaging has been proposed as one of the candidate in vivo biomarkers for tracking brain maturation and aging. While lifespan trajectories of structural white matter changes have been mapped in humans, such knowledge is not available for rhesus monkeys. We present here results of the analysis and modeling of the lifespan trajectories of white matter microstructure using in vivo diffusion imaging in a sample of 44 rhesus monkeys (age 4-27). We report and anatomically map lifespan changes related to cellular and extracellular microstructural components that are associated with white matter maturation and aging.

Unconfined lateral diffusion and an estimate of pericellular matrix viscosity revealed by measuring the mobility of gold-tagged lipids

PubMed Central

1993-01-01

Nanovid (video-enhanced) microscopy was used to determine whether lateral diffusion in the plasma membrane of colloidal gold-tagged lipid molecules is confined or is unrestricted. Confinement could be produced by domains within the plane of the plasma membrane or by filamentous barriers within the pericellular matrix. Fluorescein- phosphatidylethanolamine (F1-PE), incorporated into the plasma membranes of cultured fibroblasts, epithelial cells and keratocytes, was labeled with 30-nm colloidal gold conjugated to anti-fluorescein (anti-F1). The trajectories of the gold-labeled lipids were used to compute diffusion coefficients (DG) and to test for restricted motion. On the cell lamella, the gold-labeled lipids diffused freely in the plasma membrane. Since the gold must move through the pericellular matrix as the attached lipid diffuses in the plasma membrane, this result suggests that any extensive filamentous barriers in the pericellular matrix are at least 40 nm from the plasma membrane surface. The average diffusion coefficients ranged from 1.1 to 1.7 x 10(-9) cm2/s. These values were lower than the average diffusion coefficients (DF) (5.4 to 9.5 x 10(-9) cm2/s) obtained by FRAP. The lower DG is partially due to the pericellular matrix as demonstrated by the result that heparinase treatment of keratocytes significantly increased DG to 2.8 x 10(-9) cm2/s, but did not affect DF. Pericellular matrix viscosity was estimated from the frictional coefficients computed from DG and DF and ranged from 0.5 to 0.9 poise for untreated cells. Heparinase treatment of keratocytes decreased the apparent viscosity to approximately 0.1 poise. To evaluate the presence of domains or barriers, the trajectories and corresponding mean square displacement (MSD) plots of gold-labeled lipids were compared to the trajectories and MSD plots resulting from computer simulations of random walks within corrals. Based on these comparisons, we conclude that, if there are domains limiting the diffusion of F1-PE, most are larger than 5 microns in diameter. PMID:8416991

Stochastic lattice model of synaptic membrane protein domains.

PubMed

Li, Yiwei; Kahraman, Osman; Haselwandter, Christoph A

2017-05-01

Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments. We show that our stochastic lattice model yields quantitative agreement with mean-field models of nonlinear diffusion in crowded membranes. Through a combination of analytic and numerical solutions of the master equation governing the reaction dynamics at synaptic domains, together with kinetic Monte Carlo simulations, we find substantial discrepancies between mean-field and stochastic models for the reaction dynamics at synaptic domains. Based on the reaction and diffusion properties of synaptic receptors and scaffolds suggested by previous experiments and mean-field calculations, we show that the stochastic reaction-diffusion dynamics of synaptic receptors and scaffolds provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the observed single-molecule trajectories, and spatial heterogeneity in the effective rates at which receptors and scaffolds are recycled at the cell membrane. Our work sheds light on the physical mechanisms and principles linking the collective properties of membrane protein domains to the stochastic dynamics that rule their molecular components.

Imaging atomic-level random walk of a point defect in graphene

NASA Astrophysics Data System (ADS)

Kotakoski, Jani; Mangler, Clemens; Meyer, Jannik C.

2014-05-01

Deviations from the perfect atomic arrangements in crystals play an important role in affecting their properties. Similarly, diffusion of such deviations is behind many microstructural changes in solids. However, observation of point defect diffusion is hindered both by the difficulties related to direct imaging of non-periodic structures and by the timescales involved in the diffusion process. Here, instead of imaging thermal diffusion, we stimulate and follow the migration of a divacancy through graphene lattice using a scanning transmission electron microscope operated at 60 kV. The beam-activated process happens on a timescale that allows us to capture a significant part of the structural transformations and trajectory of the defect. The low voltage combined with ultra-high vacuum conditions ensure that the defect remains stable over long image sequences, which allows us for the first time to directly follow the diffusion of a point defect in a crystalline material.

Longitudinal in-vivo diffusion tensor imaging for assessing brain developmental changes in BALB/cJ mice, a model of reduced sociability relevant to autism.

PubMed

Kumar, Manoj; Kim, Sungheon; Pickup, Stephen; Chen, Rong; Fairless, Andrew H; Ittyerah, Ranjit; Abel, Ted; Brodkin, Edward S; Poptani, Harish

2012-05-21

Diffusion tensor imaging (DTI) is highly sensitive in detecting brain structure and connectivity phenotypes in autism spectrum disorders (ASD). Since one of the core symptoms of ASD is reduced sociability (reduced tendency to seek social interaction), we hypothesized that DTI will be sensitive in detecting neural phenotypes that correlate with decreased sociability in mouse models. Relative to C57BL/6J (B6) mice, juvenile BALB/cJ mice show reduced sociability. We performed social approach test in a three-chambered apparatus and in-vivo longitudinal DTI at post-natal days 30, 50 and 70 days-of-age in BALB/cJ (n=32) and B6 (n=15) mice to assess the correlation between DTI and sociability and to evaluate differences in DTI parameters between these two strains. Fractional anisotropy (FA) and mean diffusivity (MD) values from in-vivo DTI data were analyzed from white matter (corpus callosum, internal and external capsule) and gray matter (cerebral cortex, frontal motor cortex, hippocampus, thalamus and amygdaloid) regions based on their relevance to ASD. A moderate but significant (p<0.05) negative correlation between sociability and FA in hippocampus and frontal motor cortex was noted for BALB/cJ mice at 30 days-of-age. Significant differences in FA and MD values between BALB/cJ and B6 mice were observed in most white and gray matter areas at all three time points. Significant differences in developmental trajectories of FA and MD values from thalamus and frontal motor cortex were also observed between BALB/cJ and B6, indicating relative under-connectivity in BALB/cJ mice. These results indicate that DTI may be used as an in-vivo, non-invasive imaging method to assess developmental trajectories of brain connectivity in mouse models of neurodevelopmental and behavioral disorders. Copyright © 2012 Elsevier B.V. All rights reserved.

Longitudinal in-vivo diffusion tensor imaging for assessing brain developmental changes in BALB/cJ mice, a model of reduced sociability relevant to autism

PubMed Central

Kumar, Manoj; Kim, Sungheon; Pickup, Stephen; Chen, Rong; Fairless, Andrew H.; Ittyerah, Ranjit; Abel, Ted; Brodkin, Edward S.; Poptani, Harish

2012-01-01

Diffusion tensor imaging (DTI) is highly sensitive in detecting brain structure and connectivity phenotypes in autism spectrum disorders (ASD). Since one of the core symptoms of ASD is reduced sociability (reduced tendency to seek social interaction), we hypothesized that DTI will be sensitive in detecting neural phenotypes that correlate with decreased sociability in mouse models. Relative to C57BL/6J (B6) mice, juvenile BALB/cJ mice show reduced sociability. We performed social approach test in a three-chambered apparatus and in-vivo longitudinal DTI at post-natal days 30, 50 and 70 days-of-age in BALB/cJ (n=32) and B6 (n=15) mice to assess the correlation between DTI and sociability and to evaluate differences in DTI parameters between these two strains. Fractional anisotropy (FA) and mean diffusivity (MD) values from in-vivo DTI data were analyzed from white matter (corpus callosum, internal and external capsule) and gray matter (cerebral cortex, frontal motor cortex, hippocampus, thalamus and amygdaloid) regions based on their relevance to ASD. A moderate but significant (p<0.05) negative correlation between sociability and FA in hippocampus and frontal motor cortex was noted for BALB/cJ mice at 30 days-of-age. Significant differences in FA and MD values between BALB/cJ and B6 mice were observed in most white and gray matter areas at all three time points. Significant differences in developmental trajectories of FA and MD values from thalamus and frontal motor cortex were also observed between BALB/cJ and B6, indicating relative under-connectivity in BALB/cJ mice. These results indicate that DTI may be used as an in-vivo, non-invasive imaging method to assess developmental trajectories of brain connectivity in mouse models of neurodevelopmental and behavioral disorders. PMID:22513103

Anomalous yet Brownian.

PubMed

Wang, Bo; Anthony, Stephen M; Bae, Sung Chul; Granick, Steve

2009-09-08

We describe experiments using single-particle tracking in which mean-square displacement is simply proportional to time (Fickian), yet the distribution of displacement probability is not Gaussian as should be expected of a classical random walk but, instead, is decidedly exponential for large displacements, the decay length of the exponential being proportional to the square root of time. The first example is when colloidal beads diffuse along linear phospholipid bilayer tubes whose radius is the same as that of the beads. The second is when beads diffuse through entangled F-actin networks, bead radius being less than one-fifth of the actin network mesh size. We explore the relevance to dynamic heterogeneity in trajectory space, which has been extensively discussed regarding glassy systems. Data for the second system might suggest activated diffusion between pores in the entangled F-actin networks, in the same spirit as activated diffusion and exponential tails observed in glassy systems. But the first system shows exceptionally rapid diffusion, nearly as rapid as for identical colloids in free suspension, yet still displaying an exponential probability distribution as in the second system. Thus, although the exponential tail is reminiscent of glassy systems, in fact, these dynamics are exceptionally rapid. We also compare with particle trajectories that are at first subdiffusive but Fickian at the longest measurement times, finding that displacement probability distributions fall onto the same master curve in both regimes. The need is emphasized for experiments, theory, and computer simulation to allow definitive interpretation of this simple and clean exponential probability distribution.

Position-sensitive scanning fluorescence correlation spectroscopy.

PubMed

Skinner, Joseph P; Chen, Yan; Müller, Joachim D

2005-08-01

Fluorescence correlation spectroscopy (FCS) uses a stationary laser beam to illuminate a small sample volume and analyze the temporal behavior of the fluorescence fluctuations within the stationary observation volume. In contrast, scanning FCS (SFCS) collects the fluorescence signal from a moving observation volume by scanning the laser beam. The fluctuations now contain both temporal and spatial information about the sample. To access the spatial information we synchronize scanning and data acquisition. Synchronization allows us to evaluate correlations for every position along the scanned trajectory. We use a circular scan trajectory in this study. Because the scan radius is constant, the phase angle is sufficient to characterize the position of the beam. We introduce position-sensitive SFCS (PSFCS), where correlations are calculated as a function of lag time and phase. We present the theory of PSFCS and derive expressions for diffusion, diffusion in the presence of flow, and for immobilization. To test PSFCS we compare experimental data with theory. We determine the direction and speed of a flowing dye solution and the position of an immobilized particle. To demonstrate the feasibility of the technique for applications in living cells we present data of enhanced green fluorescent protein measured in the nucleus of COS cells.

Observing single quantum trajectories of a superconducting quantum bit

NASA Astrophysics Data System (ADS)

Murch, K. W.; Weber, S. J.; Macklin, C.; Siddiqi, I.

2013-10-01

The length of time that a quantum system can exist in a superposition state is determined by how strongly it interacts with its environment. This interaction entangles the quantum state with the inherent fluctuations of the environment. If these fluctuations are not measured, the environment can be viewed as a source of noise, causing random evolution of the quantum system from an initially pure state into a statistical mixture--a process known as decoherence. However, by accurately measuring the environment in real time, the quantum system can be maintained in a pure state and its time evolution described by a `quantum trajectory' determined by the measurement outcome. Here we use weak measurements to monitor a microwave cavity containing a superconducting quantum bit (qubit), and track the individual quantum trajectories of the system. In this set-up, the environment is dominated by the fluctuations of a single electromagnetic mode of the cavity. Using a near-quantum-limited parametric amplifier, we selectively measure either the phase or the amplitude of the cavity field, and thereby confine trajectories to either the equator or a meridian of the Bloch sphere. We perform quantum state tomography at discrete times along the trajectory to verify that we have faithfully tracked the state of the quantum system as it diffuses on the surface of the Bloch sphere. Our results demonstrate that decoherence can be mitigated by environmental monitoring, and validate the foundation of quantum feedback approaches based on Bayesian statistics. Moreover, our experiments suggest a new means of implementing `quantum steering'--the harnessing of action at a distance to manipulate quantum states through measurement.

Observing single quantum trajectories of a superconducting quantum bit.

PubMed

Murch, K W; Weber, S J; Macklin, C; Siddiqi, I

2013-10-10

The length of time that a quantum system can exist in a superposition state is determined by how strongly it interacts with its environment. This interaction entangles the quantum state with the inherent fluctuations of the environment. If these fluctuations are not measured, the environment can be viewed as a source of noise, causing random evolution of the quantum system from an initially pure state into a statistical mixture--a process known as decoherence. However, by accurately measuring the environment in real time, the quantum system can be maintained in a pure state and its time evolution described by a 'quantum trajectory' determined by the measurement outcome. Here we use weak measurements to monitor a microwave cavity containing a superconducting quantum bit (qubit), and track the individual quantum trajectories of the system. In this set-up, the environment is dominated by the fluctuations of a single electromagnetic mode of the cavity. Using a near-quantum-limited parametric amplifier, we selectively measure either the phase or the amplitude of the cavity field, and thereby confine trajectories to either the equator or a meridian of the Bloch sphere. We perform quantum state tomography at discrete times along the trajectory to verify that we have faithfully tracked the state of the quantum system as it diffuses on the surface of the Bloch sphere. Our results demonstrate that decoherence can be mitigated by environmental monitoring, and validate the foundation of quantum feedback approaches based on Bayesian statistics. Moreover, our experiments suggest a new means of implementing 'quantum steering'--the harnessing of action at a distance to manipulate quantum states through measurement.

Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA.

PubMed

Vestergaard, Christian L; Blainey, Paul C; Flyvbjerg, Henrik

2018-03-16

We reanalyze trajectories of hOGG1 repair proteins diffusing on DNA. A previous analysis of these trajectories with the popular mean-squared-displacement approach revealed only simple diffusion. Here, a new optimal estimator of diffusion coefficients reveals two-state kinetics of the protein. A simple, solvable model, in which the protein randomly switches between a loosely bound, highly mobile state and a tightly bound, less mobile state is the simplest possible dynamic model consistent with the data. It yields accurate estimates of hOGG1's (i) diffusivity in each state, uncorrupted by experimental errors arising from shot noise, motion blur and thermal fluctuations of the DNA; (ii) rates of switching between states and (iii) rate of detachment from the DNA. The protein spends roughly equal time in each state. It detaches only from the loosely bound state, with a rate that depends on pH and the salt concentration in solution, while its rates for switching between states are insensitive to both. The diffusivity in the loosely bound state depends primarily on pH and is three to ten times higher than in the tightly bound state. We propose and discuss some new experiments that take full advantage of the new tools of analysis presented here.

Evaluation of bacterial motility from non-Gaussianity of finite-sample trajectories using the large deviation principle

NASA Astrophysics Data System (ADS)

Hanasaki, Itsuo; Kawano, Satoyuki

2013-11-01

Motility of bacteria is usually recognized in the trajectory data and compared with Brownian motion, but the diffusion coefficient is insufficient to evaluate it. In this paper, we propose a method based on the large deviation principle. We show that it can be used to evaluate the non-Gaussian characteristics of model Escherichia coli motions and to distinguish combinations of the mean running duration and running speed that lead to the same diffusion coefficient. Our proposed method does not require chemical stimuli to induce the chemotaxis in a specific direction, and it is applicable to various types of self-propelling motions for which no a priori information of, for example, threshold parameters for run and tumble or head/tail direction is available. We also address the issue of the finite-sample effect on the large deviation quantities, but we propose to make use of it to characterize the nature of motility.

Q-space trajectory imaging for multidimensional diffusion MRI of the human brain

PubMed Central

Westin, Carl-Fredrik; Knutsson, Hans; Pasternak, Ofer; Szczepankiewicz, Filip; Özarslan, Evren; van Westen, Danielle; Mattisson, Cecilia; Bogren, Mats; O’Donnell, Lauren; Kubicki, Marek; Topgaard, Daniel; Nilsson, Markus

2016-01-01

This work describes a new diffusion MR framework for imaging and modeling of microstructure that we call q-space trajectory imaging (QTI). The QTI framework consists of two parts: encoding and modeling. First we propose q-space trajectory encoding, which uses time-varying gradients to probe a trajectory in q-space, in contrast to traditional pulsed field gradient sequences that attempt to probe a point in q-space. Then we propose a microstructure model, the diffusion tensor distribution (DTD) model, which takes advantage of additional information provided by QTI to estimate a distributional model over diffusion tensors. We show that the QTI framework enables microstructure modeling that is not possible with the traditional pulsed gradient encoding as introduced by Stejskal and Tanner. In our analysis of QTI, we find that the well-known scalar b-value naturally extends to a tensor-valued entity, i.e., a diffusion measurement tensor, which we call the b-tensor. We show that b-tensors of rank 2 or 3 enable estimation of the mean and covariance of the DTD model in terms of a second order tensor (the diffusion tensor) and a fourth order tensor. The QTI framework has been designed to improve discrimination of the sizes, shapes, and orientations of diffusion microenvironments within tissue. We derive rotationally invariant scalar quantities describing intuitive microstructural features including size, shape, and orientation coherence measures. To demonstrate the feasibility of QTI on a clinical scanner, we performed a small pilot study comparing a group of five healthy controls with five patients with schizophrenia. The parameter maps derived from QTI were compared between the groups, and 9 out of the 14 parameters investigated showed differences between groups. The ability to measure and model the distribution of diffusion tensors, rather than a quantity that has already been averaged within a voxel, has the potential to provide a powerful paradigm for the study of complex tissue architecture. PMID:26923372

Ion radial diffusion in an electrostatic impulse model for stormtime ring current formation

NASA Technical Reports Server (NTRS)

Chen, Margaret W.; Schulz, Michael; Lyons, Larry R.; Gorney, David J.

1992-01-01

Two refinements to the quasi-linear theory of ion radial diffusion are proposed and examined analytically with simulations of particle trajectories. The resonance-broadening correction by Dungey (1965) is applied to the quasi-linear diffusion theory by Faelthammar (1965) for an individual model storm. Quasi-linear theory is then applied to the mean diffusion coefficients resulting from simulations of particle trajectories in 20 model storms. The correction for drift-resonance broadening results in quasi-linear diffusion coefficients with discrepancies from the corresponding simulated values that are reduced by a factor of about 3. Further reductions in the discrepancies are noted following the averaging of the quasi-linear diffusion coefficients, the simulated coefficients, and the resonance-broadened coefficients for the 20 storms. Quasi-linear theory provides good descriptions of particle transport for a single storm but performs even better in conjunction with the present ensemble-averaging.

Blast and ballistic trajectories in combat casualties: a preliminary analysis using a cartesian positioning system with MDCT.

PubMed

Folio, Les R; Fischer, Tatjana; Shogan, Paul; Frew, Michael; Dwyer, Andrew; Provenzale, James M

2011-08-01

The purpose of this study is to determine the agreement with which radiologists identify wound paths in vivo on MDCT and calculate missile trajectories on the basis of Cartesian coordinates using a Cartesian positioning system (CPS). Three radiologists retrospectively identified 25 trajectories on MDCT in 19 casualties who sustained penetrating trauma in Iraq. Trajectories were described qualitatively in terms of directional path descriptors and quantitatively as trajectory vectors. Directional descriptors, trajectory angles, and angles between trajectories were calculated based on Cartesian coordinates of entrance and terminus or exit recorded in x, y image and table space (z) using a Trajectory Calculator created using spreadsheet software. The consistency of qualitative descriptor determinations was assessed in terms of frequency of observer agreement and multirater kappa statistics. Consistency of trajectory vectors was evaluated in terms of distribution of magnitude of the angles between vectors and the differences between their paraaxial and parasagittal angles. In 68% of trajectories, the observers' visual assessment of qualitative descriptors was congruent. Calculated descriptors agreed across observers in 60% of the trajectories. Estimated kappa also showed good agreement (0.65-0.79, p < 0.001); 70% of calculated paraaxial and parasagittal angles were within 20° across observers, and 61.3% of angles between trajectory vectors were within 20° across observers. Results show agreement of visually assessed and calculated qualitative descriptors and trajectory angles among observers. The Trajectory Calculator describes trajectories qualitatively similar to radiologists' visual assessment, showing the potential feasibility of automated trajectory analysis.

A multiple case history and systematic review of adoption, diffusion, implementation and impact of provincial daily physical activity policies in Canadian schools.

PubMed

Olstad, Dana Lee; Campbell, Elizabeth J; Raine, Kim D; Nykiforuk, Candace I J

2015-04-15

Few children meet physical activity (PA) recommendations, and are therefore at increased risk for overweight/obesity and adverse health outcomes. To increase children's opportunities for PA, several Canadian provinces have adopted school-based daily PA (DPA) policies. It is not clear why some jurisdictions have adopted DPA policies, and others have not, nor whether these policies have been implemented and have achieved their intended outcomes. The purpose of this study was to understand the processes underlying adoption and diffusion of Canadian DPA policies, and to review evidence regarding their implementation and impact. We adopted a multiple case history methodology in which we traced the chronological trajectory of DPA policies among Canadian provinces by compiling timelines detailing key historical events that preceded policy adoption. Publicly available documents posted on the internet were reviewed to characterize adopter innovativeness, describe the content of their DPA policies, and explore the context surrounding policy adoption. Diffusion of Innovations theory provided a conceptual framework for the analyses. A systematic literature search identified studies that had investigated adoption, diffusion, implementation or impact of Canadian DPA policies. Five of Canada's 13 provinces and territories (38.5%) have DPA policies. Although the underlying objectives of the policies are similar, there are clear differences among them and in their various policy trajectories. Adoption and diffusion of DPA policies were structured by the characteristics and capacities of adopters, the nature of their policies, and contextual factors. Limited data suggests implementation of DPA policies was moderate but inconsistent and that Canadian DPA policies have had little to no impact on school-aged children's PA levels or BMI. This study detailed the history and current status of Canadian DPA policies, highlighting the conditional nature of policy adoption and diffusion, and describing policy and adopter characteristics and political contexts that shaped policy trajectories. An understanding of the conditions associated with successful policy adoption and diffusion can help identify receptive contexts in which to pioneer novel legislative initiatives to increase PA among children. By reviewing evidence regarding policy implementation and impact, this study can also inform amendments to existing, and development of future PA policies.

A model-based approach for automated in vitro cell tracking and chemotaxis analyses.

PubMed

Debeir, Olivier; Camby, Isabelle; Kiss, Robert; Van Ham, Philippe; Decaestecker, Christine

2004-07-01

Chemotaxis may be studied in two main ways: 1) counting cells passing through an insert (e.g., using Boyden chambers), and 2) directly observing cell cultures (e.g., using Dunn chambers), both in response to stationary concentration gradients. This article promotes the use of Dunn chambers and in vitro cell-tracking, achieved by video microscopy coupled with automatic image analysis software, in order to extract quantitative and qualitative measurements characterizing the response of cells to a diffusible chemical agent. Previously, we set up a videomicroscopy system coupled with image analysis software that was able to compute cell trajectories from in vitro cell cultures. In the present study, we are introducing a new software increasing the application field of this system to chemotaxis studies. This software is based on an adapted version of the active contour methodology, enabling each cell to be efficiently tracked for hours and resulting in detailed descriptions of individual cell trajectories. The major advantages of this method come from an improved robustness with respect to variability in cell morphologies between different cell lines and dynamical changes in cell shape during cell migration. Moreover, the software includes a very small number of parameters which do not require overly sensitive tuning. Finally, the running time of the software is very short, allowing improved possibilities in acquisition frequency and, consequently, improved descriptions of complex cell trajectories, i.e. trajectories including cell division and cell crossing. We validated this software on several artificial and real cell culture experiments in Dunn chambers also including comparisons with manual (human-controlled) analyses. We developed new software and data analysis tools for automated cell tracking which enable cell chemotaxis to be efficiently analyzed. Copyright 2004 Wiley-Liss, Inc.

Seeing believes: Watching entangled sculpted branched DNA in real time

NASA Astrophysics Data System (ADS)

Jee, Ah-Young; Guan, Juan; Chen, Kejia; Granick, Steve

2015-03-01

The importance of branching in polymer physics is universally accepted but the details are disputed. We have sculpted DNA to various degrees of branching and used single-molecule tracking to image its diffusion in real time when entangled. By ligating three identical or varying length DNA segments, we construct symmetric and asymmetric ?Y? branches from elements of lambda-DNA with 16 um contour length, allowing for single-molecule visualization of equilibrium dynamics. Using home-written software, a full statistical distribution based on at least hundreds of trajectories is quantified with focus on discriminating arm-retraction from branch point motion. Some part of our observations is consistent with the anticipated ?relaxation through arm retraction? mechanism but other observations do not appear to be anticipated theoretically. Currently working as a researcher in Institute for Basic Science.

Simulations of Lateral Transport and Dropout Structure of Energetic Particles from Impulsive Solar Flares

NASA Astrophysics Data System (ADS)

Tooprakai, P.; Seripienlert, A.; Ruffolo, D.; Chuychai, P.; Matthaeus, W. H.

2016-11-01

We simulate trajectories of energetic particles from impulsive solar flares for 2D+slab models of magnetic turbulence in spherical geometry to study dropout features, I.e., sharp, repeated changes in the particle density. Among random-phase realizations of two-dimensional (2D) turbulence, a spherical harmonic expansion can generate homogeneous turbulence over a sphere, but a 2D fast Fourier transform (FFT) locally mapped onto the lateral coordinates in the region of interest is much faster computationally, and we show that the results are qualitatively similar. We then use the 2D FFT field as input to a 2D MHD simulation, which dynamically generates realistic features of turbulence such as coherent structures. The magnetic field lines and particles spread non-diffusively (ballistically) to a patchy distribution reaching up to 25° from the injection longitude and latitude at r ˜ 1 au. This dropout pattern in field line trajectories has sharper features in the case of the more realistic 2D MHD model, in better qualitative agreement with observations. The initial dropout pattern in particle trajectories is relatively insensitive to particle energy, though the energy affects the pattern’s evolution with time. We make predictions for future observations of solar particles near the Sun (e.g., at 0.25 au), for which we expect a sharp pulse of outgoing particles along the dropout pattern, followed by backscattering that first remains close to the dropout pattern and later exhibits cross-field transport to a distribution that is more diffusive, yet mostly contained within the dropout pattern found at greater distances.

Helical paths, gravitaxis, and separation phenomena for mass-anisotropic self-propelling colloids: Experiment versus theory

NASA Astrophysics Data System (ADS)

Campbell, Andrew I.; Wittkowski, Raphael; ten Hagen, Borge; Löwen, Hartmut; Ebbens, Stephen J.

2017-08-01

The self-propulsion mechanism of active colloidal particles often generates not only translational but also rotational motion. For particles with an anisotropic mass density under gravity, the motion is usually influenced by a downwards oriented force and an aligning torque. Here we study the trajectories of self-propelled bottom-heavy Janus particles in three spatial dimensions both in experiments and by theory. For a sufficiently large mass anisotropy, the particles typically move along helical trajectories whose axis is oriented either parallel or antiparallel to the direction of gravity (i.e., they show gravitaxis). In contrast, if the mass anisotropy is small and rotational diffusion is dominant, gravitational alignment of the trajectories is not possible. Furthermore, the trajectories depend on the angular self-propulsion velocity of the particles. If this component of the active motion is strong and rotates the direction of translational self-propulsion of the particles, their trajectories have many loops, whereas elongated swimming paths occur if the angular self-propulsion is weak. We show that the observed gravitational alignment mechanism and the dependence of the trajectory shape on the angular self-propulsion can be used to separate active colloidal particles with respect to their mass anisotropy and angular self-propulsion, respectively.

Determination of the hydrodynamic friction matrix for various anisotropic particles

NASA Astrophysics Data System (ADS)

Kraft, Daniela; Wittkowksi, Raphael; Löwen, Hartmut; Pine, David

2013-03-01

The relationship between the shape of a colloidal particle and its Brownian motion can be captured by the hydrodynamic friction matrix. It fully describes the translational and rotational diffusion along the particle's main axes as well as the coupling between rotational and translational diffusion. We observed a wide variety of anisotropic colloidal particles with confocal microscopy and calculated the hydrodynamic friction matrix from the particle trajectories. We find that symmetries in the particle shape are reflected in the entries of the friction matrix. We compare our experimentally obtained results with numerical simulations and theoretical predictions. Financial support through a Rubicon grant by the Netherlands Organisation for Scientific Research.

Colloidal diffusion over a quasicrystalline-patterned substrate

NASA Astrophysics Data System (ADS)

Su, Yun; Lai, Pik-Yin; Ackerson, Bruce; Tong, Penger

We report a systematic study of colloidal diffusion over a quasicrystalline-patterned substrate. The sample substrate is made of a flat thin layer of photoresist and contains identical cylindrical holes of diameter dh, which are arranged on a quasicrystal lattice. A monolayer of silica spheres of diameter comparable to dh diffuse over the rugged quasicrystalline-patterned substrate and experience a gravitational potential U (x , y) . With optical microscopy and the particle tracking method, we measure U (x , y) and particle's diffusion trajectories, which are found to undergo two distinct states: a trapped state when the particles are inside the holes and a free diffusion state when they are over the flat portion of the substrate. The dynamic properties of the diffusing particle, such as its mean dwell time, mean square displacement, and long-time diffusion coefficient DL are obtained from the particle trajectories. The measured DL is found to be in good agreement with the prediction of two theoretical models proposed for diffusion over a quasicrystal lattice. The experiment demonstrates the applications of this newly constructed colloidal potential landscape. This work was supported by the Research Grants Council of Hong Kong SAR.

Extreme event statistics in a drifting Markov chain

NASA Astrophysics Data System (ADS)

Kindermann, Farina; Hohmann, Michael; Lausch, Tobias; Mayer, Daniel; Schmidt, Felix; Widera, Artur

2017-07-01

We analyze extreme event statistics of experimentally realized Markov chains with various drifts. Our Markov chains are individual trajectories of a single atom diffusing in a one-dimensional periodic potential. Based on more than 500 individual atomic traces we verify the applicability of the Sparre Andersen theorem to our system despite the presence of a drift. We present detailed analysis of four different rare-event statistics for our system: the distributions of extreme values, of record values, of extreme value occurrence in the chain, and of the number of records in the chain. We observe that, for our data, the shape of the extreme event distributions is dominated by the underlying exponential distance distribution extracted from the atomic traces. Furthermore, we find that even small drifts influence the statistics of extreme events and record values, which is supported by numerical simulations, and we identify cases in which the drift can be determined without information about the underlying random variable distributions. Our results facilitate the use of extreme event statistics as a signal for small drifts in correlated trajectories.

Live Cell Imaging of the Endocytosis and the Intracellular Trafficking of Multifunctional Lipid Nanoparticles

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

Zhang, Tieqiao; Danthi, S. N.; Xie, Jianwu

Artificial lipid nanoparticles have drawn great attention due to their potential in medicine. Linked with targeting ligands, they can be used as probes and/or gene delivery vectors for specific types of target cells. Therefore, they are very promising agents in early detection, diagnosis and treatment of cancers and other genetic diseases. However, there are several barriers blocking the applications. Controlling the cellular uptake of the lipid nanoparticles is an important technical challenge to overcome. Understanding the mechanism of the endocytosis and the following intracellular trafficking is very important for improving the design and therefore the efficiency as a drug deliverymore » system. By using fluorescence microscopy methods, we studied the endocytosis of lipid nanoparticles by live M21 cells. The movements of the nanoparticles inside the cell were quantitatively characterized and classified based on the diffusion behavior. The trajectories of nanoparticles movement over the cell membrane revealed hop-diffusion behavior prior to the endocytosis. Fast movement in large steps is observed in intracellular trafficking and is attributed to active movement along microtubule. These observations help to understand the mechanism of the endocytosis and the pathway of the particles in cells.« less

Live cell imaging of the endocytosis and the intracellular trafficking of multifunctional lipid nanoparticles

NASA Astrophysics Data System (ADS)

Zhang, Tieqiao; Danthi, S. Narasimhan; Xie, Jianwu; Hu, Dehong; Lu, Peter; Li, King

2006-02-01

Artificial lipid nanoparticles have drawn great attention due to their potential in medicine. Linked with targeting ligands, they can be used as probes and/or gene delivery vectors for specific types of target cells. Therefore, they are very promising agents in early detection, diagnosis and treatment of cancers and other genetic diseases. However, there are several barriers blocking the applications. Controlling the cellular uptake of the lipid nanoparticles is an important technical challenge to overcome. Understanding the mechanism of the endocytosis and the following intracellular trafficking is very important for improving the design and therefore the efficiency as a drug delivery system. By using fluorescence microscopy methods, we studied the endocytosis of lipid nanoparticles by live M21 cells. The movements of the nanoparticles inside the cell were quantitatively characterized and classified based on the diffusion behavior. The trajectories of nanoparticles movement over the cell membrane revealed hop-diffusion behavior prior to the endocytosis. Fast movement in large steps is observed in intracellular trafficking and is attributed to active movement along microtubule. These observations help to understand the mechanism of the endocytosis and the pathway of the particles in cells.

Single-particle tracking: applications to membrane dynamics.

PubMed

Saxton, M J; Jacobson, K

1997-01-01

Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.

Folding time dependence of the motions of a molecular motor in an amorphous medium

NASA Astrophysics Data System (ADS)

Ciobotarescu, Simona; Bechelli, Solene; Rajonson, Gabriel; Migirditch, Samuel; Hester, Brooke; Hurduc, Nicolae; Teboul, Victor

2017-12-01

We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time τf. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very slowly with τf, while for rapid foldings (regime II) the diffusion increases strongly with τf(D ≈τf-2 ), suggesting two different physical mechanisms. We find that in regime I the motor's displacement during the folding process is counteracted by a reverse displacement during the unfolding, while in regime II this counteraction is much weaker. We notice that regime I behavior is reminiscent of the scallop theorem that holds for larger motors in a continuous medium. We find that the difference in the efficiency of the motor's motion explains most of the observed difference between the two regimes. For fast foldings the motor trajectories differ significantly from the opposite trajectories induced by the following unfolding process, resulting in a more efficient global motion than for slow foldings. This result agrees with the fluctuation theorems expectation for time reversal mechanisms. In agreement with the fluctuation theorems we find that the motors are unexpectedly more efficient when they are generating more entropy, a result that can be used to increase dramatically the motor's motion.

Strange kinetics of bulk-mediated diffusion on lipid bilayers

PubMed Central

Campagnola, Grace; Nepal, Kanti; Peersen, Olve B.

2016-01-01

Diffusion at solid-liquid interfaces is crucial in many technological and biophysical processes. Although its behavior seems deceivingly simple, recent studies showing passive superdiffusive transport suggest diffusion on surfaces may hide rich complexities. In particular, bulk-mediated diffusion occurs when molecules are transiently released from the surface to perform three-dimensional excursions into the liquid bulk. This phenomenon bears the dichotomy where a molecule always return to the surface but the mean jump length is infinite. Such behavior is associated with a breakdown of the central limit theorem and weak ergodicity breaking. Here, we use single-particle tracking to study the statistics of bulk-mediated diffusion on a supported lipid bilayer. We find that the time-averaged mean square displacement (MSD) of individual trajectories, the archetypal measure in diffusion processes, does not converge to the ensemble MSD but it remains a random variable, even in the long observation-time limit. The distribution of time averages is shown to agree with a Lévy flight model. Our results also unravel intriguing anomalies in the statistics of displacements. The time averaged MSD is shown to depend on experimental time and investigations of fractional moments show a scaling 〈|r(t)|q〉 ∼ tqv(q) with non-linear exponents, i.e. v(q) ≠ const. This type of behavior is termed strong anomalous diffusion and is rare among experimental observations. PMID:27095275

Normal and tumoral melanocytes exhibit q-Gaussian random search patterns.

PubMed

da Silva, Priscila C A; Rosembach, Tiago V; Santos, Anésia A; Rocha, Márcio S; Martins, Marcelo L

2014-01-01

In multicellular organisms, cell motility is central in all morphogenetic processes, tissue maintenance, wound healing and immune surveillance. Hence, failures in its regulation potentiates numerous diseases. Here, cell migration assays on plastic 2D surfaces were performed using normal (Melan A) and tumoral (B16F10) murine melanocytes in random motility conditions. The trajectories of the centroids of the cell perimeters were tracked through time-lapse microscopy. The statistics of these trajectories was analyzed by building velocity and turn angle distributions, as well as velocity autocorrelations and the scaling of mean-squared displacements. We find that these cells exhibit a crossover from a normal to a super-diffusive motion without angular persistence at long time scales. Moreover, these melanocytes move with non-Gaussian velocity distributions. This major finding indicates that amongst those animal cells supposedly migrating through Lévy walks, some of them can instead perform q-Gaussian walks. Furthermore, our results reveal that B16F10 cells infected by mycoplasmas exhibit essentially the same diffusivity than their healthy counterparts. Finally, a q-Gaussian random walk model was proposed to account for these melanocytic migratory traits. Simulations based on this model correctly describe the crossover to super-diffusivity in the cell migration tracks.

Twitching motility of bacteria with type-IV pili: Fractal walks, first passage time, and their consequences on microcolonies

NASA Astrophysics Data System (ADS)

Bisht, Konark; Klumpp, Stefan; Banerjee, Varsha; Marathe, Rahul

2017-11-01

A human pathogen, Neisseria gonorrhoeae (NG), moves on surfaces by attaching and retracting polymeric structures called Type IV pili. The tug-of-war between the pili results in a two-dimensional stochastic motion called twitching motility. In this paper, with the help of real-time NG trajectories, we develop coarse-grained models for their description. The fractal properties of these trajectories are determined and their influence on first passage time and formation of bacterial microcolonies is studied. Our main observations are as follows: (i) NG performs a fast ballistic walk on small time scales and a slow diffusive walk over long time scales with a long crossover region; (ii) there exists a characteristic persistent length lp*, which yields the fastest growth of bacterial aggregates or biofilms. Our simulations reveal that lp*˜L0.6 , where L ×L is the surface on which the bacteria move; (iii) the morphologies have distinct fractal characteristics as a consequence of the ballistic and diffusive motion of the constituting bacteria.

Modelling of Dictyostelium discoideum movement in a linear gradient of chemoattractant.

PubMed

Eidi, Zahra; Mohammad-Rafiee, Farshid; Khorrami, Mohammad; Gholami, Azam

2017-11-15

Chemotaxis is a ubiquitous biological phenomenon in which cells detect a spatial gradient of chemoattractant, and then move towards the source. Here we present a position-dependent advection-diffusion model that quantitatively describes the statistical features of the chemotactic motion of the social amoeba Dictyostelium discoideum in a linear gradient of cAMP (cyclic adenosine monophosphate). We fit the model to experimental trajectories that are recorded in a microfluidic setup with stationary cAMP gradients and extract the diffusion and drift coefficients in the gradient direction. Our analysis shows that for the majority of gradients, both coefficients decrease over time and become negative as the cells crawl up the gradient. The extracted model parameters also show that besides the expected drift in the direction of the chemoattractant gradient, we observe a nonlinear dependency of the corresponding variance on time, which can be explained by the model. Furthermore, the results of the model show that the non-linear term in the mean squared displacement of the cell trajectories can dominate the linear term on large time scales.

Active motion assisted by correlated stochastic torques.

PubMed

Weber, Christian; Radtke, Paul K; Schimansky-Geier, Lutz; Hänggi, Peter

2011-07-01

The stochastic dynamics of an active particle undergoing a constant speed and additionally driven by an overall fluctuating torque is investigated. The random torque forces are expressed by a stochastic differential equation for the angular dynamics of the particle determining the orientation of motion. In addition to a constant torque, the particle is supplemented by random torques, which are modeled as an Ornstein-Uhlenbeck process with given correlation time τ(c). These nonvanishing correlations cause a persistence of the particles' trajectories and a change of the effective spatial diffusion coefficient. We discuss the mean square displacement as a function of the correlation time and the noise intensity and detect a nonmonotonic dependence of the effective diffusion coefficient with respect to both correlation time and noise strength. A maximal diffusion behavior is obtained if the correlated angular noise straightens the curved trajectories, interrupted by small pirouettes, whereby the correlated noise amplifies a straightening of the curved trajectories caused by the constant torque.

A Comparison of the Age-Spectra from Data Assimilation Models

NASA Technical Reports Server (NTRS)

Schoeberl, Mark R.; Douglass, Anne R.; Zhu, Zheng-Xin; Pawson, Steven; Einaudi, Franco (Technical Monitor)

2002-01-01

We use kinematic and diabatic back trajectory calculations, driven by winds from a general circulation model (GCM) and two different data assimilation systems (DAS), to compute the age spectrum at three latitudes in the lower stratosphere. The age-spectra are compared to chemical transport model (CTM) calculations, and the mean ages from all of these studies are compared to observations. The age spectra computed using the GCM winds show a reasonably well-isolated tropics in good agreement with observations; however, the age spectra determined from the DAS differ from the GCM spectra. For the diabatic trajectory calculations, the age spectrum is too broad as a result of too much exchange between the tropics and mid-latitudes. The age spectrum determined using the kinematic trajectory calculation is less broad and lacks an age offset; both of these features are due to excessive vertical dispersion of parcels. The tropical and mid-latitude mean age difference between the diabatically and kinematically determined age-spectra is about one year, the former being older. The CTM calculation of the age spectrum using the DAS winds shows the same dispersive characteristics of the kinematic trajectory calculation. These results suggest that the current DAS products will not give realistic trace gas distributions for long integrations; they also help explain why the mean ages determined in a number of previous DAS driven CTM's are too young compared with observations. Finally, we note trajectory-generated age spectra show significant age anomalies correlated with the seasonal cycles, and these anomalies can be linked to year-to-year variations in the tropical heating rate. These anomalies are suppressed in the CTM spectra suggesting that the CTM transport is too diffusive.

Post-processing interstitialcy diffusion from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bhardwaj, U.; Bukkuru, S.; Warrier, M.

2016-01-01

An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms.

Post-processing interstitialcy diffusion from molecular dynamics simulations

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

Bhardwaj, U., E-mail: haptork@gmail.com; Bukkuru, S.; Warrier, M.

2016-01-15

An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures ismore » studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.« less

Swarming bacteria migrate by Lévy Walk

NASA Astrophysics Data System (ADS)

Ariel, Gil; Rabani, Amit; Benisty, Sivan; Partridge, Jonathan D.; Harshey, Rasika M.; Be'Er, Avraham

2015-09-01

Individual swimming bacteria are known to bias their random trajectories in search of food and to optimize survival. The motion of bacteria within a swarm, wherein they migrate as a collective group over a solid surface, is fundamentally different as typical bacterial swarms show large-scale swirling and streaming motions involving millions to billions of cells. Here by tracking trajectories of fluorescently labelled individuals within such dense swarms, we find that the bacteria are performing super-diffusion, consistent with Lévy walks. Lévy walks are characterized by trajectories that have straight stretches for extended lengths whose variance is infinite. The evidence of super-diffusion consistent with Lévy walks in bacteria suggests that this strategy may have evolved considerably earlier than previously thought.

Single-Molecule Resolution of Antimicrobial Peptide Interactions with Supported Lipid A Bilayers.

PubMed

Nelson, Nathaniel; Schwartz, Daniel K

2018-06-05

The molecular interactions between antimicrobial peptides (AMPs) and lipid A-containing supported lipid bilayers were probed using single-molecule total internal reflection fluorescence microscopy. Hybrid supported lipid bilayers with lipid A outer leaflets and phospholipid (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)) inner leaflets were prepared and characterized, and the spatiotemporal trajectories of individual fluorescently labeled LL37 and Melittin AMPs were determined as they interacted with the bilayer surfaces comprising either monophosphoryl or diphosphoryl lipid A (from Escherichia coli) to determine the impact of electrostatic interactions. Large numbers of trajectories were obtained and analyzed to obtain the distributions of surface residence times and the statistics of the spatial trajectories. Interestingly, the AMP species were sensitive to subtle differences in the charge of the lipid, with both peptides diffusing more slowly and residing longer on the diphosphoryl lipid A. Furthermore, the single-molecule dynamics indicated a qualitative difference between the behavior of AMPs on hybrid Lipid A bilayers and on those composed entirely of DOPE. Whereas AMPs interacting with a DOPE bilayer exhibited two-dimensional Brownian diffusion with a diffusion coefficient of ∼1.7 μm 2 /s, AMPs adsorbed to the lipid A surface exhibited much slower apparent diffusion (on the order of ∼0.1 μm 2 /s) and executed intermittent trajectories that alternated between two-dimensional Brownian diffusion and desorption-mediated three-dimensional flights. Overall, these findings suggested that bilayers with lipid A in the outer leaflet, as it is in bacterial outer membranes, are valuable model systems for the study of the initial stage of AMP-bacterium interactions. Furthermore, single-molecule dynamics was sensitive to subtle differences in electrostatic interactions between cationic AMPs and monovalent or divalent anionic lipid A moieties. Copyright © 2018 Biophysical Society. All rights reserved.

Preferential diffusion in concentrated solid solution alloys: NiFe, NiCo and NiCoCr

DOE PAGES

Zhao, Shijun; Osetsky, Yuri; Zhang, Yanwen

2017-02-13

In single-phase concentrated solid-solution alloys (CSAs), including high entropy alloys (HEAs), remarkable mechanical properties are exhibited, as well as extraordinary corrosion and radiation resistance compared to pure metals and dilute alloys. But, the mechanisms responsible for these properties are unknown in many cases. In this work, we employ ab initio molecular dynamics based on density functional theory to study the diffusion of interstitial atoms in Ni and Ni-based face-centered cubic CSAs including NiFe, NiCo and NiCoCr. We model the defect trajectories over >100 ps and estimate tracer diffusion coefficients, correlation factors and activation energies. Furthermore, we found that the diffusionmore » mass transport in CSAs is not only slower than that in pure components, i.e. sluggish diffusion, but also chemically non-homogeneous. The results obtained here can be used in understanding and predicting the atomic segregation and phase separation in CSAs under irradiation conditions.« less

SIMULATIONS OF LATERAL TRANSPORT AND DROPOUT STRUCTURE OF ENERGETIC PARTICLES FROM IMPULSIVE SOLAR FLARES

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

Tooprakai, P.; Seripienlert, A.; Ruffolo, D.

2016-11-10

We simulate trajectories of energetic particles from impulsive solar flares for 2D+slab models of magnetic turbulence in spherical geometry to study dropout features, i.e., sharp, repeated changes in the particle density. Among random-phase realizations of two-dimensional (2D) turbulence, a spherical harmonic expansion can generate homogeneous turbulence over a sphere, but a 2D fast Fourier transform (FFT) locally mapped onto the lateral coordinates in the region of interest is much faster computationally, and we show that the results are qualitatively similar. We then use the 2D FFT field as input to a 2D MHD simulation, which dynamically generates realistic features ofmore » turbulence such as coherent structures. The magnetic field lines and particles spread non-diffusively (ballistically) to a patchy distribution reaching up to 25° from the injection longitude and latitude at r ∼ 1 au. This dropout pattern in field line trajectories has sharper features in the case of the more realistic 2D MHD model, in better qualitative agreement with observations. The initial dropout pattern in particle trajectories is relatively insensitive to particle energy, though the energy affects the pattern’s evolution with time. We make predictions for future observations of solar particles near the Sun (e.g., at 0.25 au), for which we expect a sharp pulse of outgoing particles along the dropout pattern, followed by backscattering that first remains close to the dropout pattern and later exhibits cross-field transport to a distribution that is more diffusive, yet mostly contained within the dropout pattern found at greater distances.« less

Output Feedback-Based Boundary Control of Uncertain Coupled Semilinear Parabolic PDE Using Neurodynamic Programming.

PubMed

Talaei, Behzad; Jagannathan, Sarangapani; Singler, John

2018-04-01

In this paper, neurodynamic programming-based output feedback boundary control of distributed parameter systems governed by uncertain coupled semilinear parabolic partial differential equations (PDEs) under Neumann or Dirichlet boundary control conditions is introduced. First, Hamilton-Jacobi-Bellman (HJB) equation is formulated in the original PDE domain and the optimal control policy is derived using the value functional as the solution of the HJB equation. Subsequently, a novel observer is developed to estimate the system states given the uncertain nonlinearity in PDE dynamics and measured outputs. Consequently, the suboptimal boundary control policy is obtained by forward-in-time estimation of the value functional using a neural network (NN)-based online approximator and estimated state vector obtained from the NN observer. Novel adaptive tuning laws in continuous time are proposed for learning the value functional online to satisfy the HJB equation along system trajectories while ensuring the closed-loop stability. Local uniformly ultimate boundedness of the closed-loop system is verified by using Lyapunov theory. The performance of the proposed controller is verified via simulation on an unstable coupled diffusion reaction process.

TrackArt: the user friendly interface for single molecule tracking data analysis and simulation applied to complex diffusion in mica supported lipid bilayers.

PubMed

Matysik, Artur; Kraut, Rachel S

2014-05-01

Single molecule tracking (SMT) analysis of fluorescently tagged lipid and protein probes is an attractive alternative to ensemble averaged methods such as fluorescence correlation spectroscopy (FCS) or fluorescence recovery after photobleaching (FRAP) for measuring diffusion in artificial and plasma membranes. The meaningful estimation of diffusion coefficients and their errors is however not straightforward, and is heavily dependent on sample type, acquisition method, and equipment used. Many approaches require advanced computing and programming skills for their implementation. Here we present TrackArt software, an accessible graphic interface for simulation and complex analysis of multiple particle paths. Imported trajectories can be filtered to eliminate spurious or corrupted tracks, and are then analyzed using several previously described methodologies, to yield single or multiple diffusion coefficients, their population fractions, and estimated errors. We use TrackArt to analyze the single-molecule diffusion behavior of a sphingolipid analog SM-Atto647N, in mica supported DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayers. Fitting with a two-component diffusion model confirms the existence of two separate populations of diffusing particles in these bilayers on mica. As a demonstration of the TrackArt workflow, we characterize and discuss the effective activation energies required to increase the diffusion rates of these populations, obtained from Arrhenius plots of temperature-dependent diffusion. Finally, TrackArt provides a simulation module, allowing the user to generate models with multiple particle trajectories, diffusing with different characteristics. Maps of domains, acting as impermeable or permeable obstacles for particles diffusing with given rate constants and diffusion coefficients, can be simulated or imported from an image. Importantly, this allows one to use simulated data with a known diffusion behavior as a comparison for results acquired using particular algorithms on actual, "natural" samples whose diffusion behavior is to be extracted. It can also serve as a tool for demonstrating diffusion principles. TrackArt is an open source, platform-independent, Matlab-based graphical user interface, and is easy to use even for those unfamiliar with the Matlab programming environment. TrackArt can be used for accurate simulation and analysis of complex diffusion data, such as diffusion in lipid bilayers, providing publication-quality formatted results.

Distributional behavior of diffusion coefficients obtained by single trajectories in annealed transit time model

NASA Astrophysics Data System (ADS)

Akimoto, Takuma; Yamamoto, Eiji

2016-12-01

Local diffusion coefficients in disordered systems such as spin glass systems and living cells are highly heterogeneous and may change over time. Such a time-dependent and spatially heterogeneous environment results in irreproducibility of single-particle-tracking measurements. Irreproducibility of time-averaged observables has been theoretically studied in the context of weak ergodicity breaking in stochastic processes. Here, we provide rigorous descriptions of equilibrium and non-equilibrium diffusion processes for the annealed transit time model, which is a heterogeneous diffusion model in living cells. We give analytical solutions for the mean square displacement (MSD) and the relative standard deviation of the time-averaged MSD for equilibrium and non-equilibrium situations. We find that the time-averaged MSD grows linearly with time and that the time-averaged diffusion coefficients are intrinsically random (irreproducible) even in the long-time measurements in non-equilibrium situations. Furthermore, the distribution of the time-averaged diffusion coefficients converges to a universal distribution in the sense that it does not depend on initial conditions. Our findings pave the way for a theoretical understanding of distributional behavior of the time-averaged diffusion coefficients in disordered systems.

White matter tractography using diffusion tensor deflection.

PubMed

Lazar, Mariana; Weinstein, David M; Tsuruda, Jay S; Hasan, Khader M; Arfanakis, Konstantinos; Meyerand, M Elizabeth; Badie, Benham; Rowley, Howard A; Haughton, Victor; Field, Aaron; Alexander, Andrew L

2003-04-01

Diffusion tensor MRI provides unique directional diffusion information that can be used to estimate the patterns of white matter connectivity in the human brain. In this study, the behavior of an algorithm for white matter tractography is examined. The algorithm, called TEND, uses the entire diffusion tensor to deflect the estimated fiber trajectory. Simulations and imaging experiments on in vivo human brains were performed to investigate the behavior of the tractography algorithm. The simulations show that the deflection term is less sensitive than the major eigenvector to image noise. In the human brain imaging experiments, estimated tracts were generated in corpus callosum, corticospinal tract, internal capsule, corona radiata, superior longitudinal fasciculus, inferior longitudinal fasciculus, fronto-occipital fasciculus, and uncinate fasciculus. This approach is promising for mapping the organizational patterns of white matter in the human brain as well as mapping the relationship between major fiber trajectories and the location and extent of brain lesions. Copyright 2003 Wiley-Liss, Inc.

Fluctuating hydrodynamics, current fluctuations, and hyperuniformity in boundary-driven open quantum chains

NASA Astrophysics Data System (ADS)

Carollo, Federico; Garrahan, Juan P.; Lesanovsky, Igor; Pérez-Espigares, Carlos

2017-11-01

We consider a class of either fermionic or bosonic noninteracting open quantum chains driven by dissipative interactions at the boundaries and study the interplay of coherent transport and dissipative processes, such as bulk dephasing and diffusion. Starting from the microscopic formulation, we show that the dynamics on large scales can be described in terms of fluctuating hydrodynamics. This is an important simplification as it allows us to apply the methods of macroscopic fluctuation theory to compute the large deviation (LD) statistics of time-integrated currents. In particular, this permits us to show that fermionic open chains display a third-order dynamical phase transition in LD functions. We show that this transition is manifested in a singular change in the structure of trajectories: while typical trajectories are diffusive, rare trajectories associated with atypical currents are ballistic and hyperuniform in their spatial structure. We confirm these results by numerically simulating ensembles of rare trajectories via the cloning method, and by exact numerical diagonalization of the microscopic quantum generator.

Fluctuating hydrodynamics, current fluctuations, and hyperuniformity in boundary-driven open quantum chains.

PubMed

Carollo, Federico; Garrahan, Juan P; Lesanovsky, Igor; Pérez-Espigares, Carlos

2017-11-01

We consider a class of either fermionic or bosonic noninteracting open quantum chains driven by dissipative interactions at the boundaries and study the interplay of coherent transport and dissipative processes, such as bulk dephasing and diffusion. Starting from the microscopic formulation, we show that the dynamics on large scales can be described in terms of fluctuating hydrodynamics. This is an important simplification as it allows us to apply the methods of macroscopic fluctuation theory to compute the large deviation (LD) statistics of time-integrated currents. In particular, this permits us to show that fermionic open chains display a third-order dynamical phase transition in LD functions. We show that this transition is manifested in a singular change in the structure of trajectories: while typical trajectories are diffusive, rare trajectories associated with atypical currents are ballistic and hyperuniform in their spatial structure. We confirm these results by numerically simulating ensembles of rare trajectories via the cloning method, and by exact numerical diagonalization of the microscopic quantum generator.

The strengths and limitations of effective centroid force models explored by studying isotopic effects in liquid water

NASA Astrophysics Data System (ADS)

Yuan, Ying; Li, Jicun; Li, Xin-Zheng; Wang, Feng

2018-05-01

The development of effective centroid potentials (ECPs) is explored with both the constrained-centroid and quasi-adiabatic force matching using liquid water as a test system. A trajectory integrated with the ECP is free of statistical noises that would be introduced when the centroid potential is approximated on the fly with a finite number of beads. With the reduced cost of ECP, challenging experimental properties can be studied in the spirit of centroid molecular dynamics. The experimental number density of H2O is 0.38% higher than that of D2O. With the ECP, the H2O number density is predicted to be 0.42% higher, when the dispersion term is not refit. After correction of finite size effects, the diffusion constant of H2O is found to be 21% higher than that of D2O, which is in good agreement with the 29.9% higher diffusivity for H2O observed experimentally. Although the ECP is also able to capture the redshifts of both the OH and OD stretching modes in liquid water, there are a number of properties that a classical simulation with the ECP will not be able to recover. For example, the heat capacities of H2O and D2O are predicted to be almost identical and higher than the experimental values. Such a failure is simply a result of not properly treating quantized vibrational energy levels when the trajectory is propagated with classical mechanics. Several limitations of the ECP based approach without bead population reconstruction are discussed.

Military blast exposure, ageing and white matter integrity

PubMed Central

Trotter, Benjamin B.; Robinson, Meghan E.; Milberg, William P.; McGlinchey, Regina E.

2015-01-01

Mild traumatic brain injury, or concussion, is associated with a range of neural changes including altered white matter structure. There is emerging evidence that blast exposure—one of the most pervasive causes of casualties in the recent overseas conflicts in Iraq and Afghanistan—is accompanied by a range of neurobiological events that may result in pathological changes to brain structure and function that occur independently of overt concussion symptoms. The potential effects of brain injury due to blast exposure are of great concern as a history of mild traumatic brain injury has been identified as a risk factor for age-associated neurodegenerative disease. The present study used diffusion tensor imaging to investigate whether military-associated blast exposure influences the association between age and white matter tissue structure integrity in a large sample of veterans of the recent conflicts (n = 190 blast-exposed; 59 without exposure) between the ages of 19 and 62 years. Tract-based spatial statistics revealed a significant blast exposure × age interaction on diffusion parameters with blast-exposed individuals exhibiting a more rapid cross-sectional age trajectory towards reduced tissue integrity. Both distinct and overlapping voxel clusters demonstrating the interaction were observed among the examined diffusion contrast measures (e.g. fractional anisotropy and radial diffusivity). The regions showing the effect on fractional anisotropy included voxels both within and beyond the boundaries of the regions exhibiting a significant negative association between fractional anisotropy and age in the entire cohort. The regional effect was sensitive to the degree of blast exposure, suggesting a ‘dose-response’ relationship between the number of blast exposures and white matter integrity. Additionally, there was an age-independent negative association between fractional anisotropy and years since most severe blast exposure in a subset of the blast-exposed group, suggesting a specific influence of time since exposure on tissue structure, and this effect was also independent of post-traumatic stress symptoms. Overall, these data suggest that blast exposure may negatively affect brain-ageing trajectories at the microstructural tissue level. Additional work examining longitudinal changes in brain tissue integrity in individuals exposed to military blast forces will be an important future direction to the initial findings presented here. PMID:26033970

Exploring Quantum Dynamics of Continuous Measurement with a Superconducting Qubit

NASA Astrophysics Data System (ADS)

Jadbabaie, Arian; Forouzani, Neda; Tan, Dian; Murch, Kater

Weak measurements obtain partial information about a quantum state with minimal backaction. This enables state tracking without immediate collapse to eigenstates, of interest to both experimental and theoretical physics. State tomography and continuous weak measurements may be used to reconstruct the evolution of a single system, known as a quantum trajectory. We examine experimental trajectories of a two-level system at varied measurement strengths with constant unitary drive. Our analysis is applied to a transmon qubit dispersively coupled to a 3D microwave cavity in the circuit QED architecture. The weakly coupled cavity acts as pointer system for QND measurements in the qubit's energy basis. Our results indicate a marked difference in state purity between two approaches for trajectory reconstruction: the Bayesian and Stochastic Master Equation (SME) formalisms. Further, we observe the transition from diffusive to jump-like trajectories, state purity evolution, and a novel, tilted form of the Quantum Zeno effect. This work provides new insight into quantum behavior and prompts further comparison of SME and Bayesian formalisms to understand the nature of quantum systems. Our results are applicable to a variety of fields, from stochastic thermodynamics to quantum control.

Insight into the grain boundary effect on the ionic transport of yttria-stabilized zirconia at elevated temperatures from a molecular modeling perspective

NASA Astrophysics Data System (ADS)

Chang, Kai-Shiun; Lin, Yi-Feng; Tung, Kuo-Lun

A molecular dynamics (MD) simulation is used to reveal the grain boundary effect on the ionic transport of yttria-stabilized zirconia (YSZ). The oxygen ion displacements and diffusivities of the ideal and grain boundary-inserted YSZ models are analyzed at elevated temperatures. An optimized Y 2O 3 concentration within YSZ for the best ionic conductivity is achieved by balancing the trade-off between the increased vacancies and the decreased accessible free space. The mass transfer resistance of the grain boundary in YSZ can be more easily found at higher temperatures by observing the oxygen ion diffusivities or traveling trajectories. At lower temperatures, the grain interior and the grain boundary control the ionic transport. In contrast, the grain boundary effect on the diffusion barrier is gradually eliminated at elevated temperatures. The modeled results in this work agree well with previous experimental data.

How to test for partially predictable chaos.

PubMed

Wernecke, Hendrik; Sándor, Bulcsú; Gros, Claudius

2017-04-24

For a chaotic system pairs of initially close-by trajectories become eventually fully uncorrelated on the attracting set. This process of decorrelation can split into an initial exponential decrease and a subsequent diffusive process on the chaotic attractor causing the final loss of predictability. Both processes can be either of the same or of very different time scales. In the latter case the two trajectories linger within a finite but small distance (with respect to the overall extent of the attractor) for exceedingly long times and remain partially predictable. Standard tests for chaos widely use inter-orbital correlations as an indicator. However, testing partially predictable chaos yields mostly ambiguous results, as this type of chaos is characterized by attractors of fractally broadened braids. For a resolution we introduce a novel 0-1 indicator for chaos based on the cross-distance scaling of pairs of initially close trajectories. This test robustly discriminates chaos, including partially predictable chaos, from laminar flow. Additionally using the finite time cross-correlation of pairs of initially close trajectories, we are able to identify laminar flow as well as strong and partially predictable chaos in a 0-1 manner solely from the properties of pairs of trajectories.

Superdiffusive motion of membrane-targeting C2 domains

NASA Astrophysics Data System (ADS)

Campagnola, Grace; Nepal, Kanti; Schroder, Bryce W.; Peersen, Olve B.; Krapf, Diego

2015-12-01

Membrane-targeting domains play crucial roles in the recruitment of signalling molecules to the plasma membrane. For most peripheral proteins, the protein-to-membrane interaction is transient. After proteins dissociate from the membrane they have been observed to rebind following brief excursions in the bulk solution. Such membrane hops can have broad implications for the efficiency of reactions on membranes. We study the diffusion of membrane-targeting C2 domains using single-molecule tracking in supported lipid bilayers. The ensemble-averaged mean square displacement (MSD) exhibits superdiffusive behaviour. However, traditional time-averaged MSD analysis of individual trajectories remains linear and does not reveal superdiffusion. Our observations are explained in terms of bulk excursions that introduce jumps with a heavy-tail distribution. These hopping events allow proteins to explore large areas in a short time. The experimental results are shown to be consistent with analytical models of bulk-mediated diffusion and numerical simulations.

Controlling three-dimensional vortices using multiple and moving external fields

NASA Astrophysics Data System (ADS)

Das, Nirmali Prabha; Dutta, Sumana

2017-08-01

Spirals or scroll wave activities in cardiac tissues are the cause of lethal arrhythmias. The external control of these waves is thus of prime interest to scientists and physicians. In this article, we demonstrate the spatial control of scroll waves by using external electric fields and thermal gradients in experiments with the Belousov-Zhabotinsky reaction. We show that a scroll ring can be made to trace cyclic trajectories under a rotating electric field. Application of a thermal gradient in addition to the electric field deflects the motion and changes the nature of the trajectory. Our experimental results are analyzed and corroborated by numerical simulations based on an excitable reaction diffusion model.

A statistical mechanics approach to computing rare transitions in multi-stable turbulent geophysical flows

NASA Astrophysics Data System (ADS)

Laurie, J.; Bouchet, F.

2012-04-01

Many turbulent flows undergo sporadic random transitions, after long periods of apparent statistical stationarity. For instance, paths of the Kuroshio [1], the Earth's magnetic field reversal, atmospheric flows [2], MHD experiments [3], 2D turbulence experiments [4,5], 3D flows [6] show this kind of behavior. The understanding of this phenomena is extremely difficult due to the complexity, the large number of degrees of freedom, and the non-equilibrium nature of these turbulent flows. It is however a key issue for many geophysical problems. A straightforward study of these transitions, through a direct numerical simulation of the governing equations, is nearly always impracticable. This is mainly a complexity problem, due to the large number of degrees of freedom involved for genuine turbulent flows, and the extremely long time between two transitions. In this talk, we consider two-dimensional and geostrophic turbulent models, with stochastic forces. We consider regimes where two or more attractors coexist. As an alternative to direct numerical simulation, we propose a non-equilibrium statistical mechanics approach to the computation of this phenomenon. Our strategy is based on large deviation theory [7], derived from a path integral representation of the stochastic process. Among the trajectories connecting two non-equilibrium attractors, we determine the most probable one. Moreover, we also determine the transition rates, and in which cases this most probable trajectory is a typical one. Interestingly, we prove that in the class of models we consider, a mechanism exists for diffusion over sets of connected attractors. For the type of stochastic forces that allows this diffusion, the transition between attractors is not a rare event. It is then very difficult to characterize the flow as bistable. However for another class of stochastic forces, this diffusion mechanism is prevented, and genuine bistability or multi-stability is observed. We discuss how these results are probably connected to the long debated existence of multi-stability in the atmosphere and oceans.

Imaging and quantification of trans-membrane protein diffusion in living bacteria.

PubMed

Oswald, Felix; L M Bank, Ernst; Bollen, Yves J M; Peterman, Erwin J G

2014-07-07

The cytoplasmic membrane forms the barrier between any cell's interior and the outside world. It contains many proteins that enable essential processes such as the transmission of signals, the uptake of nutrients, and cell division. In the case of prokaryotes, which do not contain intracellular membranes, the cytoplasmic membrane also contains proteins for respiration and protein folding. Mutual interactions and specific localization of these proteins depend on two-dimensional diffusion driven by thermal fluctuations. The experimental investigation of membrane-protein diffusion in bacteria is challenging due to their small size, only a few times larger than the resolution of an optical microscope. Here, we review fluorescence microscopy-based methods to study diffusion of membrane proteins in living bacteria. The main focus is on data-analysis tools to extract diffusion coefficients from single-particle tracking data obtained by single-molecule fluorescence microscopy. We introduce a novel approach, IPODD (inverse projection of displacement distributions), to obtain diffusion coefficients from the usually obtained 2-D projected diffusion trajectories of the highly 3-D curved bacterial membrane. This method provides, in contrast to traditional mean-squared-displacement methods, correct diffusion coefficients and allows unravelling of heterogeneously diffusing populations.

Temporal behaviour of a corner separation in a radial vaned diffuser of a centrifugal compressor operating near surge

NASA Astrophysics Data System (ADS)

Marsan, A.; Trébinjac, I.; Coste, S.; Leroy, G.

2013-12-01

The temporal behaviour of a flow separation in the hub-suction side corner of a transonic diffuser is studied thanks to unsteady numerical simulations based on the phase-lagged approach. The validity of the numerical results is confirmed by comparison with experimental unsteady pressure measurements. An analysis of the instantaneous skin-friction pattern and particles trajectories is presented. It highlights the topology of the separation and its temporal behaviour. The major result is that, despite of a highly time-dependent core flow, the separation is found to be a "fixed unsteady separation" characterized by a fixed location of the main saddle of the separation but an extent of the stall region modulated by the pressure waves induced by the impeller-diffuser interaction.

Simultaneous Multi-Scale Diffusion Estimation and Tractography Guided by Entropy Spectrum Pathways

PubMed Central

Galinsky, Vitaly L.; Frank, Lawrence R.

2015-01-01

We have developed a method for the simultaneous estimation of local diffusion and the global fiber tracts based upon the information entropy flow that computes the maximum entropy trajectories between locations and depends upon the global structure of the multi-dimensional and multi-modal diffusion field. Computation of the entropy spectrum pathways requires only solving a simple eigenvector problem for the probability distribution for which efficient numerical routines exist, and a straight forward integration of the probability conservation through ray tracing of the convective modes guided by a global structure of the entropy spectrum coupled with a small scale local diffusion. The intervoxel diffusion is sampled by multi b-shell multi q-angle DWI data expanded in spherical waves. This novel approach to fiber tracking incorporates global information about multiple fiber crossings in every individual voxel and ranks it in the most scientifically rigorous way. This method has potential significance for a wide range of applications, including studies of brain connectivity. PMID:25532167

Key frame extraction based on spatiotemporal motion trajectory

NASA Astrophysics Data System (ADS)

Zhang, Yunzuo; Tao, Ran; Zhang, Feng

2015-05-01

Spatiotemporal motion trajectory can accurately reflect the changes of motion state. Motivated by this observation, this letter proposes a method for key frame extraction based on motion trajectory on the spatiotemporal slice. Different from the well-known motion related methods, the proposed method utilizes the inflexions of the motion trajectory on the spatiotemporal slice of all the moving objects. Experimental results show that although a similar performance is achieved in the single-objective screen, by comparing the proposed method to that achieved with the state-of-the-art methods based on motion energy or acceleration, the proposed method shows a better performance in a multiobjective video.

Coherent structure coloring: identification of coherent structures from sparse flow trajectories using graph theory

NASA Astrophysics Data System (ADS)

Schlueter, Kristy; Dabiri, John

2016-11-01

Coherent structure identification is important in many fluid dynamics applications, including transport phenomena in ocean flows and mixing and diffusion in turbulence. However, many of the techniques currently available for measuring such flows, including ocean drifter datasets and particle tracking velocimetry, only result in sparse velocity data. This is often insufficient for the use of current coherent structure detection algorithms based on analysis of the deformation gradient. Here, we present a frame-invariant method for detecting coherent structures from Lagrangian flow trajectories that can be sparse in number. The method, based on principles used in graph coloring algorithms, examines a measure of the kinematic dissimilarity of all pairs of flow trajectories, either measured experimentally, e.g. using particle tracking velocimetry; or numerically, by advecting fluid particles in the Eulerian velocity field. Coherence is assigned to groups of particles whose kinematics remain similar throughout the time interval for which trajectory data is available, regardless of their physical proximity to one another. Through the use of several analytical and experimental validation cases, this algorithm is shown to robustly detect coherent structures using significantly less flow data than is required by existing methods. This research was supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.

Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate.

PubMed

Berezhkovskii, Alexander M; Makarov, Dmitrii E

2018-05-03

In an effort to answer the much-debated question of whether the time evolution of common experimental observables can be described as one-dimensional diffusion in the potential of mean force, we propose a simple criterion that allows one to test whether the Markov assumption is applicable to a single-molecule trajectory x( t). This test does not involve fitting of the data to any presupposed model and can be applied to experimental data with relatively low temporal resolution.

Probabilistic Modeling of Aircraft Trajectories for Dynamic Separation Volumes

NASA Technical Reports Server (NTRS)

Lewis, Timothy A.

2016-01-01

With a proliferation of new and unconventional vehicles and operations expected in the future, the ab initio airspace design will require new approaches to trajectory prediction for separation assurance and other air traffic management functions. This paper presents an approach to probabilistic modeling of the trajectory of an aircraft when its intent is unknown. The approach uses a set of feature functions to constrain a maximum entropy probability distribution based on a set of observed aircraft trajectories. This model can be used to sample new aircraft trajectories to form an ensemble reflecting the variability in an aircraft's intent. The model learning process ensures that the variability in this ensemble reflects the behavior observed in the original data set. Computational examples are presented.

Elucidating fluctuating diffusivity in center-of-mass motion of polymer models with time-averaged mean-square-displacement tensor

NASA Astrophysics Data System (ADS)

Miyaguchi, Tomoshige

2017-10-01

There have been increasing reports that the diffusion coefficient of macromolecules depends on time and fluctuates randomly. Here a method is developed to elucidate this fluctuating diffusivity from trajectory data. Time-averaged mean-square displacement (MSD), a common tool in single-particle-tracking (SPT) experiments, is generalized to a second-order tensor with which both magnitude and orientation fluctuations of the diffusivity can be clearly detected. This method is used to analyze the center-of-mass motion of four fundamental polymer models: the Rouse model, the Zimm model, a reptation model, and a rigid rodlike polymer. It is found that these models exhibit distinctly different types of magnitude and orientation fluctuations of diffusivity. This is an advantage of the present method over previous ones, such as the ergodicity-breaking parameter and a non-Gaussian parameter, because with either of these parameters it is difficult to distinguish the dynamics of the four polymer models. Also, the present method of a time-averaged MSD tensor could be used to analyze trajectory data obtained in SPT experiments.

Longitudinal regression analysis of spatial-temporal growth patterns of geometrical diffusion measures in early postnatal brain development with diffusion tensor imaging

PubMed Central

Chen, Yasheng; An, Hongyu; Zhu, Hongtu; Jewells, Valerie; Armao, Diane; Shen, Dinggang; Gilmore, John H.; Lin, Weili

2011-01-01

Although diffusion tensor imaging (DTI) has provided substantial insights into early brain development, most DTI studies based on fractional anisotropy (FA) and mean diffusivity (MD) may not capitalize on the information derived from the three principal diffusivities (e.g. eigenvalues). In this study, we explored the spatial and temporal evolution of white matter structures during early brain development using two geometrical diffusion measures, namely, linear (Cl) and planar (Cp) diffusion anisotropies, from 71 longitudinal datasets acquired from 29 healthy, full-term pediatric subjects. The growth trajectories were estimated with generalized estimating equations (GEE) using linear fitting with logarithm of age (days). The presence of the white matter structures in Cl and Cp was observed in neonates, suggesting that both the cylindrical and fanning or crossing structures in various white matter regions may already have been formed at birth. Moreover, we found that both Cl and Cp evolved in a temporally nonlinear and spatially inhomogeneous manner. The growth velocities of Cl in central white matter were significantly higher when compared to peripheral, or more laterally located, white matter: central growth velocity Cl = 0.0465±0.0273/log(days), versus peripheral growth velocity Cl=0.0198±0.0127/log(days), p<10−6. In contrast, the growth velocities of Cp in central white matter were significantly lower than that in peripheral white matter: central growth velocity Cp= 0.0014±0.0058/log(days), versus peripheral growth velocity Cp = 0.0289±0.0101/log(days), p<10−6. Depending on the underlying white matter site which is analyzed, our findings suggest that ongoing physiologic and microstructural changes in the developing brain may exert different effects on the temporal evolution of these two geometrical diffusion measures. Thus, future studies utilizing DTI with correlative histological analysis in the study of early brain development are warranted. PMID:21784163

Maximum likelihood-based analysis of single-molecule photon arrival trajectories

NASA Astrophysics Data System (ADS)

Hajdziona, Marta; Molski, Andrzej

2011-02-01

In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 103 photons. When the intensity levels are well-separated and 104 photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

Simultaneous continuous measurement of non-commuting observables and correlation in qubit trajectories

NASA Astrophysics Data System (ADS)

Chantasri, Areeya; Jordan, Andrew

We consider the continuous quantum measurement of two or more non-commuting observables of a single qubit. Examples are presented for the measurement of two observables which can be mapped to two measurement axes on the Bloch sphere; a special case being the measurement along the X and Z bases. The qubit dynamics is described by the stochastic master equations which include the effect of decoherence and measurement inefficiencies. We investigate the qubit trajectories, their most likely paths, and their correlation functions using the stochastic path integral formalism. The correlation functions in qubit trajectories can be derived exactly for a special case and perturbatively for general cases. The theoretical predictions are compared with numerical simulations, as well as with trajectory data from the transmon superconducting qubit experiments.

Sub- and super-diffusion on Cantor sets: Beyond the paradox

NASA Astrophysics Data System (ADS)

K. Golmankhaneh, Alireza; Balankin, Alexander S.

2018-04-01

There is no way to build a nontrivial Markov process having continuous trajectories on a totally disconnected fractal embedded in the Euclidean space. Accordingly, in order to delineate the diffusion process on the totally disconnected fractal, one needs to relax the continuum requirement. Consequently, a diffusion process depends on how the continuum requirement is handled. This explains the emergence of different types of anomalous diffusion on the same totally disconnected set. In this regard, we argue that the number of effective spatial degrees of freedom of a random walker on the totally disconnected Cantor set is equal to nsp = [ D ] + 1, where [ D ] is the integer part of the Hausdorff dimension of the Cantor set. Conversely, the number of effective dynamical degrees of freedom (ds) depends on the definition of a Markov process on the totally disconnected Cantor set embedded in the Euclidean space En (n ≥nsp). This allows us to deduce the equation of diffusion by employing the local differential operators on the Fα-support. The exact solutions of this equation are obtained on the middle-ɛ Cantor sets for different kinds of the Markovian random processes. The relation of our findings to physical phenomena observed in complex systems is highlighted.

Flow and diffusion in channel-guided cell migration.

PubMed

Marel, Anna-Kristina; Zorn, Matthias; Klingner, Christoph; Wedlich-Söldner, Roland; Frey, Erwin; Rädler, Joachim O

2014-09-02

Collective migration of mechanically coupled cell layers is a notable feature of wound healing, embryonic development, and cancer progression. In confluent epithelial sheets, the dynamics have been found to be highly heterogeneous, exhibiting spontaneous formation of swirls, long-range correlations, and glass-like dynamic arrest as a function of cell density. In contrast, the flow-like properties of one-sided cell-sheet expansion in confining geometries are not well understood. Here, we studied the short- and long-term flow of Madin-Darby canine kidney (MDCK) cells as they moved through microchannels. Using single-cell tracking and particle image velocimetry (PIV), we found that a defined averaged stationary cell current emerged that exhibited a velocity gradient in the direction of migration and a plug-flow-like profile across the advancing sheet. The observed flow velocity can be decomposed into a constant term of directed cell migration and a diffusion-like contribution that increases with density gradient. The diffusive component is consistent with the cell-density profile and front propagation speed predicted by the Fisher-Kolmogorov equation. To connect diffusion-mediated transport to underlying cellular motility, we studied single-cell trajectories and occurrence of vorticity. We discovered that the directed large-scale cell flow altered fluctuations in cellular motion at short length scales: vorticity maps showed a reduced frequency of swirl formation in channel flow compared with resting sheets of equal cell density. Furthermore, under flow, single-cell trajectories showed persistent long-range, random-walk behavior superimposed on drift, whereas cells in resting tissue did not show significant displacements with respect to neighboring cells. Our work thus suggests that active cell migration manifests itself in an underlying, spatially uniform drift as well as in randomized bursts of short-range correlated motion that lead to a diffusion-mediated transport. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Intercomparison of meteorological analyses and trajectories in the Antarctic lower stratosphere with Concordiasi superpressure balloon observations

NASA Astrophysics Data System (ADS)

Hoffmann, Lars; Hertzog, Albert; Rößler, Thomas; Stein, Olaf; Wu, Xue

2017-07-01

In this study we compared temperatures and horizontal winds of meteorological analyses in the Antarctic lower stratosphere, a region of the atmosphere that is of major interest regarding chemistry and dynamics of the polar vortex. The study covers the European Centre for Medium-Range Weather Forecasts (ECMWF) operational analysis, the ERA-Interim reanalysis, the Modern-Era Retrospective analysis for Research and Applications version 1 and 2 (MERRA and MERRA-2), and the National Centers for Environmental Prediction and National Center for Atmospheric Research (NCEP/NCAR) reanalysis. The comparison was performed with respect to long-duration observations from 19 superpressure balloon flights during the Concordiasi field campaign in September 2010 to January 2011. Most of the balloon measurements were conducted at altitudes of 17-18.5 km and latitudes of 60-85° S. We found that large-scale state temperatures of the analyses have a mean precision of 0.5-1.4 K and a warm bias of 0.4-2.1 K with respect to the balloon data. Zonal and meridional winds have a mean precision of 0.9-2.3 m s-1 and a bias below ±0.5 m s-1. Standard deviations related to small-scale fluctuations due to gravity waves are reproduced at levels of 15-60 % for temperature and 30-60 % for the horizontal winds. Considering the fact that the balloon observations have been assimilated into all analyses, except for NCEP/NCAR, notable differences found here indicate that other observations, the forecast models, and the data assimilation procedures have a significant impact on the analyses as well. We also used the balloon observations to evaluate trajectory calculations with our new Lagrangian transport model Massive-Parallel Trajectory Calculations (MPTRAC), where vertical motions of simulated trajectories were nudged to pressure measurements of the balloons. We found relative horizontal transport deviations of 4-12 % and error growth rates of 60-170 km day-1 for 15-day trajectories. Dispersion simulations revealed some difficulties with the representation of subgrid-scale wind fluctuations in MPTRAC, as the spread of air parcels simulated with different analyses was not consistent. However, although case studies suggest that the accuracy of trajectory calculations is influenced by meteorological complexity, diffusion generally does not contribute significantly to transport deviations in our analysis. Overall, evaluation results are satisfactory and compare well to earlier studies using superpressure balloon observations.

Simulations of Lateral Transport and Dropout Structure of Energetic Particles from Impulsive Solar Flares

NASA Astrophysics Data System (ADS)

Matthaeus, W. H.; Ruffolo, D. J.; Tooprakai, P.; Seripienlert, A.; Chuychai, P.

2016-12-01

We simulate trajectories of energetic particles from impulsive solar flares for 2D+slab models of magnetic turbulence in spherical geometry to study dropout features, i.e., sharp, repeated changes in the particle density, and the particles' lateral transport. Among random-phase realizations of 2D turbulence, a spherical harmonic expansion can generate homogeneous turbulence over a sphere, but a 2D fast Fourier transform (FFT) locally mapped onto the lateral coordinates in the region of interest is much faster computationally, and we show that the results are qualitatively similar. We then use the 2D FFT field as input to a 2D MHD simulation, which dynamically generates realistic features of turbulence such as coherent structures. The magnetic field lines and particles spread non-diffusively (ballistically) to a patchy distribution reaching up to 25° from the injection longitude and latitude at r 1 AU. This dropout pattern in field line trajectories has sharper features in the case of the more realistic 2D MHD model, in better qualitative agreement with observations. The initial dropout pattern in particle trajectories is relatively insensitive to particle energy, though the energy affects the pattern's evolution with time. We make predictions for future observations of solar particles near the Sun (e.g., at 0.25 AU), for which we expect a sharp pulse of outgoing particles along the dropout pattern, followed by backscattering that first remains close to the dropout pattern and later exhibits cross-field transport to a distribution that is more diffusive, yet mostly contained within the dropout pattern found at greater distances. Partially supported by the Thailand Research Fund (Grants BRG5880009 and RTA5980003), the U.S. NSF (AGS-1063439), NASA (NNX14AI63G & NNX15AB88G), and the Solar Probe Plus/ISIS project.

Diffusion maps for high-dimensional single-cell analysis of differentiation data.

PubMed

Haghverdi, Laleh; Buettner, Florian; Theis, Fabian J

2015-09-15

Single-cell technologies have recently gained popularity in cellular differentiation studies regarding their ability to resolve potential heterogeneities in cell populations. Analyzing such high-dimensional single-cell data has its own statistical and computational challenges. Popular multivariate approaches are based on data normalization, followed by dimension reduction and clustering to identify subgroups. However, in the case of cellular differentiation, we would not expect clear clusters to be present but instead expect the cells to follow continuous branching lineages. Here, we propose the use of diffusion maps to deal with the problem of defining differentiation trajectories. We adapt this method to single-cell data by adequate choice of kernel width and inclusion of uncertainties or missing measurement values, which enables the establishment of a pseudotemporal ordering of single cells in a high-dimensional gene expression space. We expect this output to reflect cell differentiation trajectories, where the data originates from intrinsic diffusion-like dynamics. Starting from a pluripotent stage, cells move smoothly within the transcriptional landscape towards more differentiated states with some stochasticity along their path. We demonstrate the robustness of our method with respect to extrinsic noise (e.g. measurement noise) and sampling density heterogeneities on simulated toy data as well as two single-cell quantitative polymerase chain reaction datasets (i.e. mouse haematopoietic stem cells and mouse embryonic stem cells) and an RNA-Seq data of human pre-implantation embryos. We show that diffusion maps perform considerably better than Principal Component Analysis and are advantageous over other techniques for non-linear dimension reduction such as t-distributed Stochastic Neighbour Embedding for preserving the global structures and pseudotemporal ordering of cells. The Matlab implementation of diffusion maps for single-cell data is available at https://www.helmholtz-muenchen.de/icb/single-cell-diffusion-map. fbuettner.phys@gmail.com, fabian.theis@helmholtz-muenchen.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Statistical properties of the anomalous scaling exponent estimator based on time-averaged mean-square displacement

NASA Astrophysics Data System (ADS)

Sikora, Grzegorz; Teuerle, Marek; Wyłomańska, Agnieszka; Grebenkov, Denis

2017-08-01

The most common way of estimating the anomalous scaling exponent from single-particle trajectories consists of a linear fit of the dependence of the time-averaged mean-square displacement on the lag time at the log-log scale. We investigate the statistical properties of this estimator in the case of fractional Brownian motion (FBM). We determine the mean value, the variance, and the distribution of the estimator. Our theoretical results are confirmed by Monte Carlo simulations. In the limit of long trajectories, the estimator is shown to be asymptotically unbiased, consistent, and with vanishing variance. These properties ensure an accurate estimation of the scaling exponent even from a single (long enough) trajectory. As a consequence, we prove that the usual way to estimate the diffusion exponent of FBM is correct from the statistical point of view. Moreover, the knowledge of the estimator distribution is the first step toward new statistical tests of FBM and toward a more reliable interpretation of the experimental histograms of scaling exponents in microbiology.

Promoting Effective Teacher-Feedback: From Theory to Practice through a Multiple Component Trajectory for Professional Development

ERIC Educational Resources Information Center

Voerman, Lia; Meijer, Paulien C.; Korthagen, Fred; Simons, Robert Jan

2015-01-01

This study describes an evaluation of a theory-based trajectory for professional development called FeTiP (Feedback-Theory into Practice) that aims to have an observable effect on teacher classroom behavior. FeTiP is a multicomponent trajectory for professional development and combines several types of interventions. Its goal is to help teachers…

NextGen Far-Term Concept Exploration for Integrated Gate-to-Gate Trajectory-Based Operations

NASA Technical Reports Server (NTRS)

Johnson, Sally C.; Barmore, Bryan E.

2016-01-01

NASA is currently conducting concept exploration studies toward the definition of a far-term, gate-to-gate concept for Trajectory-Based Operations. This paper presents a basic architectural framework for the far-term concept and discusses some observations about implementation of trajectory-based operations in the National Airspace System. Within the concept, operators and service providers collaboratively negotiate aircraft trajectories, providing agile, optimized, aircraft-specific routing to meet service provider gate-to-gate flow-management constraints and increasing capacity by smoothly and effectively combining flight-deck-based and ground-based metering, merging, and spacing in a mixed-equipage environment. The far-term TBO concept is intended to influence the direction of mid-term TBO research and to inform the definition of stable requirements and standards for TBO communications infrastructure and user equipage.

Droplet swimmers in complex geometries: Autochemotaxis and trapping at pillars.

NASA Astrophysics Data System (ADS)

Maass, Corinna; Jin, Chenyu; Krueger, Carsten; Vajdi Hokmabad, Babak

Autochemotaxis is a key feature of communication between microorganisms, via their emission of a slowly diffusing chemoattractant or repellent. We present a well-controlled, tunable artificial model to study autochemotaxis in complex geometries, using microfluidic assays of self-propelling liquid crystal droplets in an aqueous surfactant solution. Droplets gain propulsion energy by micellar solubilisation, with filled micelles acting as a chemical repellent by diffusive phoretic gradient forces. We can tune the key parameters swimmer size, velocity and persistence length. If a swimming droplet approaches a wall, it will provide a boundary to both the hydrodynamic flow field and the spread of phoretic gradients, determining the interaction between swimmer and wall. Pillar arrays of variable sizes and shapes provide a convex wall interacting with the swimmer and in the case of attachment bending its trajectory and forcing it to revert to its own trail. We observe different behavior based on the interplay of wall curvature and negative auto-chemotaxis, i. e., no attachment for highly curved interfaces, stable trapping at large pillars, and a narrow transition region where negative autochemotaxis makes the swimmers detach after a single orbit. Work funded by the DFG SPP 1726 ''Microswimmers''.

Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

NASA Astrophysics Data System (ADS)

Ferguson, Andrew L.; Panagiotopoulos, Athanassios Z.; Debenedetti, Pablo G.; Kevrekidis, Ioannis G.

2011-04-01

Nonlinear dimensionality reduction techniques can be applied to molecular simulation trajectories to systematically extract a small number of variables with which to parametrize the important dynamical motions of the system. For molecular systems exhibiting free energy barriers exceeding a few kBT, inadequate sampling of the barrier regions between stable or metastable basins can lead to a poor global characterization of the free energy landscape. We present an adaptation of a nonlinear dimensionality reduction technique known as the diffusion map that extends its applicability to biased umbrella sampling simulation trajectories in which restraining potentials are employed to drive the system into high free energy regions and improve sampling of phase space. We then propose a bootstrapped approach to iteratively discover good low-dimensional parametrizations by interleaving successive rounds of umbrella sampling and diffusion mapping, and we illustrate the technique through a study of alanine dipeptide in explicit solvent.

Drift-wave turbulence and zonal flow generation.

PubMed

Balescu, R

2003-10-01

Drift-wave turbulence in a plasma is analyzed on the basis of the wave Liouville equation, describing the evolution of the distribution function of wave packets (quasiparticles) characterized by position x and wave vector k. A closed kinetic equation is derived for the ensemble-averaged part of this function by the methods of nonequilibrium statistical mechanics. It has the form of a non-Markovian advection-diffusion equation describing coupled diffusion processes in x and k spaces. General forms of the diffusion coefficients are obtained in terms of Lagrangian velocity correlations. The latter are calculated in the decorrelation trajectory approximation, a method recently developed for an accurate measure of the important trapping phenomena of particles in the rugged electrostatic potential. The analysis of individual decorrelation trajectories provides an illustration of the fragmentation of drift-wave structures in the radial direction and the generation of long-wavelength structures in the poloidal direction that are identified as zonal flows.

The Usefulness of Diffusion Tensor Imaging and Tractography in Surgery of Brainstem Cavernous Malformations.

PubMed

Januszewski, Jacob; Albert, Lauren; Black, Karen; Dehdashti, Amir R

2016-09-01

Diffusion tensor imaging (DTI) estimates the course and connectivity patterns of white matter tracts. The objective of this study is to evaluate whether findings in the brain stem modify the preoperative surgical trajectory planning or postoperative outcome in patients with brain stem cavernous malformations. Ten patients with symptomatic brainstem cavernous malformation underwent surgical resection. Five patients received preoperative DTI evaluation and the remaining 5 did not. Reconstructed DTI tracts consisted of corticospinal, medial lemnisci, and cerebellar peduncles. The surgical planning and postoperative outcome were evaluated. In 5 patients with no preoperative DTI evaluation, surgical planning was based on anatomic landmark and the 2-point technique. The other 5 patients underwent preoperative DTI, and findings were factored into the selection of the surgical approach. In 3 of the 5 cases with DTI evaluation, the 2-point technique suggested a similar trajectory. In the other 2, the DTI findings suggested a different approach to avoid damage to the white matter tract. Two patients in the group with no DTI had immediate postoperative new or worsened deficit, which improved at long-term follow-up. No patient in the DTI group had a new neurologic deficit. Compared with the standard magnetic resonance imaging, DTI provided improved visualization of cavernous malformation involvement in eloquent fiber tracts of the brainstem. This additional information might help in selecting a more appropriate surgical trajectory in selected lesions. Larger patient cohorts are needed to assess the effect of this modality in patients' outcome. Published by Elsevier Inc.

A stochastic method for Brownian-like optical transport calculations in anisotropic biosuspensions and blood

NASA Astrophysics Data System (ADS)

Miller, Steven

1998-03-01

A generic stochastic method is presented that rapidly evaluates numerical bulk flux solutions to the one-dimensional integrodifferential radiative transport equation, for coherent irradiance of optically anisotropic suspensions of nonspheroidal bioparticles, such as blood. As Fermat rays or geodesics enter the suspension, they evolve into a bundle of random paths or trajectories due to scattering by the suspended bioparticles. Overall, this can be interpreted as a bundle of Markov trajectories traced out by a "gas" of Brownian-like point photons being scattered and absorbed by the homogeneous distribution of uncorrelated cells in suspension. By considering the cumulative vectorial intersections of a statistical bundle of random trajectories through sets of interior data planes in the space containing the medium, the effective equivalent information content and behavior of the (generally unknown) analytical flux solutions of the radiative transfer equation rapidly emerges. The fluxes match the analytical diffuse flux solutions in the diffusion limit, which verifies the accuracy of the algorithm. The method is not constrained by the diffusion limit and gives correct solutions for conditions where diffuse solutions are not viable. Unlike conventional Monte Carlo and numerical techniques adapted from neutron transport or nuclear reactor problems that compute scalar quantities, this vectorial technique is fast, easily implemented, adaptable, and viable for a wide class of biophotonic scenarios. By comparison, other analytical or numerical techniques generally become unwieldy, lack viability, or are more difficult to utilize and adapt. Illustrative calculations are presented for blood medias at monochromatic wavelengths in the visible spectrum.

Maximum likelihood-based analysis of single-molecule photon arrival trajectories.

PubMed

Hajdziona, Marta; Molski, Andrzej

2011-02-07

In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 10(3) photons. When the intensity levels are well-separated and 10(4) photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

Random walks of colloidal probes in viscoelastic materials

NASA Astrophysics Data System (ADS)

Khan, Manas; Mason, Thomas G.

2014-04-01

To overcome limitations of using a single fixed time step in random walk simulations, such as those that rely on the classic Wiener approach, we have developed an algorithm for exploring random walks based on random temporal steps that are uniformly distributed in logarithmic time. This improvement enables us to generate random-walk trajectories of probe particles that span a highly extended dynamic range in time, thereby facilitating the exploration of probe motion in soft viscoelastic materials. By combining this faster approach with a Maxwell-Voigt model (MVM) of linear viscoelasticity, based on a slowly diffusing harmonically bound Brownian particle, we rapidly create trajectories of spherical probes in soft viscoelastic materials over more than 12 orders of magnitude in time. Appropriate windowing of these trajectories over different time intervals demonstrates that random walk for the MVM is neither self-similar nor self-affine, even if the viscoelastic material is isotropic. We extend this approach to spatially anisotropic viscoelastic materials, using binning to calculate the anisotropic mean square displacements and creep compliances along different orthogonal directions. The elimination of a fixed time step in simulations of random processes, including random walks, opens up interesting possibilities for modeling dynamics and response over a highly extended temporal dynamic range.

Residual sweeping errors in turbulent particle pair diffusion in a Lagrangian diffusion model.

PubMed

Malik, Nadeem A

2017-01-01

Thomson, D. J. & Devenish, B. J. [J. Fluid Mech. 526, 277 (2005)] and others have suggested that sweeping effects make Lagrangian properties in Kinematic Simulations (KS), Fung et al [Fung J. C. H., Hunt J. C. R., Malik N. A. & Perkins R. J. J. Fluid Mech. 236, 281 (1992)], unreliable. However, such a conclusion can only be drawn under the assumption of locality. The major aim here is to quantify the sweeping errors in KS without assuming locality. Through a novel analysis based upon analysing pairs of particle trajectories in a frame of reference moving with the large energy containing scales of motion it is shown that the normalized integrated error [Formula: see text] in the turbulent pair diffusivity (K) due to the sweeping effect decreases with increasing pair separation (σl), such that [Formula: see text] as σl/η → ∞; and [Formula: see text] as σl/η → 0. η is the Kolmogorov turbulence microscale. There is an intermediate range of separations 1 < σl/η < ∞ in which the error [Formula: see text] remains negligible. Simulations using KS shows that in the swept frame of reference, this intermediate range is large covering almost the entire inertial subrange simulated, 1 < σl/η < 105, implying that the deviation from locality observed in KS cannot be atributed to sweeping errors. This is important for pair diffusion theory and modeling. PACS numbers: 47.27.E?, 47.27.Gs, 47.27.jv, 47.27.Ak, 47.27.tb, 47.27.eb, 47.11.-j.

Curved trajectories of actin-based motility in two dimensions

NASA Astrophysics Data System (ADS)

Wen, Fu-Lai; Leung, Kwan-tai; Chen, Hsuan-Yi

2012-05-01

Recent experiments have reported fascinating geometrical trajectories for actin-based motility of bacteria Listeria monocytogenes and functionalized beads. To understand the physical mechanism for these trajectories, we constructed a phenomenological model to study the motion of an actin-propelled disk in two dimensions. In our model, the force and actin density on the surface of the disk are influenced by the translation and rotation of the disk, which in turn is induced by the asymmetric distributions of those densities. We show that this feedback can destabilize a straight trajectory, leading to circular, S-shape and other geometrical trajectories observed in the experiments through bifurcations in the distributions of the force and actin density. The relation between our model and the models for self-propelled deformable particles is emphasized and discussed.

DLA based compressed sensing for high resolution MR microscopy of neuronal tissue

NASA Astrophysics Data System (ADS)

Nguyen, Khieu-Van; Li, Jing-Rebecca; Radecki, Guillaume; Ciobanu, Luisa

2015-10-01

In this work we present the implementation of compressed sensing (CS) on a high field preclinical scanner (17.2 T) using an undersampling trajectory based on the diffusion limited aggregation (DLA) random growth model. When applied to a library of images this approach performs better than the traditional undersampling based on the polynomial probability density function. In addition, we show that the method is applicable to imaging live neuronal tissues, allowing significantly shorter acquisition times while maintaining the image quality necessary for identifying the majority of neurons via an automatic cell segmentation algorithm.

Micro-scale pollution mechanism of dust diffusion in a blasting driving face based on CFD-DEM coupled model.

PubMed

Yu, Haiming; Cheng, Weimin; Xie, Yao; Peng, Huitian

2018-05-23

In order to investigate the diffuse pollution mechanisms of high-concentration dusts in the blasting driving face, the airflow-dust coupled model was constructed based on CFD-DEM coupled model; the diffusion rules of the dusts with different diameters at microscopic scale were analyzed in combination with the field measured results. The simulation results demonstrate that single-exhaust ventilation exhibited more favorable dust suppression performance than single-forced ventilation. Under single-exhaust ventilation condition, the motion trajectories of the dusts with the diameter smaller than 20 μm were close to the airflow streamline and these dusts were mainly distributed near the footway walls; by contrast, under single-forced ventilation condition, the motion trajectories of the dust particles with a diameter range of 20~40 μm were close to the airflow streamlines, and a large number of dusts with the diameter smaller than 20 μm accumulated in the regions 5 m and 17~25 m away from the head-on section. Moreover, under the single-exhaust ventilation, the relationship between dust diameter D and negative-pressured-induced dust emission ratio P can be expressed as P = - 25.03ln(D) + 110.39, and the dust emission ratio was up to 74.36% for 7-μm dusts, and the path-dependent settling behaviors of the dusts mainly occurred around the head-on section; under single-forced ventilation condition, the z value of the dusts with the diameter over 20 μm decreased and the dusts with a diameter smaller than 7 μm are particularly harmful to human health, but their settling ratios were below 22.36%. Graphical abstract The airflow-dust CFD-DEM coupling model was established. The numerical simulation results were verified. The migration laws of airflow field were obtained in a blasting driving face. The diffusion laws of dusts were obtained after blasting.

Image encryption using random sequence generated from generalized information domain

NASA Astrophysics Data System (ADS)

Xia-Yan, Zhang; Guo-Ji, Zhang; Xuan, Li; Ya-Zhou, Ren; Jie-Hua, Wu

2016-05-01

A novel image encryption method based on the random sequence generated from the generalized information domain and permutation-diffusion architecture is proposed. The random sequence is generated by reconstruction from the generalized information file and discrete trajectory extraction from the data stream. The trajectory address sequence is used to generate a P-box to shuffle the plain image while random sequences are treated as keystreams. A new factor called drift factor is employed to accelerate and enhance the performance of the random sequence generator. An initial value is introduced to make the encryption method an approximately one-time pad. Experimental results show that the random sequences pass the NIST statistical test with a high ratio and extensive analysis demonstrates that the new encryption scheme has superior security.

Prediction of the Aerothermodynamic Environment of the Huygens Probe

NASA Technical Reports Server (NTRS)

Hollis, Brian R.; Striepe, Scott A.; Wright, Michael J.; Bose, Deepak; Sutton, Kenneth; Takashima, Naruhisa

2005-01-01

An investigation of the aerothermodynamic environment of the Huygens entry probe has been conducted. A Monte Carlo simulation of the trajectory of the probe during entry into Titan's atmosphere was performed to identify a worst-case heating rate trajectory. Flowfield and radiation transport computations were performed at points along this trajectory to obtain convective and radiative heat-transfer distributions on the probe's heat shield. This investigation identified important physical and numerical factors, including atmospheric CH4 concentration, transition to turbulence, numerical diffusion modeling, and radiation modeling, which strongly influenced the aerothermodynamic environment.

Consequences of using nonlinear particle trajectories to compute spatial diffusion coefficients. [for cosmic ray propagation in interstellar and interplanetary space

NASA Technical Reports Server (NTRS)

Goldstein, M. L.

1977-01-01

In a study of cosmic ray propagation in interstellar and interplanetary space, a perturbed orbit resonant scattering theory for pitch angle diffusion in a slab model of magnetostatic turbulence is slightly generalized and used to compute the diffusion coefficient for spatial propagation parallel to the mean magnetic field. This diffusion coefficient has been useful for describing the solar modulation of the galactic cosmic rays, and for explaining the diffusive phase in solar flares in which the initial anisotropy of the particle distribution decays to isotropy.

Data mining of molecular dynamics data reveals Li diffusion characteristics in garnet Li7La3Zr2O12

PubMed Central

Chen, Chi; Lu, Ziheng; Ciucci, Francesco

2017-01-01

Understanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate compared to its tetragonal counterpart, most of the Li hops in the cubic LLZO do not contribute to the diffusivity due to the dominance of back-and-forth type jumps. The hopping analysis and local Li configuration statistics give evidence that Li diffusivity in cubic LLZO is limited by the low vacancy concentration. The hopping statistics also shows uncorrelated Poisson-like diffusion for Li in the cubic LLZO, and correlated diffusion for Li in the tetragonal LLZO in the temporal scale. Further analysis of the spatio-temporal correlation using site-to-site mutual information confirms the weak site dependence of Li diffusion in the cubic LLZO as the origin for the uncorrelated diffusion. This work puts forward a perspective on combining machine learning and information theory to interpret results of molecular dynamics simulations. PMID:28094317

Evaluation of Proteins' Rotational Diffusion Coefficients from Simulations of Their Free Brownian Motion in Volume-Occupied Environments.

PubMed

Długosz, Maciej; Antosiewicz, Jan M

2014-01-14

We have investigated the rotational dynamics of hen egg white lysozyme in monodisperse aqueous solutions of concentrations up to 250 mg/mL, using a rigid-body Brownian dynamics method that accurately accounts for anisotropies of diffusing objects. We have examined the validity of the free diffusion concept in the analysis of computer simulations of volume-occupied molecular solutions. We have found that, when as the only intermolecular interaction, the excluded volume effect is considered, rotational diffusion of molecules adheres to the free diffusion model. Further, we present a method based on the exact (in the case of the free diffusion) analytic forms of autocorrelation functions of particular vectors rigidly attached to diffusing objects, which allows one to obtain from results of molecular simulations the three principal rotational diffusion coefficients characterizing rotational Brownian motion of an arbitrarily shaped rigid particle for an arbitrary concentration of crowders. We have applied this approach to trajectories resulting from Brownian dynamics simulations of hen egg white lysozyme solutions. We show that the apparent anisotropy of proteins' rotational motions increases with an increasing degree of crowding. Finally, we demonstrate that even if the hydrodynamic anisotropy of molecules is neglected and molecules are simulated using their average translational and rotational diffusion coefficients, excluded volume effects still lead to their anisotropic rotational dynamics.

Data mining of molecular dynamics data reveals Li diffusion characteristics in garnet Li7La3Zr2O12

NASA Astrophysics Data System (ADS)

Chen, Chi; Lu, Ziheng; Ciucci, Francesco

2017-01-01

Understanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate compared to its tetragonal counterpart, most of the Li hops in the cubic LLZO do not contribute to the diffusivity due to the dominance of back-and-forth type jumps. The hopping analysis and local Li configuration statistics give evidence that Li diffusivity in cubic LLZO is limited by the low vacancy concentration. The hopping statistics also shows uncorrelated Poisson-like diffusion for Li in the cubic LLZO, and correlated diffusion for Li in the tetragonal LLZO in the temporal scale. Further analysis of the spatio-temporal correlation using site-to-site mutual information confirms the weak site dependence of Li diffusion in the cubic LLZO as the origin for the uncorrelated diffusion. This work puts forward a perspective on combining machine learning and information theory to interpret results of molecular dynamics simulations.

Structural and water diffusion of poly(acryl amide)/poly(vinyl alcohol) blend films: Experiment and molecular dynamics simulations.

PubMed

Wang, Yanen; Wei, Qinghua; Wang, Shuzhi; Chai, Weihong; Zhang, Yingfeng

2017-01-01

To study the effects of composition ratios and temperature on the diffusion of water molecules in PVA/PAM blend films, five simulation models of PVA/PAM with ten water molecules at different composition ratios (4/0, 3/1, 2/2, 1/3, 0/4) were constructed and simulated by using a molecular dynamics (MD) simulation. The diffusion behavior of water molecules in blends were investigated from the aspects of the diffusion coefficient, free volume, pair correlation function (PCF) and trajectories of water molecules, respectively. And the hydrophilicity of blend composite was studied based on the contact angle and equilibrium water content (EWC) of the blend films. The simulation results show that the diffusion coefficient of water molecules and fractional free volume (FFV) of blend membranes increase with the addition of PAM, and a higher temperature can also improve the diffusion of water molecules. Additionally, the analysis of PCFs reveals the main reason why the diffusion coefficient of water in blend system increases with the addition of PAM. The measurement results of contact angle and EWC of blend films indicate that the hydrophilicity of blend films decreases with the addition of PAM, but the EWC of blends increases with the addition of PAM. Copyright © 2016 Elsevier Inc. All rights reserved.

Trajectory-Based Takeoff Time Predictions Applied to Tactical Departure Scheduling: Concept Description, System Design, and Initial Observations

NASA Technical Reports Server (NTRS)

Engelland, Shawn A.; Capps, Alan

2011-01-01

Current aircraft departure release times are based on manual estimates of aircraft takeoff times. Uncertainty in takeoff time estimates may result in missed opportunities to merge into constrained en route streams and lead to lost throughput. However, technology exists to improve takeoff time estimates by using the aircraft surface trajectory predictions that enable air traffic control tower (ATCT) decision support tools. NASA s Precision Departure Release Capability (PDRC) is designed to use automated surface trajectory-based takeoff time estimates to improve en route tactical departure scheduling. This is accomplished by integrating an ATCT decision support tool with an en route tactical departure scheduling decision support tool. The PDRC concept and prototype software have been developed, and an initial test was completed at air traffic control facilities in Dallas/Fort Worth. This paper describes the PDRC operational concept, system design, and initial observations.

Measurement tensors in diffusion MRI: generalizing the concept of diffusion encoding.

PubMed

Westin, Carl-Fredrik; Szczepankiewicz, Filip; Pasternak, Ofer; Ozarslan, Evren; Topgaard, Daniel; Knutsson, Hans; Nilsson, Markus

2014-01-01

In traditional diffusion MRI, short pulsed field gradients (PFG) are used for the diffusion encoding. The standard Stejskal-Tanner sequence uses one single pair of such gradients, known as single-PFG (sPFG). In this work we describe how trajectories in q-space can be used for diffusion encoding. We discuss how such encoding enables the extension of the well-known scalar b-value to a tensor-valued entity we call the diffusion measurement tensor. The new measurements contain information about higher order diffusion propagator covariances not present in sPFG. As an example analysis, we use this new information to estimate a Gaussian distribution over diffusion tensors in each voxel, described by its mean (a diffusion tensor) and its covariance (a 4th order tensor).

Longitudinal Study of White Matter Development and Outcomes in Children Born Very Preterm.

PubMed

Young, Julia M; Morgan, Benjamin R; Whyte, Hilary E A; Lee, Wayne; Smith, Mary Lou; Raybaud, Charles; Shroff, Manohar M; Sled, John G; Taylor, Margot J

2017-08-01

Identifying trajectories of early white matter development is important for understanding atypical brain development and impaired functional outcomes in children born very preterm (<32 weeks gestational age [GA]). In this study, 161 diffusion images were acquired in children born very preterm (median GA: 29 weeks) shortly following birth (75), term-equivalent (39), 2 years (18), and 4 years of age (29). Diffusion tensors were computed to obtain measures of fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD), which were aligned and averaged. A paediatric atlas was applied to obtain diffusion metrics within 12 white matter tracts. Developmental trajectories across time points demonstrated age-related changes which plateaued between term-equivalent and 2 years of age in the majority of posterior tracts and between 2 and 4 years of age in anterior tracts. Between preterm and term-equivalent scans, FA rates of change were slower in anterior than posterior tracts. Partial least squares analyses revealed associations between slower MD and RD rates of change within the external and internal capsule with lower intelligence quotients and language scores at 4 years of age. These results uniquely demonstrate early white matter development and its linkage to cognitive functions. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Lagrangian Statistics of Slightly Buoyant Droplets in Isotropic Turbulence

NASA Astrophysics Data System (ADS)

Gopalan, Balaji; Malkiel, Edwin; Katz, Joseph

2006-11-01

This project examines the dynamics of slightly buoyant diesel droplets in isotropic turbulence using high speed in-line digital Holographic PIV. A cloud of droplets with specific gravity of 0.85 is injected into the central portion of an isotropic turbulence facility. The droplet trajectories are measured in a 50x50x50 mm̂3 sample volume using high speed in-line digital holography. An automated program has been developed to obtain accurate time history of droplet velocities. Data analysis determines the PDF of velocity and acceleration in three dimensions. The time histories enable us to calculate the three dimensional Lagrangian velocity autocorrelation function, and from them the diffusion coefficients. Due to buoyancy the vertical diffusion time scale exceeds the horizontal one by about 65% .The diffusion coefficients vary between 2.8 cm̂2/sec in the horizontal direction to 5.5 cm̂2/sec in the vertical direction. For droplets with size varying from 2 to 11 Kolmogorov scales there are no clear trends with size. The variations of diffusion rates for different turbulent intensities and the effect of finite window size are presently examined. For shorter time scales, when the diffusion need not be Fickian the three dimensional trajectories can be used to calculate the generalized dispersion tensor and measure the time elapsed for diffusion to become Fickian.

The special theory of Brownian relativity: equivalence principle for dynamic and static random paths and uncertainty relation for diffusion.

PubMed

Mezzasalma, Stefano A

2007-03-15

The theoretical basis of a recent theory of Brownian relativity for polymer solutions is deepened and reexamined. After the problem of relative diffusion in polymer solutions is addressed, its two postulates are formulated in all generality. The former builds a statistical equivalence between (uncorrelated) timelike and shapelike reference frames, that is, among dynamical trajectories of liquid molecules and static configurations of polymer chains. The latter defines the "diffusive horizon" as the invariant quantity to work with in the special version of the theory. Particularly, the concept of universality in polymer physics corresponds in Brownian relativity to that of covariance in the Einstein formulation. Here, a "universal" law consists of a privileged observation, performed from the laboratory rest frame and agreeing with any diffusive reference system. From the joint lack of covariance and simultaneity implied by the Brownian Lorentz-Poincaré transforms, a relative uncertainty arises, in a certain analogy with quantum mechanics. It is driven by the difference between local diffusion coefficients in the liquid solution. The same transformation class can be used to infer Fick's second law of diffusion, playing here the role of a gauge invariance preserving covariance of the spacetime increments. An overall, noteworthy conclusion emerging from this view concerns the statistics of (i) static macromolecular configurations and (ii) the motion of liquid molecules, which would be much more related than expected.

Fractal analysis of lateral movement in biomembranes.

PubMed

Gmachowski, Lech

2018-04-01

Lateral movement of a molecule in a biomembrane containing small compartments (0.23-μm diameter) and large ones (0.75 μm) is analyzed using a fractal description of its walk. The early time dependence of the mean square displacement varies from linear due to the contribution of ballistic motion. In small compartments, walking molecules do not have sufficient time or space to develop an asymptotic relation and the diffusion coefficient deduced from the experimental records is lower than that measured without restrictions. The model makes it possible to deduce the molecule step parameters, namely the step length and time, from data concerning confined and unrestricted diffusion coefficients. This is also possible using experimental results for sub-diffusive transport. The transition from normal to anomalous diffusion does not affect the molecule step parameters. The experimental literature data on molecular trajectories recorded at a high time resolution appear to confirm the modeled value of the mean free path length of DOPE for Brownian and anomalous diffusion. Although the step length and time give the proper values of diffusion coefficient, the DOPE speed calculated as their quotient is several orders of magnitude lower than the thermal speed. This is interpreted as a result of intermolecular interactions, as confirmed by lateral diffusion of other molecules in different membranes. The molecule step parameters are then utilized to analyze the problem of multiple visits in small compartments. The modeling of the diffusion exponent results in a smooth transition to normal diffusion on entering a large compartment, as observed in experiments.

The Dynamics of Son Preference, Technology Diffusion, and Fertility Decline Underlying Distorted Sex Ratios at Birth: A Simulation Approach.

PubMed

Kashyap, Ridhi; Villavicencio, Francisco

2016-10-01

We present a micro-founded simulation model that formalizes the "ready, willing, and able" framework, originally used to explain historical fertility decline, to the practice of prenatal sex selection. The model generates sex ratio at birth (SRB) distortions from the bottom up and attempts to quantify plausible levels, trends, and interactions of son preference, technology diffusion, and fertility decline that underpin SRB trajectories at the macro level. Calibrating our model for South Korea, we show how even as the proportion with a preference for sons was declining, SRB distortions emerged due to rapid diffusion of prenatal sex determination technology combined with small but growing propensities to abort at low birth parities. Simulations reveal that relatively low levels of son preference (about 20 % to 30 % wanting one son) can result in skewed SRB levels if technology diffuses early and steadily, and if fertility falls rapidly to encourage sex-selective abortion at low parities. Model sensitivity analysis highlights how the shape of sex ratio trajectories is particularly sensitive to the timing and speed of prenatal sex-determination technology diffusion. The maximum SRB levels reached in a population are influenced by how the readiness to abort rises as a function of the fertility decline.

Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

NASA Astrophysics Data System (ADS)

Grazioli, Gianmarc

Calculating the kinetics of conformational changes in macromolecules, such as proteins and nucleic acids, is still very much an open problem in theoretical chemistry and computational biophysics. If it were feasible to run large sets of molecular dynamics trajectories that begin in one configuration and terminate when reaching another configuration of interest, calculating kinetics from molecular dynamics simulations would be simple, but in practice, configuration spaces encompassing all possible configurations for even the simplest of macromolecules are far too vast for such a brute force approach. In fact, many problems related to searches of configuration spaces, such as protein structure prediction, are considered to be NP-hard. Two approaches to addressing this problem are to either develop methods for enhanced sampling of trajectories that confine the search to productive trajectories without loss of temporal information, or coarse-grained methodologies that recast the problem in reduced spaces that can be exhaustively searched. This thesis will begin with a description of work carried out in the vein of the second approach, where a Smoluchowski diffusion equation model was developed that accurately reproduces the rate vs. force relationship observed in the mechano-catalytic disulphide bond cleavage observed in thioredoxin-catalyzed reduction of disulphide bonds. Next, three different novel enhanced sampling methods developed in the vein of the first approach will be described, which can be employed either separately or in conjunction with each other to autonomously define a set of energetically relevant subspaces in configuration space, accelerate trajectories between the interfaces dividing the subspaces while preserving the distribution of unassisted transition times between subspaces, and approximate time correlation functions from the kinetic data collected from the transitions between interfaces.

Young adults' trajectories of Ecstasy use: a population based study.

PubMed

Smirnov, Andrew; Najman, Jake M; Hayatbakhsh, Reza; Plotnikova, Maria; Wells, Helene; Legosz, Margot; Kemp, Robert

2013-11-01

Young adults' Ecstasy use trajectories have important implications for individual and population-level consequences of Ecstasy use, but little relevant research has been conducted. This study prospectively examines Ecstasy trajectories in a population-based sample. Data are from the Natural History Study of Drug Use, a retrospective/prospective cohort study conducted in Australia. Population screening identified a probability sample of Ecstasy users aged 19-23 years. Complete data for 30 months of follow-up, comprising 4 time intervals, were available for 297 participants (88.4% of sample). Trajectories were derived using cluster analysis based on recent Ecstasy use at each interval. Trajectory predictors were examined using a generalized ordered logit model and included Ecstasy dependence (World Mental Health Composite International Diagnostic Instrument), psychological distress (Hospital Anxiety Depression Scale), aggression (Young Adult Self Report) and contextual factors (e.g. attendance at electronic/dance music events). Three Ecstasy trajectories were identified (low, intermediate and high use). At its peak, the high-use trajectory involved 1-2 days Ecstasy use per week. Decreasing frequency of use was observed for intermediate and high-use trajectories from 12 months, independently of market factors. Intermediate and high-use trajectory membership was predicted by past Ecstasy consumption (>70 pills) and attendance at electronic/dance music events. High-use trajectory members were unlikely to have used Ecstasy for more than 3 years and tended to report consistently positive subjective effects at baseline. Given the social context and temporal course of Ecstasy use, Ecstasy trajectories might be better understood in terms of instrumental rather than addictive drug use patterns. © 2013 Elsevier Ltd. All rights reserved.

Fast Ion and Thermal Plasma Transport in Turbulent Waves in the Large Plasma Device (LAPD)

NASA Astrophysics Data System (ADS)

Zhou, Shu

2011-10-01

The transport of fast ions and thermal plasmas in electrostatic microturbulence is studied. Strong density and potential fluctuations (δn / n ~ δϕ / kTe ~ 0 . 5 , f ~5-50 kHz) are observed in the LAPD in density gradient regions produced by obstacles with slab or cylindrical geometry. Wave characteristics and the associated plasma transport are modified by driving sheared E ×B drift through biasing the obstacle, and by modification of the axial magnetic fields (Bz) and the plasma species. Cross-field plasma transport is suppressed with small bias and large Bz, and is enhanced with large bias and small Bz. Suppressed cross-field thermal transport coincides with a 180° phase shift between the density and potential fluctuations in the radial direction, while the enhanced thermal transport is associated with modes having low mode number (m = 1) and long radial correlation length. Large gyroradius lithium ions (ρfast /ρs ~ 10) orbit through the turbulent region. Scans with a collimated analyzer and with Langmuir probes give detailed profiles of the fast ion spatial-temporal distribution and of the fluctuating fields. Fast-ion transport decreases rapidly with increasing fast-ion gyroradius. Background waves with different scale lengths also alter the fast ion transport: Beam diffusion is smaller in waves with smaller structures (higher mode number); also, coherent waves with long correlation length cause less beam diffusion than turbulent waves. Experimental results agree well with gyro-averaging theory. When the fast ion interacts with the wave for most of a wave period, a transition from super-diffusive to sub-diffusive transport is observed, as predicted by diffusion theory. A Monte Carlo trajectory-following code simulates the interaction of the fast ions with the measured turbulent fields. Good agreement between observation and modeling is observed. Work funded by DOE and NSF and performed at the Basic Plasma Science Facility.

Stochastic field-line wandering in magnetic turbulence with shear. II. Decorrelation trajectory method

NASA Astrophysics Data System (ADS)

Negrea, M.; Petrisor, I.; Shalchi, A.

2017-11-01

We study the diffusion of magnetic field lines in turbulence with magnetic shear. In the first part of the series, we developed a quasi-linear theory for this type of scenario. In this article, we employ the so-called DeCorrelation Trajectory method in order to compute the diffusion coefficients of stochastic magnetic field lines. The magnetic field configuration used here contains fluctuating terms which are described by the dimensionless functions bi(X, Y, Z), i = (x, y) and they are assumed to be Gaussian processes and are perpendicular with respect to the main magnetic field B0. Furthermore, there is also a z-component of the magnetic field depending on radial coordinate x (representing the gradient of the magnetic field) and a poloidal average component. We calculate the diffusion coefficients for magnetic field lines for different values of the magnetic Kubo number K, the dimensionless inhomogeneous magnetic parallel and perpendicular Kubo numbers KB∥, KB⊥ , as well as Ka v=bya vKB∥/KB⊥ .

Crawling and turning in a minimal reaction-diffusion cell motility model: Coupling cell shape and biochemistry

NASA Astrophysics Data System (ADS)

Camley, Brian A.; Zhao, Yanxiang; Li, Bo; Levine, Herbert; Rappel, Wouter-Jan

2017-01-01

We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which controls the locations where actin polymerization occurs, and the physical properties of the cell, including its membrane tension. We find in our model both highly persistent trajectories, in which the cell crawls in a straight line, and turning trajectories, where the cell transitions from crawling in a line to crawling in a circle. We discuss the controlling variables for this turning instability and argue that turning arises from a coupling between the reaction-diffusion mechanism and the shape of the cell. This emphasizes the surprising features that can arise from simple links between cell mechanics and biochemistry. Our results suggest that similar instabilities may be present in a broad class of biochemical descriptions of cell polarity.

Longitudinal diffusion changes following postoperative delirium in older people without dementia.

PubMed

Cavallari, Michele; Dai, Weiying; Guttmann, Charles R G; Meier, Dominik S; Ngo, Long H; Hshieh, Tammy T; Fong, Tamara G; Schmitt, Eva; Press, Daniel Z; Travison, Thomas G; Marcantonio, Edward R; Jones, Richard N; Inouye, Sharon K; Alsop, David C

2017-09-05

To investigate the effect of postoperative delirium on longitudinal brain microstructural changes, as measured by diffusion tensor imaging. We studied a subset of the larger Successful Aging after Elective Surgery (SAGES) study cohort of older adults (≥70 years) without dementia undergoing elective surgery: 113 participants who had diffusion tensor imaging before and 1 year after surgery. Postoperative delirium severity and occurrence were assessed during the hospital stay using the Confusion Assessment Method and a validated chart review method. We investigated the association of delirium severity and occurrence with longitudinal diffusion changes across 1 year, adjusting for age, sex, vascular comorbidity, and baseline cognitive performance. We also assessed the association between changes in diffusion and cognitive performance across the 1-year follow-up period, adjusting for age, sex, education, and baseline cognitive performance. Postoperative delirium occurred in 25 participants (22%). Delirium severity and occurrence were associated with longitudinal diffusion changes in the periventricular, frontal, and temporal white matter. Diffusion changes were also associated with changes in cognitive performance across 1 year, although the cognitive changes did not show significant association with delirium severity or occurrence. Our study raises the possibility that delirium has an effect on the development of brain microstructural abnormalities, which may reflect brain changes underlying cognitive trajectories. Future studies are warranted to clarify whether delirium is the driving factor of the observed changes or rather a correlate of a vulnerable brain that is at high risk for neurodegenerative processes. © 2017 American Academy of Neurology.

DLA based compressed sensing for high resolution MR microscopy of neuronal tissue.

PubMed

Nguyen, Khieu-Van; Li, Jing-Rebecca; Radecki, Guillaume; Ciobanu, Luisa

2015-10-01

In this work we present the implementation of compressed sensing (CS) on a high field preclinical scanner (17.2 T) using an undersampling trajectory based on the diffusion limited aggregation (DLA) random growth model. When applied to a library of images this approach performs better than the traditional undersampling based on the polynomial probability density function. In addition, we show that the method is applicable to imaging live neuronal tissues, allowing significantly shorter acquisition times while maintaining the image quality necessary for identifying the majority of neurons via an automatic cell segmentation algorithm. Copyright © 2015 Elsevier Inc. All rights reserved.

Self-Diffusion of Drops in a Dilute Sheared Emulsion

NASA Technical Reports Server (NTRS)

Loewenberg, Michael; Hinch, E. J.

1996-01-01

Self-diffusion coefficients that describe cross-flow migration of non-Brownian drops in a dilute sheared emulsion were obtained by trajectory calculations. A boundary integral formulation was used to describe pairwise interactions between deformable drops; interactions between undeformed drops were described with mobility functions for spherical drops. The results indicate that drops have large anisotropic self-diffusivities which depend strongly on the drop viscosity and modestly on the shear-rate. Pairwise interactions between drops in shear-flow do not appreciably promote drop breakup.

Diffusion tensor tracking of neuronal fiber pathways in the living human brain

NASA Astrophysics Data System (ADS)

Lori, Nicolas Francisco

2001-11-01

The technique of diffusion tensor tracking (DTT) is described, in which diffusion tensor magnetic resonance imaging (DT-MRI) data are processed to allow the visualization of white matter (WM) tracts in a living human brain. To illustrate the methods, a detailed description is given of the physics of DT-MRI, the structure of the DT-MRI experiment, the computer tools that were developed to visualize WM tracts, the anatomical consistency of the obtained WM tracts, and the accuracy and precision of DTT using computer simulations. When presenting the physics of DT-MRI, a completely quantum-mechanical view of DT-MRI is given where some of the results are new. Examples of anatomical tracts viewed using DTT are presented, including the genu and the splenium of the corpus callosum, the ventral pathway with its amygdala connection highlighted, the geniculo- calcarine tract separated into anterior and posterior parts, the geniculo-calcarine tract defined using functional magnetic resonance imaging (MRI), and U- fibers. In the simulation, synthetic DT-MRI data were constructed that would be obtained for a cylindrical WM tract with a helical trajectory surrounded by gray matter. Noise was then added to the synthetic DT-MRI data, and DTT trajectories were calculated using the noisy data (realistic tracks). Simulated DTT errors were calculated as the vector distance between the realistic tracks and the ideal trajectory. The simulation tested the effects of a comprehensive set of experimental conditions, including voxel size, data sampling, data averaging, type of tract tissue, tract diameter and type of tract trajectory. Simulated DTT accuracy and precision were typically below the voxel dimension, and precision was compatible with the experimental results.

Quantification of errors induced by temporal resolution on Lagrangian particles in an eddy-resolving model

NASA Astrophysics Data System (ADS)

Qin, Xuerong; van Sebille, Erik; Sen Gupta, Alexander

2014-04-01

Lagrangian particle tracking within ocean models is an important tool for the examination of ocean circulation, ventilation timescales and connectivity and is increasingly being used to understand ocean biogeochemistry. Lagrangian trajectories are obtained by advecting particles within velocity fields derived from hydrodynamic ocean models. For studies of ocean flows on scales ranging from mesoscale up to basin scales, the temporal resolution of the velocity fields should ideally not be more than a few days to capture the high frequency variability that is inherent in mesoscale features. However, in reality, the model output is often archived at much lower temporal resolutions. Here, we quantify the differences in the Lagrangian particle trajectories embedded in velocity fields of varying temporal resolution. Particles are advected from 3-day to 30-day averaged fields in a high-resolution global ocean circulation model. We also investigate whether adding lateral diffusion to the particle movement can compensate for the reduced temporal resolution. Trajectory errors reveal the expected degradation of accuracy in the trajectory positions when decreasing the temporal resolution of the velocity field. Divergence timescales associated with averaging velocity fields up to 30 days are faster than the intrinsic dispersion of the velocity fields but slower than the dispersion caused by the interannual variability of the velocity fields. In experiments focusing on the connectivity along major currents, including western boundary currents, the volume transport carried between two strategically placed sections tends to increase with increased temporal averaging. Simultaneously, the average travel times tend to decrease. Based on these two bulk measured diagnostics, Lagrangian experiments that use temporal averaging of up to nine days show no significant degradation in the flow characteristics for a set of six currents investigated in more detail. The addition of random-walk-style diffusion does not mitigate the errors introduced by temporal averaging for large-scale open ocean Lagrangian simulations.

Straight trajectory planning for keyhole neurosurgery in sheep with automatic brain structures segmentation

NASA Astrophysics Data System (ADS)

Favaro, Alberto; Lad, Akash; Formenti, Davide; Zani, Davide Danilo; De Momi, Elena

2017-03-01

In a translational neuroscience/neurosurgery perspective, sheep are considered good candidates to study because of the similarity between their brain and the human one. Automatic planning systems for safe keyhole neurosurgery maximize the probe/catheter distance from vessels and risky structures. This work consists in the development of a trajectories planner for straight catheters placement intended to be used for investigating the drug diffusivity mechanisms in sheep brain. Automatic brain segmentation of gray matter, white matter and cerebrospinal fluid is achieved using an online available sheep atlas. Ventricles, midbrain and cerebellum segmentation have been also carried out. The veterinary surgeon is asked to select a target point within the white matter to be reached by the probe and to define an entry area on the brain cortex. To mitigate the risk of hemorrhage during the insertion process, which can prevent the success of the insertion procedure, the trajectory planner performs a curvature analysis of the brain cortex and wipes out from the poll of possible entry points the sulci, as part of brain cortex where superficial blood vessels are naturally located. A limited set of trajectories is then computed and presented to the surgeon, satisfying an optimality criteria based on a cost function which considers the distance from critical brain areas and the whole trajectory length. The planner proved to be effective in defining rectilinear trajectories accounting for the safety constraints determined by the brain morphology. It also demonstrated a short computational time and good capability in segmenting gyri and sulci surfaces.

Persistence of abnormalities in white matter in children with type 1 diabetes.

PubMed

Fox, Larry A; Hershey, Tamara; Mauras, Nelly; Arbeláez, Ana Maria; Tamborlane, William V; Buckingham, Bruce; Tsalikian, Eva; Englert, Kim; Raman, Mira; Jo, Booil; Shen, Hanyang; Reiss, Allan; Mazaika, Paul

2018-07-01

Prior studies suggest white matter growth is reduced and white matter microstructure is altered in the brains of young children with type 1 diabetes when compared with brains of non-diabetic children, due in part to adverse effects of hyperglycaemia. This longitudinal observational study examines whether dysglycaemia alters the developmental trajectory of white matter microstructure over time in young children with type 1 diabetes. One hundred and eighteen children, aged 4 to <10 years old with type 1 diabetes and 58 age-matched, non-diabetic children were studied at baseline and 18 months, at five Diabetes Research in Children Network clinical centres. We analysed longitudinal trajectories of white matter using diffusion tensor imaging. Continuous glucose monitoring profiles and HbA 1c levels were obtained every 3 months. Axial diffusivity was lower in children with diabetes at baseline (p = 0.022) and at 18 months (p = 0.015), indicating that differences in white matter microstructure persist over time in children with diabetes. Within the diabetes group, lower exposure to hyperglycaemia, averaged over the time since diagnosis, was associated with higher fractional anisotropy (p = 0.037). Fractional anisotropy was positively correlated with performance (p < 0.002) and full-scale IQ (p < 0.02). These results suggest that hyperglycaemia is associated with altered white matter development, which may contribute to the mild cognitive deficits in this population.

Hayabusa Re-Entry: Trajectory Analysis and Observation Mission Design

NASA Technical Reports Server (NTRS)

Cassell, Alan M.; Winter, Michael W.; Allen, Gary A.; Grinstead, Jay H.; Antimisiaris, Manny E.; Albers, James; Jenniskens, Peter

2011-01-01

On June 13th, 2010, the Hayabusa sample return capsule successfully re-entered Earth s atmosphere over the Woomera Prohibited Area in southern Australia in its quest to return fragments from the asteroid 1998 SF36 Itokawa . The sample return capsule entered at a super-orbital velocity of 12.04 km/sec (inertial), making it the second fastest human-made object to traverse the atmosphere. The NASA DC-8 airborne observatory was utilized as an instrument platform to record the luminous portion of the sample return capsule re-entry (60 sec) with a variety of on-board spectroscopic imaging instruments. The predicted sample return capsule s entry state information at 200 km altitude was propagated through the atmosphere to generate aerothermodynamic and trajectory data used for initial observation flight path design and planning. The DC- 8 flight path was designed by considering safety, optimal sample return capsule viewing geometry and aircraft capabilities in concert with key aerothermodynamic events along the predicted trajectory. Subsequent entry state vector updates provided by the Deep Space Network team at NASA s Jet Propulsion Laboratory were analyzed after the planned trajectory correction maneuvers to further refine the DC-8 observation flight path. Primary and alternate observation flight paths were generated during the mission planning phase which required coordination with Australian authorities for pre-mission approval. The final observation flight path was chosen based upon trade-offs between optimal viewing requirements, ground based observer locations (to facilitate post-flight trajectory reconstruction), predicted weather in the Woomera Prohibited Area and constraints imposed by flight path filing deadlines. To facilitate sample return capsule tracking by the instrument operators, a series of two racetrack flight path patterns were performed prior to the observation leg so the instruments could be pointed towards the region in the star background where the sample return capsule was expected to become visible. An overview of the design methodologies and trade-offs used in the Hayabusa re-entry observation campaign are presented.

Uncovering Implicit Assumptions: A Large-Scale Study on Students' Mental Models of Diffusion

ERIC Educational Resources Information Center

Stains, Marilyne; Sevian, Hannah

2015-01-01

Students' mental models of diffusion in a gas phase solution were studied through the use of the Structure and Motion of Matter (SAMM) survey. This survey permits identification of categories of ways students think about the structure of the gaseous solute and solvent, the origin of motion of gas particles, and trajectories of solute particles in…

Lagrangian Transport Model Forecasts as Useful Support of the Flight Planning During the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2k2) Measurement Campaign

NASA Astrophysics Data System (ADS)

Forster, C.; Cooper, O.; Stohl, A.; Eckhardt, S.; James, P.; Dunlea, E.; Nicks, D. K.; Holloway, J. S.; Hübler, G.; Parrish, D. D.; Ryerson, T. B.; Trainer, M.

2002-12-01

In this study, the Lagrangian tracer transport model FLEXPART is shown to be a useful forecasting tool for the flight planning during the ITCT 2k2 (Intercontinental Transport and Chemical Transformation 2002) aircraft measurement campaign. The advantages of this model are that it requires only a short computation time, has a finer spatial resolution and does not suffer numerical diffusion compared to chemistry transport models (CTMs). It is a compromise between simple trajectory calculations and complex CTMs that makes best use of available computer hardware. During the campaign FLEXPART provided three-day forecasts for four different anthropogenic CO tracers: Asian, North American, Japanese, and European. The forecasts were based on data from the Aviation model (AVN) of the National Center for Environmental Prediction (NCEP) and relied on the EDGAR emission inventory for the base year 1990. In two case studies, the forecast abilities of FLEXPART are analysed and discussed by comparing the forecasts with measurement data, results from the post analysis modelling, infrared satellite images, and backward trajectories calculated with two different Lagrangian trajectory models. It is shown that intercontinental transport and dispersion of pollution plumes were qualitatively well predicted, and the aircraft could successfully be directed into the polluted air masses.

An Eulerian/Lagrangian coupling procedure for three-dimensional vortical flows

NASA Technical Reports Server (NTRS)

Felici, Helene M.; Drela, Mark

1993-01-01

A coupled Eulerian/Lagrangian method is presented for the reduction of numerical diffusion observed in solutions of 3D vortical flows using standard Eulerian finite-volume time-marching procedures. A Lagrangian particle tracking method, added to the Eulerian time-marching procedure, provides a correction of the Eulerian solution. In turn, the Eulerian solution is used to integrate the Lagrangian state-vector along the particles trajectories. While the Eulerian solution ensures the conservation of mass and sets the pressure field, the particle markers describe accurately the convection properties and enhance the vorticity and entropy capturing capabilities of the Eulerian solver. The Eulerian/Lagrangian coupling strategies are discussed and the combined scheme is tested on a constant stagnation pressure flow in a 90 deg bend and on a swirling pipe flow. As the numerical diffusion is reduced when using the Lagrangian correction, a vorticity gradient augmentation is identified as a basic problem of this inviscid calculation.

The Decline in Diffuse Support for National Politics

PubMed Central

Jennings, Will; Clarke, Nick; Moss, Jonathan; Stoker, Gerry

2017-01-01

Abstract This research note considers how to track long-term trajectories of political discontent in Britain. Many accounts are confined to using either survey data drawn from recent decades or imperfect behavioral measures such as voting or party membership as indicators of political disengagement. We instead develop an approach that provides the long view on political disaffection. We first consider time-series data available from repeated survey measures. We next replicate historic survey questions to observe change in public opinion relative to earlier points in time. Finally, we use Stimson’s (1991) dyad-ratios algorithm to construct an over-time index of political discontent that combines data from multiple poll series. This reveals rising levels of political discontent for both specific and diffuse measures of mass opinion. Our method and findings offer insights into the rising tide of disillusionment afflicting many contemporary democracies. PMID:29731522

The Decline in Diffuse Support for National Politics: The Long View on Political Discontent in Britain.

PubMed

Jennings, Will; Clarke, Nick; Moss, Jonathan; Stoker, Gerry

2017-09-01

This research note considers how to track long-term trajectories of political discontent in Britain. Many accounts are confined to using either survey data drawn from recent decades or imperfect behavioral measures such as voting or party membership as indicators of political disengagement. We instead develop an approach that provides the long view on political disaffection. We first consider time-series data available from repeated survey measures. We next replicate historic survey questions to observe change in public opinion relative to earlier points in time. Finally, we use Stimson's (1991) dyad-ratios algorithm to construct an over-time index of political discontent that combines data from multiple poll series. This reveals rising levels of political discontent for both specific and diffuse measures of mass opinion. Our method and findings offer insights into the rising tide of disillusionment afflicting many contemporary democracies.

Principal component analysis for protein folding dynamics.

PubMed

Maisuradze, Gia G; Liwo, Adam; Scheraga, Harold A

2009-01-09

Protein folding is considered here by studying the dynamics of the folding of the triple beta-strand WW domain from the Formin-binding protein 28. Starting from the unfolded state and ending either in the native or nonnative conformational states, trajectories are generated with the coarse-grained united residue (UNRES) force field. The effectiveness of principal components analysis (PCA), an already established mathematical technique for finding global, correlated motions in atomic simulations of proteins, is evaluated here for coarse-grained trajectories. The problems related to PCA and their solutions are discussed. The folding and nonfolding of proteins are examined with free-energy landscapes. Detailed analyses of many folding and nonfolding trajectories at different temperatures show that PCA is very efficient for characterizing the general folding and nonfolding features of proteins. It is shown that the first principal component captures and describes in detail the dynamics of a system. Anomalous diffusion in the folding/nonfolding dynamics is examined by the mean-square displacement (MSD) and the fractional diffusion and fractional kinetic equations. The collisionless (or ballistic) behavior of a polypeptide undergoing Brownian motion along the first few principal components is accounted for.

Early maternal depressive symptom trajectories: Associations with 7-year maternal depressive symptoms and child behavior.

PubMed

Buckingham-Howes, Stacy; Oberlander, Sarah E; Wang, Yan; Black, Maureen M

2017-06-01

This study examines potential mechanisms linking maternal depressive symptoms over 2 years postpartum with child behavior problems at school-age in a sample of adolescent mothers and their first-born child. Potential mechanisms include: mother-reported caregiving engagement at 6 months; observed parental nurturance and control, and child competence and affect at 24 months; and mother-reported resilience at 7 years based on achievement of adult developmental tasks. One hundred eighteen low-income African American adolescent mothers were recruited at delivery and followed through child age 7 years. Maternal depressive symptom trajectories over 24 months were estimated (low, medium, and high) based on mother-reported depressive symptoms. Direct and indirect associations between depressive symptom trajectories with 7-year maternal depressive symptoms and child behavior problems were examined. The high maternal depressive symptom trajectory was associated with 7-year maternal depressive symptoms (b = 5.52, SE = 1.65, p < .01) and child internalizing problems (b = 7.60, SE = 3.12, p = .02) and externalizing problems (b = 6.23, SE = 3.22, p = .05). Caregiving engagement among high depressive symptom trajectory mothers was significantly associated with observed child affect (b = -0.21, SE = 0.11, p = 0.05). Parental nurturance in toddlerhood mediated the association between high maternal depressive symptom trajectory and child internalizing problems at 7 years (indirect effect b = 2.33, 95% CI: 0.32-5.88). Findings suggest that family based interventions to promote parenting and adolescent resiliency strengthening may be beneficial in this population. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Evaluation of altimetry-derived surface current products using Lagrangian drifter trajectories in the eastern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Liu, Yonggang; Weisberg, Robert H.; Vignudelli, Stefano; Mitchum, Gary T.

2014-05-01

Lagrangian particle trajectory models based on several altimetry-derived surface current products are used to hindcast the drifter trajectories observed in the eastern Gulf of Mexico during May to August 2010 (the Deepwater Horizon oil spill incident). The performances of the trajectory models are gauged in terms of Lagrangian separation distances (d) and a nondimensional skill score (s), respectively. A series of numerical experiments show that these altimetry-based trajectory models have about the same performance, with a certain improvement by adding surface wind Ekman components, especially over the shelf region. However, their hindcast skills are slightly better than those of the data assimilative numerical model output. After 3 days' simulation the altimetry-based trajectory models have mean d values of 75-83 and 34-42 km (s values of 0.49-0.51 and 0.35-0.43) in the Gulf of Mexico deep water area and on the West Florida Continental Shelf, respectively. These satellite altimetry data products are useful for providing essential information on ocean surface currents of use in water property transports, offshore oil and gas operations, hazardous spill mitigation, search and rescue, etc.

Optic radiation structure and anatomy in the normally developing brain determined using diffusion MRI and tractography.

PubMed

Dayan, Michael; Munoz, Monica; Jentschke, Sebastian; Chadwick, Martin J; Cooper, Janine M; Riney, Kate; Vargha-Khadem, Faraneh; Clark, Chris A

2015-01-01

The optic radiation (OR) is a component of the visual system known to be myelin mature very early in life. Diffusion tensor imaging (DTI) and its unique ability to reconstruct the OR in vivo were used to study structural maturation through analysis of DTI metrics in a cohort of 90 children aged 5-18 years. As the OR is at risk of damage during epilepsy surgery, we measured its position relative to characteristic anatomical landmarks. Anatomical distances, DTI metrics and volume of the OR were investigated for age, gender and hemisphere effects. We observed changes in DTI metrics with age comparable to known trajectories in other white matter tracts. Left lateralization of DTI metrics was observed that showed a gender effect in lateralization. Sexual dimorphism of DTI metrics in the right hemisphere was also found. With respect to OR dimensions, volume was shown to be right lateralised and sexual dimorphism demonstrated for the extent of the left OR. The anatomical results presented for the OR have potentially important applications for neurosurgical planning.

Causal Inferences with Group Based Trajectory Models

ERIC Educational Resources Information Center

Haviland, Amelia M.; Nagin, Daniel S.

2005-01-01

A central theme of research on human development and psychopathology is whether a therapeutic intervention or a turning-point event, such as a family break-up, alters the trajectory of the behavior under study. This paper lays out and applies a method for using observational longitudinal data to make more confident causal inferences about the…

An efficient quasi-3D particle tracking-based approach for transport through fractures with application to dynamic dispersion calculation.

PubMed

Wang, Lichun; Cardenas, M Bayani

2015-08-01

The quantitative study of transport through fractured media has continued for many decades, but has often been constrained by observational and computational challenges. Here, we developed an efficient quasi-3D random walk particle tracking (RWPT) algorithm to simulate solute transport through natural fractures based on a 2D flow field generated from the modified local cubic law (MLCL). As a reference, we also modeled the actual breakthrough curves (BTCs) through direct simulations with the 3D advection-diffusion equation (ADE) and Navier-Stokes equations. The RWPT algorithm along with the MLCL accurately reproduced the actual BTCs calculated with the 3D ADE. The BTCs exhibited non-Fickian behavior, including early arrival and long tails. Using the spatial information of particle trajectories, we further analyzed the dynamic dispersion process through moment analysis. From this, asymptotic time scales were determined for solute dispersion to distinguish non-Fickian from Fickian regimes. This analysis illustrates the advantage and benefit of using an efficient combination of flow modeling and RWPT. Copyright © 2015 Elsevier B.V. All rights reserved.

Ion acceleration in a plasma focus

NASA Technical Reports Server (NTRS)

Gary, S. P.

1974-01-01

The electric and magnetic fields associated with anomalous diffusion to the axis of a linear plasma discharge are used to compute representative ion trajectories. Substantial axial acceleration of the ions is demonstrated.

Sex-Specific Alterations of White Matter Developmental Trajectories in Infants With Prenatal Exposure to Methamphetamine and Tobacco.

PubMed

Chang, Linda; Oishi, Kenichi; Skranes, Jon; Buchthal, Steven; Cunningham, Eric; Yamakawa, Robyn; Hayama, Sara; Jiang, Caroline S; Alicata, Daniel; Hernandez, Antonette; Cloak, Christine; Wright, Tricia; Ernst, Thomas

2016-12-01

Methamphetamine is a common illicit drug used worldwide. Methamphetamine and/or tobacco use by pregnant women remains prevalent. However, little is known about the effect of comorbid methamphetamine and tobacco use on human fetal brain development. To investigate whether microstructural brain abnormalities reported in children with prenatal methamphetamine and/or tobacco exposure are present at birth before childhood environmental influences. A prospective, longitudinal study was conducted between September 17, 2008, and February 28, 2015, at an ambulatory academic medical center. A total of 752 infant-mother dyads were screened and 139 of 195 qualified neonates were evaluated (36 methamphetamine/tobacco exposed, 32 tobacco exposed, and 71 unexposed controls). They were recruited consecutively from the community. Prenatal methamphetamine and/or tobacco exposure. Quantitative neurologic examination and diffusion tensor imaging performed 1 to 3 times through age 4 months; diffusivities and fractional anisotropy (FA) assessed in 7 white matter tracts and 4 subcortical brain regions using an automated atlas-based method. Of the 139 infants evaluated, 72 were female (51.8%); the mean (SE) postmenstrual age at baseline was 41.5 (0.27) weeks. Methamphetamine/tobacco-exposed infants showed delayed developmental trajectories on active muscle tone (group × age, P < .001) and total neurologic scores (group × age, P = .01) that normalized by ages 3 to 4 months. Only methamphetamine/tobacco-exposed boys had lower FA (group × age, P = .02) and higher diffusivities in superior (SCR) and posterior corona radiatae (PCR) (group × age × sex, P = .002; group × age × sex, P = .01) at baseline that normalized by age 3 months. Only methamphetamine/tobacco- and tobacco-exposed girls showed persistently lower FA in anterior corona radiata (ACR) (group, P = .04; group × age × sex, P = .01). Tobacco-exposed infants showed persistently lower axial diffusion in the thalamus and internal capsule across groups (P = .02). Prenatal methamphetamine/tobacco exposure may lead to delays in motor development, with less coherent fibers and less myelination in SCR and PCR only in male infants, but these abnormalities may normalize by ages 3 to 4 months after cessation of stimulant exposure. In contrast, persistently less coherent ACR fibers were observed in methamphetamine/tobacco- and tobacco-exposed girls, possibly from increased dendritic branching or spine density due to epigenetic influences. Persistently lower diffusivity in the thalamus and internal capsule of all tobacco-exposed infants suggests aberrant axonal development. Collectively, prenatal methamphetamine and/or tobacco exposure may lead to delayed motor development and white matter maturation in sex- and regional-specific manners.

Oxygen Nanobubble Tracking by Light Scattering in Single Cells and Tissues.

PubMed

Bhandari, Pushpak; Wang, Xiaolei; Irudayaraj, Joseph

2017-03-28

Oxygen nanobubbles (ONBs) have significant potential in targeted imaging and treatment in cancer diagnosis and therapy. Precise localization and tracking of single ONBs is demonstrated based on hyperspectral dark-field microscope (HSDFM) to image and track single oxygen nanobubbles in single cells. ONBs were proposed as promising contrast-generating imaging agents due to their strong light scattering generated from nonuniformity of refractive index at the interface. With this powerful platform, we have revealed the trajectories and quantities of ONBs in cells, and demonstrated the relation between the size and diffusion coefficient. We have also evaluated the presence of ONBs in the nucleus with respect to an increase in incubation time and have quantified the uptake in single cells in ex vivo tumor tissues. Our results demonstrate that HSDFM can be a versatile platform to detect and measure cellulosic nanoparticles at the single-cell level and to assess the dynamics and trajectories of this delivery system.

A Technology-Enhanced Unit of Modeling Static Electricity: Integrating scientific explanations and everyday observations

NASA Astrophysics Data System (ADS)

Shen, Ji; Linn, Marcia C.

2011-08-01

What trajectories do students follow as they connect their observations of electrostatic phenomena to atomic-level visualizations? We designed an electrostatics unit, using the knowledge integration framework to help students link observations and scientific ideas. We analyze how learners integrate ideas about charges, charged particles, energy, and observable events. We compare learning enactments in a typical school and a magnet school in the USA. We use pre-tests, post-tests, embedded notes, and delayed post-tests to capture the trajectories of students' knowledge integration. We analyze how visualizations help students grapple with abstract electrostatics concepts such as induction. We find that overall students gain more sophisticated ideas. They can interpret dynamic, interactive visualizations, and connect charge- and particle-based explanations to interpret observable events. Students continue to have difficulty in applying the energy-based explanation.

Interplanetary Trajectory Design for the Asteroid Robotic Redirect Mission Alternate Approach Trade Study

NASA Technical Reports Server (NTRS)

Merrill, Raymond Gabriel; Qu, Min; Vavrina, Matthew A.; Englander, Jacob A.; Jones, Christopher A.

2014-01-01

This paper presents mission performance analysis methods and results for the Asteroid Robotic Redirect Mission (ARRM) option to capture a free standing boulder on the surface of a 100 m or larger NEA. It details the optimization and design of heliocentric low-thrust trajectories to asteroid targets for the ARRM solar electric propulsion spacecraft. Extensive searches were conducted to determine asteroid targets with large pick-up mass potential and potential observation opportunities. Interplanetary trajectory approximations were developed in method based tools for Itokawa, Bennu, 1999 JU3, and 2008 EV5 and were validated by end-to-end integrated trajectories.

Interaction dynamics of two diffusing particles: contact times and influence of nearby surfaces.

PubMed

Tränkle, B; Ruh, D; Rohrbach, A

2016-03-14

Interactions of diffusing particles are governed by hydrodynamics on different length and timescales. The local hydrodynamics can be influenced substantially by simple interfaces. Here, we investigate the interaction dynamics of two micron-sized spheres close to plane interfaces to mimic more complex biological systems or microfluidic environments. Using scanned line optical tweezers and fast 3D interferometric particle tracking, we are able to track the motion of each bead with precisions of a few nanometers and at a rate of 10 kilohertz. From the recorded trajectories, all spatial and temporal information is accessible. This way, we measure diffusion coefficients for two coupling particles at varying distances h to one or two glass interfaces. We analyze their coupling strength and length by cross-correlation analysis relative to h and find a significant decrease in the coupling length when a second particle diffuses nearby. By analysing the times the particles are in close contact, we find that the influence of nearby surfaces and interaction potentials reduce the diffusivity strongly, although we found that the diffusivity hardly affects the contact times and the binding probability between the particles. All experimental results are compared to a theoretical model, which is based on the number of possible diffusion paths following the Catalan numbers and a diffusion probability, which is biased by the spheres' surface potential. The theoretical and experimental results agree very well and therefore enable a better understanding of hydrodynamically coupled interaction processes.

Efficacy of Distortion Correction on Diffusion Imaging: Comparison of FSL Eddy and Eddy_Correct Using 30 and 60 Directions Diffusion Encoding

PubMed Central

Yamada, Haruyasu; Abe, Osamu; Shizukuishi, Takashi; Kikuta, Junko; Shinozaki, Takahiro; Dezawa, Ko; Nagano, Akira; Matsuda, Masayuki; Haradome, Hiroki; Imamura, Yoshiki

2014-01-01

Diffusion imaging is a unique noninvasive tool to detect brain white matter trajectory and integrity in vivo. However, this technique suffers from spatial distortion and signal pileup or dropout originating from local susceptibility gradients and eddy currents. Although there are several methods to mitigate these problems, most techniques can be applicable either to susceptibility or eddy-current induced distortion alone with a few exceptions. The present study compared the correction efficiency of FSL tools, “eddy_correct” and the combination of “eddy” and “topup” in terms of diffusion-derived fractional anisotropy (FA). The brain diffusion images were acquired from 10 healthy subjects using 30 and 60 directions encoding schemes based on the electrostatic repulsive forces. For the 30 directions encoding, 2 sets of diffusion images were acquired with the same parameters, except for the phase-encode blips which had opposing polarities along the anteroposterior direction. For the 60 directions encoding, non–diffusion-weighted and diffusion-weighted images were obtained with forward phase-encoding blips and non–diffusion-weighted images with the same parameter, except for the phase-encode blips, which had opposing polarities. FA images without and with distortion correction were compared in a voxel-wise manner with tract-based spatial statistics. We showed that images corrected with eddy and topup possessed higher FA values than images uncorrected and corrected with eddy_correct with trilinear (FSL default setting) or spline interpolation in most white matter skeletons, using both encoding schemes. Furthermore, the 60 directions encoding scheme was superior as measured by increased FA values to the 30 directions encoding scheme, despite comparable acquisition time. This study supports the combination of eddy and topup as a superior correction tool in diffusion imaging rather than the eddy_correct tool, especially with trilinear interpolation, using 60 directions encoding scheme. PMID:25405472

Efficacy of distortion correction on diffusion imaging: comparison of FSL eddy and eddy_correct using 30 and 60 directions diffusion encoding.

PubMed

Yamada, Haruyasu; Abe, Osamu; Shizukuishi, Takashi; Kikuta, Junko; Shinozaki, Takahiro; Dezawa, Ko; Nagano, Akira; Matsuda, Masayuki; Haradome, Hiroki; Imamura, Yoshiki

2014-01-01

Diffusion imaging is a unique noninvasive tool to detect brain white matter trajectory and integrity in vivo. However, this technique suffers from spatial distortion and signal pileup or dropout originating from local susceptibility gradients and eddy currents. Although there are several methods to mitigate these problems, most techniques can be applicable either to susceptibility or eddy-current induced distortion alone with a few exceptions. The present study compared the correction efficiency of FSL tools, "eddy_correct" and the combination of "eddy" and "topup" in terms of diffusion-derived fractional anisotropy (FA). The brain diffusion images were acquired from 10 healthy subjects using 30 and 60 directions encoding schemes based on the electrostatic repulsive forces. For the 30 directions encoding, 2 sets of diffusion images were acquired with the same parameters, except for the phase-encode blips which had opposing polarities along the anteroposterior direction. For the 60 directions encoding, non-diffusion-weighted and diffusion-weighted images were obtained with forward phase-encoding blips and non-diffusion-weighted images with the same parameter, except for the phase-encode blips, which had opposing polarities. FA images without and with distortion correction were compared in a voxel-wise manner with tract-based spatial statistics. We showed that images corrected with eddy and topup possessed higher FA values than images uncorrected and corrected with eddy_correct with trilinear (FSL default setting) or spline interpolation in most white matter skeletons, using both encoding schemes. Furthermore, the 60 directions encoding scheme was superior as measured by increased FA values to the 30 directions encoding scheme, despite comparable acquisition time. This study supports the combination of eddy and topup as a superior correction tool in diffusion imaging rather than the eddy_correct tool, especially with trilinear interpolation, using 60 directions encoding scheme.

Evaluation of balloon trajectory forecast routines for GAINS

NASA Astrophysics Data System (ADS)

Collander, R.; Girz, C.

The Global Air-ocean IN-situ System (GAINS) is a global observing system designed to augment current environmental observing and monitoring networks. GAINS is a network of long-duration, stratospheric platforms that carry onboard sensors and hundreds of dropsondes to acquire meteorological, air chemistry, and climate data over oceans and in remote land regions of the globe. Although GAINS platforms will include balloons and Remotely Operated Aircraft (ROA), the scope of this paper is limited to balloon-based platforms. A primary goal of GAINS balloon test flights is post-flight recovery of the balloon shell and payload, which requires information on the expected flight path and landing site prior to launch. Software has been developed for the prediction of the balloon trajectory and landing site, with separate versions written to generate predictions based upon rawinsonde data and model output. Balloon positions are calculated in 1-min increments based on wind data from the closest rawinsonde site or model grid point, given a known launch point, ascent and descent rate and flight duration. For short flights (< 6h), rawinsonde winds interpolated to 10-mb levels are used for trajectory calculations. Predictions for flight durations of 6 to 48h are based upon the initialization and 3 h forecast wind fields from NOAA's global aviation- (AVN) and Rapid Update Cycle (RUC) models. Given a limited number of actual balloon launches, trajectories computed from a chronological series of hourly RUC initializations are used as the baseline for comparison purposes. These baseline trajectories are compared to trajectory predictions from the rawinsonde and model-based versions on a monthly and seasonal basis over a 1-year period (January 1 - December 31, 2001) for flight durations of 3h, 6h and 48h. Predicted trajectories diverge from the baseline path, with the divergence increasing with increasing time. We examine the zonal, meridional and net magnitudes of these deviations, and attempt to determine directional biases in the predictions. This paper gives an overview of the software, including methods employed, physical considerations and limitations, and discusses results of this evaluation.

Precisely and Accurately Inferring Single-Molecule Rate Constants

PubMed Central

Kinz-Thompson, Colin D.; Bailey, Nevette A.; Gonzalez, Ruben L.

2017-01-01

The kinetics of biomolecular systems can be quantified by calculating the stochastic rate constants that govern the biomolecular state versus time trajectories (i.e., state trajectories) of individual biomolecules. To do so, the experimental signal versus time trajectories (i.e., signal trajectories) obtained from observing individual biomolecules are often idealized to generate state trajectories by methods such as thresholding or hidden Markov modeling. Here, we discuss approaches for idealizing signal trajectories and calculating stochastic rate constants from the resulting state trajectories. Importantly, we provide an analysis of how the finite length of signal trajectories restrict the precision of these approaches, and demonstrate how Bayesian inference-based versions of these approaches allow rigorous determination of this precision. Similarly, we provide an analysis of how the finite lengths and limited time resolutions of signal trajectories restrict the accuracy of these approaches, and describe methods that, by accounting for the effects of the finite length and limited time resolution of signal trajectories, substantially improve this accuracy. Collectively, therefore, the methods we consider here enable a rigorous assessment of the precision, and a significant enhancement of the accuracy, with which stochastic rate constants can be calculated from single-molecule signal trajectories. PMID:27793280

Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

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

Larriba, Carlos, E-mail: clarriba@umn.edu; Hogan, Christopher J.

2013-10-15

The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission ismore » largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas molecule collisions (gas molecules with altered trajectories by the potential interaction) without tracking grazing trajectories are further discussed. The presented calculation techniques should enable more accurate collision cross section predictions under experimentally relevant conditions than pre-existing approaches, and should enhance the ability of collision cross section measurement schemes to discern the structures of gas phase entities.« less

Gauging of the PhoE channel by a single freely diffusing proton.

PubMed

Bransburg-Zabary, Sharron; Nachliel, Esther; Gutman, Menachem

2002-12-01

In the present study we combined a continuum approximation with a detailed mapping of the electrostatic potential inside an ionic channel to define the most probable trajectory for proton propagation through the channel (propagation along a structure-supported trajectory (PSST)). The conversion of the three-dimensional diffusion space into propagation along a one-dimensional pathway permits reconstruction of an ion motion by a short calculation (a few seconds on a state-of-the-art workstation) rather than a laborious, time-consuming random walk simulations. The experimental system selected for testing the accuracy of this concept was the reversible dissociation of a proton from a single pyranine molecule (8-hydroxypyrene-1,2,3-trisulfonate) bound by electrostatic forces inside the PhoE ionic channel of the Escherichia coli outer membrane. The crystal structure coordinates were used for calculation of the intra-cavity electrostatic potential, and the reconstruction of the observed fluorescence decay curve was carried out using the dielectric constant of the intra-cavity space as an adjustable parameter. The fitting of past experimental observations (Shimoni, E., Y. Tsfadia, E. Nachliel, and M. Gutman. 1993. Biophys. J. 64:472-479) was carried out by a modified version of the Agmon geminate recombination program (Krissinel, E. B., and N. Agmon. 1996. J. Comp. Chem. 17:1085-1098), where the gradient of the electrostatic potential and the entropic terms were calculated by the PSST program. The best-fitted reconstruction of the observed dynamics was attained when the water in the cavity was assigned epsilon

Disentangling Random Motion and Flow in a Complex Medium

PubMed Central

Koslover, Elena F.; Chan, Caleb K.; Theriot, Julie A.

2016-01-01

We describe a technique for deconvolving the stochastic motion of particles from large-scale fluid flow in a dynamic environment such as that found in living cells. The method leverages the separation of timescales to subtract out the persistent component of motion from single-particle trajectories. The mean-squared displacement of the resulting trajectories is rescaled so as to enable robust extraction of the diffusion coefficient and subdiffusive scaling exponent of the stochastic motion. We demonstrate the applicability of the method for characterizing both diffusive and fractional Brownian motion overlaid by flow and analytically calculate the accuracy of the method in different parameter regimes. This technique is employed to analyze the motion of lysosomes in motile neutrophil-like cells, showing that the cytoplasm of these cells behaves as a viscous fluid at the timescales examined. PMID:26840734

A fractal derivative model for the characterization of anomalous diffusion in magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Liang, Yingjie; Ye, Allen Q.; Chen, Wen; Gatto, Rodolfo G.; Colon-Perez, Luis; Mareci, Thomas H.; Magin, Richard L.

2016-10-01

Non-Gaussian (anomalous) diffusion is wide spread in biological tissues where its effects modulate chemical reactions and membrane transport. When viewed using magnetic resonance imaging (MRI), anomalous diffusion is characterized by a persistent or 'long tail' behavior in the decay of the diffusion signal. Recent MRI studies have used the fractional derivative to describe diffusion dynamics in normal and post-mortem tissue by connecting the order of the derivative with changes in tissue composition, structure and complexity. In this study we consider an alternative approach by introducing fractal time and space derivatives into Fick's second law of diffusion. This provides a more natural way to link sub-voxel tissue composition with the observed MRI diffusion signal decay following the application of a diffusion-sensitive pulse sequence. Unlike previous studies using fractional order derivatives, here the fractal derivative order is directly connected to the Hausdorff fractal dimension of the diffusion trajectory. The result is a simpler, computationally faster, and more direct way to incorporate tissue complexity and microstructure into the diffusional dynamics. Furthermore, the results are readily expressed in terms of spectral entropy, which provides a quantitative measure of the overall complexity of the heterogeneous and multi-scale structure of biological tissues. As an example, we apply this new model for the characterization of diffusion in fixed samples of the mouse brain. These results are compared with those obtained using the mono-exponential, the stretched exponential, the fractional derivative, and the diffusion kurtosis models. Overall, we find that the order of the fractal time derivative, the diffusion coefficient, and the spectral entropy are potential biomarkers to differentiate between the microstructure of white and gray matter. In addition, we note that the fractal derivative model has practical advantages over the existing models from the perspective of computational accuracy and efficiency.

Evaluation of the HF-Radar network system around Taiwan using normalized cumulative Lagrangian separation.

NASA Astrophysics Data System (ADS)

Fredj, Erick; Kohut, Josh; Roarty, Hugh; Lai, Jian-Wu

2017-04-01

The Lagrangian separation distance between the endpoints of simulated and observed drifter trajectories is often used to assess the performance of numerical particle trajectory models. However, the separation distance fails to indicate relative model performance in weak and strong current regions, such as over continental shelves and the adjacent deep ocean. A skill score described in detail by (Lui et.al. 2011) was applied to estimate the cumulative Lagrangian separation distances normalized by the associated cumulative trajectory lengths. In contrast, the Lagrangian separation distance alone gives a misleading result. The proposed dimensionless skill score is particularly useful when the number of drifter trajectories is limited and neither a conventional Eulerian-based velocity nor a Lagrangian based probability density function may be estimated. The skill score assesses The Taiwan Ocean Radar Observing System (TOROS) performance. TOROS consists of 17 SeaSonde type radars around the Taiwan Island. The currents off Taiwan are significantly influenced by the nearby Kuroshio current. The main stream of the Kuroshio flows along the east coast of Taiwan to the north throughout the year. Sometimes its branch current also bypasses the south end of Taiwan and goes north along the west coast of Taiwan. The Kuroshio is also prone to seasonal change in its speed of flow, current capacity, distribution width, and depth. The evaluations of HF-Radar National Taiwanese network performance using Lagrangian drifter records demonstrated the high quality and robustness of TOROS HF-Radar data using a purely trajectory-based non-dimensional index. Yonggang Liu and Robert H. Weisberg, "Evaluation of trajectory modeling in different dynamic regions using normalized cumulative Lagrangian separation", Journal of Geophysical Research, Vol. 116, C09013, doi:10.1029/2010JC006837, 2011

Coarse analysis of collective behaviors: Bifurcation analysis of the optimal velocity model for traffic jam formation

NASA Astrophysics Data System (ADS)

Miura, Yasunari; Sugiyama, Yuki

2017-12-01

We present a general method for analyzing macroscopic collective phenomena observed in many-body systems. For this purpose, we employ diffusion maps, which are one of the dimensionality-reduction techniques, and systematically define a few relevant coarse-grained variables for describing macroscopic phenomena. The time evolution of macroscopic behavior is described as a trajectory in the low-dimensional space constructed by these coarse variables. We apply this method to the analysis of the traffic model, called the optimal velocity model, and reveal a bifurcation structure, which features a transition to the emergence of a moving cluster as a traffic jam.

Investigating the Eddy Diffusivity Concept in the Coastal Ocean

NASA Astrophysics Data System (ADS)

Rypina, I.; Kirincich, A.; Lentz, S. J.; Sundermeyer, M. A.

2016-12-01

We test the validity, utility, and limitations of the lateral eddy diffusivity concept in a coastal environment through analyzing data from coupled drifter and dye releases within the footprint of a high-resolution (800 m) high-frequency radar south of Martha's Vineyard, Massachusetts. Specifically, we investigate how well a combination of radar-based velocities and drifter-derived diffusivities can reproduce observed dye spreading over an 8-h time interval. A drifter-based estimate of an anisotropic diffusivity tensor is used to parameterize small-scale motions that are unresolved and under-resolved by the radar system. This leads to a significant improvement in the ability of the radar to reproduce the observed dye spreading. Our drifter-derived diffusivity estimates are O(10 m2/s), are consistent with the diffusivity inferred from aerial images of the dye taken using the quadcopter-mounted digital camera during the dye release, and are roughly an order of magnitude larger than diffusivity estimates of Okubo (O(1 m2/s)) for similar spatial scales ( 1 km). Despite the fact that the drifter-based diffusivity approach was successful in improving the ability of the radar to reproduce the observed dye spreading, the dispersion of drifters was, for the most part, not consistent with the diffusive spreading regime.

Bootstrapping Least Squares Estimates in Biochemical Reaction Networks

PubMed Central

Linder, Daniel F.

2015-01-01

The paper proposes new computational methods of computing confidence bounds for the least squares estimates (LSEs) of rate constants in mass-action biochemical reaction network and stochastic epidemic models. Such LSEs are obtained by fitting the set of deterministic ordinary differential equations (ODEs), corresponding to the large volume limit of a reaction network, to network’s partially observed trajectory treated as a continuous-time, pure jump Markov process. In the large volume limit the LSEs are asymptotically Gaussian, but their limiting covariance structure is complicated since it is described by a set of nonlinear ODEs which are often ill-conditioned and numerically unstable. The current paper considers two bootstrap Monte-Carlo procedures, based on the diffusion and linear noise approximations for pure jump processes, which allow one to avoid solving the limiting covariance ODEs. The results are illustrated with both in-silico and real data examples from the LINE 1 gene retrotranscription model and compared with those obtained using other methods. PMID:25898769

Biased Brownian dynamics for rate constant calculation.

PubMed

Zou, G; Skeel, R D; Subramaniam, S

2000-08-01

An enhanced sampling method-biased Brownian dynamics-is developed for the calculation of diffusion-limited biomolecular association reaction rates with high energy or entropy barriers. Biased Brownian dynamics introduces a biasing force in addition to the electrostatic force between the reactants, and it associates a probability weight with each trajectory. A simulation loses weight when movement is along the biasing force and gains weight when movement is against the biasing force. The sampling of trajectories is then biased, but the sampling is unbiased when the trajectory outcomes are multiplied by their weights. With a suitable choice of the biasing force, more reacted trajectories are sampled. As a consequence, the variance of the estimate is reduced. In our test case, biased Brownian dynamics gives a sevenfold improvement in central processing unit (CPU) time with the choice of a simple centripetal biasing force.

Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam.

PubMed

Rydzewski, J; Nowak, W

2016-04-12

In this work we propose an application of a nonlinear dimensionality reduction method to represent the high-dimensional configuration space of the ligand-protein dissociation process in a manner facilitating interpretation. Rugged ligand expulsion paths are mapped into 2-dimensional space. The mapping retains the main structural changes occurring during the dissociation. The topological similarity of the reduced paths may be easily studied using the Fréchet distances, and we show that this measure facilitates machine learning classification of the diffusion pathways. Further, low-dimensional configuration space allows for identification of residues active in transport during the ligand diffusion from a protein. The utility of this approach is illustrated by examination of the configuration space of cytochrome P450cam involved in expulsing camphor by means of enhanced all-atom molecular dynamics simulations. The expulsion trajectories are sampled and constructed on-the-fly during molecular dynamics simulations using the recently developed memetic algorithms [ Rydzewski, J.; Nowak, W. J. Chem. Phys. 2015 , 143 ( 12 ), 124101 ]. We show that the memetic algorithms are effective for enforcing the ligand diffusion and cavity exploration in the P450cam-camphor complex. Furthermore, we demonstrate that machine learning techniques are helpful in inspecting ligand diffusion landscapes and provide useful tools to examine structural changes accompanying rare events.

Sex differences in white matter development during adolescence: a DTI study.

PubMed

Wang, Yingying; Adamson, Chris; Yuan, Weihong; Altaye, Mekibib; Rajagopal, Akila; Byars, Anna W; Holland, Scott K

2012-10-10

Adolescence is a complex transitional period in human development, composing physical maturation, cognitive and social behavioral changes. The objective of this study is to investigate sex differences in white matter development and the associations between intelligence and white matter microstructure in the adolescent brain using diffusion tensor imaging (DTI) and tract-based spatial statistics (TBSS). In a cohort of 16 typically-developing adolescents aged 13 to 17 years, longitudinal DTI data were recorded from each subject at two time points that were one year apart. We used TBSS to analyze the diffusion indices including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD). Our results suggest that boys (13-18 years) continued to demonstrate white matter maturation, whereas girls appeared to reach mature levels earlier. In addition, we identified significant positive correlations between FA and full-scale intelligence quotient (IQ) in the right inferior fronto-occipital fasciculus when both sexes were looked at together. Only girls showed significant positive correlations between FA and verbal IQ in the left cortico-spinal tract and superior longitudinal fasciculus. The preliminary evidence presented in this study supports that boys and girls have different developmental trajectories in white matter microstructure. Copyright © 2012 Elsevier B.V. All rights reserved.

Quasiclassical trajectory calculations to evaluate a kinematic constraint on internal energy in suprathreshold collision energy abstraction reactions

NASA Astrophysics Data System (ADS)

Shuman, Nicholas S.; Mihok, Morgan; Fistik, Margaret; Valentini, James J.

2005-08-01

Experimentally observed product quantum state distributions across a wide range of abstraction reactions at suprathreshold collision energies have shown a strong bias against product internal energy. Only a fraction, sometimes quite a small fraction, of the energetically accessible product quantum states are populated. Picconatto et al. [J. Chem. Phys. 114, 1663 (2001)] noted a simple mathematical relationship between the highest-energy rovibrational states observed and the kinematics of the reaction system. They proposed a reaction model based on reaction kinematics that quantitatively explains this behavior. The model is in excellent agreement with measured quantum state distributions. The assumptions of the model invoke detailed characteristics of reactive trajectories at suprathreshold collision energies. Here we test those assumptions using quasiclassical trajectory calculations for the abstraction reactions H +HCl→H2+Cl, D +HCl→HD+Cl, and H +DCl→HD+Cl. Trajectories were run on a potential-energy surface calculated with a London-Eyring-Polyani-Sato function with a localized 3-center term (LEPS-3C) previously shown to accurately reproduce experimentally observed product state distributions for the H +HCl abstraction reaction. The trajectories sample collision energies near threshold and also substantially above it. Although the trajectories demonstrate some aspects of the model, they show that it is not valid. However, the inadequacy of the proposed model does not invalidate the apparent kinematic basis of the observed energy constraint. The present results show that there must be some other molecular behavior rooted in the reaction kinematics that is the explanation and the source of the constraint.

Cortical fibers orientation mapping using in-vivo whole brain 7 T diffusion MRI.

PubMed

Gulban, Omer F; De Martino, Federico; Vu, An T; Yacoub, Essa; Uğurbil, Kamil; Lenglet, Christophe

2018-05-10

Diffusion MRI of the cortical gray matter is challenging because the micro-environment probed by water molecules is much more complex than within the white matter. High spatial and angular resolutions are therefore necessary to uncover anisotropic diffusion patterns and laminar structures, which provide complementary (e.g. to anatomical and functional MRI) microstructural information about the cortex architectonic. Several ex-vivo and in-vivo MRI studies have recently addressed this question, however predominantly with an emphasis on specific cortical areas. There is currently no whole brain in-vivo data leveraging multi-shell diffusion MRI acquisition at high spatial resolution, and depth dependent analysis, to characterize the complex organization of cortical fibers. Here, we present unique in-vivo human 7T diffusion MRI data, and a dedicated cortical depth dependent analysis pipeline. We leverage the high spatial (1.05 mm isotropic) and angular (198 diffusion gradient directions) resolution of this whole brain dataset to improve cortical fiber orientations mapping, and study neurites (axons and/or dendrites) trajectories across cortical depths. Tangential fibers in superficial cortical depths and crossing fiber configurations in deep cortical depths are identified. Fibers gradually inserting into the gyral walls are visualized, which contributes to mitigating the gyral bias effect. Quantitative radiality maps and histograms in individual subjects and cortex-based aligned datasets further support our results. Copyright © 2018 Elsevier Inc. All rights reserved.

Scout trajectory error propagation computer program

NASA Technical Reports Server (NTRS)

Myler, T. R.

1982-01-01

Since 1969, flight experience has been used as the basis for predicting Scout orbital accuracy. The data used for calculating the accuracy consists of errors in the trajectory parameters (altitude, velocity, etc.) at stage burnout as observed on Scout flights. Approximately 50 sets of errors are used in Monte Carlo analysis to generate error statistics in the trajectory parameters. A covariance matrix is formed which may be propagated in time. The mechanization of this process resulted in computer program Scout Trajectory Error Propagation (STEP) and is described herein. Computer program STEP may be used in conjunction with the Statistical Orbital Analysis Routine to generate accuracy in the orbit parameters (apogee, perigee, inclination, etc.) based upon flight experience.

Combining Group-Based Trajectory Modeling and Propensity Score Matching for Causal Inferences in Nonexperimental Longitudinal Data

ERIC Educational Resources Information Center

Haviland, Amelia; Nagin, Daniel S.; Rosenbaum, Paul R.; Tremblay, Richard E.

2008-01-01

A central theme of research on human development and psychopathology is whether a therapeutic intervention or a turning-point event, such as a family break-up, alters the trajectory of the behavior under study. This article describes and applies a method for using observational longitudinal data to make more transparent causal inferences about the…

Characterizing the pain score trajectories of hospitalized adult medical and surgical patients: a retrospective cohort study.

PubMed

Kannampallil, Thomas; Galanter, William L; Falck, Suzanne; Gaunt, Michael J; Gibbons, Robert D; McNutt, Robert; Odwazny, Richard; Schiff, Gordon; Vaida, Allen J; Wilkie, Diana J; Lambert, Bruce L

2016-12-01

Pain care for hospitalized patients is often suboptimal. Representing pain scores as a graphical trajectory may provide insights into the understanding and treatment of pain. We describe a 1-year, retrospective, observational study to characterize pain trajectories of hospitalized adults during the first 48 hours after admission at an urban academic medical center. Using a subgroup of patients who presented with significant pain (pain score >4; n = 7762 encounters), we characterized pain trajectories and measured area under the curve, slope of the trajectory for the first 2 hours after admission, and pain intensity at plateau. We used mixed-effects regression to assess the association between pain score and sociodemographics (age, race, and gender), pain medication orders (opioids, nonopioids, and no medications), and medical service (obstetrics, psychiatry, surgery, sickle cell, intensive care unit, and medicine). K-means clustering was used to identify patient subgroups with similar trajectories. Trajectories showed differences based on race, gender, service, and initial pain score. Patients presumed to have dissimilar pain experiences (eg, sickle vs obstetrical) had markedly different pain trajectories. Patients with higher initial pain had a more rapid reduction during their first 2 hours of treatment. Pain reduction achieved in the 48 hours after admission was approximately 50% of the initial pain, regardless of the initial pain. Most patients' pain failed to fully resolve, plateauing at a pain score of 4 or greater. Visualizing pain scores as graphical trajectories illustrates the dynamic variability in pain, highlighting pain responses over a period of observation, and may yield new insights for quality improvement and research.

Simulating Flying Insects Using Dynamics and Data-Driven Noise Modeling to Generate Diverse Collective Behaviors

PubMed Central

Ren, Jiaping; Wang, Xinjie; Manocha, Dinesh

2016-01-01

We present a biologically plausible dynamics model to simulate swarms of flying insects. Our formulation, which is based on biological conclusions and experimental observations, is designed to simulate large insect swarms of varying densities. We use a force-based model that captures different interactions between the insects and the environment and computes collision-free trajectories for each individual insect. Furthermore, we model the noise as a constructive force at the collective level and present a technique to generate noise-induced insect movements in a large swarm that are similar to those observed in real-world trajectories. We use a data-driven formulation that is based on pre-recorded insect trajectories. We also present a novel evaluation metric and a statistical validation approach that takes into account various characteristics of insect motions. In practice, the combination of Curl noise function with our dynamics model is used to generate realistic swarm simulations and emergent behaviors. We highlight its performance for simulating large flying swarms of midges, fruit fly, locusts and moths and demonstrate many collective behaviors, including aggregation, migration, phase transition, and escape responses. PMID:27187068

Trajectories of Listeria-type motility in two dimensions

NASA Astrophysics Data System (ADS)

Wen, Fu-Lai; Leung, Kwan-tai; Chen, Hsuan-Yi

2012-12-01

Force generated by actin polymerization is essential in cell motility and the locomotion of organelles or bacteria such as Listeria monocytogenes. Both in vivo and in vitro experiments on actin-based motility have observed geometrical trajectories including straight lines, circles, S-shaped curves, and translating figure eights. This paper reports a phenomenological model of an actin-propelled disk in two dimensions that generates geometrical trajectories. Our model shows that when the evolutions of actin density and force per filament on the disk are strongly coupled to the disk self-rotation, it is possible for a straight trajectory to lose its stability. When the instability is due to a pitchfork bifurcation, the resulting trajectory is a circle; a straight trajectory can also lose stability through a Hopf bifurcation, and the resulting trajectory is an S-shaped curve. We also show that a half-coated disk, which mimics the distribution of functionalized proteins in Listeria, also undergoes similar symmetry-breaking bifurcations when the straight trajectory loses stability. For both a fully coated disk and a half-coated disk, when the trajectory is an S-shaped curve, the angular frequency of the disk self-rotation is different from that of the disk trajectory. However, for circular trajectories, these angular frequencies are different for a fully coated disk but the same for a half-coated disk.

Tetramethylpyrazine-Loaded Hydrogels: Preparation, Penetration Through a Subcutaneous-Mucous-Membrane Model, and a Molecular Dynamics Simulation.

PubMed

Xia, Hongmei; Xu, Yinxiang; Cheng, Zhiqing; Cheng, Yongfeng

2017-07-01

Tetramethylpyrazine (TMP) was extracted from Ligusticum chuanxiong hort. The compound is known to have a variety of medicinal functions; in particular, it is used for the treatment of cerebral ischemic diseases. TMP-loaded hydrogels offer an excellent preparation with the capacity to bypass the blood-brain barrier, allowing treatment of the brain through intranasal administration. We prepared TMP-loaded hydrogels using carbomer 940 and evaluated the release of TMP from the hydrogel. We determined the release rate using Franz-type diffusion cell experiments with a subcutaneous-mucous-membrane model and also by a molecular dynamics (MD) simulation. In general, the former method was more complicated than the latter was. The dynamic behavior of TMP release from the hydrogel was revealed by analysis of the mean square displacement of the trajectory in the MD simulation. The coefficient of TMP diffusion from the hydrogel was calculated at different temperatures (277, 298, and 310 K) by using MD software. The results showed that the coefficient of diffusion increased with an increase in temperature. This trend was observed both experimentally and in the MD simulation. Therefore, the MD simulation was a complementary method to verify the experimental data.

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers

NASA Astrophysics Data System (ADS)

Pitman, Michael C.; Suits, Frank; Gawrisch, Klaus; Feller, Scott E.

2005-06-01

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of H2 spin-lattice relaxation rates, nuclear overhauser enhancement spectroscopy (NOESY) cross-relaxation rates, and lateral diffusion coefficients. Additionally, we describe the dynamics of hydrogen bonding through an analysis of hydrogen bond lifetimes and the time evolution of clusters of hydrogen bonded lipids. The simulated trajectory is shown to be consistent with experimental measures of internal, intermolecular, and diffusive motion. Consistent with our analysis of SOPE structure in the companion paper, we see hydrogen bonding dominating the dynamics of the interface region. Comparison of H2 T1 relaxation rates for chain methylene segments in phosphatidylcholine and phosphatidylethanolamine bilayers indicates that slower motion resulting from hydrogen bonding extends at least three carbons into the hydrophobic core. NOESY cross-relaxation rates compare well with experimental values, indicating the observed hydrogen bonding dynamics are realistic. Calculated lateral diffusion rates (4±1×10-8cm2/s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.

Anomalous transport of charged dust grains in a magnetized collisional plasma: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Bezbaruah, Pratikshya; Das, Nilakshi

2018-05-01

Anomalous diffusion of charged dust grains immersed in a plasma in the presence of strong ion-neutral collision, flowing ions, and a magnetic field has been observed. Molecular Dynamics simulation confirms the deviation from normal diffusion in an ensemble of dust grains probed in laboratory plasma chambers. Collisional effects are significant in governing the nature of diffusion. In order to have a clear idea on the transport of particles in a real experimental situation, the contribution of streaming ions and the magnetic field along with collision is considered through the relevant interaction potential. The nonlinear evolution of Mean Square Displacement is an indication of the modification in particle trajectories due to several effects as mentioned above. It is found that strong collision and ion flow significantly affect the interparticle interaction potential in the presence of the magnetic field and lead to the appearance of the asymmetric type of Debye Hückel (D H) potential. Due to the combined effect of the magnetic field, ion flow, and collision, dusty plasma exhibits a completely novel behavior. The coupling parameter Γ enhances the asymmetric D H type potential arising due to ion flow, and this may drive the system to a disordered state.

High-precision tracking of brownian boomerang colloidal particles confined in quasi two dimensions.

PubMed

Chakrabarty, Ayan; Wang, Feng; Fan, Chun-Zhen; Sun, Kai; Wei, Qi-Huo

2013-11-26

In this article, we present a high-precision image-processing algorithm for tracking the translational and rotational Brownian motion of boomerang-shaped colloidal particles confined in quasi-two-dimensional geometry. By measuring mean square displacements of an immobilized particle, we demonstrate that the positional and angular precision of our imaging and image-processing system can achieve 13 nm and 0.004 rad, respectively. By analyzing computer-simulated images, we demonstrate that the positional and angular accuracies of our image-processing algorithm can achieve 32 nm and 0.006 rad. Because of zero correlations between the displacements in neighboring time intervals, trajectories of different videos of the same particle can be merged into a very long time trajectory, allowing for long-time averaging of different physical variables. We apply this image-processing algorithm to measure the diffusion coefficients of boomerang particles of three different apex angles and discuss the angle dependence of these diffusion coefficients.

Entrainment and scattering in microswimmer-colloid interactions

NASA Astrophysics Data System (ADS)

Shum, Henry; Yeomans, Julia M.

2017-11-01

We use boundary element simulations to study the interaction of model microswimmers with a neutrally buoyant spherical particle. The ratio of the size of the particle to that of the swimmer is varied from RP/RS≪1 , corresponding to swimmer-tracer scattering, to RP/RS≫1 , approximately equivalent to the swimmer interacting with a fixed, flat surface. We find that details of the swimmer and particle trajectories vary for different swimmers. However, the overall characteristics of the scattering event fall into two regimes, depending on the relative magnitudes of the impact parameter, ρ , and the collision radius, Rcoll=RP+RS . The range of particle motion, defined as the maximum distance between two points on the trajectory, has only a weak dependence on the impact parameter when ρ Rcoll the range decreases as a power law in ρ and is insensitive to the size of the particle. We also demonstrate that large particles can cause swimmers to be deflected through large angles. In some instances, this swimmer deflection can lead to larger net displacements of the particle. Based on these results, we estimate the effective diffusivity of a particle in a dilute bath of swimmers and show that there is a nonmonotonic dependence on particle radius. Similarly, we show that the effective diffusivity of a swimmer scattering in a suspension of particles varies nonmonotonically with particle radius.

Evolution of diffusion and dissemination theory.

PubMed

Dearing, James W

2008-01-01

The article provides a review and considers how the diffusion of innovations Research paradigm has changed, and offers suggestions for the further development of this theory of social change. Main emphases of diffusion Research studies are compared over time, with special attention to applications of diffusion theory-based concepts as types of dissemination science. A considerable degree of paradigmatic evolution is observed. The classical diffusion model focused on adopter innovativeness, individuals as the locus of decision, communication channels, and adoption as the primary outcome measures in post hoc observational study designs. The diffusion systems in question were centralized, with fidelity of implementation often assumed. Current dissemination Research and practice is better characterized by tests of interventions that operationalize one or more diffusion theory-based concepts and concepts from other change approaches, involve complex organizations as the units of adoption, and focus on implementation issues. Foment characterizes dissemination and implementation Research, Reflecting both its interdisciplinary Roots and the imperative of spreading evidence-based innovations as a basis for a new paradigm of translational studies of dissemination science.

Anomalous, non-Gaussian tracer diffusion in crowded two-dimensional environments

NASA Astrophysics Data System (ADS)

Ghosh, Surya K.; Cherstvy, Andrey G.; Grebenkov, Denis S.; Metzler, Ralf

2016-01-01

A topic of intense current investigation pursues the question of how the highly crowded environment of biological cells affects the dynamic properties of passively diffusing particles. Motivated by recent experiments we report results of extensive simulations of the motion of a finite sized tracer particle in a heterogeneously crowded environment made up of quenched distributions of monodisperse crowders of varying sizes in finite circular two-dimensional domains. For given spatial distributions of monodisperse crowders we demonstrate how anomalous diffusion with strongly non-Gaussian features arises in this model system. We investigate both biologically relevant situations of particles released either at the surface of an inner domain or at the outer boundary, exhibiting distinctly different features of the observed anomalous diffusion for heterogeneous distributions of crowders. Specifically we reveal an asymmetric spreading of tracers even at moderate crowding. In addition to the mean squared displacement (MSD) and local diffusion exponent we investigate the magnitude and the amplitude scatter of the time averaged MSD of individual tracer trajectories, the non-Gaussianity parameter, and the van Hove correlation function. We also quantify how the average tracer diffusivity varies with the position in the domain with a heterogeneous radial distribution of crowders and examine the behaviour of the survival probability and the dynamics of the tracer survival probability. Inter alia, the systems we investigate are related to the passive transport of lipid molecules and proteins in two-dimensional crowded membranes or the motion in colloidal solutions or emulsions in effectively two-dimensional geometries, as well as inside supercrowded, surface adhered cells.

SPECTRAL EVOLUTION OF ANOMALOUS COSMIC RAYS AT VOYAGER 1 BEYOND THE TERMINATION SHOCK

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

Senanayake, U. K.; Florinski, V.; Cummings, A. C.

When the Voyager 1 spacecraft crossed the termination shock (TS) on 2004 December 16, the energy spectra of anomalous cosmic rays (ACRs) could not have been produced by steady-state diffusive shock acceleration. However, over the next few years, in the declining phase of the solar cycle, the spectra began to evolve into the expected power-law profile. Observations at the shock led to a broad range of alternative theories for ACR acceleration. In spite of that, in this work we show that the observations could be explained by assuming ACRs are accelerated at the TS. In this paper, we propose thatmore » the solar cycle had an important effect on the unrolling of the spectra in the heliosheath. To investigate the spectral evolution of ACRs, a magnetohydrodynamic background model with stationary solar-wind inner boundary conditions was used to model the transport of helium and oxygen ions. We used a backward-in-time stochastic integration technique where phase-space trajectories are integrated until the so-called “injection energy” is reached. Our simulation results were compared with Voyager 1 observations using three different diffusion models. It is shown that the spectral evolution of ACRs in the heliosheath at Voyager 1 could be explained by an increase in the source strength and an enhancement in diffusion as a result of a decrease of the turbulent correlation length in the declining phase of the solar cycle. At the same time, drift effects seem to have had a smaller effect on the evolution of the spectra.« less

Extending the Functionality of Behavioural Change-Point Analysis with k-Means Clustering: A Case Study with the Little Penguin (Eudyptula minor)

PubMed Central

Zhang, Jingjing; Dennis, Todd E.

2015-01-01

We present a simple framework for classifying mutually exclusive behavioural states within the geospatial lifelines of animals. This method involves use of three sequentially applied statistical procedures: (1) behavioural change point analysis to partition movement trajectories into discrete bouts of same-state behaviours, based on abrupt changes in the spatio-temporal autocorrelation structure of movement parameters; (2) hierarchical multivariate cluster analysis to determine the number of different behavioural states; and (3) k-means clustering to classify inferred bouts of same-state location observations into behavioural modes. We demonstrate application of the method by analysing synthetic trajectories of known ‘artificial behaviours’ comprised of different correlated random walks, as well as real foraging trajectories of little penguins (Eudyptula minor) obtained by global-positioning-system telemetry. Our results show that the modelling procedure correctly classified 92.5% of all individual location observations in the synthetic trajectories, demonstrating reasonable ability to successfully discriminate behavioural modes. Most individual little penguins were found to exhibit three unique behavioural states (resting, commuting/active searching, area-restricted foraging), with variation in the timing and locations of observations apparently related to ambient light, bathymetry, and proximity to coastlines and river mouths. Addition of k-means clustering extends the utility of behavioural change point analysis, by providing a simple means through which the behaviours inferred for the location observations comprising individual movement trajectories can be objectively classified. PMID:25922935

Extending the Functionality of Behavioural Change-Point Analysis with k-Means Clustering: A Case Study with the Little Penguin (Eudyptula minor).

PubMed

Zhang, Jingjing; O'Reilly, Kathleen M; Perry, George L W; Taylor, Graeme A; Dennis, Todd E

2015-01-01

We present a simple framework for classifying mutually exclusive behavioural states within the geospatial lifelines of animals. This method involves use of three sequentially applied statistical procedures: (1) behavioural change point analysis to partition movement trajectories into discrete bouts of same-state behaviours, based on abrupt changes in the spatio-temporal autocorrelation structure of movement parameters; (2) hierarchical multivariate cluster analysis to determine the number of different behavioural states; and (3) k-means clustering to classify inferred bouts of same-state location observations into behavioural modes. We demonstrate application of the method by analysing synthetic trajectories of known 'artificial behaviours' comprised of different correlated random walks, as well as real foraging trajectories of little penguins (Eudyptula minor) obtained by global-positioning-system telemetry. Our results show that the modelling procedure correctly classified 92.5% of all individual location observations in the synthetic trajectories, demonstrating reasonable ability to successfully discriminate behavioural modes. Most individual little penguins were found to exhibit three unique behavioural states (resting, commuting/active searching, area-restricted foraging), with variation in the timing and locations of observations apparently related to ambient light, bathymetry, and proximity to coastlines and river mouths. Addition of k-means clustering extends the utility of behavioural change point analysis, by providing a simple means through which the behaviours inferred for the location observations comprising individual movement trajectories can be objectively classified.

Brownian dynamics of confined rigid bodies

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

Delong, Steven; Balboa Usabiaga, Florencio; Donev, Aleksandar, E-mail: donev@courant.nyu.edu

2015-10-14

We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust, space efficient, and easy to accumulate. We construct a system of overdamped Langevin equations in the quaternion representation that accounts for hydrodynamic effects, preserves the unit-norm constraint on the quaternion, and is time reversible with respect to the Gibbs-Boltzmann distribution at equilibrium. We introduce two schemes for temporal integration of the overdamped Langevin equations of motion, one based on the Fixman midpoint method and the othermore » based on a random finite difference approach, both of which ensure that the correct stochastic drift term is captured in a computationally efficient way. We study several examples of rigid colloidal particles diffusing near a no-slip boundary and demonstrate the importance of the choice of tracking point on the measured translational mean square displacement (MSD). We examine the average short-time as well as the long-time quasi-two-dimensional diffusion coefficient of a rigid particle sedimented near a bottom wall due to gravity. For several particle shapes, we find a choice of tracking point that makes the MSD essentially linear with time, allowing us to estimate the long-time diffusion coefficient efficiently using a Monte Carlo method. However, in general, such a special choice of tracking point does not exist, and numerical techniques for simulating long trajectories, such as the ones we introduce here, are necessary to study diffusion on long time scales.« less

Analytical modeling of operating characteristics of premixing-prevaporizing fuel-air mixing passages. Volume 1: Analysis and results

NASA Technical Reports Server (NTRS)

Anderson, O. L.; Chiappetta, L. M.; Edwards, D. E.; Mcvey, J. B.

1982-01-01

A model for predicting the distribution of liquid fuel droplets and fuel vapor in premixing-prevaporizing fuel-air mixing passages of the direct injection type is reported. This model consists of three computer programs; a calculation of the two dimensional or axisymmetric air flow field neglecting the effects of fuel; a calculation of the three dimensional fuel droplet trajectories and evaporation rates in a known, moving air flow; a calculation of fuel vapor diffusing into a moving three dimensional air flow with source terms dependent on the droplet evaporation rates. The fuel droplets are treated as individual particle classes each satisfying Newton's law, a heat transfer, and a mass transfer equation. This fuel droplet model treats multicomponent fuels and incorporates the physics required for the treatment of elastic droplet collisions, droplet shattering, droplet coalescence and droplet wall interactions. The vapor diffusion calculation treats three dimensional, gas phase, turbulent diffusion processes. The analysis includes a model for the autoignition of the fuel air mixture based upon the rate of formation of an important intermediate chemical species during the preignition period.

Transport Coefficients from Large Deviation Functions

NASA Astrophysics Data System (ADS)

Gao, Chloe; Limmer, David

2017-10-01

We describe a method for computing transport coefficients from the direct evaluation of large deviation function. This method is general, relying on only equilibrium fluctuations, and is statistically efficient, employing trajectory based importance sampling. Equilibrium fluctuations of molecular currents are characterized by their large deviation functions, which is a scaled cumulant generating function analogous to the free energy. A diffusion Monte Carlo algorithm is used to evaluate the large deviation functions, from which arbitrary transport coefficients are derivable. We find significant statistical improvement over traditional Green-Kubo based calculations. The systematic and statistical errors of this method are analyzed in the context of specific transport coefficient calculations, including the shear viscosity, interfacial friction coefficient, and thermal conductivity.

Chaotic Lagrangian models for turbulent relative dispersion.

PubMed

Lacorata, Guglielmo; Vulpiani, Angelo

2017-04-01

A deterministic multiscale dynamical system is introduced and discussed as a prototype model for relative dispersion in stationary, homogeneous, and isotropic turbulence. Unlike stochastic diffusion models, here trajectory transport and mixing properties are entirely controlled by Lagrangian chaos. The anomalous "sweeping effect," a known drawback common to kinematic simulations, is removed through the use of quasi-Lagrangian coordinates. Lagrangian dispersion statistics of the model are accurately analyzed by computing the finite-scale Lyapunov exponent (FSLE), which is the optimal measure of the scaling properties of dispersion. FSLE scaling exponents provide a severe test to decide whether model simulations are in agreement with theoretical expectations and/or observation. The results of our numerical experiments cover a wide range of "Reynolds numbers" and show that chaotic deterministic flows can be very efficient, and numerically low-cost, models of turbulent trajectories in stationary, homogeneous, and isotropic conditions. The mathematics of the model is relatively simple, and, in a geophysical context, potential applications may regard small-scale parametrization issues in general circulation models, mixed layer, and/or boundary layer turbulence models as well as Lagrangian predictability studies.

Swimming path statistics of an active Brownian particle with time-dependent self-propulsion

NASA Astrophysics Data System (ADS)

Babel, S.; ten Hagen, B.; Löwen, H.

2014-02-01

Typically, in the description of active Brownian particles, a constant effective propulsion force is assumed, which is then subjected to fluctuations in orientation and translation, leading to a persistent random walk with an enlarged long-time diffusion coefficient. Here, we generalize previous results for the swimming path statistics to a time-dependent, and thus in many situations more realistic, propulsion which is a prescribed input. We analytically calculate both the noise-free and the noise-averaged trajectories for time-periodic propulsion under the action of an additional torque. In the deterministic case, such an oscillatory microswimmer moves on closed paths that can be much more complicated than the commonly observed straight lines and circles. When exposed to random fluctuations, the mean trajectories turn out to be self-similar curves which bear the characteristics of their noise-free counterparts. Furthermore, we consider a propulsion force which scales in time t as ∝tα (with α = 0,1,2, …) and analyze the resulting superdiffusive behavior. Our predictions are verifiable for diffusiophoretic artificial microswimmers with prescribed propulsion protocols.

Chaotic Lagrangian models for turbulent relative dispersion

NASA Astrophysics Data System (ADS)

Lacorata, Guglielmo; Vulpiani, Angelo

2017-04-01

A deterministic multiscale dynamical system is introduced and discussed as a prototype model for relative dispersion in stationary, homogeneous, and isotropic turbulence. Unlike stochastic diffusion models, here trajectory transport and mixing properties are entirely controlled by Lagrangian chaos. The anomalous "sweeping effect," a known drawback common to kinematic simulations, is removed through the use of quasi-Lagrangian coordinates. Lagrangian dispersion statistics of the model are accurately analyzed by computing the finite-scale Lyapunov exponent (FSLE), which is the optimal measure of the scaling properties of dispersion. FSLE scaling exponents provide a severe test to decide whether model simulations are in agreement with theoretical expectations and/or observation. The results of our numerical experiments cover a wide range of "Reynolds numbers" and show that chaotic deterministic flows can be very efficient, and numerically low-cost, models of turbulent trajectories in stationary, homogeneous, and isotropic conditions. The mathematics of the model is relatively simple, and, in a geophysical context, potential applications may regard small-scale parametrization issues in general circulation models, mixed layer, and/or boundary layer turbulence models as well as Lagrangian predictability studies.

Estimating the Diffusion Coefficients of Sugars Using Diffusion Experiments in Agar-Gel and Computer Simulations.

PubMed

Miyamoto, Shuichi; Atsuyama, Kenji; Ekino, Keisuke; Shin, Takashi

2018-01-01

The isolation of useful microbes is one of the traditional approaches for the lead generation in drug discovery. As an effective technique for microbe isolation, we recently developed a multidimensional diffusion-based gradient culture system of microbes. In order to enhance the utility of the system, it is favorable to have diffusion coefficients of nutrients such as sugars in the culture medium beforehand. We have, therefore, built a simple and convenient experimental system that uses agar-gel to observe diffusion. Next, we performed computer simulations-based on random-walk concepts-of the experimental diffusion system and derived correlation formulas that relate observable diffusion data to diffusion coefficients. Finally, we applied these correlation formulas to our experimentally-determined diffusion data to estimate the diffusion coefficients of sugars. Our values for these coefficients agree reasonably well with values published in the literature. The effectiveness of our simple technique, which has elucidated the diffusion coefficients of some molecules which are rarely reported (e.g., galactose, trehalose, and glycerol) is demonstrated by the strong correspondence between the literature values and those obtained in our experiments.

Trajectories of dental anxiety in a birth cohort

PubMed Central

Thomson, W. M.; Broadbent, J. M.; Locker, D.; Poulton, R.

2010-01-01

Objective To examine predictors of dental anxiety trajectories in a longitudinal study of New Zealanders. Methods Prospective study of a complete birth cohort born in 1972/73 in Dunedin, New Zealand, with dental anxiety scale (DAS) scores and dental utilization determined at ages 15, 18, 26 and 32 years. Personality traits were assessed at a superfactor and (more fine-grained) subscale level via the Multidimensional Personality Questionnaire at age 18 years. Group-based trajectory analysis was used to identify dental anxiety trajectories. Results DAS scores from at least three assessments were available for 828 participants. Six dental anxiety trajectories were observed: stable nonanxious low (39.6%); stable nonanxious medium (37.9%); recovery (1.6%); adult-onset anxious (7.7%); stable anxious (7.2%) and adolescent-onset anxious (5.9%). Multivariate analysis showed that males and those with higher DMFS at age 15 years were more likely to be in the stable nonanxious low trajectory group. Membership of the stable nonanxious medium group was predicted by the dental caries experience at age 15 years. Participants who had lost one or more teeth between ages 26 and 32 years had almost twice the relative risk for membership of the adult-onset anxious group. Personality traits predicted group membership. Specifically, high scorers (via median split) on the ‘stress reaction’ subscale had over twice the risk of being in the stable anxious group; low scorers on the traditionalism subscale were more likely to be members of the recovery trajectory group; and high scorers on the ‘social closeness’ subscale had half the risk of being in the stable anxious group. Dental caries experience at age 5 years was also a predictor for the stable anxious group. Membership of the late-adolescent-onset anxious group was predicted by higher dental caries experience by age 15 years, but none of the other predictors was significant. Conclusion Six discrete trajectories of dental anxiety have been observed. Some trajectories (totalling more than 90% of the cohort) had clear associations with external influences, but others were more strongly associated with characteristics such as personality traits. A mix of both influences was observed with only the stable anxious dental anxiety trajectory. PMID:19508269

Non-local transport in turbulent MHD convection

NASA Technical Reports Server (NTRS)

Miesch, Mark; Brandenburg, Axel; Zweibel, Ellen; Toomre, Juri

1995-01-01

The nonlocal non-diffusive transport of passive scalars in turbulent magnetohydrodynamic (MHD) convection is investigated using transilient matrices. These matrices describe the probability that a tracer particle beginning at one position in a flow will be advected to another position after some time. A method for the calculation of these matrices from simulation data which involves following the trajectories of passive tracer particles and calculating their transport statistics, is presented. The method is applied to study the transport in several simulations of turbulent, rotating, three dimensional compressible, penetrative MDH convection. Transport coefficients and other diagnostics are used to quantify the transport, which is found to resemble advection more closely than diffusion. Some of the results are found to have direct relevance to other physical problems, such as the light element depletion in sun-type stars. The large kurtosis found for downward moving particles at the base of the convection zone implies several extreme events.

Engine Damage to a NASA DC-8-72 Airplane From a High-Altitude Encounter With a Diffuse Volcanic Ash Cloud

NASA Technical Reports Server (NTRS)

Grindle, Thomas J.; Burcham, Frank W., Jr.

2003-01-01

The National Aeronautics and Space Administration (NASA) DC-8 airborne sciences research airplane inadvertently flew through a diffuse volcanic ash cloud of the Mt. Hekla volcano in February 2000 during a flight from Edwards Air Force Base (Edwards, California) to Kiruna, Sweden. Although the ash plume was not visible to the flight crew, sensitive research experiments and instruments detected it. In-flight performance checks and postflight visual inspections revealed no damage to the airplane or engine first-stage fan blades; subsequent detailed examination of the engines revealed clogged turbine cooling air passages. The engines were removed and overhauled. This paper presents volcanic ash plume analysis, trajectory from satellites, analysis of ash particles collected in cabin air heat exchanger filters and removed from the engines, and data from onboard instruments and engine conditions.

Interactive, computer-assisted tracking of speckle trajectories in fluorescence microscopy: application to actin polymerization and membrane fusion.

PubMed

Smith, Matthew B; Karatekin, Erdem; Gohlke, Andrea; Mizuno, Hiroaki; Watanabe, Naoki; Vavylonis, Dimitrios

2011-10-05

Analysis of particle trajectories in images obtained by fluorescence microscopy reveals biophysical properties such as diffusion coefficient or rates of association and dissociation. Particle tracking and lifetime measurement is often limited by noise, large mobilities, image inhomogeneities, and path crossings. We present Speckle TrackerJ, a tool that addresses some of these challenges using computer-assisted techniques for finding positions and tracking particles in different situations. A dynamic user interface assists in the creation, editing, and refining of particle tracks. The following are results from application of this program: 1), Tracking single molecule diffusion in simulated images. The shape of the diffusing marker on the image changes from speckle to cloud, depending on the relationship of the diffusion coefficient to the camera exposure time. We use these images to illustrate the range of diffusion coefficients that can be measured. 2), We used the program to measure the diffusion coefficient of capping proteins in the lamellipodium. We found values ∼0.5 μm(2)/s, suggesting capping protein association with protein complexes or the membrane. 3), We demonstrate efficient measuring of appearance and disappearance of EGFP-actin speckles within the lamellipodium of motile cells that indicate actin monomer incorporation into the actin filament network. 4), We marked appearance and disappearance events of fluorescently labeled vesicles to supported lipid bilayers and tracked single lipids from the fused vesicle on the bilayer. This is the first time, to our knowledge, that vesicle fusion has been detected with single molecule sensitivity and the program allowed us to perform a quantitative analysis. 5), By discriminating between undocking and fusion events, dwell times for vesicle fusion after vesicle docking to membranes can be measured. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Determination of the Trajectory of Ballistic Missiles Using a Dense GPS Array

NASA Astrophysics Data System (ADS)

Heki, K.; Ozeki, M.

2009-12-01

The dense array of ~1000 Global Positioning System (GPS) receivers in Japan provides useful information on atmosphere and ionosphere in terms of delays of microwaves in propagation media. Here we introduce its brand-new application, determination of the trajectories of ballistic missiles by using their electron depletion signatures in ionosphere. Booker (1961) first detected F-region ion depletion associated with a missile passage. Later, formation of an ionospheric hole by the launch of Skylab was observed, and Mendillo et al. (1975) attributed the electron depletion to the water molecules in the rocket exhaust. In Japan, ionospheric depletion after the launch of the H-IIA rocket was observed at GPS receivers in southern Japan using differences in phases between the two carrier frequencies L1 and L2 (Furuya & Heki, 2008). The so-called Taepodong-1, and -2 (the North Korean government claims that they successfully launched satellites), ballistic missiles with liquid fuel engines, were launched from Musudanri, North Korea, in August 1998, and April 2009, respectively. Their first stage engines splashed down onto the Japan Sea, and their second stage engines flew over northeastern Japan and reached the Pacific Ocean. We investigated GPS data before and after the launches, and detected that linear electron depletion areas appear in the northern part of the Japan Sea (~300 km east of the launch pad) approximately six minutes after the launch. Such electron depletion occurs as a result of exchange of positive charges between oxygen ions and water molecules, and dissociative recombination of water with electrons. The ionospheric hole rapidly grows and gradually decays as the water molecules diffuse. By comparing the numerical simulation results of ionospheric hole formation (water diffusion and chemical reaction) and the observed change in ionospheric total electron content (TEC), we conclude that the Taepodong-1 exhaust included water molecules ~0.5 percent of those in the H-IIA rocket. Taepodong-2, on the other hand, made a larger and longer-lasting hole and water molecules in its exhaust appear to be eight times as many as in Taepodong-1. This perhaps reflects improvement in thrust of the Taepodong series. We estimated the most likely trajectory of the Taepodong-2 constraining the coordinates of the launch pad and splashdown point. The missile reached the ionospheric F region in six minutes after the launch and flew above northeastern Japan about 9-10 minutes after the launch.

Lagrangian predictability characteristics of an Ocean Model

NASA Astrophysics Data System (ADS)

Lacorata, Guglielmo; Palatella, Luigi; Santoleri, Rosalia

2014-11-01

The Mediterranean Forecasting System (MFS) Ocean Model, provided by INGV, has been chosen as case study to analyze Lagrangian trajectory predictability by means of a dynamical systems approach. To this regard, numerical trajectories are tested against a large amount of Mediterranean drifter data, used as sample of the actual tracer dynamics across the sea. The separation rate of a trajectory pair is measured by computing the Finite-Scale Lyapunov Exponent (FSLE) of first and second kind. An additional kinematic Lagrangian model (KLM), suitably treated to avoid "sweeping"-related problems, has been nested into the MFS in order to recover, in a statistical sense, the velocity field contributions to pair particle dispersion, at mesoscale level, smoothed out by finite resolution effects. Some of the results emerging from this work are: (a) drifter pair dispersion displays Richardson's turbulent diffusion inside the [10-100] km range, while numerical simulations of MFS alone (i.e., without subgrid model) indicate exponential separation; (b) adding the subgrid model, model pair dispersion gets very close to observed data, indicating that KLM is effective in filling the energy "mesoscale gap" present in MFS velocity fields; (c) there exists a threshold size beyond which pair dispersion becomes weakly sensitive to the difference between model and "real" dynamics; (d) the whole methodology here presented can be used to quantify model errors and validate numerical current fields, as far as forecasts of Lagrangian dispersion are concerned.

Monte Carlo simulations of protein micropatterning in biomembranes: effects of immobile sticky obstacles

NASA Astrophysics Data System (ADS)

Arnold, Andreas M.; Sevcsik, Eva; Schütz, Gerhard J.

2016-09-01

Single molecule trajectories of lipids and proteins can yield valuable information about the nanoscopic organization of the plasma membrane itself. The interpretation of such trajectories, however, is complicated, as the mobility of molecules can be affected by the presence of immobile obstacles, and the transient binding of the tracers to these obstacles. We have previously developed a micropatterning approach that allows for immobilizing a plasma membrane protein and probing the diffusional behavior of a putative interaction partner in living cells. Here, we provide guidelines on how this micropatterning approach can be extended to quantify interaction parameters between plasma membrane constituents in their natural environment. We simulated a patterned membrane system and evaluated the effect of different surface densities of patterned immobile obstacles on the relative mobility as well as the surface density of diffusing tracers. In the case of inert obstacles, the size of the obstacle can be assessed from its surface density at the percolation threshold, which in turn can be extracted from the diffusion behavior of the tracer. For sticky obstacles, 2D dissociation constants can be determined from the tracer diffusion or surface density.

Revealing the cerebello-ponto-hypothalamic pathway in the human brain.

PubMed

Kamali, Arash; Karbasian, Niloofar; Rabiei, Pejman; Cano, Andres; Riascos, Roy F; Tandon, Nitin; Arevalo, Octavio; Ocasio, Laura; Younes, Kyan; Khayat-Khoei, Mahsa; Mirbagheri, Saeedeh; Hasan, Khader M

2018-06-11

The cerebellum is shown to be involved in some limbic functions of the human brain such as emotion and affect. The major connection of the cerebellum with the limbic system is known to be through the cerebello-hypothalamic pathways. The consensus is that the projections from the cerebellar nuclei to the limbic system, and particularly the hypothalamus, or from the hypothalamus to the cerebellar nuclei, are through multisynaptic pathways in the bulbar reticular formation. The detailed anatomy of the pathways responsible for mediating these responses, however, is yet to be determined. Diffusion tensor imaging may be helpful in better visualizing the surgical anatomy of the cerebello-ponto-hypothalamic (CPH) pathway. This study aimed to investigate the utility of high-spatial-resolution diffusion tensor tractography for mapping the trajectory of the CPH tract in the human brain. Fifteen healthy adults were studied. We delineated, for the first time, the detailed trajectory of the CPH tract of the human brain in fifteen normal adult subjects using high-spatial-resolution diffusion tensor tractography. We further revealed the close relationship of the CPH tract with the optic tract, temporo-pontine tract, amygdalofugal tract and the fornix in the human brain. Copyright © 2018 Elsevier B.V. All rights reserved.

Adaptive Trajectory Prediction Algorithm for Climbing Flights

NASA Technical Reports Server (NTRS)

Schultz, Charles Alexander; Thipphavong, David P.; Erzberger, Heinz

2012-01-01

Aircraft climb trajectories are difficult to predict, and large errors in these predictions reduce the potential operational benefits of some advanced features for NextGen. The algorithm described in this paper improves climb trajectory prediction accuracy by adjusting trajectory predictions based on observed track data. It utilizes rate-of-climb and airspeed measurements derived from position data to dynamically adjust the aircraft weight modeled for trajectory predictions. In simulations with weight uncertainty, the algorithm is able to adapt to within 3 percent of the actual gross weight within two minutes of the initial adaptation. The root-mean-square of altitude errors for five-minute predictions was reduced by 73 percent. Conflict detection performance also improved, with a 15 percent reduction in missed alerts and a 10 percent reduction in false alerts. In a simulation with climb speed capture intent and weight uncertainty, the algorithm improved climb trajectory prediction accuracy by up to 30 percent and conflict detection performance, reducing missed and false alerts by up to 10 percent.

A Radiation Chemistry Code Based on the Greens Functions of the Diffusion Equation

NASA Technical Reports Server (NTRS)

Plante, Ianik; Wu, Honglu

2014-01-01

Ionizing radiation produces several radiolytic species such as.OH, e-aq, and H. when interacting with biological matter. Following their creation, radiolytic species diffuse and chemically react with biological molecules such as DNA. Despite years of research, many questions on the DNA damage by ionizing radiation remains, notably on the indirect effect, i.e. the damage resulting from the reactions of the radiolytic species with DNA. To simulate DNA damage by ionizing radiation, we are developing a step-by-step radiation chemistry code that is based on the Green's functions of the diffusion equation (GFDE), which is able to follow the trajectories of all particles and their reactions with time. In the recent years, simulations based on the GFDE have been used extensively in biochemistry, notably to simulate biochemical networks in time and space and are often used as the "gold standard" to validate diffusion-reaction theories. The exact GFDE for partially diffusion-controlled reactions is difficult to use because of its complex form. Therefore, the radial Green's function, which is much simpler, is often used. Hence, much effort has been devoted to the sampling of the radial Green's functions, for which we have developed a sampling algorithm This algorithm only yields the inter-particle distance vector length after a time step; the sampling of the deviation angle of the inter-particle vector is not taken into consideration. In this work, we show that the radial distribution is predicted by the exact radial Green's function. We also use a technique developed by Clifford et al. to generate the inter-particle vector deviation angles, knowing the inter-particle vector length before and after a time step. The results are compared with those predicted by the exact GFDE and by the analytical angular functions for free diffusion. This first step in the creation of the radiation chemistry code should help the understanding of the contribution of the indirect effect in the formation of DNA damage and double-strand breaks.

Spatio-Temporal Constrained Human Trajectory Generation from the PIR Motion Detector Sensor Network Data: A Geometric Algebra Approach

PubMed Central

Yu, Zhaoyuan; Yuan, Linwang; Luo, Wen; Feng, Linyao; Lv, Guonian

2015-01-01

Passive infrared (PIR) motion detectors, which can support long-term continuous observation, are widely used for human motion analysis. Extracting all possible trajectories from the PIR sensor networks is important. Because the PIR sensor does not log location and individual information, none of the existing methods can generate all possible human motion trajectories that satisfy various spatio-temporal constraints from the sensor activation log data. In this paper, a geometric algebra (GA)-based approach is developed to generate all possible human trajectories from the PIR sensor network data. Firstly, the representation of the geographical network, sensor activation response sequences and the human motion are represented as algebraic elements using GA. The human motion status of each sensor activation are labeled using the GA-based trajectory tracking. Then, a matrix multiplication approach is developed to dynamically generate the human trajectories according to the sensor activation log and the spatio-temporal constraints. The method is tested with the MERL motion database. Experiments show that our method can flexibly extract the major statistical pattern of the human motion. Compared with direct statistical analysis and tracklet graph method, our method can effectively extract all possible trajectories of the human motion, which makes it more accurate. Our method is also likely to provides a new way to filter other passive sensor log data in sensor networks. PMID:26729123

Spatio-Temporal Constrained Human Trajectory Generation from the PIR Motion Detector Sensor Network Data: A Geometric Algebra Approach.

PubMed

Yu, Zhaoyuan; Yuan, Linwang; Luo, Wen; Feng, Linyao; Lv, Guonian

2015-12-30

Passive infrared (PIR) motion detectors, which can support long-term continuous observation, are widely used for human motion analysis. Extracting all possible trajectories from the PIR sensor networks is important. Because the PIR sensor does not log location and individual information, none of the existing methods can generate all possible human motion trajectories that satisfy various spatio-temporal constraints from the sensor activation log data. In this paper, a geometric algebra (GA)-based approach is developed to generate all possible human trajectories from the PIR sensor network data. Firstly, the representation of the geographical network, sensor activation response sequences and the human motion are represented as algebraic elements using GA. The human motion status of each sensor activation are labeled using the GA-based trajectory tracking. Then, a matrix multiplication approach is developed to dynamically generate the human trajectories according to the sensor activation log and the spatio-temporal constraints. The method is tested with the MERL motion database. Experiments show that our method can flexibly extract the major statistical pattern of the human motion. Compared with direct statistical analysis and tracklet graph method, our method can effectively extract all possible trajectories of the human motion, which makes it more accurate. Our method is also likely to provides a new way to filter other passive sensor log data in sensor networks.

Altitude-dependent Drift of a Chemical Release Cloud at Middle Latitudes

NASA Astrophysics Data System (ADS)

Pedersen, T.; Holmes, J. M.; Sutton, E. K.

2017-12-01

A chemical release experiment conducted at the White Sands Missile Range in February 2015 consisted of firing of three identical canisters at different altitudes along a near-vertical trajectory, creating a large structured cloud after diffusion and expansion of the three initial dispersals. Dedicated optical observations from near the launch site and a remote site allow determination of the position and motion of the extended optical cloud as a function of time, while photographs captured and posted by members of the general public provide additional look angles to constrain the cloud shape in more detail. We compare the observed drift and evolution of the cloud with empirical and theoretical models of the neutral winds to examine the altitudinal shear in the neutral winds and their effects on the motion and shape of the extended optical cloud.

Actin-based motility of Listeria: Right-handed helical trajectories

NASA Astrophysics Data System (ADS)

Rangarajan, Murali

2012-06-01

Bacteria such as Listeria monocytogenes recruit cellular machinery to move in and between cells. Understanding the mechanism of motility, including force and torque generation and the resultant displacements, holds keys to numerous applications in medicine and biosensing. In this work, a simple back-of-the-envelope calculation is presented to illustrate that a biomechanical model of actin-based motility of a rigid surface through persistently attached filaments propelled by affinity-modulated molecular motors can produce a right-handed helical trajectory consistent with experimental observations. The implications of the mechanism to bacterial motility are discussed.

Ballistic projectile trajectory determining system

DOEpatents

Karr, Thomas J.

1997-01-01

A computer controlled system determines the three-dimensional trajectory of a ballistic projectile. To initialize the system, predictions of state parameters for a ballistic projectile are received at an estimator. The estimator uses the predictions of the state parameters to estimate first trajectory characteristics of the ballistic projectile. A single stationary monocular sensor then observes the actual first trajectory characteristics of the ballistic projectile. A comparator generates an error value related to the predicted state parameters by comparing the estimated first trajectory characteristics of the ballistic projectile with the observed first trajectory characteristics of the ballistic projectile. If the error value is equal to or greater than a selected limit, the predictions of the state parameters are adjusted. New estimates for the trajectory characteristics of the ballistic projectile are made and are then compared with actual observed trajectory characteristics. This process is repeated until the error value is less than the selected limit. Once the error value is less than the selected limit, a calculator calculates trajectory characteristics such a the origin and destination of the ballistic projectile.

Passivity/Lyapunov based controller design for trajectory tracking of flexible joint manipulators

NASA Technical Reports Server (NTRS)

Sicard, Pierre; Wen, John T.; Lanari, Leonardo

1992-01-01

A passivity and Lyapunov based approach for the control design for the trajectory tracking problem of flexible joint robots is presented. The basic structure of the proposed controller is the sum of a model-based feedforward and a model-independent feedback. Feedforward selection and solution is analyzed for a general model for flexible joints, and for more specific and practical model structures. Passivity theory is used to design a motor state-based controller in order to input-output stabilize the error system formed by the feedforward. Observability conditions for asymptotic stability are stated and verified. In order to accommodate for modeling uncertainties and to allow for the implementation of a simplified feedforward compensation, the stability of the system is analyzed in presence of approximations in the feedforward by using a Lyapunov based robustness analysis. It is shown that under certain conditions, e.g., the desired trajectory is varying slowly enough, stability is maintained for various approximations of a canonical feedforward.

High Speed Videometric Monitoring of Rock Breakage

NASA Astrophysics Data System (ADS)

Allemand, J.; Shortis, M. R.; Elmouttie, M. K.

2018-05-01

Estimation of rock breakage characteristics plays an important role in optimising various industrial and mining processes used for rock comminution. Although little research has been undertaken into 3D photogrammetric measurement of the progeny kinematics, there is promising potential to improve the efficacy of rock breakage characterisation. In this study, the observation of progeny kinematics was conducted using a high speed, stereo videometric system based on laboratory experiments with a drop weight impact testing system. By manually tracking individual progeny through the captured video sequences, observed progeny coordinates can be used to determine 3D trajectories and velocities, supporting the idea that high speed video can be used for rock breakage characterisation purposes. An analysis of the results showed that the high speed videometric system successfully observed progeny trajectories and showed clear projection of the progeny away from the impact location. Velocities of the progeny could also be determined based on the trajectories and the video frame rate. These results were obtained despite the limitations of the photogrammetric system and experiment processes observed in this study. Accordingly there is sufficient evidence to conclude that high speed videometric systems are capable of observing progeny kinematics from drop weight impact tests. With further optimisation of the systems and processes used, there is potential for improving the efficacy of rock breakage characterisation from measurements with high speed videometric systems.

Disturbance observer based model predictive control for accurate atmospheric entry of spacecraft

NASA Astrophysics Data System (ADS)

Wu, Chao; Yang, Jun; Li, Shihua; Li, Qi; Guo, Lei

2018-05-01

Facing the complex aerodynamic environment of Mars atmosphere, a composite atmospheric entry trajectory tracking strategy is investigated in this paper. External disturbances, initial states uncertainties and aerodynamic parameters uncertainties are the main problems. The composite strategy is designed to solve these problems and improve the accuracy of Mars atmospheric entry. This strategy includes a model predictive control for optimized trajectory tracking performance, as well as a disturbance observer based feedforward compensation for external disturbances and uncertainties attenuation. 500-run Monte Carlo simulations show that the proposed composite control scheme achieves more precise Mars atmospheric entry (3.8 km parachute deployment point distribution error) than the baseline control scheme (8.4 km) and integral control scheme (5.8 km).

Trajectory mapping of middle atmospheric water vapor by a mini network of NDACC instruments

NASA Astrophysics Data System (ADS)

Lainer, M.; Kämpfer, N.; Tschanz, B.; Nedoluha, G. E.; Ka, S.; Oh, J. J.

2015-08-01

The important task to observe the global coverage of middle atmospheric trace gases like water vapor or ozone usually is accomplished by satellites. Climate and atmospheric studies rely upon the knowledge of trace gas distributions throughout the stratosphere and mesosphere. Many of these gases are currently measured from satellites, but it is not clear whether this capability will be maintained in the future. This could lead to a significant knowledge gap of the state of the atmosphere. We explore the possibilities of mapping middle atmospheric water vapor in the Northern Hemisphere by using Lagrangian trajectory calculations and water vapor profile data from a small network of five ground-based microwave radiometers. Four of them are operated within the frame of NDACC (Network for the Detection of Atmospheric Composition Change). Keeping in mind that the instruments are based on different hardware and calibration setups, a height-dependent bias of the retrieved water vapor profiles has to be expected among the microwave radiometers. In order to correct and harmonize the different data sets, the Microwave Limb Sounder (MLS) on the Aura satellite is used to serve as a kind of traveling standard. A domain-averaging TM (trajectory mapping) method is applied which simplifies the subsequent validation of the quality of the trajectory-mapped water vapor distribution towards direct satellite observations. Trajectories are calculated forwards and backwards in time for up to 10 days using 6 hourly meteorological wind analysis fields. Overall, a total of four case studies of trajectory mapping in different meteorological regimes are discussed. One of the case studies takes place during a major sudden stratospheric warming (SSW) accompanied by the polar vortex breakdown; a second takes place after the reformation of stable circulation system. TM cases close to the fall equinox and June solstice event from the year 2012 complete the study, showing the high potential of a network of ground-based remote sensing instruments to synthesize hemispheric maps of water vapor.

Trajectory mapping of middle atmospheric water vapor by a mini network of NDACC instruments

NASA Astrophysics Data System (ADS)

Lainer, M.; Kämpfer, N.; Tschanz, B.; Nedoluha, G. E.; Ka, S.; Oh, J. J.

2015-04-01

The important task to observe the global coverage of middle atmospheric trace gases like water vapor or ozone usually is accomplished by satellites. Climate and atmospheric studies rely upon the knowledge of trace gas distributions throughout the stratosphere and mesosphere. Many of these gases are currently measured from satellites, but it is not clear whether this capability will be maintained in the future. This could lead to a significant knowledge gap of the state of the atmosphere. We explore the possibilities of mapping middle atmospheric water vapor in the Northern Hemisphere by using Lagrangian trajectory calculations and water vapor profile data from a small network of five ground-based microwave radiometers. Four of them are operated within the frame of NDACC (Network for the Detection of Atmospheric Composition Change). Keeping in mind that the instruments are based on different hardware and calibration setups, a height dependent bias of the retrieved water vapor profiles has to be expected among the microwave radiometers. In order to correct and harmonize the different datasets, the Microwave Limb Sounder (MLS) on the Aura satellite is used to serve as a kind of travelling standard. A domain-averaging TM (trajectory mapping) method is applied which simplifies the subsequent validation of the quality of the trajectory mapped water vapor distribution towards direct satellite observations. Trajectories are calculated forwards and backwards in time for up to 10 days using 6 hourly meteorological wind analysis fields. Overall, a total of four case studies of trajectory mapping in different meteorological regimes are discussed. One of the case studies takes place during a major sudden stratospheric warming (SSW) accompanied by the polar vortex breakdown, a second takes place after the reformation of stable circulation system. TM cases close to the fall equinox and June solstice event from the year 2012 complete the study, showing the high potential of a network of ground-based remote sensing instruments to synthesize hemispheric maps of water vapor.

Investigating the longer-term health consequences of work-related injuries among youth.

PubMed

Koehoorn, Mieke; Breslin, F Curtis; Xu, Fan

2008-11-01

To investigate the longer-term health consequences of work injuries among youth aged 15-24 years using a population-based, longitudinal study (1991-2001) of merged health care and workers' compensation records. A group-based modeling approach was used (1) to identify unique trajectories of health care use defined by general practitioner visits among the study sample stratified by gender, and (2) to determine the injury factors that predict a youth's membership in a trajectory, adjusted for sociodemographic factors. Four long-term trajectories of health care use were identified among young injured workers, for both males and females. Similar trajectories were observed among a comparison, noninjured sample but the magnitude of health care use was consistently higher among the injured worker cohort, especially for females (attributable to general practitioner [GP] visits for symptoms, signs and ill-defined diagnoses), and a notable "spike" in health care use occurred in the year immediately after a work injury for both males and females that was not observed in the comparison population during the matched year (attributable to GP visits for musculoskeletal and injury diagnoses). For males, the type of work injury mattered with an increased odds of belonging to the higher health care trajectories associated with a musculoskeletal injury (odds ratio [OR] = 1.57, 95% CI = .76, 3.23; and OR = 1.61, 95% CI 1.08, 2.41 for the postinjury trajectories), adjusted for age, occupation, socioeconomic status, and geographic location. Persistent use of health care services may represent a cumulative burden of morbidity over the life course as a result of a work-related injury in general among young women and as a result of musculoskeletal injuries in particular among males.

Massively Parallel Simulations of Diffusion in Dense Polymeric Structures

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

Faulon, Jean-Loup, Wilcox, R.T.

1997-11-01

An original computational technique to generate close-to-equilibrium dense polymeric structures is proposed. Diffusion of small gases are studied on the equilibrated structures using massively parallel molecular dynamics simulations running on the Intel Teraflops (9216 Pentium Pro processors) and Intel Paragon(1840 processors). Compared to the current state-of-the-art equilibration methods this new technique appears to be faster by some orders of magnitude.The main advantage of the technique is that one can circumvent the bottlenecks in configuration space that inhibit relaxation in molecular dynamics simulations. The technique is based on the fact that tetravalent atoms (such as carbon and silicon) fit in themore » center of a regular tetrahedron and that regular tetrahedrons can be used to mesh the three-dimensional space. Thus, the problem of polymer equilibration described by continuous equations in molecular dynamics is reduced to a discrete problem where solutions are approximated by simple algorithms. Practical modeling applications include the constructing of butyl rubber and ethylene-propylene-dimer-monomer (EPDM) models for oxygen and water diffusion calculations. Butyl and EPDM are used in O-ring systems and serve as sealing joints in many manufactured objects. Diffusion coefficients of small gases have been measured experimentally on both polymeric systems, and in general the diffusion coefficients in EPDM are an order of magnitude larger than in butyl. In order to better understand the diffusion phenomena, 10, 000 atoms models were generated and equilibrated for butyl and EPDM. The models were submitted to a massively parallel molecular dynamics simulation to monitor the trajectories of the diffusing species.« less

Exploring the propagation of relativistic quantum wavepackets in the trajectory-based formulation

NASA Astrophysics Data System (ADS)

Tsai, Hung-Ming; Poirier, Bill

2016-03-01

In the context of nonrelativistic quantum mechanics, Gaussian wavepacket solutions of the time-dependent Schrödinger equation provide useful physical insight. This is not the case for relativistic quantum mechanics, however, for which both the Klein-Gordon and Dirac wave equations result in strange and counterintuitive wavepacket behaviors, even for free-particle Gaussians. These behaviors include zitterbewegung and other interference effects. As a potential remedy, this paper explores a new trajectory-based formulation of quantum mechanics, in which the wavefunction plays no role [Phys. Rev. X, 4, 040002 (2014)]. Quantum states are represented as ensembles of trajectories, whose mutual interaction is the source of all quantum effects observed in nature—suggesting a “many interacting worlds” interpretation. It is shown that the relativistic generalization of the trajectory-based formulation results in well-behaved free-particle Gaussian wavepacket solutions. In particular, probability density is positive and well-localized everywhere, and its spatial integral is conserved over time—in any inertial frame. Finally, the ensemble-averaged wavepacket motion is along a straight line path through spacetime. In this manner, the pathologies of the wave-based relativistic quantum theory, as applied to wavepacket propagation, are avoided.

Synthesis of asymmetric movement trajectories in timed rhythmic behaviour by means of frequency modulation.

PubMed

Waadeland, Carl Haakon

2017-01-01

Results from different empirical investigations on gestural aspects of timed rhythmic movements indicate that the production of asymmetric movement trajectories is a feature that seems to be a common characteristic of various performances of repetitive rhythmic patterns. The behavioural or neural origin of these asymmetrical trajectories is, however, not identified. In the present study we outline a theoretical model that is capable of producing syntheses of asymmetric movement trajectories documented in empirical investigations by Balasubramaniam et al. (2004). Characteristic qualities of the extension/flexion profiles in the observed asymmetric trajectories are reproduced, and we conduct an experiment similar to Balasubramaniam et al. (2004) to show that the empirically documented movement trajectories and our modelled approximations share the same spectral components. The model is based on an application of frequency modulated movements, and a theoretical interpretation offered by the model is to view paced rhythmic movements as a result of an unpaced movement being "stretched" and "compressed", caused by the presence of a metronome. We discuss our model construction within the framework of event-based and emergent timing, and argue that a change between these timing modes might be reflected by the strength of the modulation in our model. Copyright © 2016 Elsevier B.V. All rights reserved.

Scale-Invariant Transition Probabilities in Free Word Association Trajectories

PubMed Central

Costa, Martin Elias; Bonomo, Flavia; Sigman, Mariano

2009-01-01

Free-word association has been used as a vehicle to understand the organization of human thoughts. The original studies relied mainly on qualitative assertions, yielding the widely intuitive notion that trajectories of word associations are structured, yet considerably more random than organized linguistic text. Here we set to determine a precise characterization of this space, generating a large number of word association trajectories in a web implemented game. We embedded the trajectories in the graph of word co-occurrences from a linguistic corpus. To constrain possible transport models we measured the memory loss and the cycling probability. These two measures could not be reconciled by a bounded diffusive model since the cycling probability was very high (16% of order-2 cycles) implying a majority of short-range associations whereas the memory loss was very rapid (converging to the asymptotic value in ∼7 steps) which, in turn, forced a high fraction of long-range associations. We show that memory loss and cycling probabilities of free word association trajectories can be simultaneously accounted by a model in which transitions are determined by a scale invariant probability distribution. PMID:19826622

Lagrangian analysis of premixed turbulent combustion in hydrogen-air flames

NASA Astrophysics Data System (ADS)

Darragh, Ryan; Poludnenko, Alexei; Hamlington, Peter

2016-11-01

Lagrangian analysis has long been a tool used to analyze non-reacting turbulent flows, and has recently gained attention in the reacting flow and combustion communities. The approach itself allows one to separate local molecular effects, such as those due to reactions or diffusion, from turbulent advective effects along fluid pathlines, or trajectories. Accurate calculation of these trajectories can, however, be rather difficult due to the chaotic nature of turbulent flows and the added complexity of reactions. In order to determine resolution requirements and verify the numerical algorithm, extensive tests are described in this talk for prescribed steady, unsteady, and chaotic flows, as well as for direct numerical simulations (DNS) of non-reacting homogeneous isotropic turbulence. The Lagrangian analysis is then applied to DNS of premixed hydrogen-air flames at two different turbulence intensities for both single- and multi-step chemical mechanisms. Non-monotonic temperature and fuel-mass fraction evolutions are found to exist along trajectories passing through the flame brush. Such non-monotonicity is shown to be due to molecular diffusion resulting from large spatial gradients created by turbulent advection. This work was supported by the Air Force Office of Scientific Research (AFOSR) under Award No. FA9550-14-1-0273, and the Department of Defense (DoD) High Performance Computing Modernization Program (HPCMP) under a Frontier project award.

Self-Organizing Map With Time-Varying Structure to Plan and Control Artificial Locomotion.

PubMed

Araujo, Aluizio F R; Santana, Orivaldo V

2015-08-01

This paper presents an algorithm, self-organizing map-state trajectory generator (SOM-STG), to plan and control legged robot locomotion. The SOM-STG is based on an SOM with a time-varying structure characterized by constructing autonomously close-state trajectories from an arbitrary number of robot postures. Each trajectory represents a cyclical movement of the limbs of an animal. The SOM-STG was designed to possess important features of a central pattern generator, such as rhythmic pattern generation, synchronization between limbs, and swapping between gaits following a single command. The acquisition of data for SOM-STG is based on learning by demonstration in which the data are obtained from different demonstrator agents. The SOM-STG can construct one or more gaits for a simulated robot with six legs, can control the robot with any of the gaits learned, and can smoothly swap gaits. In addition, SOM-STG can learn to construct a state trajectory form observing an animal in locomotion. In this paper, a dog is the demonstrator agent.

Spontaneous symmetry breaking for geometrical trajectories of actin-based motility in three dimensions

NASA Astrophysics Data System (ADS)

Wen, Fu-Lai; Leung, Kwan-tai; Chen, Hsuan-Yi

2016-07-01

Actin-based motility is important for many cellular processes. In this article we extend our previous studies of an actin-propelled circular disk in two dimensions to an actin-propelled spherical bead in three dimensions. We find that for an achiral load the couplings between the motion of the load and the actin network induce a series of bifurcations, starting with a transition from rest to moving state, followed by a transition from straight to planar curves, and finally a further transition from motion in a plane to one with torsion. To address the intriguing, experimentally observed chiral motility of the bacterium Listeria monocytogenes, we also study the motility of a spherical load with a built-in chirality. For such a chiral load, stable circular trajectories are no longer found in numerical simulations. Instead, helical trajectories with handedness that depends on the chirality of the load are found. Our results reveal the relation between the symmetry of actin network and the trajectories of actin-propelled loads.

Cascading Walks Model for Human Mobility Patterns

PubMed Central

Han, Xiao-Pu; Wang, Xiang-Wen; Yan, Xiao-Yong; Wang, Bing-Hong

2015-01-01

Background Uncovering the mechanism behind the scaling laws and series of anomalies in human trajectories is of fundamental significance in understanding many spatio-temporal phenomena. Recently, several models, e.g. the explorations-returns model (Song et al., 2010) and the radiation model for intercity travels (Simini et al., 2012), have been proposed to study the origin of these anomalies and the prediction of human movements. However, an agent-based model that could reproduce most of empirical observations without priori is still lacking. Methodology/Principal Findings In this paper, considering the empirical findings on the correlations of move-lengths and staying time in human trips, we propose a simple model which is mainly based on the cascading processes to capture the human mobility patterns. In this model, each long-range movement activates series of shorter movements that are organized by the law of localized explorations and preferential returns in prescribed region. Conclusions/Significance Based on the numerical simulations and analytical studies, we show more than five statistical characters that are well consistent with the empirical observations, including several types of scaling anomalies and the ultraslow diffusion properties, implying the cascading processes associated with the localized exploration and preferential returns are indeed a key in the understanding of human mobility activities. Moreover, the model shows both of the diverse individual mobility and aggregated scaling displacements, bridging the micro and macro patterns in human mobility. In summary, our model successfully explains most of empirical findings and provides deeper understandings on the emergence of human mobility patterns. PMID:25860140

Cascading walks model for human mobility patterns.

PubMed

Han, Xiao-Pu; Wang, Xiang-Wen; Yan, Xiao-Yong; Wang, Bing-Hong

2015-01-01

Uncovering the mechanism behind the scaling laws and series of anomalies in human trajectories is of fundamental significance in understanding many spatio-temporal phenomena. Recently, several models, e.g. the explorations-returns model (Song et al., 2010) and the radiation model for intercity travels (Simini et al., 2012), have been proposed to study the origin of these anomalies and the prediction of human movements. However, an agent-based model that could reproduce most of empirical observations without priori is still lacking. In this paper, considering the empirical findings on the correlations of move-lengths and staying time in human trips, we propose a simple model which is mainly based on the cascading processes to capture the human mobility patterns. In this model, each long-range movement activates series of shorter movements that are organized by the law of localized explorations and preferential returns in prescribed region. Based on the numerical simulations and analytical studies, we show more than five statistical characters that are well consistent with the empirical observations, including several types of scaling anomalies and the ultraslow diffusion properties, implying the cascading processes associated with the localized exploration and preferential returns are indeed a key in the understanding of human mobility activities. Moreover, the model shows both of the diverse individual mobility and aggregated scaling displacements, bridging the micro and macro patterns in human mobility. In summary, our model successfully explains most of empirical findings and provides deeper understandings on the emergence of human mobility patterns.

POCS-based reconstruction of multiplexed sensitivity encoded MRI (POCSMUSE): a general algorithm for reducing motion-related artifacts

PubMed Central

Chu, Mei-Lan; Chang, Hing-Chiu; Chung, Hsiao-Wen; Truong, Trong-Kha; Bashir, Mustafa R.; Chen, Nan-kuei

2014-01-01

Purpose A projection onto convex sets reconstruction of multiplexed sensitivity encoded MRI (POCSMUSE) is developed to reduce motion-related artifacts, including respiration artifacts in abdominal imaging and aliasing artifacts in interleaved diffusion weighted imaging (DWI). Theory Images with reduced artifacts are reconstructed with an iterative POCS procedure that uses the coil sensitivity profile as a constraint. This method can be applied to data obtained with different pulse sequences and k-space trajectories. In addition, various constraints can be incorporated to stabilize the reconstruction of ill-conditioned matrices. Methods The POCSMUSE technique was applied to abdominal fast spin-echo imaging data, and its effectiveness in respiratory-triggered scans was evaluated. The POCSMUSE method was also applied to reduce aliasing artifacts due to shot-to-shot phase variations in interleaved DWI data corresponding to different k-space trajectories and matrix condition numbers. Results Experimental results show that the POCSMUSE technique can effectively reduce motion-related artifacts in data obtained with different pulse sequences, k-space trajectories and contrasts. Conclusion POCSMUSE is a general post-processing algorithm for reduction of motion-related artifacts. It is compatible with different pulse sequences, and can also be used to further reduce residual artifacts in data produced by existing motion artifact reduction methods. PMID:25394325

Diffusion of torqued active particles

NASA Astrophysics Data System (ADS)

Sandoval, Mario; Lauga, Eric

2012-11-01

Motivated by swimming microorganisms whose trajectories are affected by the presence of an external torque, we calculate the diffusivity of an active particle subject to an external torque and in a fluctuating environment. The analytical results are compared with Brownian dynamics simulations showing excellent agreement between theory and numerical experiments. This work was funded in part by the Consejo Nacional de Ciencia y Tecnologia of Mexico (Conacyt postdoctoral fellowship to M. S.) and the US National Science Foundation (Grant CBET-0746285 to E.L.).

User's guide to the MESOI diffusion model and to the utility programs UPDATE and LOGRVU

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

Athey, G.F.; Allwine, K.J.; Ramsdell, J.V.

MESOI is an interactive, Lagrangian puff trajectory diffusion model. The model is documented separately (Ramsdell and Athey, 1981); this report is intended to provide MESOI users with the information needed to successfully conduct model simulations. The user is also provided with guidance in the use of the data file maintenance and review programs; UPDATE and LOGRVU. Complete examples are given for the operaton of all three programs and an appendix documents UPDATE and LOGRVU.

Coordinated observations of chemical releases from the ground and from aircraft at high latitudes

NASA Technical Reports Server (NTRS)

Romick, G. J.

1973-01-01

The ground observations of the Na-Li trail released from a Nike-Apache rocket obtained by the Geophysical Institute are discussed. By using the nominal trajectory for a 60 pound payload and the particular rocket, a best fit trajectory was determined based on the Ester Dome photographic data, launch time and earth-sun geometrical shadow height. From these calculations, the height of obvious features along the trail were determined and their velocity estimated. A clockwise rotation of the velocity vector with increasing height was observed. Velocities deduced at various altitudes were then compared to meter radar data also obtained during this period. The comparisons of these two neutral wind measurements techniques are satisfactory.

Reactive-Diffusive-Advective Traveling Waves in a Family of Degenerate Nonlinear Equations.

PubMed

Sánchez-Garduño, Faustino; Pérez-Velázquez, Judith

This paper deals with the analysis of existence of traveling wave solutions (TWS) for a diffusion-degenerate (at D (0) = 0) and advection-degenerate (at h '(0) = 0) reaction-diffusion-advection (RDA) equation. Diffusion is a strictly increasing function and the reaction term generalizes the kinetic part of the Fisher-KPP equation. We consider different forms of the convection term h ( u ): (1)   h '( u ) is constant k , (2)   h '( u ) = ku with k > 0, and (3) it is a quite general form which guarantees the degeneracy in the advective term. In Case 1, we prove that the task can be reduced to that for the corresponding equation, where k = 0, and then previous results reported from the authors can be extended. For the other two cases, we use both analytical and numerical tools. The analysis we carried out is based on the restatement of searching TWS for the full RDA equation into a two-dimensional dynamical problem. This consists of searching for the conditions on the parameter values for which there exist heteroclinic trajectories of the ordinary differential equations (ODE) system in the traveling wave coordinates. Throughout the paper we obtain the dynamics by using tools coming from qualitative theory of ODE.

Reactive-Diffusive-Advective Traveling Waves in a Family of Degenerate Nonlinear Equations

PubMed Central

Sánchez-Garduño, Faustino

2016-01-01

This paper deals with the analysis of existence of traveling wave solutions (TWS) for a diffusion-degenerate (at D(0) = 0) and advection-degenerate (at h′(0) = 0) reaction-diffusion-advection (RDA) equation. Diffusion is a strictly increasing function and the reaction term generalizes the kinetic part of the Fisher-KPP equation. We consider different forms of the convection term h(u): (1)  h′(u) is constant k, (2)  h′(u) = ku with k > 0, and (3) it is a quite general form which guarantees the degeneracy in the advective term. In Case 1, we prove that the task can be reduced to that for the corresponding equation, where k = 0, and then previous results reported from the authors can be extended. For the other two cases, we use both analytical and numerical tools. The analysis we carried out is based on the restatement of searching TWS for the full RDA equation into a two-dimensional dynamical problem. This consists of searching for the conditions on the parameter values for which there exist heteroclinic trajectories of the ordinary differential equations (ODE) system in the traveling wave coordinates. Throughout the paper we obtain the dynamics by using tools coming from qualitative theory of ODE. PMID:27689131

Physics of knuckleballs

NASA Astrophysics Data System (ADS)

Darbois Texier, Baptiste; Cohen, Caroline; Quéré, David; Clanet, Christophe

2016-07-01

Zigzag paths in sports ball trajectories are exceptional events. They have been reported in baseball (from where the word knuckleball comes from), in volleyball and in soccer. Such trajectories are associated with intermittent breaking of the lateral symmetry in the surrounding flow. The different scenarios proposed in the literature (such as the effect of seams in baseball) are first discussed and compared to existing data. We then perform experiments on zigzag trajectories and propose a new explanation based on unsteady lift forces. In a second step, we exploit wind tunnel measurements of these unsteady lift forces to solve the equations of motion for various sports and deduce the characteristics of the zigzags, pointing out the role of the drag crisis. Finally, the conditions for the observation of such trajectories in sports are discussed.

Detection of confinement and jumps in single-molecule membrane trajectories

NASA Astrophysics Data System (ADS)

Meilhac, N.; Le Guyader, L.; Salomé, L.; Destainville, N.

2006-01-01

We propose a variant of the algorithm by [R. Simson, E. D. Sheets, and K. Jacobson, Biophys. 69, 989 (1995)]. Their algorithm was developed to detect transient confinement zones in experimental single-particle tracking trajectories of diffusing membrane proteins or lipids. We show that our algorithm is able to detect confinement in a wider class of confining potential shapes than that of Simson Furthermore, it enables to detect not only temporary confinement but also jumps between confinement zones. Jumps are predicted by membrane skeleton fence and picket models. In the case of experimental trajectories of μ -opioid receptors, which belong to the family of G-protein-coupled receptors involved in a signal transduction pathway, this algorithm confirms that confinement cannot be explained solely by rigid fences.

José Bleger: Jew, Marxist and psychoanalyst.

PubMed

Plotkin, Mariano

2011-01-01

The article analyses the trajectory of Dr. José Bleger (1922-1972), an Argentine psychoanalyst who tried to articulate his triple identity as a Jew, a Marxist, and a psychoanalyst. Bleger played a central role in the constitution of the 'psy movement' and, in more general terms, in the diffusion of a 'psy culture' in Argentina, a country that today is considered as one of the 'world capitals of psychoanalysis'. However, his trajectory showed not only the limits of his projects in the increasingly politically polarized Argentina of the 1960s, as well as their internal contradictions, but also the difficulties of articulating different identities in those agitated times. Through an analysis of Bleger's trajectory this article explores larger issues of Argentine political culture and their relations with the emergence of a psychoanalytic culture.

Seasonal Variability in Global Eddy Diffusion and the Effect on Thermospheric Neutral Density

NASA Astrophysics Data System (ADS)

Pilinski, M.; Crowley, G.

2014-12-01

We describe a method for making single-satellite estimates of the seasonal variability in global-average eddy diffusion coefficients. Eddy diffusion values as a function of time between January 2004 and January 2008 were estimated from residuals of neutral density measurements made by the CHallenging Minisatellite Payload (CHAMP) and simulations made using the Thermosphere Ionosphere Mesosphere Electrodynamics - Global Circulation Model (TIME-GCM). The eddy diffusion coefficient results are quantitatively consistent with previous estimates based on satellite drag observations and are qualitatively consistent with other measurement methods such as sodium lidar observations and eddy-diffusivity models. The eddy diffusion coefficient values estimated between January 2004 and January 2008 were then used to generate new TIME-GCM results. Based on these results, the RMS difference between the TIME-GCM model and density data from a variety of satellites is reduced by an average of 5%. This result, indicates that global thermospheric density modeling can be improved by using data from a single satellite like CHAMP. This approach also demonstrates how eddy diffusion could be estimated in near real-time from satellite observations and used to drive a global circulation model like TIME-GCM. Although the use of global values improves modeled neutral densities, there are some limitations of this method, which are discussed, including that the latitude-dependence of the seasonal neutral-density signal is not completely captured by a global variation of eddy diffusion coefficients. This demonstrates the need for a latitude-dependent specification of eddy diffusion consistent with diffusion observations made by other techniques.

Seasonal variability in global eddy diffusion and the effect on neutral density

NASA Astrophysics Data System (ADS)

Pilinski, M. D.; Crowley, G.

2015-04-01

We describe a method for making single-satellite estimates of the seasonal variability in global-average eddy diffusion coefficients. Eddy diffusion values as a function of time were estimated from residuals of neutral density measurements made by the Challenging Minisatellite Payload (CHAMP) and simulations made using the thermosphere-ionosphere-mesosphere electrodynamics global circulation model (TIME-GCM). The eddy diffusion coefficient results are quantitatively consistent with previous estimates based on satellite drag observations and are qualitatively consistent with other measurement methods such as sodium lidar observations and eddy diffusivity models. Eddy diffusion coefficient values estimated between January 2004 and January 2008 were then used to generate new TIME-GCM results. Based on these results, the root-mean-square sum for the TIME-GCM model is reduced by an average of 5% when compared to density data from a variety of satellites, indicating that the fidelity of global density modeling can be improved by using data from a single satellite like CHAMP. This approach also demonstrates that eddy diffusion could be estimated in near real-time from satellite observations and used to drive a global circulation model like TIME-GCM. Although the use of global values improves modeled neutral densities, there are limitations to this method, which are discussed, including that the latitude dependence of the seasonal neutral-density signal is not completely captured by a global variation of eddy diffusion coefficients. This demonstrates the need for a latitude-dependent specification of eddy diffusion which is also consistent with diffusion observations made by other techniques.

Comparison of two trajectory based models for locating particle sources for two rural New York sites

NASA Astrophysics Data System (ADS)

Zhou, Liming; Hopke, Philip K.; Liu, Wei

Two back trajectory-based statistical models, simplified quantitative transport bias analysis and residence-time weighted concentrations (RTWC) have been compared for their capabilities of identifying likely locations of source emissions contributing to observed particle concentrations at Potsdam and Stockton, New York. Quantitative transport bias analysis (QTBA) attempts to take into account the distribution of concentrations around the directions of the back trajectories. In full QTBA approach, deposition processes (wet and dry) are also considered. Simplified QTBA omits the consideration of deposition. It is best used with multiple site data. Similarly the RTWC approach uses concentrations measured at different sites along with the back trajectories to distribute the concentration contributions across the spatial domain of the trajectories. In this study, these models are used in combination with the source contribution values obtained by the previous positive matrix factorization analysis of particle composition data from Potsdam and Stockton. The six common sources for the two sites, sulfate, soil, zinc smelter, nitrate, wood smoke and copper smelter were analyzed. The results of the two methods are consistent and locate large and clearly defined sources well. RTWC approach can find more minor sources but may also give unrealistic estimations of the source locations.

A special protection scheme utilizing trajectory sensitivity analysis in power transmission

NASA Astrophysics Data System (ADS)

Suriyamongkol, Dan

In recent years, new measurement techniques have provided opportunities to improve the North American Power System observability, control and protection. This dissertation discusses the formulation and design of a special protection scheme based on a novel utilization of trajectory sensitivity techniques with inputs consisting of system state variables and parameters. Trajectory sensitivity analysis (TSA) has been used in previous publications as a method for power system security and stability assessment, and the mathematical formulation of TSA lends itself well to some of the time domain power system simulation techniques. Existing special protection schemes often have limited sets of goals and control actions. The proposed scheme aims to maintain stability while using as many control actions as possible. The approach here will use the TSA in a novel way by using the sensitivities of system state variables with respect to state parameter variations to determine the state parameter controls required to achieve the desired state variable movements. The initial application will operate based on the assumption that the modeled power system has full system observability, and practical considerations will be discussed.

Dim target trajectory-associated detection in bright earth limb background

NASA Astrophysics Data System (ADS)

Chen, Penghui; Xu, Xiaojian; He, Xiaoyu; Jiang, Yuesong

2015-09-01

The intensive emission of earth limb in the field of view of sensors contributes much to the observation images. Due to the low signal-to-noise ratio (SNR), it is a challenge to detect small targets in earth limb background, especially for the detection of point-like targets from a single frame. To improve the target detection, track before detection (TBD) based on the frame sequence is performed. In this paper, a new technique is proposed to determine the target associated trajectories, which jointly carries out background removing, maximum value projection (MVP) and Hough transform. The background of the bright earth limb in the observation images is removed according to the profile characteristics. For a moving target, the corresponding pixels in the MVP image are shifting approximately regularly in time sequence. And the target trajectory is determined by Hough transform according to the pixel characteristics of the target and the clutter and noise. Comparing with traditional frame-by-frame methods, determining associated trajectories from MVP reduces the computation load. Numerical simulations are presented to demonstrate the effectiveness of the approach proposed.

Ballistic projectile trajectory determining system

DOEpatents

Karr, T.J.

1997-05-20

A computer controlled system determines the three-dimensional trajectory of a ballistic projectile. To initialize the system, predictions of state parameters for a ballistic projectile are received at an estimator. The estimator uses the predictions of the state parameters to estimate first trajectory characteristics of the ballistic projectile. A single stationary monocular sensor then observes the actual first trajectory characteristics of the ballistic projectile. A comparator generates an error value related to the predicted state parameters by comparing the estimated first trajectory characteristics of the ballistic projectile with the observed first trajectory characteristics of the ballistic projectile. If the error value is equal to or greater than a selected limit, the predictions of the state parameters are adjusted. New estimates for the trajectory characteristics of the ballistic projectile are made and are then compared with actual observed trajectory characteristics. This process is repeated until the error value is less than the selected limit. Once the error value is less than the selected limit, a calculator calculates trajectory characteristics such a the origin and destination of the ballistic projectile. 8 figs.

Diffusion approximations to the chemical master equation only have a consistent stochastic thermodynamics at chemical equilibrium

NASA Astrophysics Data System (ADS)

Horowitz, Jordan M.

2015-07-01

The stochastic thermodynamics of a dilute, well-stirred mixture of chemically reacting species is built on the stochastic trajectories of reaction events obtained from the chemical master equation. However, when the molecular populations are large, the discrete chemical master equation can be approximated with a continuous diffusion process, like the chemical Langevin equation or low noise approximation. In this paper, we investigate to what extent these diffusion approximations inherit the stochastic thermodynamics of the chemical master equation. We find that a stochastic-thermodynamic description is only valid at a detailed-balanced, equilibrium steady state. Away from equilibrium, where there is no consistent stochastic thermodynamics, we show that one can still use the diffusive solutions to approximate the underlying thermodynamics of the chemical master equation.

Diffusion approximations to the chemical master equation only have a consistent stochastic thermodynamics at chemical equilibrium.

PubMed

Horowitz, Jordan M

2015-07-28

The stochastic thermodynamics of a dilute, well-stirred mixture of chemically reacting species is built on the stochastic trajectories of reaction events obtained from the chemical master equation. However, when the molecular populations are large, the discrete chemical master equation can be approximated with a continuous diffusion process, like the chemical Langevin equation or low noise approximation. In this paper, we investigate to what extent these diffusion approximations inherit the stochastic thermodynamics of the chemical master equation. We find that a stochastic-thermodynamic description is only valid at a detailed-balanced, equilibrium steady state. Away from equilibrium, where there is no consistent stochastic thermodynamics, we show that one can still use the diffusive solutions to approximate the underlying thermodynamics of the chemical master equation.

Demystifying the memory effect: A geometrical approach to understanding speckle correlations

NASA Astrophysics Data System (ADS)

Prunty, Aaron C.; Snieder, Roel K.

2017-05-01

The memory effect has seen a surge of research into its fundamental properties and applications since its discovery by Feng et al. [Phys. Rev. Lett. 61, 834 (1988)]. While the wave trajectories for which the memory effect holds are hidden implicitly in the diffusion probability function [Phys. Rev. B 40, 737 (1989)], the physical intuition of why these trajectories satisfy the memory effect has often been masked by the derivation of the memory correlation function itself. In this paper, we explicitly derive the specific trajectories through a random medium for which the memory effect holds. Our approach shows that the memory effect follows from a simple conservation argument, which imposes geometrical constraints on the random trajectories that contribute to the memory effect. We illustrate the time-domain effects of these geometrical constraints with numerical simulations of pulse transmission through a random medium. The results of our derivation and numerical simulations are consistent with established theory and experimentation.

Perception of object motion in three-dimensional space induced by cast shadows.

PubMed

Katsuyama, Narumi; Usui, Nobuo; Nose, Izuru; Taira, Masato

2011-01-01

Cast shadows can be salient depth cues in three-dimensional (3D) vision. Using a motion illusion in which a ball is perceived to roll in depth on the bottom or to flow in the front plane depending on the slope of the trajectory of its cast shadow, we investigated cortical mechanisms underlying 3D vision based on cast shadows using fMRI techniques. When modified versions of the original illusion, in which the slope of the shadow trajectory (shadow slope) was changed in 5 steps from the same one as the ball trajectory to the horizontal, were presented to participants, their perceived ball trajectory shifted gradually from rolling on the bottom to floating in the front plane as the change of the shadow slope. This observation suggests that the perception of the ball trajectory in this illusion is strongly affected by the motion of the cast shadow. In the fMRI study, cortical activity during observation of the movies of the illusion was investigated. We found that the bilateral posterior-occipital sulcus (POS) and right ventral precuneus showed activation related to the perception of the ball trajectory induced by the cast shadows in the illusion. Of these areas, it was suggested that the right POS may be involved in the inferring of the ball trajectory by the given spatial relation between the ball and the shadow. Our present results suggest that the posterior portion of the medial parietal cortex may be involved in 3D vision by cast shadows. Copyright © 2010 Elsevier Inc. All rights reserved.

Terbutaline causes immobilization of single β2-adrenergic receptor-ligand complexes in the plasma membrane of living A549 cells as revealed by single-molecule microscopy

NASA Astrophysics Data System (ADS)

Sieben, Anne; Kaminski, Tim; Kubitscheck, Ulrich; Häberlein, Hanns

2011-02-01

G-protein-coupled receptors are important targets for various drugs. After signal transduction, regulatory processes, such as receptor desensitization and internalization, change the lateral receptor mobility. In order to study the lateral diffusion of β2-adrenergic receptors (β2AR) complexed with fluorescently labeled noradrenaline (Alexa-NA) in plasma membranes of A549 cells, trajectories of single receptor-ligand complexes were monitored using single-particle tracking. We found that a fraction of 18% of all β2ARs are constitutively immobile. About 2/3 of the β2ARs moved with a diffusion constant of D2 = 0.03+/-0.001 μm2/s and about 17% were diffusing five-fold faster (D3 = 0.15+/-0.02 μm2/s). The mobile receptors moved within restricted domains and also showed a discontinuous diffusion behavior. Analysis of the trajectory lengths revealed two different binding durations with τ1 = 77+/-1 ms and τ2 = 388+/-11 ms. Agonistic stimulation of the β2AR-Alexa-NA complexes with 1 μM terbutaline caused immobilization of almost 50% of the receptors within 35 min. Simultaneously, the mean area covered by the mobile receptors decreased significantly. Thus, we demonstrated that agonistic stimulation followed by cell regulatory processes results in a change in β2AR mobility suggesting that different receptor dynamics characterize different receptor states.

Anomalous Diffusion of Water in Lamellar Membranes Formed by Pluronic Polymers

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Ohl, Michael; Han, Youngkyu; Smith, Gregory; Do, Changwoo; Biology; Soft-Matter Division, Oak Ridge National Laboratory Team; Julich CenterNeutron Science Team

Water diffusion is playing an important role in polymer systems. We calculated the water diffusion coefficient at different layers along z-direction which is perpendicular to the lamellar membrane formed by Pluronic block copolymers (L62: (EO6-PO34-EO6)) with the molecular dynamics simulation trajectories. Water molecules at bulk layers are following the normal diffusion, while that at hydration layers formed by polyethylene oxide (PEO) and hydrophobic layers formed by polypropylene oxide (PPO) are following anomalous diffusion. We find that although the subdiffusive regimes at PEO layers and PPO layers are the same, which is the fractional Brownian motion, however, the dynamics are different, i.e. diffusion at the PEO layers is much faster than that at the PPO layers, and meanwhile it exhibits a normal diffusive approximation within a short time period which is governed by the localized free self-diffusion, but becomes subdiffusive after t >8 ps, which is governed by the viscoelastic medium. The Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy; and Zhe Zhang gratefully acknowledges financial support from Julich Center for Neutron Science.

Generating Pedestrian Trajectories Consistent with the Fundamental Diagram Based on Physiological and Psychological Factors

PubMed Central

Narang, Sahil; Best, Andrew; Curtis, Sean; Manocha, Dinesh

2015-01-01

Pedestrian crowds often have been modeled as many-particle system including microscopic multi-agent simulators. One of the key challenges is to unearth governing principles that can model pedestrian movement, and use them to reproduce paths and behaviors that are frequently observed in human crowds. To that effect, we present a novel crowd simulation algorithm that generates pedestrian trajectories that exhibit the speed-density relationships expressed by the Fundamental Diagram. Our approach is based on biomechanical principles and psychological factors. The overall formulation results in better utilization of free space by the pedestrians and can be easily combined with well-known multi-agent simulation techniques with little computational overhead. We are able to generate human-like dense crowd behaviors in large indoor and outdoor environments and validate the results with captured real-world crowd trajectories. PMID:25875932

Green-noise halftoning with dot diffusion

NASA Astrophysics Data System (ADS)

Lippens, Stefaan; Philips, Wilfried

2007-02-01

Dot diffusion is a halftoning technique that is based on the traditional error diffusion concept, but offers a high degree of parallel processing by its block based approach. Traditional dot diffusion however suffers from periodicity artifacts. To limit the visibility of these artifacts, we propose grid diffusion, which applies different class matrices for different blocks. Furthermore, in this paper we will discuss two approaches in the dot diffusion framework to generate green-noise halftone patterns. The first approach is based on output dependent feedback (hysteresis), analogous to the standard green-noise error diffusion techniques. We observe that the resulting halftones are rather coarse and highly dependent on the used dot diffusion class matrices. In the second approach we don't limit the diffusion to the nearest neighbors. This leads to less coarse halftones, compared to the first approach. The drawback is that it can only cope with rather limited cluster sizes. We can reduce these drawbacks by combining the two approaches.

Ion Pairing and Diffusion in Magnesium Electrolytes Based on Magnesium Borohydride.

PubMed

Samuel, Devon; Steinhauser, Carl; Smith, Jeffrey G; Kaufman, Aaron; Radin, Maxwell D; Naruse, Junichi; Hiramatsu, Hidehiko; Siegel, Donald J

2017-12-20

One obstacle to realizing a practical, rechargeable magnesium-ion battery is the development of efficient Mg electrolytes. Electrolytes based on simple Mg(BH 4 ) 2 salts suffer from poor salt solubility and/or low conductivity, presumably due to strong ion pairing. Understanding the molecular-scale processes occurring in these electrolytes would aid in overcoming these performance limitations. Toward this goal, the present study examines the solvation, agglomeration, and transport properties of a family of Mg electrolytes based on the Mg(BH 4 ) 2 salt using classical molecular dynamics. These properties were examined across five different solvents (tetrahydrofuran and the glymes G1-G4) and at four salt concentrations ranging from the dilute limit up to 0.4 M. Significant and irreversible salt agglomeration was observed in all solvents at all nondilute Mg(BH 4 ) 2 concentrations. The degree of clustering observed in these divalent Mg systems is much larger than that reported for electrolytes containing monovalent cations, such as Li. The salt agglomeration rate and diffusivity of Mg 2+ were both observed to correlate with solvent self-diffusivity: electrolytes using longer- (shorter-) chain solvents had the lowest (highest) Mg 2+ diffusivity and agglomeration rates. Incorporation of Mg 2+ into Mg 2+ -BH 4 - clusters significantly reduces the diffusivity of Mg 2+ by restricting displacements to localized motion within largely immobile agglomerates. Consequently, diffusion is increasingly impeded with increasing Mg(BH 4 ) 2 concentration. These data are consistent with the solubility limitations observed experimentally for Mg(BH 4 ) 2 -based electrolytes and highlight the need for strategies that minimize salt agglomeration in electrolytes containing divalent cations.

Can Universal SEL Programs Benefit Universally? Effects of the Positive Action Program on Multiple Trajectories of Social-Emotional and Misconduct Behaviors.

PubMed

Duncan, Robert; Washburn, Isaac J; Lewis, Kendra M; Bavarian, Niloofar; DuBois, David L; Acock, Alan C; Vuchinich, Samuel; Flay, Brian R

2017-02-01

Behavioral trajectories during middle childhood are predictive of consequential outcomes later in life (e.g., substance abuse, violence). Social and emotional learning (SEL) programs are designed to promote trajectories that reflect both growth in positive behaviors and inhibited development of negative behaviors. The current study used growth mixture models to examine effects of the Positive Action (PA) program on behavioral trajectories of social-emotional and character development (SECD) and misconduct using data from a cluster-randomized trial that involved 14 schools and a sample of predominately low-income, urban youth followed from 3rd through 8th grade. For SECD, findings indicated that PA was similarly effective at improving trajectories within latent classes characterized as "high/declining" and "low/stable". Favorable program effects were likewise evident to a comparable degree for misconduct across observed latent classes that reflected "low/rising" and "high/rising" trajectories. These findings suggest that PA and perhaps other school-based universal SEL programs have the potential to yield comparable benefits across subgroups of youth with differing trajectories of positive and negative behaviors, making them promising strategies for achieving the intended goal of school-wide improvements in student outcomes.

Adaptive boundary concentration control using Zakai equation

NASA Astrophysics Data System (ADS)

Tenno, R.; Mendelson, A.

2010-06-01

A mean-variance control problem is formulated with respect to a partially observed nonlinear system that includes unknown constant parameters. A physical prototype of the system is the cathode surface reaction in an electrolysis cell, where the controller aim is to keep the boundary concentration of species in the near vicinity of the cathode surface low but not zero. The boundary concentration is a diffusion-controlled process observed through the measured current density and, in practice, controlled through the applied voltage. The former incomplete data control problem is converted to complete data-to the so-called separated control problem whose solution is given by the infinite-dimensional Zakai equation. In this article, the separated control problem is solved numerically using pathwise integration of the Zakai equation. This article demonstrates precise tracking of the target trajectory with a rapid convergence of estimates to unknown parameters, which take place simultaneously with control.

Computing the Rotational Diffusion of Biomolecules via Molecular Dynamics Simulation and Quaternion Orientations.

PubMed

Chen, Po-Chia; Hologne, Maggy; Walker, Olivier

2017-03-02

Rotational diffusion (D rot ) is a fundamental property of biomolecules that contains information about molecular dimensions and solute-solvent interactions. While ab initio D rot prediction can be achieved by explicit all-atom molecular dynamics simulations, this is hindered by both computational expense and limitations in water models. We propose coarse-grained force fields as a complementary solution, and show that the MARTINI force field with elastic networks is sufficient to compute D rot in >10 proteins spanning 5-157 kDa. We also adopt a quaternion-based approach that computes D rot orientation directly from autocorrelations of best-fit rotations as used in, e.g., RMSD algorithms. Over 2 μs trajectories, isotropic MARTINI+EN tumbling replicates experimental values to within 10-20%, with convergence analyses suggesting a minimum sampling of >50 × τ theor to achieve sufficient precision. Transient fluctuations in anisotropic tumbling cause decreased precision in predictions of axisymmetric anisotropy and rhombicity, the latter of which cannot be precisely evaluated within 2000 × τ theor for GB3. Thus, we encourage reporting of axial decompositions D x , D y , D z to ease comparability between experiment and simulation. Where protein disorder is absent, we observe close replication of MARTINI+EN D rot orientations versus CHARMM22*/TIP3p and experimental data. This work anticipates the ab initio prediction of NMR-relaxation by combining coarse-grained global motions with all-atom local motions.

Extended state observer-based motion synchronisation control for hybrid actuation system of large civil aircraft

NASA Astrophysics Data System (ADS)

Wang, Xingjian; Shi, Cun; Wang, Shaoping

2017-07-01

Hybrid actuation system with dissimilar redundant actuators, which is composed of a hydraulic actuator (HA) and an electro-hydrostatic actuator (EHA), has been applied on modern civil aircraft to improve the reliability. However, the force fighting problem arises due to different dynamic performances between HA and EHA. This paper proposes an extended state observer (ESO)-based motion synchronisation control method. To cope with the problem of unavailability of the state signals, the well-designed ESO is utilised to observe the HA and EHA state variables which are unmeasured. In particular, the extended state of ESO can estimate the lumped effect of the unknown external disturbances acting on the control surface, the nonlinear dynamics, uncertainties, and the coupling term between HA and EHA. Based on the observed states of ESO, motion synchronisation controllers are presented to make HA and EHA to simultaneously track the desired motion trajectories, which are generated by a trajectory generator. Additionally, the unknown disturbances and the coupling terms can be compensated by using the extended state of the proposed ESO. Finally, comparative simulation results indicate that the proposed ESO-based motion synchronisation controller can achieve great force fighting reduction between HA and EHA.

Tuning Monotonic Basin Hopping: Improving the Efficiency of Stochastic Search as Applied to Low-Thrust Trajectory Optimization

NASA Technical Reports Server (NTRS)

Englander, Jacob; Englander, Arnold

2014-01-01

Trajectory optimization methods using MBH have become well developed during the past decade. An essential component of MBH is a controlled random search through the multi-dimensional space of possible solutions. Historically, the randomness has been generated by drawing RVs from a uniform probability distribution. Here, we investigate the generating the randomness by drawing the RVs from Cauchy and Pareto distributions, chosen because of their characteristic long tails. We demonstrate that using Cauchy distributions (as first suggested by Englander significantly improves MBH performance, and that Pareto distributions provide even greater improvements. Improved performance is defined in terms of efficiency and robustness, where efficiency is finding better solutions in less time, and robustness is efficiency that is undiminished by (a) the boundary conditions and internal constraints of the optimization problem being solved, and (b) by variations in the parameters of the probability distribution. Robustness is important for achieving performance improvements that are not problem specific. In this work we show that the performance improvements are the result of how these long-tailed distributions enable MBH to search the solution space faster and more thoroughly. In developing this explanation, we use the concepts of sub-diffusive, normally-diffusive, and super-diffusive RWs originally developed in the field of statistical physics.

Analysing the diffusion and adoption of mobile IT across social worlds.

PubMed

Nielsen, Jeppe Agger; Mengiste, Shegaw Anagaw

2014-06-01

The diffusion and adoption of information technology innovations (e.g. mobile information technology) in healthcare organizations involves a dynamic process of change with multiple stakeholders with competing interests, varying commitments, and conflicting values. Nevertheless, the extant literature on mobile information technology diffusion and adoption has predominantly focused on organizations and individuals as the unit of analysis, with little emphasis on the environment in which healthcare organizations are embedded. We propose the social worlds approach as a promising theoretical lens for dealing with this limitation together with reports from a case study of a mobile information technology innovation in elderly home care in Denmark including both the sociopolitical and organizational levels in the analysis. Using the notions of social worlds, trajectories, and boundary objects enables us to show how mobile information technology innovation in Danish home care can facilitate negotiation and collaboration across different social worlds in one setting while becoming a source of tension and conflicts in others. The trajectory of mobile information technology adoption was shaped by influential stakeholders in the Danish home care sector. Boundary objects across multiple social worlds legitimized the adoption, but the use arrangement afforded by the new technology interfered with important aspects of home care practices, creating resistance among the healthcare personnel.

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

Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories inmore » a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.« less

Tracing compartment exchange by NMR diffusometry: Water in lithium-exchanged low-silica X zeolites

NASA Astrophysics Data System (ADS)

Lauerer, A.; Kurzhals, R.; Toufar, H.; Freude, D.; Kärger, J.

2018-04-01

The two-region model for analyzing signal attenuation in pulsed field gradient (PFG) NMR diffusion studies with molecules in compartmented media implies that, on their trajectory, molecules get from one region (one type of compartment) into the other one with a constant (i.e. a time-invariant) probability. This pattern has proved to serve as a good approach for considering guest diffusion in beds of nanoporous host materials, with the two regions ("compartments") identified as the intra- and intercrystalline pore spaces. It is obvious, however, that the requirements of the application of the two-region model are not strictly fulfilled given the correlation between the covered diffusion path lengths in the intracrystalline pore space and the probability of molecular "escape" from the individual crystallites. On considering water diffusion in lithium-exchanged low-silica X zeolite, we are now assuming a different position since this type of material is known to offer "traps" in the trajectories of the water molecules. Now, on attributing the water molecules in the traps and outside of the traps to these two types of regions, we perfectly comply with the requirements of the two-region model. We do, moreover, benefit from the option of high-resolution measurements owing to the combination of magic angle spinning (MAS) with PFG NMR. Data analysis via the two-region model under inclusion of the influence of nuclear magnetic relaxation yields satisfactory agreement between experimental evidence and theoretical estimates. Limitations in accuracy are shown to result from the fact that mass transfer outside of the traps is too complicated for being adequately reflected by simple Fick's laws with but one diffusivity.

Long-period comet impact risk mitigation with Earth-based laser arrays

NASA Astrophysics Data System (ADS)

Zhang, Qicheng; Lubin, Philip M.; Hughes, Gary B.

2017-09-01

Long-period comets (LPCs) frequently transit the inner solar system, and like near-Earth asteroids (NEAs), pose a continued risk of impact with Earth. Unlike NEAs, LPCs follow nearly parabolic trajectories and approach from the distant outer solar system where they cannot be observed. An LPC on an Earth-impact trajectory is unlikely to be discovered more than a few years in advance of its arrival, even with significant advancements in sky survey detection capabilities, likely leaving insufficient time to develop and deliver an interception mission to deflect the comet. However, recent proposals have called for the development of one or more large ˜ 1 km laser arrays placed on or near Earth primarily as a means for photon propulsion of low-mass spacecraft at delta-v above what would be feasible by traditional chemical or ion propulsion methods. Such a laser array can also be directed to target and heat a threatening comet, sublimating its ices and activating jets of dust and vapor which alter the comet's trajectory in a manner similar to rocket propulsion. Simulations of directed energy comet deflection were previously developed from astrometric models of nongravitational orbital perturbations from solar heating, an analogous process that has been observed in numerous comets. These simulations are used together with the distribution of known LPC trajectories to evaluate the effect of an operational Earth-based laser array on the LPC impact risk.

The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations.

PubMed

Anselmi, Massimiliano; Di Nola, Alfredo; Amadei, Andrea

2011-03-01

By using multiple molecular dynamics (MD) trajectories, a quantitative description of carbon monoxide (CO) migration within crystal of L29F myoglobin mutant (L29F-Mb) was obtained. The aim was to provide a detailed model for ligand diffusion in the protein to be compared to the available L29F-Mb experimental-computational data and to the corresponding model kinetics we previously obtained for photolyzed CO within crystallized wild-type myoglobin (wt-Mb). Results suggest a clear migration pathway from distal pocket to the proximal site, similar to the one observed in wt-Mb, with a relaxation kinetics differing from the wt-Mb one essentially for the escape rate which is much higher in the mutant. Moreover MD data indicated a clear correlation between CO location within the protein and the conformation adopted by Phe29, well matching the available experimental data as obtained by time-resolved X-ray density maps. Such data, further validating the model used in the simulations, point out the subtle mutual effect between ligand diffusion and protein functional motions possibly explaining the observed dramatic variation of CO exit rate in L29F-Mb. Copyright © 2010 Wiley-Liss, Inc.

Observability-Based Guidance and Sensor Placement

NASA Astrophysics Data System (ADS)

Hinson, Brian T.

Control system performance is highly dependent on the quality of sensor information available. In a growing number of applications, however, the control task must be accomplished with limited sensing capabilities. This thesis addresses these types of problems from a control-theoretic point-of-view, leveraging system nonlinearities to improve sensing performance. Using measures of observability as an information quality metric, guidance trajectories and sensor distributions are designed to improve the quality of sensor information. An observability-based sensor placement algorithm is developed to compute optimal sensor configurations for a general nonlinear system. The algorithm utilizes a simulation of the nonlinear system as the source of input data, and convex optimization provides a scalable solution method. The sensor placement algorithm is applied to a study of gyroscopic sensing in insect wings. The sensor placement algorithm reveals information-rich areas on flexible insect wings, and a comparison to biological data suggests that insect wings are capable of acting as gyroscopic sensors. An observability-based guidance framework is developed for robotic navigation with limited inertial sensing. Guidance trajectories and algorithms are developed for range-only and bearing-only navigation that improve navigation accuracy. Simulations and experiments with an underwater vehicle demonstrate that the observability measure allows tuning of the navigation uncertainty.

Automated correction of improperly rotated diffusion gradient orientations in diffusion weighted MRI.

PubMed

Jeurissen, Ben; Leemans, Alexander; Sijbers, Jan

2014-10-01

Ensuring one is using the correct gradient orientations in a diffusion MRI study can be a challenging task. As different scanners, file formats and processing tools use different coordinate frame conventions, in practice, users can end up with improperly oriented gradient orientations. Using such wrongly oriented gradient orientations for subsequent diffusion parameter estimation will invalidate all rotationally variant parameters and fiber tractography results. While large misalignments can be detected by visual inspection, small rotations of the gradient table (e.g. due to angulation of the acquisition plane), are much more difficult to detect. In this work, we propose an automated method to align the coordinate frame of the gradient orientations with that of the corresponding diffusion weighted images, using a metric based on whole brain fiber tractography. By transforming the gradient table and measuring the average fiber trajectory length, we search for the transformation that results in the best global 'connectivity'. To ensure a fast calculation of the metric we included a range of algorithmic optimizations in our tractography routine. To make the optimization routine robust to spurious local maxima, we use a stochastic optimization routine that selects a random set of seed points on each evaluation. Using simulations, we show that our method can recover the correct gradient orientations with high accuracy and precision. In addition, we demonstrate that our technique can successfully recover rotated gradient tables on a wide range of clinically realistic data sets. As such, our method provides a practical and robust solution to an often overlooked pitfall in the processing of diffusion MRI. Copyright © 2014 Elsevier B.V. All rights reserved.

Locating multiple diffusion sources in time varying networks from sparse observations.

PubMed

Hu, Zhao-Long; Shen, Zhesi; Cao, Shinan; Podobnik, Boris; Yang, Huijie; Wang, Wen-Xu; Lai, Ying-Cheng

2018-02-08

Data based source localization in complex networks has a broad range of applications. Despite recent progress, locating multiple diffusion sources in time varying networks remains to be an outstanding problem. Bridging structural observability and sparse signal reconstruction theories, we develop a general framework to locate diffusion sources in time varying networks based solely on sparse data from a small set of messenger nodes. A general finding is that large degree nodes produce more valuable information than small degree nodes, a result that contrasts that for static networks. Choosing large degree nodes as the messengers, we find that sparse observations from a few such nodes are often sufficient for any number of diffusion sources to be located for a variety of model and empirical networks. Counterintuitively, sources in more rapidly varying networks can be identified more readily with fewer required messenger nodes.

Estimation of Center of Mass Trajectory using Wearable Sensors during Golf Swing.

PubMed

Najafi, Bijan; Lee-Eng, Jacqueline; Wrobel, James S; Goebel, Ruben

2015-06-01

This study suggests a wearable sensor technology to estimate center of mass (CoM) trajectory during a golf swing. Groups of 3, 4, and 18 participants were recruited, respectively, for the purpose of three validation studies. Study 1 examined the accuracy of the system to estimate a 3D body segment angle compared to a camera-based motion analyzer (Vicon®). Study 2 assessed the accuracy of three simplified CoM trajectory models. Finally, Study 3 assessed the accuracy of the proposed CoM model during multiple golf swings. A relatively high agreement was observed between wearable sensors and the reference (Vicon®) for angle measurement (r > 0.99, random error <1.2° (1.5%) for anterior-posterior; <0.9° (2%) for medial-lateral; and <3.6° (2.5%) for internal-external direction). The two-link model yielded a better agreement with the reference system compared to one-link model (r > 0.93 v. r = 0.52, respectively). On the same note, the proposed two-link model estimated CoM trajectory during golf swing with relatively good accuracy (r > 0.9, A-P random error <1cm (7.7%) and <2cm (10.4%) for M-L). The proposed system appears to accurately quantify the kinematics of CoM trajectory as a surrogate of dynamic postural control during an athlete's movement and its portability, makes it feasible to fit the competitive environment without restricting surface type. Key pointsThis study demonstrates that wearable technology based on inertial sensors are accurate to estimate center of mass trajectory in complex athletic task (e.g., golf swing)This study suggests that two-link model of human body provides optimum tradeoff between accuracy and minimum number of sensor module for estimation of center of mass trajectory in particular during fast movements.Wearable technologies based on inertial sensors are viable option for assessing dynamic postural control in complex task outside of gait laboratory and constraints of cameras, surface, and base of support.

Transport and Deposition of Nanoparticles in the Pore Network of a Reservoir Rock: Effects of Pore Surface Heterogeneity and Radial Diffusion

NASA Astrophysics Data System (ADS)

Pham, Ngoc; Papavassiliou, Dimitrios

2014-03-01

In this study, transport behavior of nanoparticles under different pore surface conditions of consolidated Berea sandstone is numerically investigated. Micro-CT scanning technique is applied to obtain 3D grayscale images of the rock sample geometry. Quantitative characterization, which is based on image analysis is done to obtain physical properties of the pore network, such as the pore size distribution and the type of each pore (dead-end, isolated, and fully connected pore). Transport of water through the rock is simulated by employing a 3D lattice Boltzmann method. The trajectories of nanopaticles moving under convection in the simulated flow field and due to molecular diffusion are monitored in the Lagrangian framework. It is assumed in the model that the particle adsorption on the pore surface, which is modeled as a pseudo-first order adsorption, is the only factor hindering particle propagation. The effect of pore surface heterogeneity to the particle breakthrough is considered, and the role of particle radial diffusion is also addressed in details. The financial support of the Advanced Energy Consortium (AEC BEG08-022) and the computational support of XSEDE (CTS090017) are acknowledged.

Fluctuating observation time ensembles in the thermodynamics of trajectories

NASA Astrophysics Data System (ADS)

Budini, Adrián A.; Turner, Robert M.; Garrahan, Juan P.

2014-03-01

The dynamics of stochastic systems, both classical and quantum, can be studied by analysing the statistical properties of dynamical trajectories. The properties of ensembles of such trajectories for long, but fixed, times are described by large-deviation (LD) rate functions. These LD functions play the role of dynamical free energies: they are cumulant generating functions for time-integrated observables, and their analytic structure encodes dynamical phase behaviour. This ‘thermodynamics of trajectories’ approach is to trajectories and dynamics what the equilibrium ensemble method of statistical mechanics is to configurations and statics. Here we show that, just like in the static case, there are a variety of alternative ensembles of trajectories, each defined by their global constraints, with that of trajectories of fixed total time being just one of these. We show how the LD functions that describe an ensemble of trajectories where some time-extensive quantity is constant (and large) but where total observation time fluctuates can be mapped to those of the fixed-time ensemble. We discuss how the correspondence between generalized ensembles can be exploited in path sampling schemes for generating rare dynamical trajectories.

STATISTICAL GROWTH MODELING OF LONGITUDINAL DT-MRI FOR REGIONAL CHARACTERIZATION OF EARLY BRAIN DEVELOPMENT.

PubMed

Sadeghi, Neda; Prastawa, Marcel; Fletcher, P Thomas; Gilmore, John H; Lin, Weili; Gerig, Guido

2012-01-01

A population growth model that represents the growth trajectories of individual subjects is critical to study and understand neurodevelopment. This paper presents a framework for jointly estimating and modeling individual and population growth trajectories, and determining significant regional differences in growth pattern characteristics applied to longitudinal neuroimaging data. We use non-linear mixed effect modeling where temporal change is modeled by the Gompertz function. The Gompertz function uses intuitive parameters related to delay, rate of change, and expected asymptotic value; all descriptive measures which can answer clinical questions related to growth. Our proposed framework combines nonlinear modeling of individual trajectories, population analysis, and testing for regional differences. We apply this framework to the study of early maturation in white matter regions as measured with diffusion tensor imaging (DTI). Regional differences between anatomical regions of interest that are known to mature differently are analyzed and quantified. Experiments with image data from a large ongoing clinical study show that our framework provides descriptive, quantitative information on growth trajectories that can be directly interpreted by clinicians. To our knowledge, this is the first longitudinal analysis of growth functions to explain the trajectory of early brain maturation as it is represented in DTI.

Mechanics of biomimetic systems propelled by actin comet tails

NASA Astrophysics Data System (ADS)

Kang, Hyeran; Tambe, Dhananjay; Shenoy, Vivek; Tang, Jay

2009-03-01

The motility of intracellular bacterial pathogens such as Listeria monocytogenes is driven by filamentous actin comet tails in a variety of trajectories. Here, we present the in vitro study on the actin-based movements using spherical beads of different sizes coated with VCA protein, a partial domain of N-Wasp, in platelet extracts. Long term two-dimensional trajectories of the spherical beads motility show characteristic difference than those observed for bacteria, which have both elongated shape and asymmetric expression of the polymerization inducing enzyme. The trajectories also vary sensitively with the bead size and shape. These results provide a useful test to our new analytical model including the rotation of the bead relative to the tail.

An optimal control strategy for two-dimensional motion camouflage with non-holonimic constraints.

PubMed

Rañó, Iñaki

2012-07-01

Motion camouflage is a stealth behaviour observed both in hover-flies and in dragonflies. Existing controllers for mimicking motion camouflage generate this behaviour on an empirical basis or without considering the kinematic motion restrictions present in animal trajectories. This study summarises our formal contributions to solve the generation of motion camouflage as a non-linear optimal control problem. The dynamics of the system capture the kinematic restrictions to motion of the agents, while the performance index ensures camouflage trajectories. An extensive set of simulations support the technique, and a novel analysis of the obtained trajectories contributes to our understanding of possible mechanisms to obtain sensor based motion camouflage, for instance, in mobile robots.

Intersection Detection Based on Qualitative Spatial Reasoning on Stopping Point Clusters

NASA Astrophysics Data System (ADS)

Zourlidou, S.; Sester, M.

2016-06-01

The purpose of this research is to propose and test a method for detecting intersections by analysing collectively acquired trajectories of moving vehicles. Instead of solely relying on the geometric features of the trajectories, such as heading changes, which may indicate turning points and consequently intersections, we extract semantic features of the trajectories in form of sequences of stops and moves. Under this spatiotemporal prism, the extracted semantic information which indicates where vehicles stop can reveal important locations, such as junctions. The advantage of the proposed approach in comparison with existing turning-points oriented approaches is that it can detect intersections even when not all the crossing road segments are sampled and therefore no turning points are observed in the trajectories. The challenge with this approach is that first of all, not all vehicles stop at the same location - thus, the stop-location is blurred along the direction of the road; this, secondly, leads to the effect that nearby junctions can induce similar stop-locations. As a first step, a density-based clustering is applied on the layer of stop observations and clusters of stop events are found. Representative points of the clusters are determined (one per cluster) and in a last step the existence of an intersection is clarified based on spatial relational cluster reasoning, with which less informative geospatial clusters, in terms of whether a junction exists and where its centre lies, are transformed in more informative ones. Relational reasoning criteria, based on the relative orientation of the clusters with their adjacent ones are discussed for making sense of the relation that connects them, and finally for forming groups of stop events that belong to the same junction.

QM/MD studies on graphene growth from small islands on the Ni(111) surface

NASA Astrophysics Data System (ADS)

Jiao, Menggai; Song, Wei; Qian, Hu-Jun; Wang, Ying; Wu, Zhijian; Irle, Stephan; Morokuma, Keiji

2016-01-01

Quantum chemical molecular dynamics simulations of graphene growth from small island precursors in different carbon nucleation densities on the Ni(111) surface at high temperatures have been conducted. The results indicate that small islands are not static, i.e. lateral diffusion and vertical fluctuation are frequently observed. In the case of low carbon nucleation density, carbon atoms or small carbon patches diffuse and attach to the edge of the nuclei to expand the size of the growing carbon network. The growth of graphene precursors is accompanied by the corresponding changes in the bonding of nickel atoms with the precipitation of subsurface carbon atoms. This is because the carbon-carbon interaction is stronger than the nickel-carbon interaction. In the case of high carbon nucleation densities, the dominant ripening mechanism depends on different growth stages. In the initial stage, the coalescence of carbon islands takes place via the Smoluchowski ripening mechanism. In the later stage the Smoluchowski ripening process is damped owing to the higher diffusion barrier of larger clusters and the restriction of movement by self-assembled nickel step edges. The cross-linking mechanism eventually takes over by the coalescence of extended polyyne chains between graphene islands. In either case, the Ostwald ripening process is not found in our molecular dynamics simulations due to the stability of carbon-carbon bonds within the islands. These investigations should be instructive to the control of graphene growth in experiments.Quantum chemical molecular dynamics simulations of graphene growth from small island precursors in different carbon nucleation densities on the Ni(111) surface at high temperatures have been conducted. The results indicate that small islands are not static, i.e. lateral diffusion and vertical fluctuation are frequently observed. In the case of low carbon nucleation density, carbon atoms or small carbon patches diffuse and attach to the edge of the nuclei to expand the size of the growing carbon network. The growth of graphene precursors is accompanied by the corresponding changes in the bonding of nickel atoms with the precipitation of subsurface carbon atoms. This is because the carbon-carbon interaction is stronger than the nickel-carbon interaction. In the case of high carbon nucleation densities, the dominant ripening mechanism depends on different growth stages. In the initial stage, the coalescence of carbon islands takes place via the Smoluchowski ripening mechanism. In the later stage the Smoluchowski ripening process is damped owing to the higher diffusion barrier of larger clusters and the restriction of movement by self-assembled nickel step edges. The cross-linking mechanism eventually takes over by the coalescence of extended polyyne chains between graphene islands. In either case, the Ostwald ripening process is not found in our molecular dynamics simulations due to the stability of carbon-carbon bonds within the islands. These investigations should be instructive to the control of graphene growth in experiments. Electronic supplementary information (ESI) available: There are two movies showing the simulation process and they are provided in separate files. Movie S1 is the evolution of QM/MD simulations of the growth of graphene from one C13 on the Ni(111) surface for trajectory D@C13. Movie S2 is the evolution of QM/MD simulations of the growth of graphene from two C13 species on the Ni(111) surface for trajectory C@2C13. Fig. S1 shows the optimized geometries of C13-G and C13-H on the Ni(111) surface. Fig. S2 is the final structures of trajectories A-J@C13 following 400 ps QM/MD simulation for the Ni(111) + C13 system. Fig. S3 is the final structures of trajectories A-J@2C13 following 350 ps QM/MD simulation for the Ni(111) + 2C13 system. Fig. S4 shows average polygonal carbon ring populations formed during graphene growth from the Ni(111) + C13 and Ni(111) + 2C13 systems. Fig. S5 shows the averaged δ value of the C13 clusters and the nickel catalyst in the Ni(111) + C13 and Ni(111) + 2C13 systems. Fig. S6 depicts the total Mermin free energy as a function of simulation time in the Ni(111) + 2C13 system. See DOI: 10.1039/c5nr07680c

Diffusion properties of conventional and calcium-sensitive MRI contrast agents in the rat cerebral cortex.

PubMed

Hagberg, Gisela E; Mamedov, Ilgar; Power, Anthony; Beyerlein, Michael; Merkle, Hellmut; Kiselev, Valerij G; Dhingra, Kirti; Kubìček, Vojtĕch; Angelovski, Goran; Logothetis, Nikos K

2014-01-01

Calcium-sensitive MRI contrast agents can only yield quantitative results if the agent concentration in the tissue is known. The agent concentration could be determined by diffusion modeling, if relevant parameters were available. We have established an MRI-based method capable of determining diffusion properties of conventional and calcium-sensitive agents. Simulations and experiments demonstrate that the method is applicable both for conventional contrast agents with a fixed relaxivity value and for calcium-sensitive contrast agents. The full pharmacokinetic time-course of gadolinium concentration estimates was observed by MRI before, during and after intracerebral administration of the agent, and the effective diffusion coefficient D* was determined by voxel-wise fitting of the solution to the diffusion equation. The method yielded whole brain coverage with a high spatial and temporal sampling. The use of two types of MRI sequences for sampling of the diffusion time courses was investigated: Look-Locker-based quantitative T(1) mapping, and T(1) -weighted MRI. The observation times of the proposed MRI method is long (up to 20 h) and consequently the diffusion distances covered are also long (2-4 mm). Despite this difference, the D* values in vivo were in agreement with previous findings using optical measurement techniques, based on observation times of a few minutes. The effective diffusion coefficient determined for the calcium-sensitive contrast agents may be used to determine local tissue concentrations and to design infusion protocols that maintain the agent concentration at a steady state, thereby enabling quantitative sensing of the local calcium concentration. Copyright © 2014 John Wiley & Sons, Ltd.

Exploring the complexity of quantum control optimization trajectories.

PubMed

Nanduri, Arun; Shir, Ofer M; Donovan, Ashley; Ho, Tak-San; Rabitz, Herschel

2015-01-07

The control of quantum system dynamics is generally performed by seeking a suitable applied field. The physical objective as a functional of the field forms the quantum control landscape, whose topology, under certain conditions, has been shown to contain no critical point suboptimal traps, thereby enabling effective searches for fields that give the global maximum of the objective. This paper addresses the structure of the landscape as a complement to topological critical point features. Recent work showed that landscape structure is highly favorable for optimization of state-to-state transition probabilities, in that gradient-based control trajectories to the global maximum value are nearly straight paths. The landscape structure is codified in the metric R ≥ 1.0, defined as the ratio of the length of the control trajectory to the Euclidean distance between the initial and optimal controls. A value of R = 1 would indicate an exactly straight trajectory to the optimal observable value. This paper extends the state-to-state transition probability results to the quantum ensemble and unitary transformation control landscapes. Again, nearly straight trajectories predominate, and we demonstrate that R can take values approaching 1.0 with high precision. However, the interplay of optimization trajectories with critical saddle submanifolds is found to influence landscape structure. A fundamental relationship necessary for perfectly straight gradient-based control trajectories is derived, wherein the gradient on the quantum control landscape must be an eigenfunction of the Hessian. This relation is an indicator of landscape structure and may provide a means to identify physical conditions when control trajectories can achieve perfect linearity. The collective favorable landscape topology and structure provide a foundation to understand why optimal quantum control can be readily achieved.

Self-assembly of robotic micro- and nanoswimmers using magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Cheang, U. Kei; Kim, Min Jun

2015-03-01

Micro- and nanoscale robotic swimmers are very promising to significantly enhance the performance of particulate drug delivery by providing high accuracy at extremely small scales. Here, we introduce micro- and nanoswimmers fabricated using self-assembly of nanoparticles and control via magnetic fields. Nanoparticles self-align into parallel chains under magnetization. The swimmers exhibit flexibility under a rotating magnetic field resulting in chiral structures upon deformation, thereby having the prerequisite for non-reciprocal motion to move about at low Reynolds number. The swimmers are actuated wirelessly using an external rotating magnetic field supplied by approximate Helmholtz coils. By controlling the concentration of the suspended magnetic nanoparticles, the swimmers can be modulated into different sizes. Nanoscale swimmers are largely influenced by Brownian motion, as observed from their jerky trajectories. The microswimmers, which are roughly three times larger, are less vulnerable to the effects from Brownian motion. In this paper, we demonstrate responsive directional control of micro- and nanoswimmers and compare their respective diffusivities and trajectories to characterize the implications of Brownian disturbance on the motions of small and large swimmers. We then performed a simulation using a kinematic model for the magnetic swimmers including the stochastic nature of Brownian motion.

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

NASA Astrophysics Data System (ADS)

Thapa, S.; Karki, B. B.

2017-12-01

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

Diffusion approximations to the chemical master equation only have a consistent stochastic thermodynamics at chemical equilibrium

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

Horowitz, Jordan M., E-mail: jordan.horowitz@umb.edu

The stochastic thermodynamics of a dilute, well-stirred mixture of chemically reacting species is built on the stochastic trajectories of reaction events obtained from the chemical master equation. However, when the molecular populations are large, the discrete chemical master equation can be approximated with a continuous diffusion process, like the chemical Langevin equation or low noise approximation. In this paper, we investigate to what extent these diffusion approximations inherit the stochastic thermodynamics of the chemical master equation. We find that a stochastic-thermodynamic description is only valid at a detailed-balanced, equilibrium steady state. Away from equilibrium, where there is no consistent stochasticmore » thermodynamics, we show that one can still use the diffusive solutions to approximate the underlying thermodynamics of the chemical master equation.« less

Fractional Brownian motion run with a multi-scaling clock mimics diffusion of spherical colloids in microstructural fluids.

PubMed

Park, Moongyu; Cushman, John Howard; O'Malley, Dan

2014-09-30

The collective molecular reorientations within a nematic liquid crystal fluid bathing a spherical colloid cause the colloid to diffuse anomalously on a short time scale (i.e., as a non-Brownian particle). The deformations and fluctuations of long-range orientational order in the liquid crystal profoundly influence the transient diffusive regimes. Here we show that an anisotropic fractional Brownian process run with a nonlinear multiscaling clock effectively mimics this collective and transient phenomenon. This novel process has memory, Gaussian increments, and a multiscale mean square displacement that can be chosen independently from the fractal dimension of a particle trajectory. The process is capable of modeling multiscale sub-, super-, or classical diffusion. The finite-size Lyapunov exponents for this multiscaling process are defined for future analysis of related mixing processes.

Wright-Fisher diffusion bridges.

PubMed

Griffiths, Robert C; Jenkins, Paul A; Spanò, Dario

2017-10-06

The trajectory of the frequency of an allele which begins at x at time 0 and is known to have frequency z at time T can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when x=z=0 are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time T. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy of the population in a bridge from a time t∈(0,T). In a bridge with allele frequencies of 0 at times 0 and T the coalescence structure is that the population coalesces in two directions from t to 0 and t to T such that there is just one lineage of the allele under consideration at times 0 and T. The genealogy in Wright-Fisher diffusion bridges with selection is more complex than in the neutral model, but still with the property of the population branching and coalescing in two directions from time t∈(0,T). The density of the frequency of an allele at time t is expressed in a way that shows coalescence in the two directions. A new algorithm for exact simulation of a neutral Wright-Fisher bridge is derived. This follows from knowing the density of the frequency in a bridge and exact simulation from the Wright-Fisher diffusion. The genealogy of the neutral Wright-Fisher bridge is also modelled by branching Pólya urns, extending a representation in a Wright-Fisher diffusion. This is a new very interesting representation that relates Wright-Fisher bridges to classical urn models in a Bayesian setting. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental Evaluation of an Integrated Datalink and Automation-Based Strategic Trajectory Concept

NASA Technical Reports Server (NTRS)

Mueller, Eric

2007-01-01

This paper presents research on the interoperability of trajectory-based automation concepts and technologies with modern Flight Management Systems and datalink communication available on many of today s commercial aircraft. A tight integration of trajectory-based ground automation systems with the aircraft Flight Management System through datalink will enable mid-term and far-term benefits from trajectory-based automation methods. A two-way datalink connection between the trajectory-based automation resident in the Center/TRACON Automation System and the Future Air Navigation System-1 integrated FMS/datalink in NASA Ames B747-400 Level D simulator has been established and extensive simulation of the use of datalink messages to generate strategic trajectories completed. A strategic trajectory is defined as an aircraft deviation needed to solve a conflict or honor a route request and then merge the aircraft back to its nominal preferred trajectory using a single continuous trajectory clearance. Engineers on the ground side of the datalink generated lateral and vertical trajectory clearances and transmitted them to the Flight Management System of the 747; the airborne automation then flew the new trajectory without human intervention, requiring the flight crew only to review and to accept the trajectory. This simulation established the protocols needed for a significant majority of the trajectory change types required to solve a traffic conflict or deviate around weather. This demonstration provides a basis for understanding the requirements for integration of trajectory-based automation with current Flight Management Systems and datalink to support future National Airspace System operations.

State-specific tunneling lifetimes from classical trajectories: H-atom dissociation in electronically excited pyrrole

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

Xie, Weiwei; Domcke, Wolfgang; Farantos, Stavros C.

A trajectory method of calculating tunneling probabilities from phase integrals along straight line tunneling paths, originally suggested by Makri and Miller [J. Chem. Phys. 91, 4026 (1989)] and recently implemented by Truhlar and co-workers [Chem. Sci. 5, 2091 (2014)], is tested for one- and two-dimensional ab initio based potentials describing hydrogen dissociation in the {sup 1}B{sub 1} excited electronic state of pyrrole. The primary observables are the tunneling rates in a progression of bending vibrational states lying below the dissociation barrier and their isotope dependences. Several initial ensembles of classical trajectories have been considered, corresponding to the quasiclassical and themore » quantum mechanical samplings of the initial conditions. It is found that the sampling based on the fixed energy Wigner density gives the best agreement with the quantum mechanical dissociation rates.« less

The trajectory and atmospheric impact of asteroid 2014 AA

NASA Astrophysics Data System (ADS)

Farnocchia, Davide; Chesley, Steven R.; Brown, Peter G.; Chodas, Paul W.

2016-08-01

Near-Earth asteroid 2014 AA entered the Earth's atmosphere on 2014 January 2, only 21 h after being discovered by the Catalina Sky Survey. In this paper we compute the trajectory of 2014 AA by combining the available optical astrometry, seven ground-based observations over 69 min, and the International Monitoring System detection of the atmospheric impact infrasonic airwaves in a least-squares orbit estimation filter. The combination of these two sources of observations results in a tremendous improvement in the orbit uncertainties. The impact time is 3:05 UT with a 1σ uncertainty of 6 min, while the impact location corresponds to a west longitude of 44.2° and a latitude of 13.1° with a 1σ uncertainty of 140 km. The minimum impact energy estimated from the infrasound data and the impact velocity result in an estimated minimum mass of 22.6 t. By propagating the trajectory of 2014 AA backwards we find that the only window for finding precovery observations is for the three days before its discovery.

Robust back-stepping output feedback trajectory tracking for quadrotors via extended state observer and sigmoid tracking differentiator

NASA Astrophysics Data System (ADS)

Shao, Xingling; Liu, Jun; Wang, Honglun

2018-05-01

In this paper, a robust back-stepping output feedback trajectory tracking controller is proposed for quadrotors subject to parametric uncertainties and external disturbances. Based on the hierarchical control principle, the quadrotor dynamics is decomposed into translational and rotational subsystems to facilitate the back-stepping control design. With given model information incorporated into observer design, a high-order extended state observer (ESO) that relies only on position measurements is developed to estimate the remaining unmeasurable states and the lumped disturbances in rotational subsystem simultaneously. To overcome the problem of "explosion of complexity" in the back-stepping design, the sigmoid tracking differentiator (STD) is introduced to compute the derivative of virtual control laws. The advantage is that the proposed controller via output-feedback scheme not only can ensure good tracking performance using very limited information of quadrotors, but also has the ability of handling the undesired uncertainties. The stability analysis is established using the Lyapunov theory. Simulation results demonstrate the effectiveness of the proposed control scheme in achieving a guaranteed tracking performance with respect to an 8-shaped reference trajectory.

Two Dimensional Drug Diffusion Between Nanoparticles and Fractal Tumors

NASA Astrophysics Data System (ADS)

Samioti, S. E.; Karamanos, K.; Tsiantis, A.; Papathanasiou, A.; Sarris, I.

2017-11-01

Drug delivery methods based on nanoparticles are some of the most promising medical applications in nanotechnology to treat cancer. It is observed that drug released by nanoparticles to the cancer tumors may be driven by diffusion. A fractal tumor boundary of triangular Von Koch shape is considered here and the diffusion mechanism is studied for different drug concentrations and increased fractality. A high order Finite Elements method based on the Fenics library is incorporated in fine meshes to fully resolve these irregular boundaries. Drug concentration, its transfer rates and entropy production are calculated in an up to forth order fractal iteration boundaries. We observed that diffusion rate diminishes for successive prefractal generations. Also, the entropy production around the system changes greatly as the order of the fractal curve increases. Results indicate with precision where the active sites are, in which most of the diffusion takes place and thus drug arrives to the tumor.

Novel algorithm and MATLAB-based program for automated power law analysis of single particle, time-dependent mean-square displacement

NASA Astrophysics Data System (ADS)

Umansky, Moti; Weihs, Daphne

2012-08-01

In many physical and biophysical studies, single-particle tracking is utilized to reveal interactions, diffusion coefficients, active modes of driving motion, dynamic local structure, micromechanics, and microrheology. The basic analysis applied to those data is to determine the time-dependent mean-square displacement (MSD) of particle trajectories and perform time- and ensemble-averaging of similar motions. The motion of particles typically exhibits time-dependent power-law scaling, and only trajectories with qualitatively and quantitatively comparable MSD should be ensembled. Ensemble averaging trajectories that arise from different mechanisms, e.g., actively driven and diffusive, is incorrect and can result inaccurate correlations between structure, mechanics, and activity. We have developed an algorithm to automatically and accurately determine power-law scaling of experimentally measured single-particle MSD. Trajectories can then categorized and grouped according to user defined cutoffs of time, amplitudes, scaling exponent values, or combinations. Power-law fits are then provided for each trajectory alongside categorized groups of trajectories, histograms of power laws, and the ensemble-averaged MSD of each group. The codes are designed to be easily incorporated into existing user codes. We expect that this algorithm and program will be invaluable to anyone performing single-particle tracking, be it in physical or biophysical systems. Catalogue identifier: AEMD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 25 892 No. of bytes in distributed program, including test data, etc.: 5 572 780 Distribution format: tar.gz Programming language: MATLAB (MathWorks Inc.) version 7.11 (2010b) or higher, program should also be backwards compatible. Symbolic Math Toolboxes (5.5) is required. The Curve Fitting Toolbox (3.0) is recommended. Computer: Tested on Windows only, yet should work on any computer running MATLAB. In Windows 7, should be used as administrator, if the user is not the administrator the program may not be able to save outputs and temporary outputs to all locations. Operating system: Any supporting MATLAB (MathWorks Inc.) v7.11 / 2010b or higher. Supplementary material: Sample output files (approx. 30 MBytes) are available. Classification: 12 External routines: Several MATLAB subfunctions (m-files), freely available on the web, were used as part of and included in, this code: count, NaN suite, parseArgs, roundsd, subaxis, wcov, wmean, and the executable pdfTK.exe. Nature of problem: In many physical and biophysical areas employing single-particle tracking, having the time-dependent power-laws governing the time-averaged meansquare displacement (MSD) of a single particle is crucial. Those power laws determine the mode-of-motion and hint at the underlying mechanisms driving motion. Accurate determination of the power laws that describe each trajectory will allow categorization into groups for further analysis of single trajectories or ensemble analysis, e.g. ensemble and time-averaged MSD. Solution method: The algorithm in the provided program automatically analyzes and fits time-dependent power laws to single particle trajectories, then group particles according to user defined cutoffs. It accepts time-dependent trajectories of several particles, each trajectory is run through the program, its time-averaged MSD is calculated, and power laws are determined in regions where the MSD is linear on a log-log scale. Our algorithm searches for high-curvature points in experimental data, here time-dependent MSD. Those serve as anchor points for determining the ranges of the power-law fits. Power-law scaling is then accurately determined and error estimations of the parameters and quality of fit are provided. After all single trajectory time-averaged MSDs are fit, we obtain cutoffs from the user to categorize and segment the power laws into groups; cutoff are either in exponents of the power laws, time of appearance of the fits, or both together. The trajectories are sorted according to the cutoffs and the time- and ensemble-averaged MSD of each group is provided, with histograms of the distributions of the exponents in each group. The program then allows the user to generate new trajectory files with trajectories segmented according to the determined groups, for any further required analysis. Additional comments: README file giving the names and a brief description of all the files that make-up the package and clear instructions on the installation and execution of the program is included in the distribution package. Running time: On an i5 Windows 7 machine with 4 GB RAM the automated parts of the run (excluding data loading and user input) take less than 45 minutes to analyze and save all stages for an 844 trajectory file, including optional PDF save. Trajectory length did not affect run time (tested up to 3600 frames/trajectory), which was on average 3.2±0.4 seconds per trajectory.

FuzzObserver

NASA Technical Reports Server (NTRS)

Howard, Ayanna; Bayard, David

2006-01-01

Fuzzy Feature Observation Planner for Small Body Proximity Observations (FuzzObserver) is a developmental computer program, to be used along with other software, for autonomous planning of maneuvers of a spacecraft near an asteroid, comet, or other small astronomical body. Selection of terrain features and estimation of the position of the spacecraft relative to these features is an essential part of such planning. FuzzObserver contributes to the selection and estimation by generating recommendations for spacecraft trajectory adjustments to maintain the spacecraft's ability to observe sufficient terrain features for estimating position. The input to FuzzObserver consists of data from terrain images, including sets of data on features acquired during descent toward, or traversal of, a body of interest. The name of this program reflects its use of fuzzy logic to reason about the terrain features represented by the data and extract corresponding trajectory-adjustment rules. Linguistic fuzzy sets and conditional statements enable fuzzy systems to make decisions based on heuristic rule-based knowledge derived by engineering experts. A major advantage of using fuzzy logic is that it involves simple arithmetic calculations that can be performed rapidly enough to be useful for planning within the short times typically available for spacecraft maneuvers.

Theoretical Relationships between Luminescence and Hillslope Soil Vertical Diffusivity: a Numerical Modeling Approach

NASA Astrophysics Data System (ADS)

Gray, H. J.; Tucker, G. E.; Mahan, S.

2017-12-01

Luminescence is a property of matter that can be used to obtain depositional ages from fine sand. Luminescence generates due to exposure to background ionizing radiation and is removed by sunlight exposure in a process known as bleaching. There is evidence to suggest that luminescence can also serve as a sediment tracer in fluvial and hillslope environments. For hillslope environments, it has been suggested that the magnitude of luminescence as a function of soil depth is related to the strength of soil mixing. Hillslope soils with a greater extent of mixing will have previously surficial sand grains moved to greater depths in a soil column. These previously surface-exposed grains will contain a lower luminescence than those which have never seen the surface. To attempt to connect luminescence profiles with soil mixing rate, here defined as the soil vertical diffusivity, I conduct numerical modelling of particles in hillslope soils coupled with equations describing the physics of luminescence. I use recently published equations describing the trajectories of particles under both exponential and uniform soil velocity soils profiles and modify them to include soil diffusivity. Results from the model demonstrates a strong connection between soil diffusivity and luminescence. Both the depth profiles of luminescence and the total percent of surface exposed grains will change drastically based on the magnitude of the diffusivity. This suggests that luminescence could potentially be used to infer the magnitude of soil diffusivity. However, I test other variables such as the soil production rate, e-folding length of soil velocity, background dose rate, and soil thickness, and I find these other variables can also affect the relationship between luminescence and diffusivity. This suggests that these other variables may need to be constrained prior to any inferences of soil diffusivity from luminescence measurements. Further field testing of the model in areas where the soil vertical diffusivity and other parameters are independently known will provide a test of this potential new method.

Trajectories of thermospheric air parcels flowing over Alaska, reconstructed from ground-based wind measurements

NASA Astrophysics Data System (ADS)

Dhadly, Manbharat; Conde, Mark

2017-06-01

It is widely presumed that the convective stability and enormous kinematic viscosity of Earth's upper thermosphere hinders development of both horizontal and vertical wind shears and other gradients. Any strong local structure (over scale sizes of several hundreds of kilometers) that might somehow form would be expected to dissipate rapidly. Air flow in such an atmosphere should be relatively simple, and transport effects only slowly disperse and mix air masses. However, our observations show that wind fields in Earth's thermosphere have much more local-scale structure than usually predicated by current modeling techniques, at least at auroral latitudes; they complicate air parcel trajectories enormously, relative to typical expectations. For tracing air parcels, we used wind measurements of an all-sky Scanning Doppler Fabry-Perot interferometer and reconstructed time-resolved two-dimensional maps of the horizontal vector wind field to infer forward and backward air parcel trajectories over time. This is the first comprehensive study to visualize the complex motions of thermospheric air parcels carried through the actual observed local-scale structures in the high-latitude winds. Results show that thermospheric air parcel transport is a very difficult observational problem, because the trajectories followed are very sensitive to the detailed features of the driving wind field. To reconstruct the actual motion of a given air parcel requires wind measurements everywhere along the trajectory followed, with spatial resolutions of 100 km or less, and temporal resolutions of a few minutes or better. Understanding such transport is important, for example, in predicting the global-scale impacts of aurorally generated composition perturbations.

Influence of air parcel trajectories on CO2 and CH4 concentrations in the northern plateau of the Iberian Peninsula

NASA Astrophysics Data System (ADS)

Pérez, Isidro A.; Sánchez, M. Luisa; García, M. Ángeles; Pardo, Nuria

2018-01-01

This study presents a simpler procedure for grouping air parcel back trajectories than others previously applied. Two-day air parcel back trajectories reaching an unpolluted site in the centre of the northern plateau of the Iberian Peninsula were calculated over a three-year period using the METEX model. A procedure based on the kernel density calculation was applied to the direction of each trajectory centroid to determine groups of trajectories. This method is much faster than the cluster procedure when it comes to retaining the directional details of groups. Seasonal analysis of six groups of trajectories revealed that the Atlantic origin prevailed against displacement from northern Europe. Moreover, Mediterranean and particularly African trajectories were infrequent, probably due to the rough peninsular orography in these directions. The location of air trajectories reaching the study site was described using a surface classification below the air parcels with improved spatial resolution compared to previous analyses. Local contribution was very marked, particularly in summer. Mean trajectories were calculated for each group together with meteorological features and CO2 and CH4 concentrations. Groups may be identified by their mean temperature, wind speed, elevation and distance values. However, only two groups should be considered when analysing the two trace gases, one for trajectories from the Atlantic Ocean and the second for trajectories from the continent. Contrasts of about 4 ppm for CO2 in summer and 0.023 ppm for CH4 in winter were observed, revealing that air trajectories from the Atlantic Ocean were cleaner than those arriving from the continent. These differences were attributed to higher air stagnation over land.

Trajectory Optimization Using Adjoint Method and Chebyshev Polynomial Approximation for Minimizing Fuel Consumption During Climb

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Hornby, Gregory; Ishihara, Abe

2013-01-01

This paper describes two methods of trajectory optimization to obtain an optimal trajectory of minimum-fuel- to-climb for an aircraft. The first method is based on the adjoint method, and the second method is based on a direct trajectory optimization method using a Chebyshev polynomial approximation and cubic spine approximation. The approximate optimal trajectory will be compared with the adjoint-based optimal trajectory which is considered as the true optimal solution of the trajectory optimization problem. The adjoint-based optimization problem leads to a singular optimal control solution which results in a bang-singular-bang optimal control.

Statistical signatures of a targeted search by bacteria

NASA Astrophysics Data System (ADS)

Jashnsaz, Hossein; Anderson, Gregory G.; Pressé, Steve

2017-12-01

Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium’s natural habitat, striking phenomena—such as the volcano effect or banding—have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources. Here we use a theoretical model to identify statistical signatures of a targeted search toward point food sources, such as prey. Our model is constructed on the basis that bacteria use temporal comparisons to bias their random walk, exhibit finite memory and are subject to random (Brownian) motion as well as signaling noise. The advantage with using a stochastic model-based approach is that a stochastic model may be parametrized from individual stochastic bacterial trajectories but may then be used to generate a very large number of simulated trajectories to explore average behaviors obtained from stochastic search strategies. For example, our model predicts that a bacterium’s diffusion coefficient increases as it approaches the point source and that, in the presence of multiple sources, bacteria may take substantially longer to locate their first source giving the impression of an untargeted search strategy.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

NASA Astrophysics Data System (ADS)

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-09-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

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

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlapmore » with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.« less

Callosal degeneration topographically correlated with cognitive function in amnestic mild cognitive impairment and Alzheimer's disease dementia.

PubMed

Wang, Pei-Ning; Chou, Kun-Hsien; Chang, Ni-Jung; Lin, Ker-Neng; Chen, Wei-Ta; Lan, Gong-Yau; Lin, Ching-Po; Lirng, Jiing-Feng

2014-04-01

Degeneration of the corpus callosum (CC) is evident in the pathogenesis of Alzheimer's disease (AD). However, the correlation of microstructural damage in the CC on the cognitive performance of patients with amnestic mild cognitive impairment (aMCI) and AD dementia is undetermined. We enrolled 26 normal controls, 24 patients with AD dementia, and 40 single-domain aMCI patients with at least grade 1 hippocampal atrophy and isolated memory impairment. Diffusion tensor imaging (DTI) with fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (DA), and radial diffusivity (DR) were measured. The entire CC was parcellated based on fiber trajectories to specific cortical Brodmann areas using a probabilistic tractography method. The relationship between the DTI measures in the subregions of the CC and cognitive performance was examined. Although the callosal degeneration in the patients with aMCI was less extended than in the patients with AD dementia, degeneration was already exhibited in several subregions of the CC at the aMCI stage. Scores of various neuropsychological tests were correlated to the severity of microstructural changes in the subregional CC connecting to functionally corresponding cortical regions. Our results confirm that CC degeneration is noticeable as early as the aMCI stage of AD and the disconnection of the CC subregional fibers to the corresponding Brodmann areas has an apparent impact on the related cognitive performance. Copyright © 2013 Wiley Periodicals, Inc.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

PubMed Central

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-01-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space. PMID:25240340

Two-photon time-lapse microscopy of BODIPY-cholesterol reveals anomalous sterol diffusion in chinese hamster ovary cells

PubMed Central

2012-01-01

Background Cholesterol is an important membrane component, but our knowledge about its transport in cells is sparse. Previous imaging studies using dehydroergosterol (DHE), an intrinsically fluorescent sterol from yeast, have established that vesicular and non-vesicular transport modes contribute to sterol trafficking from the plasma membrane. Significant photobleaching, however, limits the possibilities for in-depth analysis of sterol dynamics using DHE. Co-trafficking studies with DHE and the recently introduced fluorescent cholesterol analog BODIPY-cholesterol (BChol) suggested that the latter probe has utility for prolonged live-cell imaging of sterol transport. Results We found that BChol is very photostable under two-photon (2P)-excitation allowing the acquisition of several hundred frames without significant photobleaching. Therefore, long-term tracking and diffusion measurements are possible. Two-photon temporal image correlation spectroscopy (2P-TICS) provided evidence for spatially heterogeneous diffusion constants of BChol varying over two orders of magnitude from the cell interior towards the plasma membrane, where D ~ 1.3 μm2/s. Number and brightness (N&B) analysis together with stochastic simulations suggest that transient partitioning of BChol into convoluted membranes slows local sterol diffusion. We observed sterol endocytosis as well as fusion and fission of sterol-containing endocytic vesicles. The mobility of endocytic vesicles, as studied by particle tracking, is well described by a model for anomalous subdiffusion on short time scales with an anomalous exponent α ~ 0.63 and an anomalous diffusion constant of Dα = 1.95 x 10-3 μm2/sα. On a longer time scale (t > ~5 s), a transition to superdiffusion consistent with slow directed transport with an average velocity of v ~ 6 x 10-3 μm/s was observed. We present an analytical model that bridges the two regimes and fit this model to vesicle trajectories from control cells and cells with disrupted microtubule or actin filaments. Both treatments reduced the anomalous diffusion constant and the velocity by ~40-50%. Conclusions The mobility of sterol-containing vesicles on the short time scale could reflect dynamic rearrangements of the cytoskeleton, while directed transport of sterol vesicles occurs likely along both, microtubules and actin filaments. Spatially varying anomalous diffusion could contribute to fine-tuning and local regulation of intracellular sterol transport. PMID:23078907

Analysis of Bacteriophage Motion Through a Non-Static Medium

NASA Astrophysics Data System (ADS)

Dickey, Samuel A.

In this work, I investigated the motion of bacteriophages (phages) through their mucosal environment. Recently, biologists here at San Diego State University have proposed a model in which phages move sub-diffusively through mucosal fibers in their hunt for bacteria to prey upon. Through a Hoc protein located upon the capsid of the wild type phages, these phages are allowed to bind to mucosal fibers, and extend the amount of time spent in a single location hunting for bacteria. Contrarily, the delta hoc phages are unable to. The ability of the wild type phages to attach itself to mucosal fibers is what enables its subdiffusive behavior. This study investigates the diffusive behavior of these phages in different mucus concentrations. It expands on previous studies in which only short tracks could be observed. In the study at hand, phages are imaged in a highly doped optical fiber with varying concentrations of mucus present in solution. Through rigorous image processing techniques, trajectories of these phages are created with a minimized noise level. We developed code that created position-versus-time files for each phage present in the experimental data. These files were then further analyzed. The sub-diffusive behavior is investigated via mean squared displacement versus time. The diffusive exponent can be obtained from fits to these data. For large enough time intervals, I always obtained an exponent of one for space and time averaged data. This indicates that the diffusion is normal, or sub-diffusive of the CTRW type. CTRW sub-diffusive motion is characterized by waiting times that resemble a power law distribution and have long tails. I investigate these stuck time distributions, however am unable to determine if a power law or exponential fits the data best. Moreover, the distribution gives the same power law exponent for phages moving through water, or mucus, for wild type and delta hoc phages. These exponents would predict super-diffusive instead of sub-diffusive behavior. We conclude that many of these problems result from the small amount of data available to us and the still primitive conditions of the setup at the time the data were collected.

Trajectory-Based Loads for the Ares I-X Test Flight Vehicle

NASA Technical Reports Server (NTRS)

Vause, Roland F.; Starr, Brett R.

2011-01-01

In trajectory-based loads, the structural engineer treats each point on the trajectory as a load case. Distributed aero, inertial, and propulsion forces are developed for the structural model which are equivalent to the integrated values of the trajectory model. Free-body diagrams are then used to solve for the internal forces, or loads, that keep the applied aero, inertial, and propulsion forces in dynamic equilibrium. There are several advantages to using trajectory-based loads. First, consistency is maintained between the integrated equilibrium equations of the trajectory analysis and the distributed equilibrium equations of the structural analysis. Second, the structural loads equations are tied to the uncertainty model for the trajectory systems analysis model. Atmosphere, aero, propulsion, mass property, and controls uncertainty models all feed into the dispersions that are generated for the trajectory systems analysis model. Changes in any of these input models will affect structural loads response. The trajectory systems model manages these inputs as well as the output from the structural model over thousands of dispersed cases. Large structural models with hundreds of thousands of degrees of freedom would execute too slowly to be an efficient part of several thousand system analyses. Trajectory-based loads provide a means for the structures discipline to be included in the integrated systems analysis. Successful applications of trajectory-based loads methods for the Ares I-X vehicle are covered in this paper. Preliminary design loads were based on 2000 trajectories using Monte Carlo dispersions. Range safety loads were tied to 8423 malfunction turn trajectories. In addition, active control system loads were based on 2000 preflight trajectories using Monte Carlo dispersions.

Trajectories of change in depression severity during treatment with antidepressants.

PubMed

Uher, R; Muthén, B; Souery, D; Mors, O; Jaracz, J; Placentino, A; Petrovic, A; Zobel, A; Henigsberg, N; Rietschel, M; Aitchison, K J; Farmer, A; McGuffin, P

2010-08-01

Response and remission defined by cut-off values on the last observed depression severity score are commonly used as outcome criteria in clinical trials, but ignore the time course of symptomatic change and may lead to inefficient analyses. We explore alternative categorization of outcome by naturally occurring trajectories of symptom change. Growth mixture models were applied to repeated measurements of depression severity in 807 participants with major depression treated for 12 weeks with escitalopram or nortriptyline in the part-randomized Genome-based Therapeutic Drugs for Depression study. Latent trajectory classes were validated as outcomes in drug efficacy comparison and pharmacogenetic analyses. The final two-piece growth mixture model categorized participants into a majority (75%) following a gradual improvement trajectory and the remainder following a trajectory with rapid initial improvement. The rapid improvement trajectory was over-represented among nortriptyline-treated participants and showed an antidepressant-specific pattern of pharmacogenetic associations. In contrast, conventional response and remission favoured escitalopram and produced chance results in pharmacogenetic analyses. Controlling for drop-out reduced drug differences on response and remission but did not affect latent trajectory results. Latent trajectory mixture models capture heterogeneity in the development of clinical response after the initiation of antidepressants and provide an outcome that is distinct from traditional endpoint measures. It differentiates between antidepressants with different modes of action and is robust against bias due to differential discontinuation.

Can Universal SEL Programs Benefit Universally? Effects of the Positive Action Program on Multiple Trajectories of Social-Emotional and Misconduct Behaviors

PubMed Central

Duncan, Robert; Washburn, Isaac J.; Lewis, Kendra M.; Bavarian, Niloofar; DuBois, David L.; Acock, Alan C.; Vuchinich, Samuel; Flay, Brian R.

2016-01-01

Behavioral trajectories during middle childhood are predictive of consequential outcomes later in life (e.g., substance abuse, violence). Social and emotional learning (SEL) programs are designed to promote trajectories that reflect both growth in positive behaviors and inhibited development of negative behaviors. The current study used growth mixture models to examine effects of the Positive Action program (PA) on behavioral trajectories of social-emotional and character development (SECD) and misconduct using data from a cluster-randomized trial that involved 14 schools and a sample of predominately low-income, urban youth followed from 3rd through 8th grade. For SECD, findings indicated that PA was similarly effective at improving trajectories within latent classes characterized as “High/declining” and “Low/stable”. Favorable program effects were likewise evident to a comparable degree for misconduct across observed latent classes that reflected “Low/rising” and “High/rising” trajectories. These findings suggest that PA and perhaps other school-based universal SEL programs have the potential to yield comparable benefits across subgroups of youth with differing trajectories of positive and negative behaviors, making them promising strategies for achieving the intended goal of school-wide improvements in student outcomes. PMID:28028741

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

PubMed Central

Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D.; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll.

2016-01-01

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. PMID:26612862

Aging underdamped scaled Brownian motion: Ensemble- and time-averaged particle displacements, nonergodicity, and the failure of the overdamping approximation.

PubMed

Safdari, Hadiseh; Cherstvy, Andrey G; Chechkin, Aleksei V; Bodrova, Anna; Metzler, Ralf

2017-01-01

We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times. In particular, we quantify the ballistic regime for the MSD and the time-averaged MSD as well as the spread of individual time-averaged MSD trajectories. One of the main effects we observe is that, both for the MSD and the time-averaged MSD, for superdiffusive UDSBM the ballistic regime is much shorter than for ordinary Brownian motion. In contrast, for subdiffusive UDSBM, the ballistic region extends to much longer diffusion times. Therefore, particular care needs to be taken under what conditions the overdamped limit indeed provides a correct description, even in the long time limit. We also analyze to what extent ergodicity in the Boltzmann-Khinchin sense in this nonstationary system is broken, both for subdiffusive and superdiffusive UDSBM. Finally, the limiting case of ultraslow UDSBM is considered, with a mixed logarithmic and power-law dependence of the ensemble- and time-averaged MSDs of the particles. In the limit of strong aging, remarkably, the ordinary UDSBM and the ultraslow UDSBM behave similarly in the short time ballistic limit. The approaches developed here open ways for considering other stochastic processes under physically important conditions when a finite particle mass and aging in the system cannot be neglected.

Aging underdamped scaled Brownian motion: Ensemble- and time-averaged particle displacements, nonergodicity, and the failure of the overdamping approximation

NASA Astrophysics Data System (ADS)

Safdari, Hadiseh; Cherstvy, Andrey G.; Chechkin, Aleksei V.; Bodrova, Anna; Metzler, Ralf

2017-01-01

We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times. In particular, we quantify the ballistic regime for the MSD and the time-averaged MSD as well as the spread of individual time-averaged MSD trajectories. One of the main effects we observe is that, both for the MSD and the time-averaged MSD, for superdiffusive UDSBM the ballistic regime is much shorter than for ordinary Brownian motion. In contrast, for subdiffusive UDSBM, the ballistic region extends to much longer diffusion times. Therefore, particular care needs to be taken under what conditions the overdamped limit indeed provides a correct description, even in the long time limit. We also analyze to what extent ergodicity in the Boltzmann-Khinchin sense in this nonstationary system is broken, both for subdiffusive and superdiffusive UDSBM. Finally, the limiting case of ultraslow UDSBM is considered, with a mixed logarithmic and power-law dependence of the ensemble- and time-averaged MSDs of the particles. In the limit of strong aging, remarkably, the ordinary UDSBM and the ultraslow UDSBM behave similarly in the short time ballistic limit. The approaches developed here open ways for considering other stochastic processes under physically important conditions when a finite particle mass and aging in the system cannot be neglected.

New aspects in single-body meteor physics

NASA Astrophysics Data System (ADS)

Pecina, P.; Ceplecha, Z.

1983-03-01

An exact analytical solution of the atmospheric meteoroid single-body problem is presented expressing the distance along the trajectory as a function of time, which yields a least-square fit of the observed trajectory, and analytical expressions for the velocity at the point of maximum deceleration are derived. These results are used to determine the ablation coefficient from observations. These methods are applied to 17 Prairie Network fireballs observed below the maximum deceleration point and to the Innisfree fireball, and the results are found to be superior to the ones obtained with the usual interpolation formula. A model of luminous efficiencies for small velocities and for masses up to several hundred grams based on data on Innisfree and on artificial rocketry meteors is proposed and applied to separate the shape-density coefficient from the meteoroid mass.

Multicellular Self-Organization of P. aeruginosa due to Interactions with Secreted Trails.

PubMed

Gelimson, Anatolij; Zhao, Kun; Lee, Calvin K; Kranz, W Till; Wong, Gerard C L; Golestanian, Ramin

2016-10-21

Guided movement in response to slowly diffusing polymeric trails provides a unique mechanism for self-organization of some microorganisms. To elucidate how this signaling route leads to microcolony formation, we experimentally probe the trajectory and orientation of Pseudomonas aeruginosa that propel themselves on a surface using type IV pili motility appendages, which preferentially attach to deposited exopolysaccharides. We construct a stochastic model by analyzing single-bacterium trajectories and show that the resulting theoretical prediction for the many-body behavior of the bacteria is in quantitative agreement with our experimental characterization of how cells explore the surface via a power-law strategy.

Longitudinal modelling of theory-based depressive vulnerabilities, depression trajectories and poor outcomes post-ACS.

PubMed

Keegan, Conor; Conroy, Ronán; Doyle, Frank

2016-02-01

Depression is associated with increased mortality in patients with acute coronary syndrome (ACS). However, little is known about the theoretical causes of depression trajectories post-ACS, and whether these trajectories predict subsequent morbidity/mortality. We tested a longitudinal model of depressive vulnerabilities, trajectories and mortality. A prospective observational study of 374 ACS patients was conducted. Participants completed questionnaires on theoretical vulnerabilities (interpersonal life events, reinforcing events, cognitive distortions, and Type D personality) during hospitalisation and depression at baseline and 3, 6 and 12 months post-hospitalisation. Latent class analysis determined trajectories of depression. Path analysis was used to test relationships among vulnerabilities, depression trajectories and outcomes (combination of 1-year morbidity and 7-year mortality). Vulnerabilities independently predicted persistent and subthreshold depression trajectory categories, with effect sizes significantly highest for persistent depression. Both subthreshold and persistent depression trajectories were significant predictors of morbidity/mortality (e.g. persistent depression OR=2.4, 95% CI=1.8-3.1, relative to never depressed). Causality cannot be inferred from these associations. We had no measures of history of depression or treatments, which may affect associations. Theoretical vulnerabilities predicted depression trajectories, which in turn predicted increased morbidity/mortality, demonstrating for the first time a potential longitudinal chain of events post-ACS. This longitudinal model has important practical implications as clinicians can use vulnerability measures to identify those at most risk of poor outcomes. Copyright © 2015. Published by Elsevier B.V.

An incremental DPMM-based method for trajectory clustering, modeling, and retrieval.

PubMed

Hu, Weiming; Li, Xi; Tian, Guodong; Maybank, Stephen; Zhang, Zhongfei

2013-05-01

Trajectory analysis is the basis for many applications, such as indexing of motion events in videos, activity recognition, and surveillance. In this paper, the Dirichlet process mixture model (DPMM) is applied to trajectory clustering, modeling, and retrieval. We propose an incremental version of a DPMM-based clustering algorithm and apply it to cluster trajectories. An appropriate number of trajectory clusters is determined automatically. When trajectories belonging to new clusters arrive, the new clusters can be identified online and added to the model without any retraining using the previous data. A time-sensitive Dirichlet process mixture model (tDPMM) is applied to each trajectory cluster for learning the trajectory pattern which represents the time-series characteristics of the trajectories in the cluster. Then, a parameterized index is constructed for each cluster. A novel likelihood estimation algorithm for the tDPMM is proposed, and a trajectory-based video retrieval model is developed. The tDPMM-based probabilistic matching method and the DPMM-based model growing method are combined to make the retrieval model scalable and adaptable. Experimental comparisons with state-of-the-art algorithms demonstrate the effectiveness of our algorithm.

Unconventional Constraints on Nitrogen Chemistry using DC3 Observations and Trajectory-based Chemical Modeling

NASA Astrophysics Data System (ADS)

Shu, Q.; Henderson, B. H.

2017-12-01

Chemical transport models underestimate nitrogen dioxide observations in the upper troposphere (UT). Previous research in the UT succeeded in combining model predictions with field campaign measurements to demonstrate that the nitric acid formation rate (HO + NO2 → HNO3 (R1)) is overestimated by 22% (Henderson et al., 2012). A subsequent publication (Seltzer et al., 2015) demonstrated that single chemical constraint alters ozone and aerosol formation/composition. This work attempts to replicate previous chemical constraints with newer observations and a different modeling framework. We apply the previously successful constraint framework to Deep Convection Clouds and Chemistry (DC3). DC3 is a more recent field campaign where simulated nitrogen imbalances still exist. Freshly convected air parcels, identified in the DC3 dataset, as initial coordinates to initiate Lagrangian trajectories. Along each trajectory, we simulate the air parcel chemical state. Samples along the trajectories will form ensembles that represent possible realizations of UT air parcels. We then apply Bayesian inference to constrain nitrogen chemistry and compare results to the existing literature. Our anticipated results will confirm overestimation of HNO3 formation rate in previous work and provide further constraints on other nitrogen reaction rate coefficients that affect terminal products from NOx. We will particularly focus on organic nitrate chemistry that laboratory literature has yet to fully address. The results will provide useful insights into nitrogen chemistry that affects climate and human health.

Sustained diffusion reversal with in-bore reperfusion in monkey stroke models: Confirmed by prospective magnetic resonance imaging

PubMed Central

Yi, Kyung Sik; Choi, Chi-Hoon; Lee, Sang-Rae; Lee, Hong Jun; Lee, Youngjeon; Jeong, Kang-Jin; Hwang, Jinwoo; Chang, Kyu-Tae

2016-01-01

Although early diffusion lesion reversal after recanalization treatment of acute ischaemic stroke has been observed in clinical settings, the reversibility of lesions observed by diffusion-weighted imaging remains controversial. Here, we present consistent observations of sustained diffusion lesion reversal after transient middle cerebral artery occlusion in a monkey stroke model. Seven rhesus macaques were subjected to endovascular transient middle cerebral artery occlusion with in-bore reperfusion confirmed by repeated prospective diffusion-weighted imaging. Early diffusion lesion reversal was defined as lesion reversal at 3 h after reperfusion. Sustained diffusion lesion reversal was defined as the difference between the ADC-derived pre-reperfusion maximal ischemic lesion volume (ADCD-P Match) and the lesion on 4-week follow-up FLAIR magnetic resonance imaging. Diffusion lesions were spatiotemporally assessed using a 3-D voxel-based quantitative technique. The ADCD-P Match was 9.7 ± 6.0% (mean ± SD) and the final infarct was 1.2–6.0% of the volume of the ipsilateral hemisphere. Early diffusion lesion reversal and sustained diffusion lesion reversal were observed in all seven animals, and the calculated percentages compared with their ADCD-P Match ranged from 8.3 to 51.9% (mean ± SD, 26.9 ± 15.3%) and 41.7–77.8% (mean ± SD, 65.4 ± 12.2%), respectively. Substantial sustained diffusion lesion reversal and early reversal were observed in all animals in this monkey model of transient focal cerebral ischaemia. PMID:27401804

Learning and Inferring "Dark Matter" and Predicting Human Intents and Trajectories in Videos.

PubMed

Xie, Dan; Shu, Tianmin; Todorovic, Sinisa; Zhu, Song-Chun

2018-07-01

This paper presents a method for localizing functional objects and predicting human intents and trajectories in surveillance videos of public spaces, under no supervision in training. People in public spaces are expected to intentionally take shortest paths (subject to obstacles) toward certain objects (e.g., vending machine, picnic table, dumpster etc.) where they can satisfy certain needs (e.g., quench thirst). Since these objects are typically very small or heavily occluded, they cannot be inferred by their visual appearance but indirectly by their influence on people's trajectories. Therefore, we call them "dark matter", by analogy to cosmology, since their presence can only be observed as attractive or repulsive "fields" in the public space. A person in the scene is modeled as an intelligent agent engaged in one of the "fields" selected depending his/her intent. An agent's trajectory is derived from an Agent-based Lagrangian Mechanics. The agents can change their intents in the middle of motion and thus alter the trajectory. For evaluation, we compiled and annotated a new dataset. The results demonstrate our effectiveness in predicting human intent behaviors and trajectories, and localizing and discovering distinct types of "dark matter" in wide public spaces.

EUROPA Multiple-Flyby Trajectory Design

NASA Technical Reports Server (NTRS)

Buffington, Brent; Campagnola, Stefano; Petropoulos, Anastassios

2012-01-01

As reinforced by the 2011 NRC Decadal Survey, Europa remains one of the most scientifically intriguing targets in planetary science due to its potential suitability for life. However, based on JEO cost estimates and current budgetary constraints, the Decadal Survey recommended-and later directed by NASA Headquarters-a more affordable pathway to Europa exploration be derived. In response, a flyby-only proof-of-concept trajectory has been developed to investigate Europa. The trajectory, enabled by employing a novel combination of new mission design techniques, successfully fulfills a set of Science Definition Team derived scientific objectives carried out by a notional payload including ice penetrating radar, topographic imaging, and short wavelength infrared observations, and ion neutral mass spectrometry in-situ measurements. The current baseline trajectory, referred to as 11-F5, consists of 34 Europa and 9 Ganymede flybys executed over the course of 2.4 years, reached a maximum inclination of 15 degrees, has a deterministic delta v of 157 m/s (post-PJR), and has a total ionizing dose of 2.06 Mrad (Si behind 100 mil Al, spherical shell). The 11-F5 trajectory and more generally speaking, flyby-only trajectories-exhibit a number of potential advantages over an Europa orbiter mission.

Discrimination of curvature from motion during smooth pursuit eye movements and fixation.

PubMed

Ross, Nicholas M; Goettker, Alexander; Schütz, Alexander C; Braun, Doris I; Gegenfurtner, Karl R

2017-09-01

Smooth pursuit and motion perception have mainly been investigated with stimuli moving along linear trajectories. Here we studied the quality of pursuit movements to curved motion trajectories in human observers and examined whether the pursuit responses would be sensitive enough to discriminate various degrees of curvature. In a two-interval forced-choice task subjects pursued a Gaussian blob moving along a curved trajectory and then indicated in which interval the curve was flatter. We also measured discrimination thresholds for the same curvatures during fixation. Motion curvature had some specific effects on smooth pursuit properties: trajectories with larger amounts of curvature elicited lower open-loop acceleration, lower pursuit gain, and larger catch-up saccades compared with less curved trajectories. Initially, target motion curvatures were underestimated; however, ∼300 ms after pursuit onset pursuit responses closely matched the actual curved trajectory. We calculated perceptual thresholds for curvature discrimination, which were on the order of 1.5 degrees of visual angle (°) for a 7.9° curvature standard. Oculometric sensitivity to curvature discrimination based on the whole pursuit trajectory was quite similar to perceptual performance. Oculometric thresholds based on smaller time windows were higher. Thus smooth pursuit can quite accurately follow moving targets with curved trajectories, but temporal integration over longer periods is necessary to reach perceptual thresholds for curvature discrimination. NEW & NOTEWORTHY Even though motion trajectories in the real world are frequently curved, most studies of smooth pursuit and motion perception have investigated linear motion. We show that pursuit initially underestimates the curvature of target motion and is able to reproduce the target curvature ∼300 ms after pursuit onset. Temporal integration of target motion over longer periods is necessary for pursuit to reach the level of precision found in perceptual discrimination of curvature. Copyright © 2017 the American Physiological Society.

Reduced aliasing artifacts using shaking projection k-space sampling trajectory

NASA Astrophysics Data System (ADS)

Zhu, Yan-Chun; Du, Jiang; Yang, Wen-Chao; Duan, Chai-Jie; Wang, Hao-Yu; Gao, Song; Bao, Shang-Lian

2014-03-01

Radial imaging techniques, such as projection-reconstruction (PR), are used in magnetic resonance imaging (MRI) for dynamic imaging, angiography, and short-T2 imaging. They are less sensitive to flow and motion artifacts, and support fast imaging with short echo times. However, aliasing and streaking artifacts are two main sources which degrade radial imaging quality. For a given fixed number of k-space projections, data distributions along radial and angular directions will influence the level of aliasing and streaking artifacts. Conventional radial k-space sampling trajectory introduces an aliasing artifact at the first principal ring of point spread function (PSF). In this paper, a shaking projection (SP) k-space sampling trajectory was proposed to reduce aliasing artifacts in MR images. SP sampling trajectory shifts the projection alternately along the k-space center, which separates k-space data in the azimuthal direction. Simulations based on conventional and SP sampling trajectories were compared with the same number projections. A significant reduction of aliasing artifacts was observed using the SP sampling trajectory. These two trajectories were also compared with different sampling frequencies. A SP trajectory has the same aliasing character when using half sampling frequency (or half data) for reconstruction. SNR comparisons with different white noise levels show that these two trajectories have the same SNR character. In conclusion, the SP trajectory can reduce the aliasing artifact without decreasing SNR and also provide a way for undersampling reconstruction. Furthermore, this method can be applied to three-dimensional (3D) hybrid or spherical radial k-space sampling for a more efficient reduction of aliasing artifacts.

Microscopic video observation of capillary vessel systems using diffuse back lighting

NASA Astrophysics Data System (ADS)

Sakai, Minako; Arai, Hiroki; Iwai, Toshiaki

2017-04-01

We have been developing a simple and practical video microscopy system based on absorption spectra of biological substance to perform spectroscopic observation of living tissues. The diffuse backlighting effect is actively used in the developed system, which is generated by multiple light scattering in the tissue. It is demonstrated that the light specularly reflected from the skin surface can be completely suppressed in the microscopic observation and the biological activity of the capillary vessel systems distributed under the skin can be successfully observed. As a result, we can confirm the effectiveness of the video microscopy system using diffuse backlighting and the applicability of our developed system.

Use of a minimally invasive tubular retraction system for deep-seated tumors in pediatric patients.

PubMed

Recinos, Pablo F; Raza, Shaan M; Jallo, George I; Recinos, Violette Renard

2011-05-01

Microsurgical removal is the preferred treatment for most deep-seated, intraaxial tumors in the pediatric population. The feasibility of surgery as an option has improved with advances in surgical technology and technique. Tubular retractors disperse retraction forces over a greater surface area than do conventional retractors, which can lower the risk of ischemic complications. The authors describe their experience utilizing a new tubular retractor system specifically designed for cranial applications in conjunction with frameless neuronavigation. The Vycor ViewSite retractor was used in 4 pediatric patients (ages 15 months and 9, 10, and 16 years) with deep-seated intraaxial tumors. The lesions included a papillary tumor of the pineal region, a low-grade astrocytoma in the occipital lobe, a dysembryoplastic neuroepithelial tumor arising from the basal ganglia, and an intraventricular low-grade glioma. The extent of white matter damage along the surgical trajectory (based on T2 or FLAIR and diffusion restriction/apparent diffusion coefficient signals) and the extent of resection were assessed on postoperative imaging. Satisfactory resection or biopsy was achieved in all patients. A comparison of pre- and postoperative MR imaging studies revealed evidence of white matter damage along the surgical trajectory in 1 patient. None of the patients demonstrated new neurological deficits postoperatively. Obtaining surgical access to deep-seated, intraaxial tumors is challenging. In this small series of pediatric patients, the combination of the ViewSite tubular retractor and frameless neuronavigation facilitated the surgical approach. The combination of these technologies adds to the armamentarium to safely approach tumors in deep locations.

Optimizing Likelihood Models for Particle Trajectory Segmentation in Multi-State Systems.

PubMed

Young, Dylan Christopher; Scrimgeour, Jan

2018-06-19

Particle tracking offers significant insight into the molecular mechanics that govern the behav- ior of living cells. The analysis of molecular trajectories that transition between different motive states, such as diffusive, driven and tethered modes, is of considerable importance, with even single trajectories containing significant amounts of information about a molecule's environment and its interactions with cellular structures. Hidden Markov models (HMM) have been widely adopted to perform the segmentation of such complex tracks. In this paper, we show that extensive analysis of hidden Markov model outputs using data derived from multi-state Brownian dynamics simulations can be used both for the optimization of the likelihood models used to describe the states of the system and for characterization of the technique's failure mechanisms. This analysis was made pos- sible by the implementation of parallelized adaptive direct search algorithm on a Nvidia graphics processing unit. This approach provides critical information for the visualization of HMM failure and successful design of particle tracking experiments where trajectories contain multiple mobile states. © 2018 IOP Publishing Ltd.

Monitoring of the Polar Stratospheric Clouds formation and evolution in Antarctica in August 2007 during IPY with the MATCH method applied to lidar data

NASA Astrophysics Data System (ADS)

Montoux, Nadege; David, Christine; Klekociuk, Andrew; Pitts, Michael; di Liberto, Luca; Snels, Marcel; Jumelet, Julien; Bekki, Slimane; Larsen, Niels

2010-05-01

The project ORACLE-O3 ("Ozone layer and UV RAdiation in a changing CLimate Evaluated during IPY") is one of the coordinated international proposals selected for the International Polar Year (IPY). As part of this global project, LOLITA-PSC ("Lagrangian Observations with Lidar Investigations and Trajectories in Antarctica and Arctic, of PSC") is devoted to Polar Stratospheric Clouds (PSC) studies. Indeed, understanding the formation and evolution of PSC is an important issue to quantify the impact of climate changes on their frequency of formation and, further, on chlorine activation and subsequent ozone depletion. In this framework, three lidar stations performed PSC observations in Antarctica during the 2006, 2007, and 2008 winters: Davis (68.58°S, 77.97°E), McMurdo (77.86°S, 166.48°E) and Dumont D'Urville (66.67°S, 140.01°E). The data are completed with the lidar data from CALIOP ("Cloud-Aerosol Lidar with Orthogonal Polarization") onboard the CALIPSO ("Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation") satellite. Lagrangian trajectory calculations are used to identify air masses with PSCs sounded by several ground-based lidar stations with the same method, called MATCH, applied for the first time in Arctic to study the ozone depletion with radiosoundings. The evolution of the optical properties of the PSCs and thus the type of PSCs formed (supercooled ternary solution, nitric acid trihydrate particles or ice particles) could thus be linked to the thermodynamical evolution of the air mass deduced from the trajectories. A modeling with the microphysical model of the Danish Meteorological Institute allows assessing our ability to predict PSCs for various environmental conditions. Indeed, from pressure and temperature evolution, the model allows retrieving the types of particles formed as well as their mean radii, their concentrations and could also simulate the lidar signals. In a first step, a case in August 2007 around 17-18 km, involving the three ground-based lidar stations and CALIOP has been selected. Trajectories with different models (gscf and ecmwf), grids and initializations have been computed to test the robustness of the MATCH. Then the DMI model has been used with these different trajectories to test its ability to reproduce the observations. For a same case, the temperature differences (~2-3 K) between the trajectories have a strong impact on the number density of the particles formed (factor 1000). This case is presented here in detail and a statistical comparison is planned with the numerous MATCH cases identified during the three winters and which involve most of the time two ground-based lidar stations with CALIOP.

Trajectories for spacecraft encounters with Comet Honda-Mrkos-Pajdusakova in 1996

NASA Technical Reports Server (NTRS)

Dunham, David W.; Jen, Shao-Chiang; Farquhar, Robert W.

1989-01-01

Early in 1996, the relatively bright short-period Comet Honda-Mrkos-Pajdusakova (HMP) will pass only 0.17 astronomical unit from the earth, providing both an unusually favorable apparition for ground-based observers and an opportunity for a spacecraft to reach Comet HMP on relatively low-energy trajectories. The Japanense Institute of Space and Astronautical Sciences Sakigake spacecraft is expected to fly by Comet HMP on February 3, 1996, after utilizing four earth swingbys to modify its orbit. If the camera on the ESA Giotto spacecraft is inoperable, Giotto may also be sent to Comet HMP. In addition, 1-year earth-return trajectories to Comet HMP are described, along with some that can be extended to encounter Comet Giacobini-Zinner in 1998.

The Valec fireball and predicted meteorite fall

NASA Technical Reports Server (NTRS)

Ceplecha, Z.; Spurny, P.

1987-01-01

A fireball was photographed with a luminous trajectory below a height of 20 km. On Aug. 3, 1984, seven stations photographed this slow moving fireball, which traversed 94 km of luminous trajectory in 9.2 sec and terminated its visible flight at a height of 19.1 km. The computed dark flight trajectory intersected the surface close to Valec, a small village 40 km west of Brno. The Valec fireball was the lowest photographed fireball ever. The Valec fireball was photographed by fish eye cameras. The positional precision of all the records were within the range of 1 to 2 minutes of arc. All computations were done using the FIRBAL program, a set of almost 4000 Fortran statements run on EC 1040 computer. The average computed mass at the terminal point, i.e., the predicted mass of the biggest meteorite, was 16 kg. This number is based on the dynamical data at the terminal point solely. Visual data was also collected from occasional observers. This observed phenomenon is discussed.

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

PubMed Central

Donovan, Rory M.; Tapia, Jose-Juan; Sullivan, Devin P.; Faeder, James R.; Murphy, Robert F.; Dittrich, Markus; Zuckerman, Daniel M.

2016-01-01

The long-term goal of connecting scales in biological simulation can be facilitated by scale-agnostic methods. We demonstrate that the weighted ensemble (WE) strategy, initially developed for molecular simulations, applies effectively to spatially resolved cell-scale simulations. The WE approach runs an ensemble of parallel trajectories with assigned weights and uses a statistical resampling strategy of replicating and pruning trajectories to focus computational effort on difficult-to-sample regions. The method can also generate unbiased estimates of non-equilibrium and equilibrium observables, sometimes with significantly less aggregate computing time than would be possible using standard parallelization. Here, we use WE to orchestrate particle-based kinetic Monte Carlo simulations, which include spatial geometry (e.g., of organelles, plasma membrane) and biochemical interactions among mobile molecular species. We study a series of models exhibiting spatial, temporal and biochemical complexity and show that although WE has important limitations, it can achieve performance significantly exceeding standard parallel simulation—by orders of magnitude for some observables. PMID:26845334

Understanding and controlling regime switching in molecular diffusion

NASA Astrophysics Data System (ADS)

Hallerberg, S.; de Wijn, A. S.

2014-12-01

Diffusion can be strongly affected by ballistic flights (long jumps) as well as long-lived sticking trajectories (long sticks). Using statistical inference techniques in the spirit of Granger causality, we investigate the appearance of long jumps and sticks in molecular-dynamics simulations of diffusion in a prototype system, a benzene molecule on a graphite substrate. We find that specific fluctuations in certain, but not all, internal degrees of freedom of the molecule can be linked to either long jumps or sticks. Furthermore, by changing the prevalence of these predictors with an outside influence, the diffusion of the molecule can be controlled. The approach presented in this proof of concept study is very generic and can be applied to larger and more complex molecules. Additionally, the predictor variables can be chosen in a general way so as to be accessible in experiments, making the method feasible for control of diffusion in applications. Our results also demonstrate that data-mining techniques can be used to investigate the phase-space structure of high-dimensional nonlinear dynamical systems.

Constructing an Indoor Floor Plan Using Crowdsourcing Based on Magnetic Fingerprinting

PubMed Central

Zhao, Fang; Jiang, Mengling; Ma, Hao; Zhang, Yuexia

2017-01-01

A large number of indoor positioning systems have recently been developed to cater for various location-based services. Indoor maps are a prerequisite of such indoor positioning systems; however, indoor maps are currently non-existent for most indoor environments. Construction of an indoor map by external experts excludes quick deployment and prevents widespread utilization of indoor localization systems. Here, we propose an algorithm for the automatic construction of an indoor floor plan, together with a magnetic fingerprint map of unmapped buildings using crowdsourced smartphone data. For floor plan construction, our system combines the use of dead reckoning technology, an observation model with geomagnetic signals, and trajectory fusion based on an affinity propagation algorithm. To obtain the indoor paths, the magnetic trajectory data obtained through crowdsourcing were first clustered using dynamic time warping similarity criteria. The trajectories were inferred from odometry tracing, and those belonging to the same cluster in the magnetic trajectory domain were then fused. Fusing these data effectively eliminates the inherent tracking errors originating from noisy sensors; as a result, we obtained highly accurate indoor paths. One advantage of our system is that no additional hardware such as a laser rangefinder or wheel encoder is required. Experimental results demonstrate that our proposed algorithm successfully constructs indoor floor plans with 0.48 m accuracy, which could benefit location-based services which lack indoor maps. PMID:29156639

Identity Formation Re-revisited: A Rejoinder to Waterman on Developmental and Cross-Cultural Issues.

ERIC Educational Resources Information Center

Meeus, W.; Iedema, J.; Vollebergh, W.

1999-01-01

Examines similarities and differences between American and Dutch research on identity formation and psychological well-being in adolescent and young adults. Concludes that identity development is systematically progressive and may be described with the trajectory diffusion?closure/moratorium?achieving commitment. Age differences are found in the…

Holographic Measurements of Fuel Droplet Diffusion in Isotropic Turbulence

NASA Astrophysics Data System (ADS)

Gopalan, Balaji

2005-11-01

High-speed digital holographic cinematography was used to investigate the diffusion of slightly buoyant fuel droplets in locally isotropic turbulence. High turbulence levels with a weak mean velocity was generated at the center of a tank by four rotating grids. 0.3-1.5mm droplets were injected here and tracked using in-line holography. To obtain all three components of velocity, we simultaneously recorded holograms of the central 37x37x37 mm^3 volume from two perpendicular directions. These were numerically reconstructed to provide focused images of the droplets. An automated code was developed to identify the 3-D droplet trajectories from the two views, and then calculate time series of their velocity. After subtracting the local mean fluid velocity, the time series were used to obtain the 3-D Lagrangian autocorrelation function of droplet velocity. Averaging over many trajectories provided the autocorrelation functions as a function of direction and droplet sizes. As expected, the correlation was higher in the vertical direction due to the effect of gravity. Data analysis is still in progress.

Finite Larmor radius effects on weak turbulence transport

NASA Astrophysics Data System (ADS)

Kryukov, N.; Martinell, J. J.

2018-06-01

Transport of test particles in two-dimensional weak turbulence with waves propagating along the poloidal direction is studied using a reduced model. Finite Larmor radius (FLR) effects are included by gyroaveraging over one particle orbit. For low wave amplitudes the motion is mostly regular with particles trapped in the potential wells. As the amplitude increases the trajectories become chaotic and the Larmor radius modifies the orbits. For a thermal distribution of Finite Larmor radii the particle distribution function (PDF) is Gaussian for small th$ (thermal gyroradius) but becomes non-Gaussian for large th$ . However, the time scaling of transport is diffusive, as characterized by a linear dependence of the variance of the PDF with time. An explanation for this behaviour is presented that provides an expression for an effective diffusion coefficient and reproduces the numerical results for large wave amplitudes which implies generalized chaos. When a shear flow is added in the direction of wave propagation, a modified model is obtained that produces free-streaming particle trajectories in addition to trapped ones; these contribute to ballistic transport for low wave amplitude but produce super-ballistic transport in the chaotic regime. As in the previous case, the PDF is Gaussian for low th$ becoming non-Gaussian as it increases. The perpendicular transport presents the same behaviour as in the case with no flow but the diffusion is faster in the presence of the flow.

Tuning Monotonic Basin Hopping: Improving the Efficiency of Stochastic Search as Applied to Low-Thrust Trajectory Optimization

NASA Technical Reports Server (NTRS)

Englander, Jacob A.; Englander, Arnold C.

2014-01-01

Trajectory optimization methods using monotonic basin hopping (MBH) have become well developed during the past decade [1, 2, 3, 4, 5, 6]. An essential component of MBH is a controlled random search through the multi-dimensional space of possible solutions. Historically, the randomness has been generated by drawing random variable (RV)s from a uniform probability distribution. Here, we investigate the generating the randomness by drawing the RVs from Cauchy and Pareto distributions, chosen because of their characteristic long tails. We demonstrate that using Cauchy distributions (as first suggested by J. Englander [3, 6]) significantly improves monotonic basin hopping (MBH) performance, and that Pareto distributions provide even greater improvements. Improved performance is defined in terms of efficiency and robustness. Efficiency is finding better solutions in less time. Robustness is efficiency that is undiminished by (a) the boundary conditions and internal constraints of the optimization problem being solved, and (b) by variations in the parameters of the probability distribution. Robustness is important for achieving performance improvements that are not problem specific. In this work we show that the performance improvements are the result of how these long-tailed distributions enable MBH to search the solution space faster and more thoroughly. In developing this explanation, we use the concepts of sub-diffusive, normally-diffusive, and super-diffusive random walks (RWs) originally developed in the field of statistical physics.

Clinical application of diffusion tensor magnetic resonance imaging in skeletal muscle

PubMed Central

Longwei, Xu

2012-01-01

Summary Diffusion tensor magnetic resonance imaging (DTI) is increasingly applied in the detection and characterization of skeletal muscle. This promising technique has aroused much enthusiasm and generated high expectations, because it is able to provide some specific information of skeletal muscle that is not available from other imaging modalities. Compared with conventional MRI, DTI could reconstruct the trajectories of skeletal muscle fibers. It makes it possible to non-invasively detect several physiological values (diffusion values), like fractional anisotropy (FA) and apparent diffusion coefficient (ADC), which have a great association with the muscle physiology and pathology. Furthermore, other advantages of DTI are the capability of investigating the muscle biomechanics and also investigate the pathological condition of skeletal muscle. Finally, several challenges, which limit the wide application of DTI in skeletal muscle, were discussed. It is believed that this review may arouse in-depth studies on the clinical application of DTI in skeletal muscle in future. PMID:23738269

Turbulent vertical diffusivity in the sub-tropical stratosphere

NASA Astrophysics Data System (ADS)

Pisso, I.; Legras, B.

2008-02-01

Vertical (cross-isentropic) mixing is produced by small-scale turbulent processes which are still poorly understood and paramaterized in numerical models. In this work we provide estimates of local equivalent diffusion in the lower stratosphere by comparing balloon borne high-resolution measurements of chemical tracers with reconstructed mixing ratio from large ensembles of random Lagrangian backward trajectories using European Centre for Medium-range Weather Forecasts analysed winds and a chemistry-transport model (REPROBUS). We focus on a case study in subtropical latitudes using data from HIBISCUS campaign. An upper bound on the vertical diffusivity is found in this case study to be of the order of 0.5 m2 s-1 in the subtropical region, which is larger than the estimates at higher latitudes. The relation between diffusion and dispersion is studied by estimating Lyapunov exponents and studying their variation according to the presence of active dynamical structures.

Approximation of epidemic models by diffusion processes and their statistical inference.

PubMed

Guy, Romain; Larédo, Catherine; Vergu, Elisabeta

2015-02-01

Multidimensional continuous-time Markov jump processes [Formula: see text] on [Formula: see text] form a usual set-up for modeling [Formula: see text]-like epidemics. However, when facing incomplete epidemic data, inference based on [Formula: see text] is not easy to be achieved. Here, we start building a new framework for the estimation of key parameters of epidemic models based on statistics of diffusion processes approximating [Formula: see text]. First, previous results on the approximation of density-dependent [Formula: see text]-like models by diffusion processes with small diffusion coefficient [Formula: see text], where [Formula: see text] is the population size, are generalized to non-autonomous systems. Second, our previous inference results on discretely observed diffusion processes with small diffusion coefficient are extended to time-dependent diffusions. Consistent and asymptotically Gaussian estimates are obtained for a fixed number [Formula: see text] of observations, which corresponds to the epidemic context, and for [Formula: see text]. A correction term, which yields better estimates non asymptotically, is also included. Finally, performances and robustness of our estimators with respect to various parameters such as [Formula: see text] (the basic reproduction number), [Formula: see text], [Formula: see text] are investigated on simulations. Two models, [Formula: see text] and [Formula: see text], corresponding to single and recurrent outbreaks, respectively, are used to simulate data. The findings indicate that our estimators have good asymptotic properties and behave noticeably well for realistic numbers of observations and population sizes. This study lays the foundations of a generic inference method currently under extension to incompletely observed epidemic data. Indeed, contrary to the majority of current inference techniques for partially observed processes, which necessitates computer intensive simulations, our method being mostly an analytical approach requires only the classical optimization steps.

Modeling Sediment Detention Ponds Using Reactor Theory and Advection-Diffusion Concepts

NASA Astrophysics Data System (ADS)

Wilson, Bruce N.; Barfield, Billy J.

1985-04-01

An algorithm is presented to model the sedimentation process in detention ponds. This algorithm is based on a mass balance for an infinitesimal layer that couples reactor theory concepts with advection-diffusion processes. Reactor theory concepts are used to (1) determine residence time of sediment particles and to (2) mix influent sediment with previously stored flow. Advection-diffusion processes are used to model the (1) settling characteristics of sediment and the (2) vertical diffusion of sediment due to turbulence. Predicted results of the model are compared to those observed on two pilot scale ponds for a total of 12 runs. The average percent error between predicted and observed trap efficiency was 5.2%. Overall, the observed sedimentology values were predicted with reasonable accuracy.

Teaching the principles of statistical dynamics

PubMed Central

Ghosh, Kingshuk; Dill, Ken A.; Inamdar, Mandar M.; Seitaridou, Effrosyni; Phillips, Rob

2012-01-01

We describe a simple framework for teaching the principles that underlie the dynamical laws of transport: Fick’s law of diffusion, Fourier’s law of heat flow, the Newtonian viscosity law, and the mass-action laws of chemical kinetics. In analogy with the way that the maximization of entropy over microstates leads to the Boltzmann distribution and predictions about equilibria, maximizing a quantity that E. T. Jaynes called “caliber” over all the possible microtrajectories leads to these dynamical laws. The principle of maximum caliber also leads to dynamical distribution functions that characterize the relative probabilities of different microtrajectories. A great source of recent interest in statistical dynamics has resulted from a new generation of single-particle and single-molecule experiments that make it possible to observe dynamics one trajectory at a time. PMID:23585693

Teaching the principles of statistical dynamics.

PubMed

Ghosh, Kingshuk; Dill, Ken A; Inamdar, Mandar M; Seitaridou, Effrosyni; Phillips, Rob

2006-02-01

We describe a simple framework for teaching the principles that underlie the dynamical laws of transport: Fick's law of diffusion, Fourier's law of heat flow, the Newtonian viscosity law, and the mass-action laws of chemical kinetics. In analogy with the way that the maximization of entropy over microstates leads to the Boltzmann distribution and predictions about equilibria, maximizing a quantity that E. T. Jaynes called "caliber" over all the possible microtrajectories leads to these dynamical laws. The principle of maximum caliber also leads to dynamical distribution functions that characterize the relative probabilities of different microtrajectories. A great source of recent interest in statistical dynamics has resulted from a new generation of single-particle and single-molecule experiments that make it possible to observe dynamics one trajectory at a time.

Fluorescence imaging of single-molecule retention trajectories in reversed-phase chromatographic particles.

PubMed

Cooper, Justin T; Peterson, Eric M; Harris, Joel M

2013-10-01

Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. The simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized.

Galactic Cosmic-ray Transport in the Global Heliosphere: A Four-Dimensional Stochastic Model

NASA Astrophysics Data System (ADS)

Florinski, V.

2009-04-01

We study galactic cosmic-ray transport in the outer heliosphere and heliosheath using a newly developed transport model based on stochastic integration of the phase-space trajectories of Parker's equation. The model employs backward integration of the diffusion-convection transport equation using Ito calculus and is four-dimensional in space+momentum. We apply the model to the problem of galactic proton transport in the heliosphere during a negative solar minimum. Model results are compared with the Voyager measurements of galactic proton radial gradients and spectra in the heliosheath. We show that the heliosheath is not as efficient in diverting cosmic rays during solar minima as predicted by earlier two-dimensional models.

Control of complex dynamics and chaos in distributed parameter systems

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

Chakravarti, S.; Marek, M.; Ray, W.H.

This paper discusses a methodology for controlling complex dynamics and chaos in distributed parameter systems. The reaction-diffusion system with Brusselator kinetics, where the torus-doubling or quasi-periodic (two characteristic incommensurate frequencies) route to chaos exists in a defined range of parameter values, is used as an example. Poincare maps are used for characterization of quasi-periodic and chaotic attractors. The dominant modes or topos, which are inherent properties of the system, are identified by means of the Singular Value Decomposition. Tested modal feedback control schemas based on identified dominant spatial modes confirm the possibility of stabilization of simple quasi-periodic trajectories in themore » complex quasi-periodic or chaotic spatiotemporal patterns.« less

Adjustable Trajectory Design Based on Node Density for Mobile Sink in WSNs

PubMed Central

Yang, Guisong; Liu, Shuai; He, Xingyu; Xiong, Naixue; Wu, Chunxue

2016-01-01

The design of movement trajectories for mobile sink plays an important role in data gathering for Wireless Sensor Networks (WSNs), as it affects the network coverage, and packet delivery ratio, as well as the network lifetime. In some scenarios, the whole network can be divided into subareas where the nodes are randomly deployed. The node densities of these subareas are quite different, which may result in a decreased packet delivery ratio and network lifetime if the movement trajectory of the mobile sink cannot adapt to these differences. To address these problems, we propose an adjustable trajectory design method based on node density for mobile sink in WSNs. The movement trajectory of the mobile sink in each subarea follows the Hilbert space-filling curve. Firstly, the trajectory is constructed based on network size. Secondly, the adjustable trajectory is established based on node density in specific subareas. Finally, the trajectories in each subarea are combined to acquire the whole network’s movement trajectory for the mobile sink. In addition, an adaptable power control scheme is designed to adjust nodes’ transmitting range dynamically according to the movement trajectory of the mobile sink in each subarea. The simulation results demonstrate that the proposed trajectories can adapt to network changes flexibly, thus outperform both in packet delivery ratio and in energy consumption the trajectories designed only based on the network size and the whole network node density. PMID:27941662

Lévy/Anomalous Diffusion as a Mean-Field Theory for 3D Cloud Effects in SW-RT: Empirical Support, New Analytical Formulation, and Impact on Atmospheric Absorption

NASA Astrophysics Data System (ADS)

Pfeilsticker, K.; Davis, A.; Marshak, A.; Suszcynsky, D. M.; Buldryrev, S.; Barker, H.

2001-12-01

2-stream RT models, as used in all current GCMs, are mathematically equivalent to standard diffusion theory where the physical picture is a slow propagation of the diffuse radiation by Gaussian random walks. In other words, after the conventional van de Hulst rescaling by 1/(1-g) in R3 and also by (1-g) in t, solar photons follow convoluted fractal trajectories in the atmosphere. For instance, we know that transmitted light is typically scattered about (1-g)τ 2 times while reflected light is scattered on average about τ times, where τ is the optical depth of the column. The space/time spread of this diffusion process is described exactly by a Gaussian distribution; from the statistical physics viewpoint, this follows from the convergence of the sum of many (rescaled) steps between scattering events with a finite variance. This Gaussian picture follows from directly from first principles (the RT equation) under the assumptions of horizontal uniformity and large optical depth, i.e., there is a homogeneous plane-parallel cloud somewhere in the column. The first-order effect of 3D variability of cloudiness, the main source of scattering, is to perturb the distribution of single steps between scatterings which, modulo the '1-g' rescaling, can be assumed effectively isotropic. The most natural generalization of the Gaussian distribution is the 1-parameter family of symmetric Lévy-stable distributions because the sum of many zero-mean random variables with infinite variance, but finite moments of order q < α (0 < α < 2), converge to them. It has been shown on heuristic grounds that for these Lévy-based random walks the typical number of scatterings is now (1-g)τ α for transmitted light. The appearance of a non-rational exponent is why this is referred to as anomalous diffusion. Note that standard/Gaussian diffusion is retrieved in the limit α = 2-. Lévy transport theory has been successfully used in the statistical physics to investigate a wide variety of systems with strongly nonlinear dynamics; these applications range from random advection in turbulent fluids to the erratic behavior of financial time-series and, most recently, self-regulating ecological systems. We will briefly survey the state-of-the-art observations that offer compelling empirical support for the Lévy/anomalous diffusion model in atmospheric radiation: (1) high-resolution spectroscopy of differential absorption in the O2 A-band from ground; (2) temporal transient records of lightning strokes transmitted through clouds to a sensitive detector in space; and (3) the Gamma-distributions of optical depths derived from Landsat cloud scenes at 30-m resolution. We will then introduce a rigorous analytical formulation of anomalous transport through finite media based on fractional derivatives and Sonin calculus. A remarkable result from this new theoretical development is an extremal property of the α = 1+ case (divergent mean-free-path), as is observed in the cloudy atmosphere. Finally, we will discuss the implications of anomalous transport theory for bulk 3D effects on the current enhanced absorption problem as well as its role as the basis of a next-generation GCM RT parameterization.

Monte Carlo sampling in diffusive dynamical systems

NASA Astrophysics Data System (ADS)

Tapias, Diego; Sanders, David P.; Altmann, Eduardo G.

2018-05-01

We introduce a Monte Carlo algorithm to efficiently compute transport properties of chaotic dynamical systems. Our method exploits the importance sampling technique that favors trajectories in the tail of the distribution of displacements, where deviations from a diffusive process are most prominent. We search for initial conditions using a proposal that correlates states in the Markov chain constructed via a Metropolis-Hastings algorithm. We show that our method outperforms the direct sampling method and also Metropolis-Hastings methods with alternative proposals. We test our general method through numerical simulations in 1D (box-map) and 2D (Lorentz gas) systems.

Superdiffusive Dispersals Impart the Geometry of Underlying Random Walks

NASA Astrophysics Data System (ADS)

Zaburdaev, V.; Fouxon, I.; Denisov, S.; Barkai, E.

2016-12-01

It is recognized now that a variety of real-life phenomena ranging from diffusion of cold atoms to the motion of humans exhibit dispersal faster than normal diffusion. Lévy walks is a model that excelled in describing such superdiffusive behaviors albeit in one dimension. Here we show that, in contrast to standard random walks, the microscopic geometry of planar superdiffusive Lévy walks is imprinted in the asymptotic distribution of the walkers. The geometry of the underlying walk can be inferred from trajectories of the walkers by calculating the analogue of the Pearson coefficient.

A fast random walk algorithm for computing the pulsed-gradient spin-echo signal in multiscale porous media.

PubMed

Grebenkov, Denis S

2011-02-01

A new method for computing the signal attenuation due to restricted diffusion in a linear magnetic field gradient is proposed. A fast random walk (FRW) algorithm for simulating random trajectories of diffusing spin-bearing particles is combined with gradient encoding. As random moves of a FRW are continuously adapted to local geometrical length scales, the method is efficient for simulating pulsed-gradient spin-echo experiments in hierarchical or multiscale porous media such as concrete, sandstones, sedimentary rocks and, potentially, brain or lungs. Copyright © 2010 Elsevier Inc. All rights reserved.

Comorbidity amplifies the effects of post-9/11 posttraumatic stress disorder trajectories on health-related quality of life.

PubMed

Li, Jiehui; Zweig, Kimberly Caramanica; Brackbill, Robert M; Farfel, Mark R; Cone, James E

2018-03-01

The present study aims to examine the impact of physical and mental health comorbidities on the association between post-9/11 posttraumatic stress disorder (PTSD) trajectories over 10 years and health-related quality of life (HRQOL) among 9/11-exposed persons. 30,002 responding adult World Trade Center Health Registry enrollees reporting no pre-9/11 PTSD were studied. PTSD trajectories (chronic, delayed, remitted, no PTSD) were defined based on a 17-item PTSD Checklist-Specific to 9/11 across three waves of survey data. Three indicators of poor HRQOL were defined based on CDC HRQOL-4 measures. We computed age-adjusted prevalence of physical and mental health comorbidity (depression/anxiety) by PTSD trajectory and used modified Poisson regression to assess the effect of PTSD trajectory on poor HRQOL prevalence, accounting for comorbidity. Age-adjusted prevalence of overall comorbid conditions was 95.8 and 61.4% among the chronic and no-PTSD groups, respectively. Associations between 9/11-related PTSD trajectories and poor HRQOL were significant and became greater when comorbidity was included. Adjusted prevalence ratios were elevated for fair/poor health status (APR 7.3, 95% CI 6.5, 8.2), ≥ 14 unhealthy days (4.7; 95% CI 4.4, 5.1), and ≥ 14 activity limitation days during the last 30 days (9.6; 95% CI 8.1, 11.4) in the chronic PTSD group with physical and mental health comorbidity compared to those without PTSD and comorbidity; similar associations were observed for delayed PTSD. Ten years post-9/11 physical and mental health comorbidities have a substantial impact on the PTSD trajectories and HRQOL association. The need for early identification and treatment of PTSD and comorbidity should be emphasized to potentially improve HRQOL.

Evolution of the concentration PDF in random environments modeled by global random walk

NASA Astrophysics Data System (ADS)

Suciu, Nicolae; Vamos, Calin; Attinger, Sabine; Knabner, Peter

2013-04-01

The evolution of the probability density function (PDF) of concentrations of chemical species transported in random environments is often modeled by ensembles of notional particles. The particles move in physical space along stochastic-Lagrangian trajectories governed by Ito equations, with drift coefficients given by the local values of the resolved velocity field and diffusion coefficients obtained by stochastic or space-filtering upscaling procedures. A general model for the sub-grid mixing also can be formulated as a system of Ito equations solving for trajectories in the composition space. The PDF is finally estimated by the number of particles in space-concentration control volumes. In spite of their efficiency, Lagrangian approaches suffer from two severe limitations. Since the particle trajectories are constructed sequentially, the demanded computing resources increase linearly with the number of particles. Moreover, the need to gather particles at the center of computational cells to perform the mixing step and to estimate statistical parameters, as well as the interpolation of various terms to particle positions, inevitably produce numerical diffusion in either particle-mesh or grid-free particle methods. To overcome these limitations, we introduce a global random walk method to solve the system of Ito equations in physical and composition spaces, which models the evolution of the random concentration's PDF. The algorithm consists of a superposition on a regular lattice of many weak Euler schemes for the set of Ito equations. Since all particles starting from a site of the space-concentration lattice are spread in a single numerical procedure, one obtains PDF estimates at the lattice sites at computational costs comparable with those for solving the system of Ito equations associated to a single particle. The new method avoids the limitations concerning the number of particles in Lagrangian approaches, completely removes the numerical diffusion, and speeds up the computation by orders of magnitude. The approach is illustrated for the transport of passive scalars in heterogeneous aquifers, with hydraulic conductivity modeled as a random field.

Lagrangian Photochemical Box-Model Calculations of Asian Pacific Rim Outflow During TRACE-P

NASA Astrophysics Data System (ADS)

Hamlin, A.; Crawford, J.; Olson, J.; Avery, M.; Sachse, G.; Barrick, J.; Blake, D.; Tan, D.; Sandholm, S.; Kondo, Y.; Singh, H.; Eisele, F.; Zondlo, M.; Flocke, F.; Talbot, R.

2006-12-01

NASA's TRACE-P (TRAnsport and Chemical Evolution over the Pacific) mission was conducted over the northwestern Pacific February-April, 2001. During two transit flights across the Pacific, extensive pollution was observed from an Asian outflow event that split into two branches over the central Pacific, one subsiding and moving southward over the central Pacific and the other continuing eastward in the upper troposphere. The subsiding branch was observed as a widespread stagnant pollution layer between 2 and 4 km over the central Pacific during transit flights from Kona, HI to Guam. In this region, high levels of O3 (70 ppbv), CO (217 ppbv), and NOx (114 pptv) were well in excess of typical values observed during TRACE-P along the Asian coast. Evidence suggests that the subsiding branch experienced extensive photochemical processing compared to the branch that remained at altitude. To examine the processes controlling the chemical evolution of ozone and its precursors in this outflow event, data collected during the TRACE-P mission have been combined with lagrangian photochemical box model calculations. One of the largest sources of uncertainty in these calculations was associated with predicted water vapor levels along the transport trajectories calculated using the HYSPLIT model. Water vapor levels predicted by HYSPLIT trajectory calculations in the subsiding layer ranged from 3390 to 4880 ppm, while the median level observed in the pollution layer was only 637 ppm. Simulations of ozone production and associated radical chemistry differed dramatically when using water vapor levels based on trajectory calculations versus observed water vapor levels. Levels of PAN and HO2NO2, NOx reservoir species, are also influenced by uncertainties in temperature along the trajectories. These results highlight the importance of accurately representing the humidification and warming of subsiding air masses in 3-D chemical- transport models.

SU-F-BRB-16: A Spreadsheet Based Automatic Trajectory GEnerator (SAGE): An Open Source Tool for Automatic Creation of TrueBeam Developer Mode Robotic Trajectories

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

Etmektzoglou, A; Mishra, P; Svatos, M

Purpose: To automate creation and delivery of robotic linac trajectories with TrueBeam Developer Mode, an open source spreadsheet-based trajectory generation tool has been developed, tested and made freely available. The computing power inherent in a spreadsheet environment plus additional functions programmed into the tool insulate users from the underlying schema tedium and allow easy calculation, parameterization, graphical visualization, validation and finally automatic generation of Developer Mode XML scripts which are directly loadable on a TrueBeam linac. Methods: The robotic control system platform that allows total coordination of potentially all linac moving axes with beam (continuous, step-and-shoot, or combination thereof) becomesmore » available in TrueBeam Developer Mode. Many complex trajectories are either geometric or can be described in analytical form, making the computational power, graphing and programmability available in a spreadsheet environment an easy and ideal vehicle for automatic trajectory generation. The spreadsheet environment allows also for parameterization of trajectories thus enabling the creation of entire families of trajectories using only a few variables. Standard spreadsheet functionality has been extended for powerful movie-like dynamic graphic visualization of the gantry, table, MLC, room, lasers, 3D observer placement and beam centerline all as a function of MU or time, for analysis of the motions before requiring actual linac time. Results: We used the tool to generate and deliver extended SAD “virtual isocenter” trajectories of various shapes such as parameterized circles and ellipses. We also demonstrated use of the tool in generating linac couch motions that simulate respiratory motion using analytical parameterized functions. Conclusion: The SAGE tool is a valuable resource to experiment with families of complex geometric trajectories for a TrueBeam Linac. It makes Developer Mode more accessible as a vehicle to quickly translate research ideas into machine readable scripts without programming knowledge. As an open source initiative, it also enables researcher collaboration on future developments. I am a full time employee at Varian Medical Systems, Palo Alto, California.« less

Rare behavior of growth processes via umbrella sampling of trajectories

NASA Astrophysics Data System (ADS)

Klymko, Katherine; Geissler, Phillip L.; Garrahan, Juan P.; Whitelam, Stephen

2018-03-01

We compute probability distributions of trajectory observables for reversible and irreversible growth processes. These results reveal a correspondence between reversible and irreversible processes, at particular points in parameter space, in terms of their typical and atypical trajectories. Thus key features of growth processes can be insensitive to the precise form of the rate constants used to generate them, recalling the insensitivity to microscopic details of certain equilibrium behavior. We obtained these results using a sampling method, inspired by the "s -ensemble" large-deviation formalism, that amounts to umbrella sampling in trajectory space. The method is a simple variant of existing approaches, and applies to ensembles of trajectories controlled by the total number of events. It can be used to determine large-deviation rate functions for trajectory observables in or out of equilibrium.

Effect of heterogeneity on the characterization of cell membrane compartments: I. Uniform size and permeability.

PubMed

Hall, Damien

2010-03-15

Observations of the motion of individual molecules in the membrane of a number of different cell types have led to the suggestion that the outer membrane of many eukaryotic cells may be effectively partitioned into microdomains. A major cause of this suggested partitioning is believed to be due to the direct/indirect association of the cytosolic face of the cell membrane with the cortical cytoskeleton. Such intimate association is thought to introduce effective hydrodynamic barriers into the membrane that are capable of frustrating molecular Brownian motion over distance scales greater than the average size of the compartment. To date, the standard analytical method for deducing compartment characteristics has relied on observing the random walk behavior of a labeled lipid or protein at various temporal frequencies and different total lengths of time. Simple theoretical arguments suggest that the presence of restrictive barriers imparts a characteristic turnover to a plot of mean squared displacement versus sampling period that can be interpreted to yield the average dimensions of the compartment expressed as the respective side lengths of a rectangle. In the following series of articles, we used computer simulation methods to investigate how well the conventional analytical strategy coped with heterogeneity in size, shape, and barrier permeability of the cell membrane compartments. We also explored questions relating to the necessary extent of sampling required (with regard to both the recorded time of a single trajectory and the number of trajectories included in the measurement bin) for faithful representation of the actual distribution of compartment sizes found using the SPT technique. In the current investigation, we turned our attention to the analytical characterization of diffusion through cell membrane compartments having both a uniform size and permeability. For this ideal case, we found that (i) an optimum sampling time interval existed for the analysis and (ii) the total length of time for which a trajectory was recorded was a key factor. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Estimation of Center of Mass Trajectory using Wearable Sensors during Golf Swing

PubMed Central

Najafi, Bijan; Lee-Eng, Jacqueline; Wrobel, James S.; Goebel, Ruben

2015-01-01

This study suggests a wearable sensor technology to estimate center of mass (CoM) trajectory during a golf swing. Groups of 3, 4, and 18 participants were recruited, respectively, for the purpose of three validation studies. Study 1 examined the accuracy of the system to estimate a 3D body segment angle compared to a camera-based motion analyzer (Vicon®). Study 2 assessed the accuracy of three simplified CoM trajectory models. Finally, Study 3 assessed the accuracy of the proposed CoM model during multiple golf swings. A relatively high agreement was observed between wearable sensors and the reference (Vicon®) for angle measurement (r > 0.99, random error <1.2° (1.5%) for anterior-posterior; <0.9° (2%) for medial-lateral; and <3.6° (2.5%) for internal-external direction). The two-link model yielded a better agreement with the reference system compared to one-link model (r > 0.93 v. r = 0.52, respectively). On the same note, the proposed two-link model estimated CoM trajectory during golf swing with relatively good accuracy (r > 0.9, A-P random error <1cm (7.7%) and <2cm (10.4%) for M-L). The proposed system appears to accurately quantify the kinematics of CoM trajectory as a surrogate of dynamic postural control during an athlete’s movement and its portability, makes it feasible to fit the competitive environment without restricting surface type. Key points This study demonstrates that wearable technology based on inertial sensors are accurate to estimate center of mass trajectory in complex athletic task (e.g., golf swing) This study suggests that two-link model of human body provides optimum tradeoff between accuracy and minimum number of sensor module for estimation of center of mass trajectory in particular during fast movements. Wearable technologies based on inertial sensors are viable option for assessing dynamic postural control in complex task outside of gait laboratory and constraints of cameras, surface, and base of support. PMID:25983585

Plume trajectory formation under stack tip self-enveloping

NASA Astrophysics Data System (ADS)

Gribkov, A. M.; Zroichikov, N. A.; Prokhorov, V. B.

2017-10-01

The phenomenon of stack tip self-enveloping and its influence upon the conditions of plume formation and on the trajectory of its motion are considered. Processes are described occurring in the initial part of the plume while the interaction between vertically directed flue gases outflowing from the stack and a horizontally directed moving air flow at high wind velocities that lead to the formation of a flag-like plume. Conditions responsible for the origin and evolution of interaction between these flows are demonstrated. For the first time, a plume formed under these conditions without bifurcation is registered. A photo image thereof is presented. A scheme for the calculation of the motion of a plume trajectory is proposed, the quantitative characteristics of which are obtained based on field observations. The wind velocity and direction, air temperature, and atmospheric turbulence at the level of the initial part of the trajectory have been obtained based on data obtained from an automatic meteorological system (mounted on the outer parts of a 250 m high stack no. 1 at the Naberezhnye Chelny TEPP plant) as well as based on the results of photographing and theodolite sighting of smoke puffs' trajectory taking into account their velocity within its initial part. The calculation scheme is supplemented with a new acting force—the force of self-enveloping. Based on the comparison of the new calculation scheme with the previous one, a significant contribution of this force to the development of the trajectory is revealed. A comparison of the natural full-scale data with the results of the calculation according to the proposed new scheme is made. The proposed calculation scheme has allowed us to extend the application of the existing technique to the range of high wind velocities. This approach would make it possible to simulate and investigate the trajectory and full rising height of the calculated the length above the mouth of flue-pipes, depending on various modal and meteorological parameters under the interrelation between the dynamic and thermal components of the rise as well as to obtain a universal calculation expression for determining the height of the plume rise for different classes of atmospheric stability.

Localization of diffusion sources in complex networks with sparse observations

NASA Astrophysics Data System (ADS)

Hu, Zhao-Long; Shen, Zhesi; Tang, Chang-Bing; Xie, Bin-Bin; Lu, Jian-Feng

2018-04-01

Locating sources in a large network is of paramount importance to reduce the spreading of disruptive behavior. Based on the backward diffusion-based method and integer programming, we propose an efficient approach to locate sources in complex networks with limited observers. The results on model networks and empirical networks demonstrate that, for a certain fraction of observers, the accuracy of our method for source localization will improve as the increase of network size. Besides, compared with the previous method (the maximum-minimum method), the performance of our method is much better with a small fraction of observers, especially in heterogeneous networks. Furthermore, our method is more robust against noise environments and strategies of choosing observers.

Entropic Movement Complexity Reflects Subjective Creativity Rankings of Visualized Hand Motion Trajectories

PubMed Central

Peng, Zhen; Braun, Daniel A.

2015-01-01

In a previous study we have shown that human motion trajectories can be characterized by translating continuous trajectories into symbol sequences with well-defined complexity measures. Here we test the hypothesis that the motion complexity individuals generate in their movements might be correlated to the degree of creativity assigned by a human observer to the visualized motion trajectories. We asked participants to generate 55 novel hand movement patterns in virtual reality, where each pattern had to be repeated 10 times in a row to ensure reproducibility. This allowed us to estimate a probability distribution over trajectories for each pattern. We assessed motion complexity not only by the previously proposed complexity measures on symbolic sequences, but we also propose two novel complexity measures that can be directly applied to the distributions over trajectories based on the frameworks of Gaussian Processes and Probabilistic Movement Primitives. In contrast to previous studies, these new methods allow computing complexities of individual motion patterns from very few sample trajectories. We compared the different complexity measures to how a group of independent jurors rank ordered the recorded motion trajectories according to their personal creativity judgment. We found three entropic complexity measures that correlate significantly with human creativity judgment and discuss differences between the measures. We also test whether these complexity measures correlate with individual creativity in divergent thinking tasks, but do not find any consistent correlation. Our results suggest that entropic complexity measures of hand motion may reveal domain-specific individual differences in kinesthetic creativity. PMID:26733896

Effects of the reconnection electric field on crescent electron distribution functions in asymmetric guide field reconnection

NASA Astrophysics Data System (ADS)

Bessho, N.; Chen, L. J.; Hesse, M.; Wang, S.

2017-12-01

In asymmetric reconnection with a guide field in the Earth's magnetopause, electron motion in the electron diffusion region (EDR) is largely affected by the guide field, the Hall electric field, and the reconnection electric field. The electron motion in the EDR is neither simple gyration around the guide field nor simple meandering motion across the current sheet. The combined meandering motion and gyration has essential effects on particle acceleration by the in-plane Hall electric field (existing only in the magnetospheric side) and the out-of-plane reconnection electric field. We analyze electron motion and crescent-shaped electron distribution functions in the EDR in asymmetric guide field reconnection, and perform 2-D particle-in-cell (PIC) simulations to elucidate the effect of reconnection electric field on electron distribution functions. Recently, we have analytically expressed the acceleration effect due to the reconnection electric field on electron crescent distribution functions in asymmetric reconnection without a guide field (Bessho et al., Phys. Plasmas, 24, 072903, 2017). We extend the theory to asymmetric guide field reconnection, and predict the crescent bulge in distribution functions. Assuming 1D approximation of field variations in the EDR, we derive the time period of oscillatory electron motion (meandering + gyration) in the EDR. The time period is expressed as a hybrid of the meandering period and the gyro period. Due to the guide field, electrons not only oscillate along crescent-shaped trajectories in the velocity plane perpendicular to the antiparallel magnetic fields, but also move along parabolic trajectories in the velocity plane coplanar with magnetic field. The trajectory in the velocity space gradually shifts to the acceleration direction by the reconnection electric field as multiple bounces continue. Due to the guide field, electron distributions for meandering particles are bounded by two paraboloids (or hyperboloids) in the velocity space. We compare theory and PIC simulation results of the velocity shift of crescent distribution functions based on the derived time period of bounce motion in a guide field. Theoretical predictions are applied to electron distributions observed by MMS in magnetopause reconnection to estimate the reconnection electric field.

Effective electric fields along realistic DTI-based neural trajectories for modelling the stimulation mechanisms of TMS

NASA Astrophysics Data System (ADS)

De Geeter, N.; Crevecoeur, G.; Leemans, A.; Dupré, L.

2015-01-01

In transcranial magnetic stimulation (TMS), an applied alternating magnetic field induces an electric field in the brain that can interact with the neural system. It is generally assumed that this induced electric field is the crucial effect exciting a certain region of the brain. More specifically, it is the component of this field parallel to the neuron’s local orientation, the so-called effective electric field, that can initiate neuronal stimulation. Deeper insights on the stimulation mechanisms can be acquired through extensive TMS modelling. Most models study simple representations of neurons with assumed geometries, whereas we embed realistic neural trajectories computed using tractography based on diffusion tensor images. This way of modelling ensures a more accurate spatial distribution of the effective electric field that is in addition patient and case specific. The case study of this paper focuses on the single pulse stimulation of the left primary motor cortex with a standard figure-of-eight coil. Including realistic neural geometry in the model demonstrates the strong and localized variations of the effective electric field between the tracts themselves and along them due to the interplay of factors such as the tract’s position and orientation in relation to the TMS coil, the neural trajectory and its course along the white and grey matter interface. Furthermore, the influence of changes in the coil orientation is studied. Investigating the impact of tissue anisotropy confirms that its contribution is not negligible. Moreover, assuming isotropic tissues lead to errors of the same size as rotating or tilting the coil with 10 degrees. In contrast, the model proves to be less sensitive towards the not well-known tissue conductivity values.

Developmental trajectories of self-injurious behavior, suicidal behavior and substance misuse and their association with adolescent borderline personality pathology.

PubMed

Nakar, Orit; Brunner, Romuald; Schilling, Oliver; Chanen, Andrew; Fischer, Gloria; Parzer, Peter; Carli, Vladimir; Wasserman, Danuta; Sarchiapone, Marco; Wasserman, Camilla; Hoven, Christina W; Resch, Franz; Kaess, Michael

2016-06-01

Adolescent risk-taking and self-harm behaviors are associated with affect dysregulation and impulsivity, both core features of borderline personality disorder (BPD). We hypothesized that the developmental courses of these behaviors i) tend to cluster rather than appear individually, and ii) might indicate adolescent BPD pathology. Therefore, we explored the developmental trajectories of self-injurious behavior (SIB), suicidal behavior (SB) and substance misuse (SM) in a community sample of adolescents; and we investigated the trajectories' overlap and its associations with BPD traits. 513 adolescents, aged 15-17 years, were followed for two years as part of the Saving and Empowering Young Lives in Europe study and its subsequent follow-up. Distinct developmental trajectories were explored using general growth mixture modeling. Three distinct classes were identified within each of the harmful behaviors SIB, SB and SM. Both the high-risk SIB trajectory and the high-risk SB trajectory demonstrated elevated initial degree of engagement, followed by a gradual decrease. The SM high-risk trajectory had a medium initial degree of engagement, which increased over time. There was a high degree of overlap (80-90%) among the high-risk trajectories for the three behaviors (SIB, SB and SM), and this overlap was significantly associated with elevated levels of BPD pathology. The data collection was based on participants' self-report. The findings indicate a similar pattern of reduction over time between SIB and SB for the high-risk trajectories, whereas the high-risk trajectories for SM show a pattern of increase over time. The observed symptom shift is associated with borderline personality pathology in adolescents. Therefore these behaviors might represent early indicators of risk supporting potential early detection. Copyright © 2016 Elsevier B.V. All rights reserved.

Transport of Colloids along Corners: Visualization of Evaporation-Induced Flows beyond the Axisymmetric Condition.

PubMed

Vélez-Cordero, J Rodrigo; Yáñez Soto, Bernardo; Arauz-Lara, José L

2016-08-16

Nonhomogeneous evaporation fluxes have been shown to promote the formation of internal currents in sessile droplets, explaining the patterns that suspended particles leave after the droplet has dried out. Although most evaporation experiments have been conducted using spherical-cap-shaped drops, which are essentially in an axisymmetric geometry, here we show an example of nonhomogeneous evaporation in asymmetric geometries, which is visualized by following the motion of colloidal particles along liquid fingers forming a meniscus at square corners. It is found that the particle's velocity increases with the diffusive evaporation factor [Formula: see text] for the three tested fluids: water, isopropyl alcohol (IPA), and ethanol (EtOH). Here, [Formula: see text] is the vapor diffusivity in air, RH is the relative amount of vapor in the atmosphere, and cs is the saturated vapor concentration. We observed that in IPA and EtOH the internal currents promote a 3D spiral motion, whereas in water the particle's trajectory is basically unidirectional. By adding 0.25 critical micelle concentration (CMC) of sodium dodecyl sulfate (SDS) surfactant in water, a velocity blast was observed in the whole circulation flow pattern, going from [Formula: see text] to nearly [Formula: see text] in the longitudinal velocity component. To assess the effect of breaking the axisymmetric condition on the evaporation flux profile, we numerically solved the diffusive equation in model geometries that preserve the value of the contact angle θ but introduce an additional angle ϕ that characterizes the solid substrate. By testing different combinations of θ and ϕ, we corroborated that the evaporation flux increases when the substrate and the gas-liquid curves meet at corners with increasing sharpness.

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

PubMed

Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll

2016-01-04

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Measuring molecular motions inside single cells with improved analysis of single-particle trajectories

NASA Astrophysics Data System (ADS)

Rowland, David J.; Biteen, Julie S.

2017-04-01

Single-molecule super-resolution imaging and tracking can measure molecular motions inside living cells on the scale of the molecules themselves. Diffusion in biological systems commonly exhibits multiple modes of motion, which can be effectively quantified by fitting the cumulative probability distribution of the squared step sizes in a two-step fitting process. Here we combine this two-step fit into a single least-squares minimization; this new method vastly reduces the total number of fitting parameters and increases the precision with which diffusion may be measured. We demonstrate this Global Fit approach on a simulated two-component system as well as on a mixture of diffusing 80 nm and 200 nm gold spheres to show improvements in fitting robustness and localization precision compared to the traditional Local Fit algorithm.

Sex differences in adolescent white matter architecture.

PubMed

Bava, Sunita; Boucquey, Veronique; Goldenberg, Diane; Thayer, Rachel E; Ward, Megan; Jacobus, Joanna; Tapert, Susan F

2011-02-23

Sex-specific trajectories in white matter development during adolescence may help explain cognitive and behavioral divergences between males and females. Knowledge of sex differences in typically developing adolescents can provide a basis for interpreting sexual dimorphisms in abilities and actions. We examined 58 healthy adolescents (12-14years of age) with diffusion tensor imaging (DTI). Diffusion parameters fractional anisotropy (FA), and mean (MD), radial (RD), and axial diffusivities (AD) were subjected to whole-brain voxel-wise group comparisons using tract-based spatial statistics. Sex differences in white matter microstructure were examined in relation to pubertal development. Early adolescent females (n=29) evidenced higher FA in the right superior corona radiata, higher FA and AD in bilateral corticospinal tracts (≥164μl, p<.01), and lower MD in the right inferior longitudinal fasciculus (ILF) and left forceps major (≥164μl, p<.01) than age-matched males (n=29). Males did not show any areas of higher FA or lower MD than females, but had higher AD in the right superior longitudinal fasciculus, ILF, and forceps minor (≥ 164μl, p<.01). Pubertal stage did not account for sex disparities. In early adolescence, females' motor tracts may reflect widespread changes, while males may undergo relatively more microstructural change in projection and association fibers. Copyright © 2010 Elsevier B.V. All rights reserved.

Macromolecule diffusion and confinement in prokaryotic cells.

PubMed

Mika, Jacek T; Poolman, Bert

2011-02-01

We review recent observations on the mobility of macromolecules and their spatial organization in live bacterial cells. We outline the major fluorescence microscopy-based methods to determine the mobility and thus the diffusion coefficients (D) of molecules, which is not trivial in small cells. The extremely high macromolecule crowding of prokaryotes is used to rationalize the reported lower diffusion coefficients as compared to eukaryotes, and we speculate on the nature of the barriers for diffusion observed for proteins (and mRNAs) in vivo. Building on in vitro experiments and modeling studies, we evaluate the size dependence of diffusion coefficients for macromolecules in vivo, in case of both water-soluble and integral membrane proteins. We comment on the possibilities of anomalous diffusion and provide examples where the macromolecule mobility may be limiting biological processes. Copyright © 2010 Elsevier Ltd. All rights reserved.

Quasilinear analysis of ion Bernstein and lower hybrid waves synergy

NASA Astrophysics Data System (ADS)

Paoletti, F.; Cardinali, A.; Shoucri, M.; Shkarofsky, A.; Bernabei, S.; Ono, M.

1996-02-01

A quasilinear analysis of the absorption of Ion Bernstein Wave (IBW) by the electron population of the plasma is performed. It uses an analytical calculation of the amplitude of the electric field along the trajectory to obtain the quasilinear diffusion coefficient. A numerical integration of the Fokker-Planck equation is performed together with the dynamical evolution of the IBW and Lower Hybrid Wave (LHW) ray trajectories. The damping of IBW is calculated on the distorted distribution function generated by the previous application of Lower Hybrid Current Drive (LHCD) which has bridged the n∥-gap. This calculation is particularly relevant because of the IBW/LHW experiments on the Princeton Beta Experiment-Modified (PBX-M).

Anomalous diffusion of brain metabolites evidenced by diffusion-weighted magnetic resonance spectroscopy in vivo

PubMed Central

Marchadour, Charlotte; Brouillet, Emmanuel; Hantraye, Philippe; Lebon, Vincent; Valette, Julien

2012-01-01

Translational displacement of molecules within cells is a key process in cellular biology. Molecular motion potentially depends on many factors, including active transport, cytosol viscosity and molecular crowding, tortuosity resulting from cytoskeleton and organelles, and restriction barriers. However, the relative contribution of these factors to molecular motion in the cytoplasm remains poorly understood. In this work, we designed an original diffusion-weighted magnetic resonance spectroscopy strategy to probe molecular motion at subcellular scales in vivo. This led to the first observation of anomalous diffusion, that is, dependence of the apparent diffusion coefficient (ADC) on the diffusion time, for endogenous intracellular metabolites in the brain. The observed increase of the ADC at short diffusion time yields evidence that metabolite motion is characteristic of hindered random diffusion rather than active transport, for time scales up to the dozen milliseconds. Armed with this knowledge, data modeling based on geometrically constrained diffusion was performed. Results suggest that metabolite diffusion occurs in a low-viscosity cytosol hindered by ∼2-μm structures, which is consistent with known intracellular organization. PMID:22929443

Putting atomic diffusion theory of magnetic ApBp stars to the test: evaluation of the predictions of time-dependent diffusion models

NASA Astrophysics Data System (ADS)

Kochukhov, O.; Ryabchikova, T. A.

2018-02-01

A series of recent theoretical atomic diffusion studies has address the challenging problem of predicting inhomogeneous vertical and horizontal chemical element distributions in the atmospheres of magnetic ApBp stars. Here we critically assess the most sophisticated of such diffusion models - based on a time-dependent treatment of the atomic diffusion in a magnetized stellar atmosphere - by direct comparison with observations as well by testing the widely used surface mapping tools with the spectral line profiles predicted by this theory. We show that the mean abundances of Fe and Cr are grossly underestimated by the time-dependent theoretical diffusion model, with discrepancies reaching a factor of 1000 for Cr. We also demonstrate that Doppler imaging inversion codes, based either on modelling of individual metal lines or line-averaged profiles simulated according to theoretical three-dimensional abundance distribution, are able to reconstruct correct horizontal chemical spot maps despite ignoring the vertical abundance variation. These numerical experiments justify a direct comparison of the empirical two-dimensional Doppler maps with theoretical diffusion calculations. This comparison is generally unfavourable for the current diffusion theory, as very few chemical elements are observed to form overabundance rings in the horizontal field regions as predicted by the theory and there are numerous examples of element accumulations in the vicinity of radial field zones, which cannot be explained by diffusion calculations.

Rumor Diffusion in an Interests-Based Dynamic Social Network

PubMed Central

Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping

2013-01-01

To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency. PMID:24453911

Rumor diffusion in an interests-based dynamic social network.

PubMed

Tang, Mingsheng; Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping

2013-01-01

To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency.

Improved compaction of ZnO nano-powder triggered by the presence of acetate and its effect on sintering.

PubMed

Dargatz, Benjamin; Gonzalez-Julian, Jesus; Guillon, Olivier

2015-04-01

The retention of nanocrystallinity in dense ceramic materials is still a challenge, even with the application of external pressure during sintering. The compaction behavior of high purity and acetate enriched zinc oxide (ZnO) nano-powders was investigated. It was found that acetate in combination with water plays a key role during the compaction into green bodies at moderate temperatures. Application of constant pressure resulted in a homogeneous green body with superior packing density (86% of theoretical value) at moderate temperature (85 °C) in the presence of water. In contrast, no improvement in density could be achieved if pure ZnO powder was used. This compaction behavior offers superior packing of the particles, resulting in a high relative density of the consolidated compact with negligible coarsening. Dissolution accompanying creep diffusion based matter transport is suggested to strongly support reorientation of ZnO particles towards densities beyond the theoretical limit for packing of ideal monosized spheres. Finally, the sintering trajectory reveals that grain growth is retarded compared to conventional processing up to 90% of theoretical density. Moreover, nearly no radial shrinkage was observed after sinter-forging for bodies performed with this advanced processing method.

Improved compaction of ZnO nano-powder triggered by the presence of acetate and its effect on sintering

PubMed Central

Gonzalez-Julian, Jesus; Guillon, Olivier

2015-01-01

The retention of nanocrystallinity in dense ceramic materials is still a challenge, even with the application of external pressure during sintering. The compaction behavior of high purity and acetate enriched zinc oxide (ZnO) nano-powders was investigated. It was found that acetate in combination with water plays a key role during the compaction into green bodies at moderate temperatures. Application of constant pressure resulted in a homogeneous green body with superior packing density (86% of theoretical value) at moderate temperature (85 °C) in the presence of water. In contrast, no improvement in density could be achieved if pure ZnO powder was used. This compaction behavior offers superior packing of the particles, resulting in a high relative density of the consolidated compact with negligible coarsening. Dissolution accompanying creep diffusion based matter transport is suggested to strongly support reorientation of ZnO particles towards densities beyond the theoretical limit for packing of ideal monosized spheres. Finally, the sintering trajectory reveals that grain growth is retarded compared to conventional processing up to 90% of theoretical density. Moreover, nearly no radial shrinkage was observed after sinter-forging for bodies performed with this advanced processing method. PMID:27877777

Sulfides from Martian and Lunar Basalts: Comparative Chemistry for Ni Co Cu and Se

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

J Papike; P Burger; C Shearer

2011-12-31

Here Mars and Moon are used as 'natural laboratories' with Moon displaying lower oxygen fugacities ({approx}IW-1) than Mars ({approx}IW to FMQ). Moon has lower concentrations of Ni and Co in basaltic melts than does Mars. The major sulfides are troilite (FeS) in lunar basalts and pyrrhotite (Fe{sub 1-x}S) in martian basalts. This study focuses on the concentrations of Ni, Co, Cu, and Se. We chose these elements because of their geochemical importance and the feasibility of analyzing them with a combination of synchrotron X-ray fluorescence (SXRF) and electron microprobe (EPMA) techniques. The selenium concentrations could only be analyzed, at highmore » precision, with SXRF techniques as they are <150 ppm, similar to concentrations seen in carbonaceous chondrites and interplanetary dust particles (IDPs). Nickel and Co are in higher concentrations in martian sulfides than lunar and are higher in martian olivine-bearing lithologies than olivine-free varieties. The sulfides in individual samples show very large ranges in concentration (e.g., Ni ranges from 50 000 ppm to <5 ppm). These large ranges are mainly due to compositional heterogeneities within individual grains due to diffusion and phase separation. Electron microprobe wavelength-dispersive (WDS) mapping of Ni, Co, and Cu show the diffusion trajectories. Nickel and Co have almost identical diffusion trajectories leading to the likely nucleation of pentlandite (Ni,Co,Fe){sub 9}S{sub 8}, and copper diffuses along separate pathways likely toward chalcopyrite nucleation sites (CuFeS{sub 2}). The systematics of Ni and Co in lunar and martian sulfides clearly distinguish the two parent bodies, with martian sulfides displaced to higher Ni and Co values.« less

"O tradutor e os seus trebelhos": Fred P. Ellison and Translation

ERIC Educational Resources Information Center

Frizzi, Adria

2016-01-01

In this article, Adria Frizzi provides a brief overview of Fred Ellison's work in the field of literary translation. Frizzi does so by outlining Ellison's trajectory as a translator--highlighting how his choices in this area of his scholarship fit into a broader, multipronged approach to the study and diffusion of the language, culture, and…

Global Reference Atmosphere Model (GRAM)

NASA Technical Reports Server (NTRS)

Woodrum, A. W.

1989-01-01

GRAM series of four-dimensional atmospheric model validated by years of data. GRAM program, still available. More current are Gram 86, which includes atmospheric data from 1986 and runs on DEC VAX, and GRAM 88, which runs on IBM 3084. Program generates altitude profiles of atmospheric parameters along any simulated trajectory through atmosphere, and also useful for global circulation and diffusion studies.

White Matter and Development in Children with an Autism Spectrum Disorder

ERIC Educational Resources Information Center

Mak-Fan, Kathleen M.; Morris, Drew; Vidal, Julie; Anagnostou, Evdokia; Roberts, Wendy; Taylor, Margot J.

2013-01-01

Recent research suggests that brain development follows an abnormal trajectory in children with autism spectrum disorders (ASD). The current study examined changes in diffusivity with age within defined white matter tracts in a group of typically developing children and a group of children with an ASD, aged 6 to 14 years. Age by group interactions…

Terminal altitude maximization for Mars entry considering uncertainties

NASA Astrophysics Data System (ADS)

Cui, Pingyuan; Zhao, Zeduan; Yu, Zhengshi; Dai, Juan

2018-04-01

Uncertainties present in the Mars atmospheric entry process may cause state deviations from the nominal designed values, which will lead to unexpected performance degradation if the trajectory is designed merely based on the deterministic dynamic model. In this paper, a linear covariance based entry trajectory optimization method is proposed considering the uncertainties presenting in the initial states and parameters. By extending the elements of the state covariance matrix as augmented states, the statistical behavior of the trajectory is captured to reformulate the performance metrics and path constraints. The optimization problem is solved by the GPOPS-II toolbox in MATLAB environment. Monte Carlo simulations are also conducted to demonstrate the capability of the proposed method. Primary trading performances between the nominal deployment altitude and its dispersion can be observed by modulating the weights on the dispersion penalty, and a compromised result referring to maximizing the 3σ lower bound of the terminal altitude is achieved. The resulting path constraints also show better satisfaction in a disturbed environment compared with the nominal situation.

Physical properties of meteoroids based on middle and upper atmosphere radar measurements

NASA Astrophysics Data System (ADS)

Gritsevich, M.; Kero, J.; Virtanen, J.; Szasz, C.; Nakamura, T.; Peltoniemi, J.; Koschny, D.

2014-07-01

We present a novel approach to reliably interpret the meteor head-echo scattering measurements detected by the 46.5 MHz MU radar system near Shigaraki, Japan. A meteor head echo is caused by radio waves scattered from the dense region of plasma surrounding and co-moving with a meteoroid during atmospheric flight. The signal Doppler shift and/or range rate of the target can therefore be used to determine meteoroid velocity. The data reduction steps include determining the exact trajectory of the meteoroids entering the observation volume of the antenna beam and calculating meteoroid mass and velocity as a function of time. The model is built using physically-based parametrization. The considered observation volume is narrow, elongated in the vertical direction, and its area of greatest sensitivity covers a circular area of about 10 km diameter at an altitude of 100 km above the radar. Over 100,000 meteor head echoes have been detected over past years of observations. Most of the events are faint with no alternative to be detected visually or with intensified video (ICCD) cameras. In this study we are focusing on objects which have entered the atmosphere with almost vertical trajectories, to ensure the observed segment of the trajectory to be as complete as possible, without loss of its beginning or end part due to beam-pattern-related loss of signal power. The analysis output parameters are range, altitude, radial velocity, meteoroid velocity, instantaneous target position, Radar Cross Section (RCS), meteor radiant, meteoroid ballistic and ablation coefficients, mass loss parameter and meteoroid mass, with possibility to derive other parameters.

Physical Properties of Meteoroids based on Middle and Upper Atmosphere Radar Measurements

NASA Astrophysics Data System (ADS)

Gritsevich, Maria; Nakamura, Takuji; Kero, Johan; Szasz, Csilla; Virtanen, Jenni; Peltoniemi, Jouni; Koschny, Detlef

We present a novel approach to reliably interpret the meteor head echo scattering measurements detected by the 46.5 MHz MU radar system near Shigaraki, Japan. A meteor head echo is caused by radio waves scattered from the dense region of plasma surrounding and co-moving with a meteoroid during atmospheric flight. The signal Doppler shift and/or range rate of the target can therefore be used to determine meteoroid velocity. The data reduction steps include determining the exact trajectory of the meteoroids entering the observation volume of the antenna beam and calculating meteoroid mass and velocity as a function of time. The model is built using physically based parameterization. The considered observation volume is narrow, elongated in the vertical direction, and its area of greatest sensitivity covers a circular area of about 10 km diameter at an altitude of 100 km above the radar. Over 100000 meteor head echoes have been detected over past years of observations. Most of the events are faint with no alternative to be detected visually or with intensified video (ICCD) cameras. In this study we are focusing on objects which have entered the atmosphere with almost vertical trajectories, to ensure the observed segment of the trajectory to be as complete as possible, without loss of its beginning or end part due to beam-pattern related loss of signal power. The analysis output parameters are range, altitude, radial velocity, meteoroid velocity, instantaneous target position, Radar Cross Section (RCS), meteor radiant, meteoroid ballistic and ablation coefficients, mass loss parameter and meteoroid mass, with possibility to derive other parameters.

Single-Molecule Tracking Study of the Permeability and Transverse Width of Individual Cylindrical Microdomains in Solvent-Swollen Polystyrene-block-poly(ethylene oxide) Films.

PubMed

Sapkota, Dol Raj; Tran-Ba, Khanh-Hoa; Elwell-Cuddy, Trevor; Higgins, Daniel A; Ito, Takashi

2016-12-01

Understanding the properties of solvent-swollen block copolymer (BCP) microdomains is important for better solvent-based control of microdomain morphology, orientation, and permeability. In this study, single-molecule tracking (SMT) was explored to assess the permeability and transverse width of individual cylindrical microdomains in solvent-swollen polystyrene-block-poly(ethylene oxide) (PS-b-PEO) films. PS-b-PEO films comprising shear-elongated cylindrical PEO microdomains were prepared by sandwiching its benzene or tetrahydrofuran (THF) solution between two glass substrates. SMT measurements were performed at different drying times to investigate the effects of solvent evaporation on the microdomain properties. SMT data showed one-dimensional (1D) motions of single fluorescent molecules (sulforhodamine B) based on their diffusion within the cylindrical microdomains. Microdomain permeability and transverse width were assessed from the single-molecule diffusion coefficients (D SMT ) and transverse variance of the 1D trajectories (σ δ 2 ), respectively. The D SMT and σ δ 2 values from individual 1D trajectories were widely distributed with no evidence of correlation on a single molecule basis, possibly because the individual microdomains in a film were swollen to different extents. On average, microdomain permeability (D) and effective radius (r) gradually decreased within the first 3 days of drying due to solvent evaporation, and changed negligibly thereafter. PS-b-PEO films prepared from THF solutions exhibited larger changes in D and r as compared with those from benzene solutions due to the better swelling of the PEO microdomains by THF. Importantly, changes in D were more prominent than those in r, suggesting that the permeability of the PEO microdomains is very susceptible to the presence of solvent. These results reveal the unique capability of SMT to assess the properties of individual cylindrical microdomains in a solvent-swollen BCP film.

Single-molecule tracking study of the permeability and transverse width of individual cylindrical microdomains in solvent-swollen polystyrene- block-poly(ethylene oxide) films

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

Sapkota, Dol Raj; Tran-Ba, Khanh-Hoa; Elwell-Cuddy, Trevor

Understanding the properties of solvent-swollen block copolymer (BCP) microdomains is important for better solvent-based control of microdomain morphology, orientation, and permeability. In this study, single-molecule tracking (SMT) was explored to assess the permeability and transverse width of individual cylindrical microdomains in solvent-swollen polystyrene- block-poly(ethylene oxide) (PS-b-PEO) films. PS-b-PEO films comprising shear-elongated cylindrical PEO microdomains were prepared by sandwiching its benzene or tetrahydrofuran (THF) solution between two glass substrates. In this paper, SMT measurements were performed at different drying times to investigate the effects of solvent evaporation on the microdomain properties. SMT data showed one-dimensional (1D) motions of single fluorescent moleculesmore » (sulforhodamine B) based on their diffusion within the cylindrical microdomains. Microdomain permeability and transverse width were assessed from the single-molecule diffusion coefficients (D SMT) and transverse variance of the 1D trajectories (σ δ 2), respectively. The D SMT and σ δ 2 values from individual 1D trajectories were widely distributed with no evidence of correlation on a single molecule basis, possibly because the individual microdomains in a film were swollen to different extents. On average, microdomain permeability (D) and effective radius (r) gradually decreased within the first 3 days of drying due to solvent evaporation, and changed negligibly thereafter. PS-b-PEO films prepared from THF solutions exhibited larger changes in D and r as compared with those from benzene solutions due to the better swelling of the PEO microdomains by THF. Importantly, changes in D were more prominent than those in r, suggesting that the permeability of the PEO microdomains is very susceptible to the presence of solvent. Finally, these results reveal the unique capability of SMT to assess the properties of individual cylindrical microdomains in a solvent-swollen BCP film.« less

Single-molecule tracking study of the permeability and transverse width of individual cylindrical microdomains in solvent-swollen polystyrene- block-poly(ethylene oxide) films

DOE PAGES

Sapkota, Dol Raj; Tran-Ba, Khanh-Hoa; Elwell-Cuddy, Trevor; ...

2016-11-04

Understanding the properties of solvent-swollen block copolymer (BCP) microdomains is important for better solvent-based control of microdomain morphology, orientation, and permeability. In this study, single-molecule tracking (SMT) was explored to assess the permeability and transverse width of individual cylindrical microdomains in solvent-swollen polystyrene- block-poly(ethylene oxide) (PS-b-PEO) films. PS-b-PEO films comprising shear-elongated cylindrical PEO microdomains were prepared by sandwiching its benzene or tetrahydrofuran (THF) solution between two glass substrates. In this paper, SMT measurements were performed at different drying times to investigate the effects of solvent evaporation on the microdomain properties. SMT data showed one-dimensional (1D) motions of single fluorescent moleculesmore » (sulforhodamine B) based on their diffusion within the cylindrical microdomains. Microdomain permeability and transverse width were assessed from the single-molecule diffusion coefficients (D SMT) and transverse variance of the 1D trajectories (σ δ 2), respectively. The D SMT and σ δ 2 values from individual 1D trajectories were widely distributed with no evidence of correlation on a single molecule basis, possibly because the individual microdomains in a film were swollen to different extents. On average, microdomain permeability (D) and effective radius (r) gradually decreased within the first 3 days of drying due to solvent evaporation, and changed negligibly thereafter. PS-b-PEO films prepared from THF solutions exhibited larger changes in D and r as compared with those from benzene solutions due to the better swelling of the PEO microdomains by THF. Importantly, changes in D were more prominent than those in r, suggesting that the permeability of the PEO microdomains is very susceptible to the presence of solvent. Finally, these results reveal the unique capability of SMT to assess the properties of individual cylindrical microdomains in a solvent-swollen BCP film.« less

Phenomenology and energetics of diffusion across cell phase states.

PubMed

Ashrafuzzaman, Md

2015-11-01

Cell based transport properties have been mathematically addressed. Cell contained cross boundary diffusion of materials has been explained using valid formalisms and related analytical expressions have been developed. Various distinguishable physical structures and their properties raise different general structure specific diffusion mechanisms and controlled transport related parameters. Some of these parameters play phenomenological roles and some cause regulatory effects. The cell based compartments may be divided into three major physical phase states namely liquid, plasma and solid phase states. Transport of ions, nutrients, small molecules like proteins, etc. across inter phase states and intraphase states follows general transport related formalisms. Creation of some localized permanent and/or temporary structures e.g., ion channels, clustering of constituents, etc. and the transitions between such structures appear as regulators of the transport mechanisms. In this article, I have developed mainly a theoretical analysis of the commonly observed cell transport phenomena. I have attempted to develop formalisms on general cell based diffusion followed by a few numerical computations to address the analytical expression phenomenologically. I have then extended the analysis to adopting with the local structure originated energetics. Independent or correlated molecular transport naturally relies on some general parameters that define the nature of local cell environment as well as on some occasionally raised or transiently active stochastic resonance due to localized interactions. Short and long range interaction energies play crucial roles in this regard. Physical classification of cellular compartments has led us developing analytical expressions on both biologically observed diffusion mechanisms and the diffusions's occasional stochasticity causing energetics. These analytical expressions help us address the diffusion phenomena generally considering the physical properties of the biostructures across the diffusion pathways. A specific example case of single molecule transport and localized interaction energetics in a specific cell phase has been utilized to address the diffusion quite clearly. This article helps to address the mechanisms of cell based diffusion and nutrient movements and thus helps develop strategic templates to manipulate the diffusion mechanisms. Application of the theoretical knowledge into designing or discovering drugs or small molecule inhibitors targeting cell based structures may open up new avenues in biomedical sciences.

Analysis of self-overlap reveals trade-offs in plankton swimming trajectories

PubMed Central

Bianco, Giuseppe; Mariani, Patrizio; Visser, Andre W.; Mazzocchi, Maria Grazia; Pigolotti, Simone

2014-01-01

Movement is a fundamental behaviour of organisms that not only brings about beneficial encounters with resources and mates, but also at the same time exposes the organism to dangerous encounters with predators. The movement patterns adopted by organisms should reflect a balance between these contrasting processes. This trade-off can be hypothesized as being evident in the behaviour of plankton, which inhabit a dilute three-dimensional environment with few refuges or orienting landmarks. We present an analysis of the swimming path geometries based on a volumetric Monte Carlo sampling approach, which is particularly adept at revealing such trade-offs by measuring the self-overlap of the trajectories. Application of this method to experimentally measured trajectories reveals that swimming patterns in copepods are shaped to efficiently explore volumes at small scales, while achieving a large overlap at larger scales. Regularities in the observed trajectories make the transition between these two regimes always sharper than in randomized trajectories or as predicted by random walk theory. Thus, real trajectories present a stronger separation between exploration for food and exposure to predators. The specific scale and features of this transition depend on species, gender and local environmental conditions, pointing at adaptation to state and stage-dependent evolutionary trade-offs. PMID:24789560

Observing quantum trajectories: From Mott’s problem to quantum Zeno effect and back

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

Gosson, Maurice de, E-mail: maurice.de.gosson@univie.ac.at; Hiley, Basil; TPRU, Birkbeck, University of London, Malet Street, London WC1E 7HX

2016-11-15

The experimental results of Kocsis et al., Mahler et al. and the proposed experiments of Morley et al. show that it is possible to construct “trajectories” in interference regions in a two-slit interferometer. These results call for a theoretical re-appraisal of the notion of a “quantum trajectory” first introduced by Dirac and in the present paper we re-examine this notion from the Bohm perspective based on Hamiltonian flows. In particular, we examine the short-time propagator and the role that the quantum potential plays in determining the form of these trajectories. These trajectories differ from those produced in a typical particlemore » tracker and the key to this difference lies in the active suppression of the quantum potential necessary to produce Mott-type trajectories. We show, using a rigorous mathematical argument, how the active suppression of this potential arises. Finally we discuss in detail how this suppression also accounts for the quantum Zeno effect.« less

Leidenfrost vapour layer moderation of the drag crisis and trajectories of superhydrophobic and hydrophilic spheres falling in water.

PubMed

Vakarelski, Ivan U; Chan, Derek Y C; Thoroddsen, Sigurdur T

2014-08-21

We investigate the dynamic effects of a Leidenfrost vapour layer sustained on the surface of heated steel spheres during free fall in water. We find that a stable vapour layer sustained on the textured superhydrophobic surface of spheres falling through 95 °C water can reduce the hydrodynamic drag by up to 75% and stabilize the sphere trajectory for the Reynolds number between 10(4) and 10(6), spanning the drag crisis in the absence of the vapour layer. For hydrophilic spheres under the same conditions, the transition to drag reduction and trajectory stability occurs abruptly at a temperature different from the static Leidenfrost point. The observed drag reduction effects are attributed to the disruption of the viscous boundary layer by the vapour layer whose thickness depends on the water temperature. Both the drag reduction and the trajectory stabilization effects are expected to have significant implications for development of sustainable vapour layer based technologies.

A mass diffusion-based interpretation of the effect of total solids content on solid-state anaerobic digestion of cellulosic biomass.

PubMed

Xu, Fuqing; Wang, Zhi-Wu; Tang, Li; Li, Yebo

2014-09-01

In solid-state anaerobic digestion (SS-AD) of cellulosic biomass, the volumetric methane production rate has often been found to increase with the increase in total solids (TS) content until a threshold is reached, and then to decrease. This phenomenon cannot be explained by conventional understanding derived from liquid anaerobic digestion. This study proposed that the high TS content-caused mass diffusion limitation may be responsible for the observed methane production deterioration. Based on this hypothesis, a new SS-AD model was developed by taking into account the mass diffusion limitation and hydrolysis inhibition. The good agreement between model simulation and the experimental as well as literature data verified that the observed reduction in volumetric methane production rate could be ascribed to hydrolysis inhibition as a result of the mass diffusion limitation in SS-AD. Copyright © 2014 Elsevier Ltd. All rights reserved.

On The Development of One-way Nesting of Air-pollution Model Smog Into Numerical Weather Prediction Model Eta

NASA Astrophysics Data System (ADS)

Halenka, T.; Bednar, J.; Brechler, J.

The spatial distribution of air pollution on the regional scale (Bohemian region) is simulated by means of Charles University puff model SMOG. The results are used for the assessment of the concentration fields of ozone, nitrogen oxides and other ozone precursors. Current improved version of the model covers up to 16 groups of basic compounds and it is based on trajectory computation and puff interaction both by means of Gaussian diffusion mixing and chemical reactions of basic species. Gener- ally, the method used for trajectory computation is valuable mainly for episodes sim- ulation, nevertheless, climatological study can be solved as well by means of average wind rose. For the study being presented huge database of real emission sources was incorporated with all kind of sources included. Some problem with the background values of concentrations was removed. The model SMOG has been nested into the forecast model ETA to obtain appropriate meteorological data input. We can estimate air pollution characteristics both for episodes analysis and the prediction of future air quality conditions. Necessary prognostic variables from the numerical weather pre- diction model are taken for the region of the central Bohemia, where the original puff model was tested. We used mainly 850 hPa wind field for computation of prognos- tic trajectories, the influence of surface temperature as a parameter of photochemistry reactions as well as the effect of cloudness has been tested.

Emerging Structure–Function Relations in the Developing Face Processing System

PubMed Central

Suzanne Scherf, K.; Thomas, Cibu; Doyle, Jaime; Behrmann, Marlene

2014-01-01

To evaluate emerging structure–function relations in a neural circuit that mediates complex behavior, we investigated age-related differences among cortical regions that support face recognition behavior and the fiber tracts through which they transmit and receive signals using functional neuroimaging and diffusion tensor imaging. In a large sample of human participants (aged 6–23 years), we derived the microstructural and volumetric properties of the inferior longitudinal fasciculus (ILF), the inferior fronto-occipital fasciculus, and control tracts, using independently defined anatomical markers. We also determined the functional characteristics of core face- and place-selective regions that are distributed along the trajectory of the pathways of interest. We observed disproportionately large age-related differences in the volume, fractional anisotropy, and mean and radial, but not axial, diffusivities of the ILF. Critically, these differences in the structural properties of the ILF were tightly and specifically linked with an age-related increase in the size of a key face-selective functional region, the fusiform face area. This dynamic association between emerging structural and functional architecture in the developing brain may provide important clues about the mechanisms by which neural circuits become organized and optimized in the human cortex. PMID:23765156

A principal component analysis of the dynamics of subdomains and binding sites in human serum albumin.

PubMed

Paris, Guillaume; Ramseyer, Christophe; Enescu, Mironel

2014-05-01

The conformational dynamics of human serum albumin (HSA) was investigated by principal component analysis (PCA) applied to three molecular dynamics trajectories of 200 ns each. The overlap of the essential subspaces spanned by the first 10 principal components (PC) of different trajectories was about 0.3 showing that the PCA based on a trajectory length of 200 ns is not completely convergent for this protein. The contributions of the relative motion of subdomains and of the subdomains (internal) distortion to the first 10 PCs were found to be comparable. Based on the distribution of the first 3 PC, 10 protein conformers are identified showing relative root mean square deviations (RMSD) between 2.3 and 4.6 Å. The main PCs are found to be delocalized over the whole protein structure indicating that the motions of different protein subdomains are coupled. This coupling is considered as being related to the allosteric effects observed upon ligand binding to HSA. On the other hand, the first PC of one of the three trajectories describes a conformational transition of the protein domain I that is close to that experimentally observed upon myristate binding. This is a theoretical support for the older hypothesis stating that changes of the protein onformation favorable to binding can precede the ligand complexation. A detailed all atoms PCA performed on the primary Sites 1 and 2 confirms the multiconformational character of the HSA binding sites as well as the significant coupling of their motions. Copyright © 2013 Wiley Periodicals, Inc.

Plasma diffusion at the magnetopause - The case of lower hybrid drift waves

NASA Technical Reports Server (NTRS)

Treumann, R. A.; Labelle, J.; Pottelette, R.

1991-01-01

The diffusion expected from the quasi-linear theory of the lower hybrid drift instability at the earth's magnetopause is recalculated. The resulting diffusion coefficient is marginally large enough to explain the thickness of the boundary layer under quiet conditions, based on observational upper limits for the wave intensities. Thus, one possible model for the boundary layer could involve equilibrium between the diffusion arising from lower hybrid waves and various loss processes.

Trajectory Design of the Lunar Impactor Mission Concept

NASA Technical Reports Server (NTRS)

Chung, Min-Kun J.; McElrath, Timothy P.; Roncoli, Ralph B.

2006-01-01

The National Aeronautics and Space Administration (NASA) solicited proposals in 2006 for an opportunity to include a small secondary payload with the launch of the Lunar Reconnaissance Orbiter (LRO) scheduled for October 2008. The cost cap of the proposal was between $50 and $80M, and the mass cap was 1,000 kilograms. JPL proposed a Lunar Impactor (LI) concept for this solicitation. The mission objective of LI was to impact the permanently shadowed region of a South polar crater ultimately to detect the presence of water. The detection of water ice would prove to be an important factor on future lunar exploration. NASA Ames Research Center also proposed a similar concept, the Lunar Crater observation and Sensing Satellite (LCROSS), which was selected by NASA for the mission. However, in this paper, the trajectory design of the LI proposed by JPL is considered. Since the LI spacecraft was to be launched on the LRO launch vehicle as a secondary payload, its initial trajectory must be diverted at some later time from the LRO trans-lunar trajectory for the subsequent impact. Several such trajectories have been considered, where each trajectory option fields some specific values for the mission parameters. The mission parameters include the availability of LRO instruments at the time of impact for the observation by LRO, the mission duration, the impact velocity, the impact angle, etc. It is possible for the LI to be deflected with a relatively low delta-V to impact a South polar crater at a reasonable impact velocity and impact angle directly with no delay. However, the instruments on-board LRO may not be ready for observation. Thus, several delayed trajectory options have been considered further. The lunar phase at the time of impact may also play an important factor for observation, especially from Earth. Several lunar flyby trajectory maneuvers have been identified to arrive at the Moon for impact at the desired lunar phase. By using a combination of these successive lunar flyby maneuvers, the impact lunar phase may be adjusted to the desired location. A few such trajectories have been suggested. Also, some attempts have been made to maximize the impact velocity by converting the impact trajectory into a retrograde orbit with respect to Earth. Since these types of trajectories take advantage of the Sun-Earth three-body region to minimize the delta-V, the mission duration is relatively long. A few such trajectories are suggested. Also, an attempt has been made to adjust the lunar impact within a desired time period for the optimum Earth observation for the above trajectories. The mission parameters resulting from each trajectory option above are considered and weighed against the cost and robustness of the mission in a brief summary.

Trajectory-adaptive route choice models : specification, choice set generation, and estimation.

DOT National Transportation Integrated Search

2013-03-01

The objective of the research is to investigate adaptive route choice behavior using individuallevel route choice data from GPS (Global Positioning System) observations in a real-life : network, where a traveler could revise the route choice based up...

Sliding mode based trajectory linearization control for hypersonic reentry vehicle via extended disturbance observer.

PubMed

Xingling, Shao; Honglun, Wang

2014-11-01

This paper proposes a novel hybrid control framework by combing observer-based sliding mode control (SMC) with trajectory linearization control (TLC) for hypersonic reentry vehicle (HRV) attitude tracking problem. First, fewer control consumption is achieved using nonlinear tracking differentiator (TD) in the attitude loop. Second, a novel SMC that employs extended disturbance observer (EDO) to counteract the effect of uncertainties using a new sliding surface which includes the estimation error is integrated to address the tracking error stabilization issues in the attitude and angular rate loop, respectively. In addition, new results associated with EDO are examined in terms of dynamic response and noise-tolerant performance, as well as estimation accuracy. The key feature of the proposed compound control approach is that chattering free tracking performance with high accuracy can be ensured for HRV in the presence of multiple uncertainties under control constraints. Based on finite time convergence stability theory, the stability of the resulting closed-loop system is well established. Also, comparisons and extensive simulation results are presented to demonstrate the effectiveness of the control strategy. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

Patterns of healthcare service utilisation following severe traumatic brain injury: an idiographic analysis of injury compensation claims data.

PubMed

Collie, A; Prang, K-H

2013-11-01

The rate and extent of recovery after severe traumatic brain injury (TBI) is heterogeneous making prediction of likely healthcare service utilisation (HSU) difficult. Patterns of HSU derived from nomothetic samples do not represent the diverse range of outcomes possible within this patient group. Group-based trajectory model is a semi-parametric statistical technique that seeks to identify clusters of individuals whose outcome (however measured) follows a similar pattern of change over time. To identify and characterise patterns of HSU in the 5-year period following severe TBI. Detailed healthcare treatment payments data in 316 adults with severe TBI (Glasgow Coma Scale score 3-8) from the transport accident compensation system in the state of Victoria, Australia was accessed for this analysis. A semi-parametric group-based trajectory analytical technique for longitudinal data was applied to monthly observation counts of HSU data to identify distinct clusters of participants' trajectories. Comparison between trajectory groups on demographic, injury, disability and compensation relevant outcomes was undertaken. Four distinct patterns (trajectories) of HSU were identified in the sample. The first trajectory group comprised 27% of participants and displayed a rapid decrease in HSU in the first year post-injury. The second group comprised 24% of participants and showed a sharp peak in HSU during the first 12 months post-injury followed by a decline over time. The third group comprised 32% of participants and showed a slight peak in HSU in the first few months post-injury and then a slow decline over time. The fourth group comprised 17% of participants and displayed a steady rise in HSU up to 30 months post-injury, followed by a gradual decline to a level consistent with that received in the first months post-injury. Significant differences were observed between groups on factors such as age, injury severity, and use of disability services. There is substantial variation in patterns of HSU following severe TBI. Idiographic analysis can provide rich information for describing and understanding the resources required to help people with TBI. Copyright © 2013 Elsevier Ltd. All rights reserved.

Diffusion tensor imaging in children with tuberous sclerosis complex: tract-based spatial statistics assessment of brain microstructural changes.

PubMed

Zikou, Anastasia K; Xydis, Vasileios G; Astrakas, Loukas G; Nakou, Iliada; Tzarouchi, Loukia C; Tzoufi, Meropi; Argyropoulou, Maria I

2016-07-01

There is evidence of microstructural changes in normal-appearing white matter of patients with tuberous sclerosis complex. To evaluate major white matter tracts in children with tuberous sclerosis complex using tract-based spatial statistics diffusion tensor imaging (DTI) analysis. Eight children (mean age ± standard deviation: 8.5 ± 5.5 years) with an established diagnosis of tuberous sclerosis complex and 8 age-matched controls were studied. The imaging protocol consisted of T1-weighted high-resolution 3-D spoiled gradient-echo sequence and a spin-echo, echo-planar diffusion-weighted sequence. Differences in the diffusion indices were evaluated using tract-based spatial statistics. Tract-based spatial statistics showed increased axial diffusivity in the children with tuberous sclerosis complex in the superior and anterior corona radiata, the superior longitudinal fascicle, the inferior fronto-occipital fascicle, the uncinate fascicle and the anterior thalamic radiation. No significant differences were observed in fractional anisotropy, mean diffusivity and radial diffusivity between patients and control subjects. No difference was found in the diffusion indices between the baseline and follow-up examination in the patient group. Patients with tuberous sclerosis complex have increased axial diffusivity in major white matter tracts, probably related to reduced axonal integrity.

Spiral trajectory design: a flexible numerical algorithm and base analytical equations.

PubMed

Pipe, James G; Zwart, Nicholas R

2014-01-01

Spiral-based trajectories for magnetic resonance imaging can be advantageous, but are often cumbersome to design or create. This work presents a flexible numerical algorithm for designing trajectories based on explicit definition of radial undersampling, and also gives several analytical expressions for charactering the base (critically sampled) class of these trajectories. Expressions for the gradient waveform, based on slew and amplitude limits, are developed such that a desired pitch in the spiral k-space trajectory is followed. The source code for this algorithm, written in C, is publicly available. Analytical expressions approximating the spiral trajectory (ignoring the radial component) are given to characterize measurement time, gradient heating, maximum gradient amplitude, and off-resonance phase for slew-limited and gradient amplitude-limited cases. Several numerically calculated trajectories are illustrated, and base Archimedean spirals are compared with analytically obtained results. Several different waveforms illustrate that the desired slew and amplitude limits are reached, as are the desired undersampling patterns, using the numerical method. For base Archimedean spirals, the results of the numerical and analytical approaches are in good agreement. A versatile numerical algorithm was developed, and was written in publicly available code. Approximate analytical formulas are given that help characterize spiral trajectories. Copyright © 2013 Wiley Periodicals, Inc.

Non-universal tracer diffusion in crowded media of non-inert obstacles.

PubMed

Ghosh, Surya K; Cherstvy, Andrey G; Metzler, Ralf

2015-01-21

We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer-obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer-obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer-crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids.

Back to the Future: Consistency-Based Trajectory Tracking

NASA Technical Reports Server (NTRS)

Kurien, James; Nayak, P. Pandurand; Norvig, Peter (Technical Monitor)

2000-01-01

Given a model of a physical process and a sequence of commands and observations received over time, the task of an autonomous controller is to determine the likely states of the process and the actions required to move the process to a desired configuration. We introduce a representation and algorithms for incrementally generating approximate belief states for a restricted but relevant class of partially observable Markov decision processes with very large state spaces. The algorithm presented incrementally generates, rather than revises, an approximate belief state at any point by abstracting and summarizing segments of the likely trajectories of the process. This enables applications to efficiently maintain a partial belief state when it remains consistent with observations and revisit past assumptions about the process' evolution when the belief state is ruled out. The system presented has been implemented and results on examples from the domain of spacecraft control are presented.

PROPELLER EPI: An MRI Technique Suitable for Diffusion Tensor Imaging at High Field Strength With Reduced Geometric Distortions

PubMed Central

Wang, Fu-Nien; Huang, Teng-Yi; Lin, Fa-Hsuan; Chuang, Tzu-Chao; Chen, Nan-Kuei; Chung, Hsiao-Wen; Chen, Cheng-Yu; Kwong, Kenneth K.

2013-01-01

A technique suitable for diffusion tensor imaging (DTI) at high field strengths is presented in this work. The method is based on a periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) k-space trajectory using EPI as the signal readout module, and hence is dubbed PROPELLER EPI. The implementation of PROPELLER EPI included a series of correction schemes to reduce possible errors associated with the intrinsically higher sensitivity of EPI to off-resonance effects. Experimental results on a 3.0 Tesla MR system showed that the PROPELLER EPI images exhibit substantially reduced geometric distortions compared with single-shot EPI, at a much lower RF specific absorption rate (SAR) than the original version of the PROPELLER fast spin-echo (FSE) technique. For DTI, the self-navigated phase-correction capability of the PROPELLER EPI sequence was shown to be effective for in vivo imaging. A higher signal-to-noise ratio (SNR) compared to single-shot EPI at an identical total scan time was achieved, which is advantageous for routine DTI applications in clinical practice. PMID:16206142

PROPELLER EPI: an MRI technique suitable for diffusion tensor imaging at high field strength with reduced geometric distortions.

PubMed

Wang, Fu-Nien; Huang, Teng-Yi; Lin, Fa-Hsuan; Chuang, Tzu-Chao; Chen, Nan-Kuei; Chung, Hsiao-Wen; Chen, Cheng-Yu; Kwong, Kenneth K

2005-11-01

A technique suitable for diffusion tensor imaging (DTI) at high field strengths is presented in this work. The method is based on a periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) k-space trajectory using EPI as the signal readout module, and hence is dubbed PROPELLER EPI. The implementation of PROPELLER EPI included a series of correction schemes to reduce possible errors associated with the intrinsically higher sensitivity of EPI to off-resonance effects. Experimental results on a 3.0 Tesla MR system showed that the PROPELLER EPI images exhibit substantially reduced geometric distortions compared with single-shot EPI, at a much lower RF specific absorption rate (SAR) than the original version of the PROPELLER fast spin-echo (FSE) technique. For DTI, the self-navigated phase-correction capability of the PROPELLER EPI sequence was shown to be effective for in vivo imaging. A higher signal-to-noise ratio (SNR) compared to single-shot EPI at an identical total scan time was achieved, which is advantageous for routine DTI applications in clinical practice. (c) 2005 Wiley-Liss, Inc.

Mapping the Critical Gestational Age at Birth that Alters Brain Development in Preterm-born Infants using Multi-Modal MRI

PubMed Central

Wu, Dan; Chang, Linda; Akazawa, Kentaro; Oishi, Kumiko; Skranes, Jon; Ernst, Thomas; Oishi, Kenichi

2017-01-01

Preterm birth adversely affects postnatal brain development. In order to investigate the critical gestational age at birth (GAB) that alters the developmental trajectory of gray and white matter structures in the brain, we investigated diffusion tensor and quantitative T2 mapping data in 43 term-born and 43 preterm-born infants. A novel multivariate linear model—the change point model, was applied to detect change points in fractional anisotropy, mean diffusivity, and T2 relaxation time. Change points captured the “critical” GAB value associated with a change in the linear relation between GAB and MRI measures. The analysis was performed in 126 regions across the whole brain using an atlas-based image quantification approach to investigate the spatial pattern of the critical GAB. Our results demonstrate that the critical GABs are region- and modality-specific, generally following a central-to-peripheral and bottom-to-top order of structural development. This study may offer unique insights into the postnatal neurological development associated with differential degrees of preterm birth. PMID:28111189

Mapping the critical gestational age at birth that alters brain development in preterm-born infants using multi-modal MRI.

PubMed

Wu, Dan; Chang, Linda; Akazawa, Kentaro; Oishi, Kumiko; Skranes, Jon; Ernst, Thomas; Oishi, Kenichi

2017-04-01

Preterm birth adversely affects postnatal brain development. In order to investigate the critical gestational age at birth (GAB) that alters the developmental trajectory of gray and white matter structures in the brain, we investigated diffusion tensor and quantitative T2 mapping data in 43 term-born and 43 preterm-born infants. A novel multivariate linear model-the change point model, was applied to detect change points in fractional anisotropy, mean diffusivity, and T2 relaxation time. Change points captured the "critical" GAB value associated with a change in the linear relation between GAB and MRI measures. The analysis was performed in 126 regions across the whole brain using an atlas-based image quantification approach to investigate the spatial pattern of the critical GAB. Our results demonstrate that the critical GABs are region- and modality-specific, generally following a central-to-peripheral and bottom-to-top order of structural development. This study may offer unique insights into the postnatal neurological development associated with differential degrees of preterm birth. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Rotational Fourier tracking of diffusing polygons.

PubMed

Mayoral, Kenny; Kennair, Terry P; Zhu, Xiaoming; Milazzo, James; Ngo, Kathy; Fryd, Michael M; Mason, Thomas G

2011-11-01

We use optical microscopy to measure the rotational Brownian motion of polygonal platelets that are dispersed in a liquid and confined by depletion attractions near a wall. The depletion attraction inhibits out-of-plane translational and rotational Brownian fluctuations, thereby facilitating in-plane imaging and video analysis. By taking fast Fourier transforms (FFTs) of the images and analyzing the angular position of rays in the FFTs, we determine an isolated particle's rotational trajectory, independent of its position. The measured in-plane rotational diffusion coefficients are significantly smaller than estimates for the bulk; this difference is likely due to the close proximity of the particles to the wall arising from the depletion attraction.

Identification of PM10 air pollution origins at a rural background site

NASA Astrophysics Data System (ADS)

Reizer, Magdalena; Orza, José A. G.

2018-01-01

Trajectory cluster analysis and concentration weighted trajectory (CWT) approach have been applied to investigate the origins of PM10 air pollution recorded at a rural background site in North-eastern Poland (Diabla Góra). Air mass back-trajectories used in this study have been computed with the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model for a 10-year period of 2006-2015. A cluster analysis grouped back-trajectories into 7 clusters. Most of the trajectories correspond to fast and moderately moving westerly and northerly flows (45% and 25% of the cases, respectively). However, significantly higher PM10 concentrations were observed for slow moving easterly (11%) and southerly (20%) air masses. The CWT analysis shows that high PM10 levels are observed at Diabla Góra site when air masses are originated and passed over the heavily industrialized areas in Central-Eastern Europe located to the south and south-east of the site.

Power spectral density of a single Brownian trajectory: what one can and cannot learn from it

NASA Astrophysics Data System (ADS)

Krapf, Diego; Marinari, Enzo; Metzler, Ralf; Oshanin, Gleb; Xu, Xinran; Squarcini, Alessio

2018-02-01

The power spectral density (PSD) of any time-dependent stochastic process X t is a meaningful feature of its spectral content. In its text-book definition, the PSD is the Fourier transform of the covariance function of X t over an infinitely large observation time T, that is, it is defined as an ensemble-averaged property taken in the limit T\\to ∞ . A legitimate question is what information on the PSD can be reliably obtained from single-trajectory experiments, if one goes beyond the standard definition and analyzes the PSD of a single trajectory recorded for a finite observation time T. In quest for this answer, for a d-dimensional Brownian motion (BM) we calculate the probability density function of a single-trajectory PSD for arbitrary frequency f, finite observation time T and arbitrary number k of projections of the trajectory on different axes. We show analytically that the scaling exponent for the frequency-dependence of the PSD specific to an ensemble of BM trajectories can be already obtained from a single trajectory, while the numerical amplitude in the relation between the ensemble-averaged and single-trajectory PSDs is a fluctuating property which varies from realization to realization. The distribution of this amplitude is calculated exactly and is discussed in detail. Our results are confirmed by numerical simulations and single-particle tracking experiments, with remarkably good agreement. In addition we consider a truncated Wiener representation of BM, and the case of a discrete-time lattice random walk. We highlight some differences in the behavior of a single-trajectory PSD for BM and for the two latter situations. The framework developed herein will allow for meaningful physical analysis of experimental stochastic trajectories.

Controls over spatial and seasonal variations on isotopic composition of the precipitation along the central and eastern portion of Brazil.

PubMed

Gastmans, Didier; Santos, Vinícius; Galhardi, Juliana Aparecida; Gromboni, João Felipe; Batista, Ludmila Vianna; Miotlinski, Konrad; Chang, Hung Kiang; Govone, José Silvio

2017-10-01

Based on Global Network Isotopes in Precipitation (GNIP) isotopic data set, a review of the spatial and temporal variability of δ 18 O and δ 2 H in precipitation was conducted throughout central and eastern Brazil, indicating that dynamic interactions between Intertropical and South Atlantic Convergence Zones, Amazon rainforest, and Atlantic Ocean determine the variations on the isotopic composition of precipitation over this area. Despite the seasonality and latitude effects observed, a fair correlation with precipitation amount was found. In addition, Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) air mass back trajectories were used to quantify the factors controlling daily variability in stable isotopes in precipitation. Through a linear multiple regression analysis, it was observed that temporal variations were consistent with the meteorological parameters derived from HYSPLIT, particularly precipitation amount along the trajectory and mix depth, but are not dependent on vapour residence time in the atmosphere. These findings also indicate the importance of convective systems to control the isotopic composition of precipitation in tropical and subtropical regions.

Controller Strategies for Automation Tool Use under Varying Levels of Trajectory Prediction Uncertainty

NASA Technical Reports Server (NTRS)

Morey, Susan; Prevot, Thomas; Mercer, Joey; Martin, Lynne; Bienert, Nancy; Cabrall, Christopher; Hunt, Sarah; Homola, Jeffrey; Kraut, Joshua

2013-01-01

A human-in-the-loop simulation was conducted to examine the effects of varying levels of trajectory prediction uncertainty on air traffic controller workload and performance, as well as how strategies and the use of decision support tools change in response. This paper focuses on the strategies employed by two controllers from separate teams who worked in parallel but independently under identical conditions (airspace, arrival traffic, tools) with the goal of ensuring schedule conformance and safe separation for a dense arrival flow in en route airspace. Despite differences in strategy and methods, both controllers achieved high levels of schedule conformance and safe separation. Overall, results show that trajectory uncertainties introduced by wind and aircraft performance prediction errors do not affect the controllers' ability to manage traffic. Controller strategies were fairly robust to changes in error, though strategies were affected by the amount of delay to absorb (scheduled time of arrival minus estimated time of arrival). Using the results and observations, this paper proposes an ability to dynamically customize the display of information including delay time based on observed error to better accommodate different strategies and objectives.

The effect of tensile stress on hydrogen diffusion in metal alloys

NASA Technical Reports Server (NTRS)

Danford, M. D.

1992-01-01

The effect of tensile stress on hydrogen diffusion has been determined for Type 303 stainless steel, A286 CRES, and Waspaloy and IN100 nickel-base alloys. It was found that hydrogen diffusion coefficients are not significantly affected by stress, while the hydrogen permeabilities are greatly affected in Type 303 stainless steel and A286 CRES (iron-based alloys), but are affected little in Waspaloy (nickel-base) and not affected in all in IN100 (nickel base). These observations might be taken as an indication that hydrogen permeabilities are affected by stress in iron-based alloys, but only slightly affected in nickel-based alloys. However, it is too early to make such a generalization based on the study of only these four alloys.

One-dimensional numerical study of charged particle trajectories in turbulent electrostatic wave fields

NASA Technical Reports Server (NTRS)

Graham, K. N.; Fejer, J. A.

1976-01-01

The paper describes a numerical simulation of electron trajectories in weak random electric fields under conditions that are approximately true for Langmuir waves whose wavelength is much longer than the Debye length. Two types of trajectory calculations were made: (1) the initial particle velocity was made equal to the mean phase velocity of the waves, or (2) it was equal to 0.7419 times the mean velocity of the waves, so that the initial velocity differed substantially from all phase velocities of the wave spectrum. When the autocorrelation time is much greater than the trapping time, the particle motion can change virtually instantaneously from one of three states - high-velocity, low-velocity, or trapped state - to another. The probability of instantaneous transition from a high- or low-velocity state becomes small when the difference between the particle velocity and the mean phase velocity of the waves becomes high in comparison to the trapping velocity. Diffusive motion becomes negligible under these conditions also.

Time-dependent vibrational spectral analysis of first principles trajectory of methylamine with wavelet transform.

PubMed

Biswas, Sohag; Mallik, Bhabani S

2017-04-12

The fluctuation dynamics of amine stretching frequencies, hydrogen bonds, dangling N-D bonds, and the orientation profile of the amine group of methylamine (MA) were investigated under ambient conditions by means of dispersion-corrected density functional theory-based first principles molecular dynamics (FPMD) simulations. Along with the dynamical properties, various equilibrium properties such as radial distribution function, spatial distribution function, combined radial and angular distribution functions and hydrogen bonding were also calculated. The instantaneous stretching frequencies of amine groups were obtained by wavelet transform of the trajectory obtained from FPMD simulations. The frequency-structure correlation reveals that the amine stretching frequency is weakly correlated with the nearest nitrogen-deuterium distance. The frequency-frequency correlation function has a short time scale of around 110 fs and a longer time scale of about 1.15 ps. It was found that the short time scale originates from the underdamped motion of intact hydrogen bonds of MA pairs. However, the long time scale of the vibrational spectral diffusion of N-D modes is determined by the overall dynamics of hydrogen bonds as well as the dangling ND groups and the inertial rotation of the amine group of the molecule.

ATCA observations of the MACS-Planck Radio Halo Cluster Project. II. Radio observations of an intermediate redshift cluster sample

NASA Astrophysics Data System (ADS)

Martinez Aviles, G.; Johnston-Hollitt, M.; Ferrari, C.; Venturi, T.; Democles, J.; Dallacasa, D.; Cassano, R.; Brunetti, G.; Giacintucci, S.; Pratt, G. W.; Arnaud, M.; Aghanim, N.; Brown, S.; Douspis, M.; Hurier, J.; Intema, H. T.; Langer, M.; Macario, G.; Pointecouteau, E.

2018-04-01

Aim. A fraction of galaxy clusters host diffuse radio sources whose origins are investigated through multi-wavelength studies of cluster samples. We investigate the presence of diffuse radio emission in a sample of seven galaxy clusters in the largely unexplored intermediate redshift range (0.3 < z < 0.44). Methods: In search of diffuse emission, deep radio imaging of the clusters are presented from wide band (1.1-3.1 GHz), full resolution ( 5 arcsec) observations with the Australia Telescope Compact Array (ATCA). The visibilities were also imaged at lower resolution after point source modelling and subtraction and after a taper was applied to achieve better sensitivity to low surface brightness diffuse radio emission. In case of non-detection of diffuse sources, we set upper limits for the radio power of injected diffuse radio sources in the field of our observations. Furthermore, we discuss the dynamical state of the observed clusters based on an X-ray morphological analysis with XMM-Newton. Results: We detect a giant radio halo in PSZ2 G284.97-23.69 (z = 0.39) and a possible diffuse source in the nearly relaxed cluster PSZ2 G262.73-40.92 (z = 0.421). Our sample contains three highly disturbed massive clusters without clear traces of diffuse emission at the observed frequencies. We were able to inject modelled radio haloes with low values of total flux density to set upper detection limits; however, with our high-frequency observations we cannot exclude the presence of RH in these systems because of the sensitivity of our observations in combination with the high z of the observed clusters. The reduced images are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/611/A94

The Invisible Hand: Governmental Influences on the Field of Play During the Production and Diffusion of Mobile TV

NASA Astrophysics Data System (ADS)

Lin, Su-Yi; Chiasson, Mike W.

The purpose of this paper is to examine how government agencies alter the context around the production and diffusion of technologies, and how this strengthens or weakens particular ICT trajectories. An embedded case is conducted to address this question in Taiwan, as governmental actions affected the early production and diffusion of DVB-H technology and WiMAX technology, both of which enable mobile TV services. The context around and across these two technologies are analyzed from an institutional perspective, including the framework proposed by King et al (1994). The key lesson of this paper is that government agencies are capable of influencing the diffusion of nomadic technologies through their legitimating powers, specific national policies, the allocation of radio frequency spectrum, the implementation of regulations, and the allocation of financial resources. However, the ultimate effects are determined by mixed institutional factors and sometimes contradictory governmental interventions, stemming from historical differences and conflicts across the various government agencies involved. The implications for ICT diffusion research and governmental policy makers are discussed.

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

Morales, George J.; Maggs, James E.

The project expanded and developed mathematical descriptions, and corresponding numerical modeling, of non-diffusive transport to incorporate new perspectives derived from basic transport experiments performed in the LAPD device at UCLA, and at fusion devices throughout the world. By non-diffusive it is meant that the transport of fundamental macroscopic parameters of a system, such as temperature and density, does not follow the standard diffusive behavior predicted by a classical Fokker-Planck equation. The appearance of non-diffusive behavior is often related to underlying microscopic processes that cause the value of a system parameter, at one spatial position, to be linked to distant events,more » i.e., non-locality. In the LAPD experiments the underlying process was traced to large amplitude, coherent drift-waves that give rise to chaotic trajectories. Significant advances were made in this project. The results have lead to a new perspective about the fundamentals of edge transport in magnetically confined plasmas; the insight has important consequences for worldwide studies in fusion devices. Progress was also made in advancing the mathematical techniques used to describe fractional diffusion.« less

Forecast of drifter trajectories using a Rapid Environmental Assessment based on CTD observations

NASA Astrophysics Data System (ADS)

Sorgente, R.; Tedesco, C.; Pessini, F.; De Dominicis, M.; Gerin, R.; Olita, A.; Fazioli, L.; Di Maio, A.; Ribotti, A.

2016-11-01

A high resolution submesoscale resolving ocean model was implemented in a limited area north of Island of Elba where a maritime exercise, named Serious Game 1 (SG1), took place on May 2014 in the framework of the project MEDESS-4MS (Mediterranean Decision Support System for Marine Safety). During the exercise, CTD data have been collected responding to the necessity of a Rapid Environmental Assessment, i.e. to a rapid evaluation of the marine conditions able to provide sensible information for initialisation of modelling tools, in the scenario of possible maritime accidents. The aim of this paper is to evaluate the impact of such mesoscale-resolving CTD observations on short-term forecasts of the surface currents, within the framework of possible oil-spill related emergencies. For this reason, modelling outputs were compared with Lagrangian observations at sea: the high resolution modelled currents, together with the ones of the coarser sub-regional model WMED, are used to force the MEDSLIK-II oil-spill model to simulate drifter trajectories. Both ocean models have been assessed by comparing the prognostic scalar and vector fields as an independent CTD data set and with real drifter trajectories acquired during SG1. The diagnosed and prognosed circulation reveals that the area was characterised by water masses of Atlantic origin influenced by small mesoscale cyclonic and anti-cyclonic eddies, which govern the spatial and temporal evolution of the drifter trajectories and of the water masses distribution. The assimilation of CTD data into the initial conditions of the high resolution model highly improves the accuracy of the short-term forecast in terms of location and structure of the thermocline and positively influence the ability of the model in reproducing the observed paths of the surface drifters.

Calculating tumor trajectory and dose-of-the-day using cone-beam CT projections

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

Jones, Bernard L., E-mail: bernard.jones@ucdenver.edu; Westerly, David; Miften, Moyed

2015-02-15

Purpose: Cone-beam CT (CBCT) projection images provide anatomical data in real-time over several respiratory cycles, forming a comprehensive picture of tumor movement. The authors developed and validated a method which uses these projections to determine the trajectory of and dose to highly mobile tumors during each fraction of treatment. Methods: CBCT images of a respiration phantom were acquired, the trajectory of which mimicked a lung tumor with high amplitude (up to 2.5 cm) and hysteresis. A template-matching algorithm was used to identify the location of a steel BB in each CBCT projection, and a Gaussian probability density function for themore » absolute BB position was calculated which best fit the observed trajectory of the BB in the imager geometry. Two modifications of the trajectory reconstruction were investigated: first, using respiratory phase information to refine the trajectory estimation (Phase), and second, using the Monte Carlo (MC) method to sample the estimated Gaussian tumor position distribution. The accuracies of the proposed methods were evaluated by comparing the known and calculated BB trajectories in phantom-simulated clinical scenarios using abdominal tumor volumes. Results: With all methods, the mean position of the BB was determined with accuracy better than 0.1 mm, and root-mean-square trajectory errors averaged 3.8% ± 1.1% of the marker amplitude. Dosimetric calculations using Phase methods were more accurate, with mean absolute error less than 0.5%, and with error less than 1% in the highest-noise trajectory. MC-based trajectories prevent the overestimation of dose, but when viewed in an absolute sense, add a small amount of dosimetric error (<0.1%). Conclusions: Marker trajectory and target dose-of-the-day were accurately calculated using CBCT projections. This technique provides a method to evaluate highly mobile tumors using ordinary CBCT data, and could facilitate better strategies to mitigate or compensate for motion during stereotactic body radiotherapy.« less

An agent-based model for queue formation of powered two-wheelers in heterogeneous traffic

NASA Astrophysics Data System (ADS)

Lee, Tzu-Chang; Wong, K. I.

2016-11-01

This paper presents an agent-based model (ABM) for simulating the queue formation of powered two-wheelers (PTWs) in heterogeneous traffic at a signalized intersection. The main novelty is that the proposed interaction rule describing the position choice behavior of PTWs when queuing in heterogeneous traffic can capture the stochastic nature of the decision making process. The interaction rule is formulated as a multinomial logit model, which is calibrated by using a microscopic traffic trajectory dataset obtained from video footage. The ABM is validated against the survey data for the vehicular trajectory patterns, queuing patterns, queue lengths, and discharge rates. The results demonstrate that the proposed model is capable of replicating the observed queue formation process for heterogeneous traffic.

Atomistic models of vacancy-mediated diffusion in silicon

NASA Astrophysics Data System (ADS)

Dunham, Scott T.; Wu, Can Dong

1995-08-01

Vacancy-mediated diffusion of dopants in silicon is investigated using Monte Carlo simulations of hopping diffusion, as well as analytic approximations based on atomistic considerations. Dopant/vacancy interaction potentials are assumed to extend out to third-nearest neighbor distances, as required for pair diffusion theories. Analysis focusing on the third-nearest neighbor sites as bridging configurations for uncorrelated hops leads to an improved analytic model for vacancy-mediated dopant diffusion. The Monte Carlo simulations of vacancy motion on a doped silicon lattice verify the analytic results for moderate doping levels. For very high doping (≳2×1020 cm-3) the simulations show a very rapid increase in pair diffusivity due to interactions of vacancies with more than one dopant atom. This behavior has previously been observed experimentally for group IV and V atoms in silicon [Nylandsted Larsen et al., J. Appl. Phys. 73, 691 (1993)], and the simulations predict both the point of onset and doping dependence of the experimentally observed diffusivity enhancement.

Exploring the Complex Pattern of Information Spreading in Online Blog Communities

PubMed Central

Pei, Sen; Muchnik, Lev; Tang, Shaoting; Zheng, Zhiming; Makse, Hernán A.

2015-01-01

Information spreading in online social communities has attracted tremendous attention due to its utmost practical values in applications. Despite that several individual-level diffusion data have been investigated, we still lack the detailed understanding of the spreading pattern of information. Here, by comparing information flows and social links in a blog community, we find that the diffusion processes are induced by three different spreading mechanisms: social spreading, self-promotion and broadcast. Although numerous previous studies have employed epidemic spreading models to simulate information diffusion, we observe that such models fail to reproduce the realistic diffusion pattern. In respect to users behaviors, strikingly, we find that most users would stick to one specific diffusion mechanism. Moreover, our observations indicate that the social spreading is not only crucial for the structure of diffusion trees, but also capable of inducing more subsequent individuals to acquire the information. Our findings suggest new directions for modeling of information diffusion in social systems, and could inform design of efficient propagation strategies based on users behaviors. PMID:25985081

Exploring the complex pattern of information spreading in online blog communities.

PubMed

Pei, Sen; Muchnik, Lev; Tang, Shaoting; Zheng, Zhiming; Makse, Hernán A

2015-01-01

Information spreading in online social communities has attracted tremendous attention due to its utmost practical values in applications. Despite that several individual-level diffusion data have been investigated, we still lack the detailed understanding of the spreading pattern of information. Here, by comparing information flows and social links in a blog community, we find that the diffusion processes are induced by three different spreading mechanisms: social spreading, self-promotion and broadcast. Although numerous previous studies have employed epidemic spreading models to simulate information diffusion, we observe that such models fail to reproduce the realistic diffusion pattern. In respect to users behaviors, strikingly, we find that most users would stick to one specific diffusion mechanism. Moreover, our observations indicate that the social spreading is not only crucial for the structure of diffusion trees, but also capable of inducing more subsequent individuals to acquire the information. Our findings suggest new directions for modeling of information diffusion in social systems, and could inform design of efficient propagation strategies based on users behaviors.

Mesoscale numerical investigations of air traffic emissions over the North Atlantic during SONEX flight 8: A case study

NASA Astrophysics Data System (ADS)

Bieberbach, George; Fuelberg, Henry E.; Thompson, Anne M.; Schmitt, Alfons; Hannan, John R.; Gregory, G. L.; Kondo, Yutaka; Knabb, Richard D.; Sachse, G. W.; Talbot, R. W.

2000-02-01

Chemical data from flight 8 of NASA's Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX) exhibited signatures consistent with aircraft emissions, stratospheric air, and surface-based pollution. These signatures are examined in detail, focusing on the broad aircraft emission signatures that are several hundred kilometers in length. A mesoscale meteorological model provides high-resolution wind data that are used to calculate backward trajectories arriving at locations along the flight track. These trajectories are compared to aircraft locations in the North Atlantic Flight Corridor (NAFC) over a 27-33 hour period. Time series of flight level NO and the number of trajectory/aircraft encounters within the NAFC show excellent agreement. Trajectories arriving within the stratospheric and surface-based pollution regions are found to experience very few aircraft encounters. Conversely, there are many trajectory/aircraft encounters within the two chemical signatures corresponding to aircraft emissions. Even many detailed fluctuations of NO within the two aircraft signature regions correspond to similar fluctuations in aircraft encountered. These NO spikes are due to the superposition of 14 to 25 aircraft plumes transported to the DC-8 flight track during the previous 33 hours. Results confirm that aircraft emissions were responsible for two chemical signatures observed during SONEX flight 8. They also indicate that high-resolution meteorological modeling, when coupled with detailed aircraft location data, is useful for understanding chemical signatures from aircraft emissions at scales of several hundred kilometers.

From screen to structure with a harvestable microfluidic device.

PubMed

Stojanoff, Vivian; Jakoncic, Jean; Oren, Deena A; Nagarajan, V; Poulsen, Jens-Christian Navarro; Adams-Cioaba, Melanie A; Bergfors, Terese; Sommer, Morten O A

2011-08-01

Advances in automation have facilitated the widespread adoption of high-throughput vapour-diffusion methods for initial crystallization screening. However, for many proteins, screening thousands of crystallization conditions fails to yield crystals of sufficient quality for structural characterization. Here, the rates of crystal identification for thaumatin, catalase and myoglobin using microfluidic Crystal Former devices and sitting-drop vapour-diffusion plates are compared. It is shown that the Crystal Former results in a greater number of identified initial crystallization conditions compared with vapour diffusion. Furthermore, crystals of thaumatin and lysozyme obtained in the Crystal Former were used directly for structure determination both in situ and upon harvesting and cryocooling. On the basis of these results, a crystallization strategy is proposed that uses multiple methods with distinct kinetic trajectories through the protein phase diagram to increase the output of crystallization pipelines.

A numerical study on swimming micro-organisms inside a capillary tube

NASA Astrophysics Data System (ADS)

Zhu, Lailai; Lauga, Eric; Brandt, Luca

2011-11-01

The locomotivity of micro-organisms is highly dependent on the surrounding environments such as walls, free surface and neighbouring cells. In our current work, we perform simulations of swimming micro-organisms inside a capillary tube based on boundary element method. We focus on the swimming speed, power consumption and locomotive trajectory of swimming cells for different levels of confinement. For a cell propelling itself by tangential surface deformation, we show that it will swim along a helical trajectory with a specified swimming gait. Such a helical trajectory was observed before by experiments on swimming Paramecium inside a capillary tube. Funding by VR (the Swedish Research Council) and the National Science Foundation (grant CBET-0746285 to E.L.) is gratefully acknowledged. Computer time provided by SNIC (Swedish National Infrastructure for Computing) is also acknowledged.

The General Mission Analysis Tool (GMAT): Current Features And Adding Custom Functionality

NASA Technical Reports Server (NTRS)

Conway, Darrel J.; Hughes, Steven P.

2010-01-01

The General Mission Analysis Tool (GMAT) is a software system for trajectory optimization, mission analysis, trajectory estimation, and prediction developed by NASA, the Air Force Research Lab, and private industry. GMAT's design and implementation are based on four basic principles: open source visibility for both the source code and design documentation; platform independence; modular design; and user extensibility. The system, released under the NASA Open Source Agreement, runs on Windows, Mac and Linux. User extensions, loaded at run time, have been built for optimization, trajectory visualization, force model extension, and estimation, by parties outside of GMAT's development group. The system has been used to optimize maneuvers for the Lunar Crater Observation and Sensing Satellite (LCROSS) and ARTEMIS missions and is being used for formation design and analysis for the Magnetospheric Multiscale Mission (MMS).

Towards Assessing the Human Trajectory Planning Horizon

PubMed Central

Nitsch, Verena; Meinzer, Dominik; Wollherr, Dirk

2016-01-01

Mobile robots are envisioned to cooperate closely with humans and to integrate seamlessly into a shared environment. For locomotion, these environments resemble traversable areas which are shared between multiple agents like humans and robots. The seamless integration of mobile robots into these environments requires accurate predictions of human locomotion. This work considers optimal control and model predictive control approaches for accurate trajectory prediction and proposes to integrate aspects of human behavior to improve their performance. Recently developed models are not able to reproduce accurately trajectories that result from sudden avoidance maneuvers. Particularly, the human locomotion behavior when handling disturbances from other agents poses a problem. The goal of this work is to investigate whether humans alter their trajectory planning horizon, in order to resolve abruptly emerging collision situations. By modeling humans as model predictive controllers, the influence of the planning horizon is investigated in simulations. Based on these results, an experiment is designed to identify, whether humans initiate a change in their locomotion planning behavior while moving in a complex environment. The results support the hypothesis, that humans employ a shorter planning horizon to avoid collisions that are triggered by unexpected disturbances. Observations presented in this work are expected to further improve the generalizability and accuracy of prediction methods based on dynamic models. PMID:27936015

Towards Assessing the Human Trajectory Planning Horizon.

PubMed

Carton, Daniel; Nitsch, Verena; Meinzer, Dominik; Wollherr, Dirk

2016-01-01

Mobile robots are envisioned to cooperate closely with humans and to integrate seamlessly into a shared environment. For locomotion, these environments resemble traversable areas which are shared between multiple agents like humans and robots. The seamless integration of mobile robots into these environments requires accurate predictions of human locomotion. This work considers optimal control and model predictive control approaches for accurate trajectory prediction and proposes to integrate aspects of human behavior to improve their performance. Recently developed models are not able to reproduce accurately trajectories that result from sudden avoidance maneuvers. Particularly, the human locomotion behavior when handling disturbances from other agents poses a problem. The goal of this work is to investigate whether humans alter their trajectory planning horizon, in order to resolve abruptly emerging collision situations. By modeling humans as model predictive controllers, the influence of the planning horizon is investigated in simulations. Based on these results, an experiment is designed to identify, whether humans initiate a change in their locomotion planning behavior while moving in a complex environment. The results support the hypothesis, that humans employ a shorter planning horizon to avoid collisions that are triggered by unexpected disturbances. Observations presented in this work are expected to further improve the generalizability and accuracy of prediction methods based on dynamic models.

A positive-definite form of bounce-averaged quasilinear velocity diffusion for the parallel inhomogeneity in a tokamak

NASA Astrophysics Data System (ADS)

Lee, Jungpyo; Smithe, David; Wright, John; Bonoli, Paul

2018-02-01

In this paper, the analytical form of the quasilinear diffusion coefficients is modified from the Kennel-Engelmann diffusion coefficients to guarantee the positive definiteness of its bounce average in a toroidal geometry. By evaluating the parallel inhomogeneity of plasmas and magnetic fields in the trajectory integral, we can ensure the positive definiteness and help illuminate some non-resonant toroidal effects in the quasilinear diffusion. When the correlation length of the plasma-wave interaction is comparable to the magnetic field variation length, the variation becomes important and the parabolic variation at the outer-midplane, the inner-midplane, and trapping tips can be evaluated by Airy functions. The new form allows the coefficients to include both resonant and non-resonant contributions, and the correlations between the consecutive resonances and in many poloidal periods. The positive-definite form is implemented in a wave code TORIC and we present an example for ITER using this form.

What is the alternative to the Alexander-Orbach relation?

NASA Astrophysics Data System (ADS)

Sokolov, Igor M.

2016-03-01

The Alexander-Orbach (AO) relation d w = 2d f /d s connecting the fractal dimension of a random walk’s (RW) trajectory d w or the exponent of anomalous diffusion α = 2/d w on a fractal structure with the fractal and spectral dimension of the structure itself plays a key role in discussion of dynamical properties of complex systems including living cells and single biomolecules. This relation however does not hold universally and breaks down for some structures like diffusion limited aggregates and Eden trees. We show that the alternative to the AO relation is the explicit dependence of the coefficient of the anomalous diffusion on the system’s size, i.e. the absence of its thermodynamical limit. The prerequisite for its breakdown is the dependence of the local structure of possible steps of the RW on the system’s size. The discussion is illustrated by the examples of diffusion on a Koch curve (AO-conform) and on a Cantor dust (violating AO relation).

Trajectory-Oriented Approach to Managing Traffic Complexity: Trajectory Flexibility Metrics and Algorithms and Preliminary Complexity Impact Assessment

NASA Technical Reports Server (NTRS)

Idris, Husni; Vivona, Robert A.; Al-Wakil, Tarek

2009-01-01

This document describes exploratory research on a distributed, trajectory oriented approach for traffic complexity management. The approach is to manage traffic complexity based on preserving trajectory flexibility and minimizing constraints. In particular, the document presents metrics for trajectory flexibility; a method for estimating these metrics based on discrete time and degree of freedom assumptions; a planning algorithm using these metrics to preserve flexibility; and preliminary experiments testing the impact of preserving trajectory flexibility on traffic complexity. The document also describes an early demonstration capability of the trajectory flexibility preservation function in the NASA Autonomous Operations Planner (AOP) platform.

Kinematic GPS solutions for aircraft trajectories: Identifying and minimizing systematic height errors associated with atmospheric propagation delays

USGS Publications Warehouse

Shan, S.; Bevis, M.; Kendrick, E.; Mader, G.L.; Raleigh, D.; Hudnut, K.; Sartori, M.; Phillips, D.

2007-01-01

When kinematic GPS processing software is used to estimate the trajectory of an aircraft, unless the delays imposed on the GPS signals by the atmosphere are either estimated or calibrated via external observations, then vertical height errors of decimeters can occur. This problem is clearly manifested when the aircraft is positioned against multiple base stations in areas of pronounced topography because the aircraft height solutions obtained using different base stations will tend to be mutually offset, or biased, in proportion to the elevation differences between the base stations. When performing kinematic surveys in areas with significant topography it should be standard procedure to use multiple base stations, and to separate them vertically to the maximum extent possible, since it will then be much easier to detect mis-modeling of the atmosphere. Copyright 2007 by the American Geophysical Union.

Automated Generation of 3D Volcanic Gas Plume Models for Geobrowsers

NASA Astrophysics Data System (ADS)

Wright, T. E.; Burton, M.; Pyle, D. M.

2007-12-01

A network of five UV spectrometers on Etna automatically gathers column amounts of SO2 during daylight hours. Near-simultaneous scans from adjacent spectrometers, comprising 210 column amounts in total, are then converted to 2D slices showing the spatial distribution of the gas by tomographic reconstruction. The trajectory of the plume is computed using an automatically-submitted query to NOAA's HYSPLIT Trajectory Model. This also provides local estimates of air temperature, which are used to determine the atmospheric stability and therefore the degree to which the plume is dispersed by turbulence. This information is sufficient to construct an animated sequence of models which show how the plume is advected and diffused over time. These models are automatically generated in the Collada Digital Asset Exchange format and combined into a single file which displays the evolution of the plume in Google Earth. These models are useful for visualising and predicting the shape and distribution of the plume for civil defence, to assist field campaigns and as a means of communicating some of the work of volcano observatories to the public. The Simultaneous Algebraic Reconstruction Technique is used to create the 2D slices. This is a well-known method, based on iteratively updating a forward model (from 2D distribution to column amounts). Because it is based on a forward model, it also provides a simple way to quantify errors.

Observation of bow shock protons at the lunar orbit. M.S. Thesis; [particle trajectory analysis of solar protons in the lunar atmosphere

NASA Technical Reports Server (NTRS)

Benson, J. L.

1974-01-01

Protons with energies ranging from about 500 eV to 3,500 eV were observed by the Suprathermal Ion Detector Experiment (SIDE) on both the dusk and dawn sides of the magnetosphere. On each lunation these particles appeared as a rather continuous phenomenon for 3 to 5 days after crossing from the dawn-side magnetosheath into the solar wind and for about 2 days prior to entering the dusk-side magnetosheath. Data from the SIDE and from the Explorer 35 lunar orbiting magnetometer were analyzed and these data indicated that the transverse ion flows observed by the SIDE in the pre and post bow shock crossing regions of the lunar orbit are due to these deviated solar wind particles. A computer model based on drift trajectories for particles leaving the shock was developed and synthetic particle data produced by this model are in good agreement with the observed data.

Using CATS Near-Real-time Lidar Observations to Monitor and Constrain Volcanic Sulfur Dioxide (SO2) Forecasts

NASA Technical Reports Server (NTRS)

Hughes, E. J.; Yorks, J.; Krotkov, N. A.; da Silva, A. M.; Mcgill, M.

2016-01-01

An eruption of Italian volcano Mount Etna on 3 December 2015 produced fast-moving sulfur dioxide (SO2) and sulfate aerosol clouds that traveled across Asia and the Pacific Ocean, reaching North America in just 5 days. The Ozone Profiler and Mapping Suite's Nadir Mapping UV spectrometer aboard the U.S. National Polar-orbiting Partnership satellite observed the horizontal transport of the SO2 cloud. Vertical profiles of the colocated volcanic sulfate aerosols were observed between 11.5 and 13.5 km by the new Cloud Aerosol Transport System (CATS) space-based lidar aboard the International Space Station. Backward trajectory analysis estimates the SO2 cloud altitude at 7-12 km. Eulerian model simulations of the SO2 cloud constrained by CATS measurements produced more accurate dispersion patterns compared to those initialized with the back trajectory height estimate. The near-real-time data processing capabilities of CATS are unique, and this work demonstrates the use of these observations to monitor and model volcanic clouds.

Using CATS Near-Real-Time Lidar Observations to Monitor and Constrain Volcanic Sulfur Dioxide (SO2) Forecasts

NASA Technical Reports Server (NTRS)

Hughes, E. J.; Yorks, J.; Krotkov, N. A.; Da Silva, A. M.; McGill, M.

2016-01-01

An eruption of Italian volcano Mount Etna on 3 December 2015 produced fast-moving sulfur dioxide (SO2) and sulfate aerosol clouds that traveled across Asia and the Pacific Ocean, reaching North America in just 5days. The Ozone Profiler and Mapping Suite's Nadir Mapping UV spectrometer aboard the U.S. National Polar-orbiting Partnership satellite observed the horizontal transport of the SO2 cloud. Vertical profiles of the colocated volcanic sulfate aerosols were observed between 11.5 and 13.5 km by the new Cloud Aerosol Transport System (CATS) space-based lidar aboard the International Space Station. Backward trajectory analysis estimates the SO2 cloud altitude at 7-12 km. Eulerian model simulations of the SO2 cloud constrained by CATS measurements produced more accurate dispersion patterns compared to those initialized with the back trajectory height estimate. The near-real-time data processing capabilities of CATS are unique, and this work demonstrates the use of these observations to monitor and model volcanic clouds.

A novel approach to Lagrangian sampling of marine boundary layer cloud and aerosol in the northeast Pacific: case studies from CSET

NASA Astrophysics Data System (ADS)

Mohrmann, J.; Albrecht, B. A.; Bretherton, C. S.; Ghate, V. P.; Zuidema, P.; Wood, R.

2015-12-01

The Cloud System Evolution in the Trades (CSET) field campaign took place during July/August 2015 with the purpose of characterizing the cloud, aerosol and thermodynamic properties of the northeast Pacific marine boundary layer. One major science goal of the campaign was to observe a Lagrangian transition from thin stratocumulus (Sc) upwind near California to trade cumulus (Cu) nearer to Hawaii. Cloud properties were observed from the NSF/NCAR Gulfstream V research plane (GV) using the HIAPER Cloud Radar (HCR) and the HIAPER Spectral Resolution Lidar (HSRL), among other instrumentation. Aircraft observations were complemented by a suite of satellite-derived products. To observe a the evolution of airmasses over the course of two days, upwind regions were sampled on an outbound flight to from Sacramento, CA, to Kona, HI. The sampled airmasses were then tracked using HYSPLIT trajectories based on GFS model forecasts, and the return flight to California was planned to intercept those airmasses, using satellite observation to track cloud evolution in the interim. This approach required that trajectories were reasonably stable up to 3 days prior to final sampling, and also that forecast trajectories were in agreement with post-flight analysis and visual cloud feature tracking. The extent to which this was realised, and hence the validity of this new approach to Lagrangian airmass observation, is assessed here. We also present results showing that a Sc-Cu airmass transition was consistently observed during the CSET study using measurements from research flights and satellite.

Study of recognizing multiple persons' complicated hand gestures from the video sequence acquired by a moving camera

NASA Astrophysics Data System (ADS)

Dan, Luo; Ohya, Jun

2010-02-01

Recognizing hand gestures from the video sequence acquired by a dynamic camera could be a useful interface between humans and mobile robots. We develop a state based approach to extract and recognize hand gestures from moving camera images. We improved Human-Following Local Coordinate (HFLC) System, a very simple and stable method for extracting hand motion trajectories, which is obtained from the located human face, body part and hand blob changing factor. Condensation algorithm and PCA-based algorithm was performed to recognize extracted hand trajectories. In last research, this Condensation Algorithm based method only applied for one person's hand gestures. In this paper, we propose a principal component analysis (PCA) based approach to improve the recognition accuracy. For further improvement, temporal changes in the observed hand area changing factor are utilized as new image features to be stored in the database after being analyzed by PCA. Every hand gesture trajectory in the database is classified into either one hand gesture categories, two hand gesture categories, or temporal changes in hand blob changes. We demonstrate the effectiveness of the proposed method by conducting experiments on 45 kinds of sign language based Japanese and American Sign Language gestures obtained from 5 people. Our experimental recognition results show better performance is obtained by PCA based approach than the Condensation algorithm based method.

Does representational momentum reflect a distortion of the length or the endpoint of a trajectory?

PubMed

Hubbard, Timothy L; Motes, Michael A

2002-01-01

Observers viewed a moving target, and after the target vanished, indicated either the initial position or the final position of the target. In Experiment 1, an auditory tone cued observers to indicate either the initial position or the final position; in Experiment 2, different groups of observers indicated the initial position or the final position. Judgments of the initial position were displaced backward in the direction opposite to motion, and judgments of the final position were displaced forward in the direction of motion. The data suggest that the remembered trajectory is longer than the actual trajectory, and the displacement pattern is not consistent with the hypothesis that representational momentum results from a distortion of memory for the location of a trajectory.

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data.

PubMed

Ferrer-Admetlla, Anna; Leuenberger, Christoph; Jensen, Jeffrey D; Wegmann, Daniel

2016-06-01

The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional information for disentangling these effects may be obtained by observing changes in allele frequencies over multiple time points. Such data are common in experimental evolution studies, as well as in the comparison of ancient and contemporary samples. Leveraging this information, however, has been computationally challenging, particularly when considering multilocus data sets. To overcome these issues, we introduce a novel, discrete approximation for diffusion processes, termed mean transition time approximation, which preserves the long-term behavior of the underlying continuous diffusion process. We then derive this approximation for the particular case of inferring selection and demography from time series data under the classic Wright-Fisher model and demonstrate that our approximation is well suited to describe allele trajectories through time, even when only a few states are used. We then develop a Bayesian inference approach to jointly infer the population size and locus-specific selection coefficients with high accuracy and further extend this model to also infer the rates of sequencing errors and mutations. We finally apply our approach to recent experimental data on the evolution of drug resistance in influenza virus, identifying likely targets of selection and finding evidence for much larger viral population sizes than previously reported. Copyright © 2016 by the Genetics Society of America.

Microelectrode Recordings Validate the Clinical Visualization of Subthalamic-Nucleus Based on 7T Magnetic Resonance Imaging and Machine Learning for Deep Brain Stimulation Surgery.

PubMed

Shamir, Reuben R; Duchin, Yuval; Kim, Jinyoung; Patriat, Remi; Marmor, Odeya; Bergman, Hagai; Vitek, Jerrold L; Sapiro, Guillermo; Bick, Atira; Eliahou, Ruth; Eitan, Renana; Israel, Zvi; Harel, Noam

2018-05-24

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is a proven and effective therapy for the management of the motor symptoms of Parkinson's disease (PD). While accurate positioning of the stimulating electrode is critical for success of this therapy, precise identification of the STN based on imaging can be challenging. We developed a method to accurately visualize the STN on a standard clinical magnetic resonance imaging (MRI). The method incorporates a database of 7-Tesla (T) MRIs of PD patients together with machine-learning methods (hereafter 7 T-ML). To validate the clinical application accuracy of the 7 T-ML method by comparing it with identification of the STN based on intraoperative microelectrode recordings. Sixteen PD patients who underwent microelectrode-recordings guided STN DBS were included in this study (30 implanted leads and electrode trajectories). The length of the STN along the electrode trajectory and the position of its contacts to dorsal, inside, or ventral to the STN were compared using microelectrode-recordings and the 7 T-ML method computed based on the patient's clinical 3T MRI. All 30 electrode trajectories that intersected the STN based on microelectrode-recordings, also intersected it when visualized with the 7 T-ML method. STN trajectory average length was 6.2 ± 0.7 mm based on microelectrode recordings and 5.8 ± 0.9 mm for the 7 T-ML method. We observed a 93% agreement regarding contact location between the microelectrode-recordings and the 7 T-ML method. The 7 T-ML method is highly consistent with microelectrode-recordings data. This method provides a reliable and accurate patient-specific prediction for targeting the STN.

Statistical learning of movement.

PubMed

Ongchoco, Joan Danielle Khonghun; Uddenberg, Stefan; Chun, Marvin M

2016-12-01

The environment is dynamic, but objects move in predictable and characteristic ways, whether they are a dancer in motion, or a bee buzzing around in flight. Sequences of movement are comprised of simpler motion trajectory elements chained together. But how do we know where one trajectory element ends and another begins, much like we parse words from continuous streams of speech? As a novel test of statistical learning, we explored the ability to parse continuous movement sequences into simpler element trajectories. Across four experiments, we showed that people can robustly parse such sequences from a continuous stream of trajectories under increasingly stringent tests of segmentation ability and statistical learning. Observers viewed a single dot as it moved along simple sequences of paths, and were later able to discriminate these sequences from novel and partial ones shown at test. Observers demonstrated this ability when there were potentially helpful trajectory-segmentation cues such as a common origin for all movements (Experiment 1); when the dot's motions were entirely continuous and unconstrained (Experiment 2); when sequences were tested against partial sequences as a more stringent test of statistical learning (Experiment 3); and finally, even when the element trajectories were in fact pairs of trajectories, so that abrupt directional changes in the dot's motion could no longer signal inter-trajectory boundaries (Experiment 4). These results suggest that observers can automatically extract regularities in movement - an ability that may underpin our capacity to learn more complex biological motions, as in sport or dance.

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods.

PubMed

Gaspari, Roberto; Rapallo, Arnaldo

2008-06-28

In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum trajectory, with great savings in computational time required. This offers a theoretical bridge between the experimental static and dynamical properties of polymers.

Monte Carlo based investigation of berry phase for depth resolved characterization of biomedical scattering samples

NASA Astrophysics Data System (ADS)

Baba, J. S.; Koju, V.; John, D.

2015-03-01

The propagation of light in turbid media is an active area of research with relevance to numerous investigational fields, e.g., biomedical diagnostics and therapeutics. The statistical random-walk nature of photon propagation through turbid media is ideal for computational based modeling and simulation. Ready access to super computing resources provide a means for attaining brute force solutions to stochastic light-matter interactions entailing scattering by facilitating timely propagation of sufficient (>107) photons while tracking characteristic parameters based on the incorporated physics of the problem. One such model that works well for isotropic but fails for anisotropic scatter, which is the case for many biomedical sample scattering problems, is the diffusion approximation. In this report, we address this by utilizing Berry phase (BP) evolution as a means for capturing anisotropic scattering characteristics of samples in the preceding depth where the diffusion approximation fails. We extend the polarization sensitive Monte Carlo method of Ramella-Roman, et al., to include the computationally intensive tracking of photon trajectory in addition to polarization state at every scattering event. To speed-up the computations, which entail the appropriate rotations of reference frames, the code was parallelized using OpenMP. The results presented reveal that BP is strongly correlated to the photon penetration depth, thus potentiating the possibility of polarimetric depth resolved characterization of highly scattering samples, e.g., biological tissues.

Monte Carlo based investigation of Berry phase for depth resolved characterization of biomedical scattering samples

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

Baba, Justin S; John, Dwayne O; Koju, Vijay

The propagation of light in turbid media is an active area of research with relevance to numerous investigational fields, e.g., biomedical diagnostics and therapeutics. The statistical random-walk nature of photon propagation through turbid media is ideal for computational based modeling and simulation. Ready access to super computing resources provide a means for attaining brute force solutions to stochastic light-matter interactions entailing scattering by facilitating timely propagation of sufficient (>10million) photons while tracking characteristic parameters based on the incorporated physics of the problem. One such model that works well for isotropic but fails for anisotropic scatter, which is the case formore » many biomedical sample scattering problems, is the diffusion approximation. In this report, we address this by utilizing Berry phase (BP) evolution as a means for capturing anisotropic scattering characteristics of samples in the preceding depth where the diffusion approximation fails. We extend the polarization sensitive Monte Carlo method of Ramella-Roman, et al.,1 to include the computationally intensive tracking of photon trajectory in addition to polarization state at every scattering event. To speed-up the computations, which entail the appropriate rotations of reference frames, the code was parallelized using OpenMP. The results presented reveal that BP is strongly correlated to the photon penetration depth, thus potentiating the possibility of polarimetric depth resolved characterization of highly scattering samples, e.g., biological tissues.« less

Single particle tracking with sterol modulation reveals the cholesterol-mediated diffusion properties of integrin receptors.

PubMed

Arora, Neha; Syed, Aleem; Sander, Suzanne; Smith, Emily A

2014-10-07

A combination of sterol modulation with cyclodextrins plus fluorescence microscopy revealed a biophysical mechanism behind cholesterol's influence on the diffusion of a ubiquitous class of receptors called integrins. The heterogeneous diffusion of integrins bound to ligand-coated quantum dots was measured using single particle tracking (SPT), and the ensemble changes in integrin diffusion were measured by fluorescence recovery after photobleaching (FRAP). A 25 ± 1% reduction of membrane cholesterol resulted in three significant changes to the diffusion of ligand-bound αPS2CβPS integrins as measured by SPT. There was a 23% increase in ligand-bound mobile integrins; there was a statistically significant increase in the average diffusion coefficient inside zones of confined diffusion, and histograms of confined integrin trajectories showed an increased frequency in the range of 0.1-1 μm(2) s(-1) and a decreased frequency in the 0.001-0.1 μm(2) s(-1) range. No statistical change was measured in the duration of confinement nor the size of confined zones. Restoring the cholesterol-depleted cells with exogenous cholesterol or exogenous epicholesterol resulted in similar diffusion properties. Epicholesterol differs from cholesterol in the orientation of a single hydroxyl group. The ability of epicholesterol to substitute for cholesterol suggests a biophysical mechanism for cholesterol's effect on integrin diffusion. Influences of bilayer thickness, viscosity and organization are discussed as possible explanations for the measured changes in integrin diffusion when the membrane cholesterol concentration is reduced.

The heavy ion diffusion region in magnetic reconnection in the Earth's magnetotail

NASA Astrophysics Data System (ADS)

Liu, Y. H.; Mouikis, C. G.; Kistler, L. M.; Wang, S.; Roytershteyn, V.; Karimabadi, H.

2015-05-01

While the plasma in the Earth's magnetotail predominantly consists of protons and electrons, there are times when a significant amount of oxygen is present. When magnetic reconnection occurs, the behavior of these heavy ions can be significantly different from that of the protons, due to their larger gyroradius. In this study, we investigate the heavy ion distribution functions in the reconnection ion diffusion region from a 2.5D three-species particle-in-cell numerical simulation and compare those with Cluster observations from the near-Earth magnetotail. From the simulation results, we find that the heavy ions are demagnetized and accelerated in a larger diffusion region, the heavy ion diffusion region. The ion velocity distribution functions show that, inside the heavy ion diffusion region, heavy ions appear as counterstreaming beams along z in the GSM x-z plane, while drifting in y, carrying cross-tail current. We compare this result with Cluster observations in the vicinity of reconnection regions in the near-Earth magnetotail and find that the simulation predictions are consistent with the observed ion distribution functions in the ion diffusion region, as well as the inflow, exhaust, and separatrix regions. Based on the simulation and observation results, the presence of a multiscale diffusion region model, for O+ abundant reconnection events in the Earth's magnetotail, is demonstrated. A test particle simulation shows that in the diffusion region, the H+ gains energy mainly through Ex, while the O+ energy gain comes equally from Ex and Ey.

Fractal diffusion in high temperature polymer electrolyte fuel cell membranes

NASA Astrophysics Data System (ADS)

Hopfenmüller, Bernhard; Zorn, Reiner; Holderer, Olaf; Ivanova, Oxana; Lehnert, Werner; Lüke, Wiebke; Ehlers, Georg; Jalarvo, Niina; Schneider, Gerald J.; Monkenbusch, Michael; Richter, Dieter

2018-05-01

The performance of fuel cells depends largely on the proton diffusion in the proton conducting membrane, the core of a fuel cell. High temperature polymer electrolyte fuel cells are based on a polymer membrane swollen with phosphoric acid as the electrolyte, where proton conduction takes place. We studied the proton diffusion in such membranes with neutron scattering techniques which are especially sensitive to the proton contribution. Time of flight spectroscopy and backscattering spectroscopy have been combined to cover a broad dynamic range. In order to selectively observe the diffusion of protons potentially contributing to the ion conductivity, two samples were prepared, where in one of the samples the phosphoric acid was used with hydrogen replaced by deuterium. The scattering data from the two samples were subtracted in a suitable way after measurement. Thereby subdiffusive behavior of the proton diffusion has been observed and interpreted in terms of a model of fractal diffusion. For this purpose, a scattering function for fractal diffusion has been developed. The fractal diffusion dimension dw and the Hausdorff dimension df have been determined on the length scales covered in the neutron scattering experiments.

Derivation of site-specific relationships between hydraulic parameters and p-wave velocities based on hydraulic and seismic tomography

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

Brauchler, R.; Doetsch, J.; Dietrich, P.

2012-01-10

In this study, hydraulic and seismic tomographic measurements were used to derive a site-specific relationship between the geophysical parameter p-wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p-wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm, using a ray tracing technique with curved trajectories. The experimental set-up was designed such that the p-wave velocity tomogram overlaps the hydraulic tomograms by half. Themore » experiments were performed at a wellcharacterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct-push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site-specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p-wave velocities into hydraulic properties was undertaken using a k-means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.« less

ATLAS - A new Lagrangian transport and mixing model with detailed stratospheric chemistry

NASA Astrophysics Data System (ADS)

Wohltmann, I.; Rex, M.; Lehmann, R.

2009-04-01

We present a new global Chemical Transport Model (CTM) with full stratospheric chemistry and Lagrangian transport and mixing called ATLAS. Lagrangian models have some crucial advantages over Eulerian grid-box based models, like no numerical diffusion, no limitation of the time step of the model by the CFL criterion, conservation of mixing ratios by design and easy parallelization of code. The transport module is based on a trajectory code developed at the Alfred Wegener Institute. The horizontal and vertical resolution, the vertical coordinate system (pressure, potential temperature, hybrid coordinate) and the time step of the model are flexible, so that the model can be used both for process studies and long-time runs over several decades. Mixing of the Lagrangian air parcels is parameterized based on the local shear and strain of the flow with a method similar to that used in the CLaMS model, but with some modifications like a triangulation that introduces no vertical layers. The stratospheric chemistry module was developed at the Institute and includes 49 species and 170 reactions and a detailed treatment of heterogenous chemistry on polar stratospheric clouds. We present an overview over the model architecture, the transport and mixing concept and some validation results. Comparison of model results with tracer data from flights of the ER2 aircraft in the stratospheric polar vortex in 1999/2000 which are able to resolve fine tracer filaments show that excellent agreement with observed tracer structures can be achieved with a suitable mixing parameterization.

Modern Methods for Modeling Change in Obesity Research in Nursing.

PubMed

Sereika, Susan M; Zheng, Yaguang; Hu, Lu; Burke, Lora E

2017-08-01

Persons receiving treatment for weight loss often demonstrate heterogeneity in lifestyle behaviors and health outcomes over time. Traditional repeated measures approaches focus on the estimation and testing of an average temporal pattern, ignoring the interindividual variability about the trajectory. An alternate person-centered approach, group-based trajectory modeling, can be used to identify distinct latent classes of individuals following similar trajectories of behavior or outcome change as a function of age or time and can be expanded to include time-invariant and time-dependent covariates and outcomes. Another latent class method, growth mixture modeling, builds on group-based trajectory modeling to investigate heterogeneity within the distinct trajectory classes. In this applied methodologic study, group-based trajectory modeling for analyzing changes in behaviors or outcomes is described and contrasted with growth mixture modeling. An illustration of group-based trajectory modeling is provided using calorie intake data from a single-group, single-center prospective study for weight loss in adults who are either overweight or obese.

Design of fast earth-return trajectories from a lunar base

NASA Astrophysics Data System (ADS)

Anhorn, Walter

1991-09-01

The Apollo Lunar Program utilized efficient transearth trajectories which employed parking orbits in order to minimize energy requirements. This thesis concentrates on a different type of transearth trajectory. These are direct-ascent, hyperbolic trajectories which omit the parking orbits in order to achieve short flight times to and from a future lunar base. The object of the thesis is the development of a three-dimensional transearth trajectory model and associated computer program for exploring trade-offs between flight-time and energy, given various mission constraints. The program also targets the Moon with a hyperbolic trajectory, which can be used for targeting Earth impact points. The first-order model is based on an Earth-centered conic and a massless spherical Moon, using MathCAD version 3.0. This model is intended as the basis for future patched-conic formulations for the design of fast Earth-return trajectories. Applications include placing nuclear deterrent arsenals on the Moon, various space support related activities, and finally protection against Earth-threatening asteroids and comets using lunar bases.

Observation and simulation of the ionosphere disturbance waves triggered by rocket exhausts

NASA Astrophysics Data System (ADS)

Lin, Charles C. H.; Chen, Chia-Hung; Matsumura, Mitsuru; Lin, Jia-Ting; Kakinami, Yoshihiro

2017-08-01

Observations and theoretical modeling of the ionospheric disturbance waves generated by rocket launches are investigated. During the rocket passage, time rate change of total electron content (rTEC) enhancement with the V-shape shock wave signature is commonly observed, followed by acoustic wave disturbances and region of negative rTEC centered along the trajectory. Ten to fifteen min after the rocket passage, delayed disturbance waves appeared and propagated along direction normal to the V-shape wavefronts. These observation features appeared most prominently in the 2016 North Korea rocket launch showing a very distinct V-shape rTEC enhancement over enormous areas along the southeast flight trajectory despite that it was also appeared in the 2009 North Korea rocket launch with the eastward flight trajectory. Numerical simulations using the physical-based nonlinear and nonhydrostatic coupled model of neutral atmosphere and ionosphere reproduce promised results in qualitative agreement with the characteristics of ionospheric disturbance waves observed in the 2009 event by considering the released energy of the rocket exhaust as the disturbance source. Simulations reproduce the shock wave signature of electron density enhancement, acoustic wave disturbances, the electron density depletion due to the rocket-induced pressure bulge, and the delayed disturbance waves. The pressure bulge results in outward neutral wind flows carrying neutrals and plasma away from it and leading to electron density depletions. Simulations further show, for the first time, that the delayed disturbance waves are produced by the surface reflection of the earlier arrival acoustic wave disturbances.

Developmental trajectories of children's symbolic numerical magnitude processing skills and associated cognitive competencies.

PubMed

Vanbinst, Kiran; Ceulemans, Eva; Peters, Lien; Ghesquière, Pol; De Smedt, Bert

2018-02-01

Although symbolic numerical magnitude processing skills are key for learning arithmetic, their developmental trajectories remain unknown. Therefore, we delineated during the first 3years of primary education (5-8years of age) groups with distinguishable developmental trajectories of symbolic numerical magnitude processing skills using a model-based clustering approach. Three clusters were identified and were labeled as inaccurate, accurate but slow, and accurate and fast. The clusters did not differ in age, sex, socioeconomic status, or IQ. We also tested whether these clusters differed in domain-specific (nonsymbolic magnitude processing and digit identification) and domain-general (visuospatial short-term memory, verbal working memory, and processing speed) cognitive competencies that might contribute to children's ability to (efficiently) process the numerical meaning of Arabic numerical symbols. We observed minor differences between clusters in these cognitive competencies except for verbal working memory for which no differences were observed. Follow-up analyses further revealed that the above-mentioned cognitive competencies did not merely account for the cluster differences in children's development of symbolic numerical magnitude processing skills, suggesting that other factors account for these individual differences. On the other hand, the three trajectories of symbolic numerical magnitude processing revealed remarkable and stable differences in children's arithmetic fact retrieval, which stresses the importance of symbolic numerical magnitude processing for learning arithmetic. Copyright © 2017 Elsevier Inc. All rights reserved.

Longitudinal Trajectories of Metabolic Control From Childhood to Young Adulthood in Type 1 Diabetes From a Large German/Austrian Registry: A Group-Based Modeling Approach.

PubMed

Schwandt, Anke; Hermann, Julia M; Rosenbauer, Joachim; Boettcher, Claudia; Dunstheimer, Désirée; Grulich-Henn, Jürgen; Kuss, Oliver; Rami-Merhar, Birgit; Vogel, Christian; Holl, Reinhard W

2017-03-01

Worsening of glycemic control in type 1 diabetes during puberty is a common observation. However, HbA 1c remains stable or even improves for some youths. The aim is to identify distinct patterns of glycemic control in type 1 diabetes from childhood to young adulthood. A total of 6,433 patients with type 1 diabetes were selected from the prospective, multicenter diabetes patient registry Diabetes-Patienten-Verlaufsdokumentation (DPV) (follow-up from age 8 to 19 years, baseline diabetes duration ≥2 years, HbA 1c aggregated per year of life). We used latent class growth modeling as the trajectory approach to determine distinct subgroups following a similar trajectory for HbA 1c over time. Five distinct longitudinal trajectories of HbA 1c were determined, comprising group 1 = 40%, group 2 = 27%, group 3 = 15%, group 4 = 13%, and group 5 = 5% of patients. Groups 1-3 indicated stable glycemic control at different HbA 1c levels. At baseline, similar HbA 1c was observed in group 1 and group 4, but HbA 1c deteriorated in group 4 from age 8 to 19 years. Similar patterns were present in group 3 and group 5. We observed differences in self-monitoring of blood glucose, insulin therapy, daily insulin dose, physical activity, BMI SD score, body-height SD score, and migration background across all HbA 1c trajectories (all P ≤ 0.001). No sex differences were present. Comparing groups with similar initial HbA 1c but different patterns, groups with higher HbA 1c increase were characterized by lower frequency of self-monitoring of blood glucose and physical activity and reduced height (all P < 0.01). Using a trajectory approach, we determined five distinct longitudinal patterns of glycemic control from childhood to early adulthood. Diabetes self-care, treatment differences, and demographics were related to different HbA 1c courses. © 2017 by the American Diabetes Association.

On-Line Use of Three-Dimensional Marker Trajectory Estimation From Cone-Beam Computed Tomography Projections for Precise Setup in Radiotherapy for Targets With Respiratory Motion

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

Worm, Esben S., E-mail: esbeworm@rm.dk; Department of Medical Physics, Aarhus University Hospital, Aarhus; Hoyer, Morten

2012-05-01

Purpose: To develop and evaluate accurate and objective on-line patient setup based on a novel semiautomatic technique in which three-dimensional marker trajectories were estimated from two-dimensional cone-beam computed tomography (CBCT) projections. Methods and Materials: Seven treatment courses of stereotactic body radiotherapy for liver tumors were delivered in 21 fractions in total to 6 patients by a linear accelerator. Each patient had two to three gold markers implanted close to the tumors. Before treatment, a CBCT scan with approximately 675 two-dimensional projections was acquired during a full gantry rotation. The marker positions were segmented in each projection. From this, the three-dimensionalmore » marker trajectories were estimated using a probability based method. The required couch shifts for patient setup were calculated from the mean marker positions along the trajectories. A motion phantom moving with known tumor trajectories was used to examine the accuracy of the method. Trajectory-based setup was retrospectively used off-line for the first five treatment courses (15 fractions) and on-line for the last two treatment courses (6 fractions). Automatic marker segmentation was compared with manual segmentation. The trajectory-based setup was compared with setup based on conventional CBCT guidance on the markers (first 15 fractions). Results: Phantom measurements showed that trajectory-based estimation of the mean marker position was accurate within 0.3 mm. The on-line trajectory-based patient setup was performed within approximately 5 minutes. The automatic marker segmentation agreed with manual segmentation within 0.36 {+-} 0.50 pixels (mean {+-} SD; pixel size, 0.26 mm in isocenter). The accuracy of conventional volumetric CBCT guidance was compromised by motion smearing ({<=}21 mm) that induced an absolute three-dimensional setup error of 1.6 {+-} 0.9 mm (maximum, 3.2) relative to trajectory-based setup. Conclusions: The first on-line clinical use of trajectory estimation from CBCT projections for precise setup in stereotactic body radiotherapy was demonstrated. Uncertainty in the conventional CBCT-based setup procedure was eliminated with the new method.« less

Sparse and Adaptive Diffusion Dictionary (SADD) for recovering intra-voxel white matter structure.

PubMed

Aranda, Ramon; Ramirez-Manzanares, Alonso; Rivera, Mariano

2015-12-01

On the analysis of the Diffusion-Weighted Magnetic Resonance Images, multi-compartment models overcome the limitations of the well-known Diffusion Tensor model for fitting in vivo brain axonal orientations at voxels with fiber crossings, branching, kissing or bifurcations. Some successful multi-compartment methods are based on diffusion dictionaries. The diffusion dictionary-based methods assume that the observed Magnetic Resonance signal at each voxel is a linear combination of the fixed dictionary elements (dictionary atoms). The atoms are fixed along different orientations and diffusivity profiles. In this work, we present a sparse and adaptive diffusion dictionary method based on the Diffusion Basis Functions Model to estimate in vivo brain axonal fiber populations. Our proposal overcomes the following limitations of the diffusion dictionary-based methods: the limited angular resolution and the fixed shapes for the atom set. We propose to iteratively re-estimate the orientations and the diffusivity profile of the atoms independently at each voxel by using a simplified and easier-to-solve mathematical approach. As a result, we improve the fitting of the Diffusion-Weighted Magnetic Resonance signal. The advantages with respect to the former Diffusion Basis Functions method are demonstrated on the synthetic data-set used on the 2012 HARDI Reconstruction Challenge and in vivo human data. We demonstrate that improvements obtained in the intra-voxel fiber structure estimations benefit brain research allowing to obtain better tractography estimations. Hence, these improvements result in an accurate computation of the brain connectivity patterns. Copyright © 2015 Elsevier B.V. All rights reserved.

Signal detectability in diffusive media using phased arrays in conjunction with detector arrays.

PubMed

Kang, Dongyel; Kupinski, Matthew A

2011-06-20

We investigate Hotelling observer performance (i.e., signal detectability) of a phased array system for tasks of detecting small inhomogeneities and distinguishing adjacent abnormalities in uniform diffusive media. Unlike conventional phased array systems where a single detector is located on the interface between two sources, we consider a detector array, such as a CCD, on a phantom exit surface for calculating the Hotelling observer detectability. The signal detectability for adjacent small abnormalities (2 mm displacement) for the CCD-based phased array is related to the resolution of reconstructed images. Simulations show that acquiring high-dimensional data from a detector array in a phased array system dramatically improves the detectability for both tasks when compared to conventional single detector measurements, especially at low modulation frequencies. It is also observed in all studied cases that there exists the modulation frequency optimizing CCD-based phased array systems, where detectability for both tasks is consistently high. These results imply that the CCD-based phased array has the potential to achieve high resolution and signal detectability in tomographic diffusive imaging while operating at a very low modulation frequency. The effect of other configuration parameters, such as a detector pixel size, on the observer performance is also discussed.

Trajectory Studies of Large HNO3-Containing PSC Particles in the Arctic: Evidence for the Role of NAT

NASA Technical Reports Server (NTRS)

McKinney, K. A.; Wennberg, P. O.; Dhaniyala, S.; Fahey, D. W.; Northway, M. J.; Kuenzi, K. F.; Kleinboehl, A.; Sinnhuber, M.; Kuellmann, H.; Bremer, H.;

Hand interception of occluded motion in humans: a test of model-based vs. on-line control

PubMed Central

Zago, Myrka; Lacquaniti, Francesco

2015-01-01

Two control schemes have been hypothesized for the manual interception of fast visual targets. In the model-free on-line control, extrapolation of target motion is based on continuous visual information, without resorting to physical models. In the model-based control, instead, a prior model of target motion predicts the future spatiotemporal trajectory. To distinguish between the two hypotheses in the case of projectile motion, we asked participants to hit a ball that rolled down an incline at 0.2 g and then fell in air at 1 g along a parabola. By varying starting position, ball velocity and trajectory differed between trials. Motion on the incline was always visible, whereas parabolic motion was either visible or occluded. We found that participants were equally successful at hitting the falling ball in both visible and occluded conditions. Moreover, in different trials the intersection points were distributed along the parabolic trajectories of the ball, indicating that subjects were able to extrapolate an extended segment of the target trajectory. Remarkably, this trend was observed even at the very first repetition of movements. These results are consistent with the hypothesis of model-based control, but not with on-line control. Indeed, ball path and speed during the occlusion could not be extrapolated solely from the kinematic information obtained during the preceding visible phase. The only way to extrapolate ball motion correctly during the occlusion was to assume that the ball would fall under gravity and air drag when hidden from view. Such an assumption had to be derived from prior experience. PMID:26133803

Eight-Year Latent Class Trajectories of Academic and Social Functioning in Children with Attention-Deficit/Hyperactivity Disorder.

PubMed

DuPaul, George J; Morgan, Paul L; Farkas, George; Hillemeier, Marianne M; Maczuga, Steve

2017-09-15

We examined trajectories of academic and social functioning in children with attention-deficit/hyperactivity disorder (ADHD) to identify those who might be at risk for especially severe levels of academic and social impairment over time. We estimated a series of growth mixture models using data from two subsamples of children participating in the NIMH Collaborative Multisite Multimodal Treatment Study of Children with ADHD (MTA) including those with at least baseline and 96-month data for reading and mathematics achievement (n = 392; 77.3% male; M age = 7.7; SD = 0.8) or social skills ratings from teachers (n = 259; 74.9% male; M age = 7.6; SD = 0.8). We compared latent trajectories for children with ADHD to mean observed trajectories obtained from a local normative (i.e., non-ADHD) comparison group (n = 289; 80.6% male; M age = 9.9; SD = 1.1). Results indicated six latent trajectory classes for reading and mathematics and four classes for teacher social skills ratings. There was not only a relationship between trajectories of inattention symptoms and academic impairment, but also a similarly strong association between trajectory classes of hyperactive-impulsive symptoms and achievement. Trajectory class membership correlated with socio-demographic and diagnostic characteristics, inattention and hyperactive-impulsive symptom trajectories, externalizing behavior in school, and treatment receipt and dosage. Although children with ADHD display substantial heterogeneity in their reading, math, and social skills growth trajectories, those with behavioral and socio-demographic disadvantages are especially likely to display severe levels of academic and social impairment over time. Evidence-based early screening and intervention that directly address academic and social impairments in elementary school-aged children with ADHD are warranted. The ClinicalTrials.gov identifier is NCT00000388.

Chemotactic droplet swimmers in complex geometries

NASA Astrophysics Data System (ADS)

Jin, Chenyu; Hokmabad, Babak V.; Baldwin, Kyle A.; Maass, Corinna C.

2018-02-01

Chemotaxis1 and auto-chemotaxis are key mechanisms in the dynamics of micro-organisms, e.g. in the acquisition of nutrients and in the communication between individuals, influencing the collective behaviour. However, chemical signalling and the natural environment of biological swimmers are generally complex, making them hard to access analytically. We present a well-controlled, tunable artificial model to study chemotaxis and autochemotaxis in complex geometries, using microfluidic assays of self-propelling oil droplets in an aqueous surfactant solution (Herminghaus et al 2014 Soft Matter 10 7008-22 Krüger et al 2016 Phys. Rev. Lett. 117). Droplets propel via interfacial Marangoni stresses powered by micellar solubilisation. Moreover, filled micelles act as a chemical repellent by diffusive phoretic gradient forces. We have studied these chemotactic effects in a series of microfluidic geometries, as published in Jin et al (2017 Proc. Natl Acad. Sci. 114 5089-94): first, droplets are guided along the shortest path through a maze by surfactant diffusing into the maze from the exit. Second, we let auto-chemotactic droplet swimmers pass through bifurcating microfluidic channels and record anticorrelations between the branch choices of consecutive droplets. We present an analytical Langevin model matching the experimental data. In a previously unpublished experiment, pillar arrays of variable sizes and shapes provide a convex wall interacting with the swimmer and, in the case of attachment, bending its trajectory and forcing it to revert to its own trail. We observe different behaviours based on the interplay of wall curvature and negative autochemotaxis, i.e. no attachment for highly curved interfaces, stable trapping at large pillars, and a narrow transition region where negative autochemotaxis makes the swimmers detach after a single orbit.