Science.gov

Sample records for affine motion model

  1. Performance comparison of rigid and affine models for motion estimation using ultrasound radio-frequency signals.

    PubMed

    Pan, Xiaochang; Liu, Ke; Shao, Jinghua; Gao, Jing; Huang, Lingyun; Bai, Jing; Luo, Jianwen

    2015-11-01

    Tissue motion estimation is widely used in many ultrasound techniques. Rigid-model-based and nonrigid-modelbased methods are two main groups of space-domain methods of tissue motion estimation. The affine model is one of the commonly used nonrigid models. The performances of the rigid model and affine model have not been compared on ultrasound RF signals, which have been demonstrated to obtain higher accuracy, precision, and resolution in motion estimation compared with B-mode images. In this study, three methods, i.e., the normalized cross-correlation method with rigid model (NCC), the optical flow method with rigid model (OFRM), and the optical flow method with affine model (OFAM), are compared using ultrasound RF signals, rather than the B-mode images used in previous studies. Simulations, phantom, and in vivo experiments are conducted to make the comparison. In the simulations, the root-mean-square errors (RMSEs) of axial and lateral displacements and strains are used to assess the accuracy of motion estimation, and the elastographic signal-tonoise ratio (SNRe) and contrast-to-noise ratio (CNRe) are used to evaluate the quality of axial strain images. In the phantom experiments, the registration error between the pre- and postdeformation RF signals, as well as the SNRe and CNRe of axial strain images, are utilized as the evaluation criteria. In the in vivo experiments, the registration error is used to evaluate the estimation performance. The results show that the affinemodel- based method (i.e., OFAM) obtains the lowest RMSE or registration error and the highest SNRe and CNRe among all the methods. The affine model is demonstrated to be superior to the rigid model in motion estimation based on RF signals. PMID:26559623

  2. Speckle reduction in optical coherence tomography imaging by affine-motion image registration

    NASA Astrophysics Data System (ADS)

    Alonso-Caneiro, David; Read, Scott A.; Collins, Michael J.

    2011-11-01

    Signal-degrading speckle is one factor that can reduce the quality of optical coherence tomography images. We demonstrate the use of a hierarchical model-based motion estimation processing scheme based on an affine-motion model to reduce speckle in optical coherence tomography imaging, by image registration and the averaging of multiple B-scans. The proposed technique is evaluated against other methods available in the literature. The results from a set of retinal images show the benefit of the proposed technique, which provides an improvement in signal-to-noise ratio of the square root of the number of averaged images, leading to clearer visual information in the averaged image. The benefits of the proposed technique are also explored in the case of ocular anterior segment imaging.

  3. On Affine Fusion and the Phase Model

    NASA Astrophysics Data System (ADS)

    Walton, Mark A.

    2012-11-01

    A brief review is given of the integrable realization of affine fusion discovered recently by Korff and Stroppel. They showed that the affine fusion of the su(n) Wess-Zumino-Novikov-Witten (WZNW) conformal field theories appears in a simple integrable system known as the phase model. The Yang-Baxter equation leads to the construction of commuting operators as Schur polynomials, with noncommuting hopping operators as arguments. The algebraic Bethe ansatz diagonalizes them, revealing a connection to the modular S matrix and fusion of the su(n) WZNW model. The noncommutative Schur polynomials play roles similar to those of the primary field operators in the corresponding WZNW model. In particular, their 3-point functions are the su(n) fusion multiplicities. We show here how the new phase model realization of affine fusion makes obvious the existence of threshold levels, and how it accommodates higher-genus fusion.

  4. Fan Affinity Laws from a Collision Model

    ERIC Educational Resources Information Center

    Bhattacharjee, Shayak

    2012-01-01

    The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour…

  5. Brownian-motion based simulation of stochastic reaction-diffusion systems for affinity based sensors

    NASA Astrophysics Data System (ADS)

    Tulzer, Gerhard; Heitzinger, Clemens

    2016-04-01

    In this work, we develop a 2D algorithm for stochastic reaction-diffusion systems describing the binding and unbinding of target molecules at the surfaces of affinity-based sensors. In particular, we simulate the detection of DNA oligomers using silicon-nanowire field-effect biosensors. Since these devices are uniform along the nanowire, two dimensions are sufficient to capture the kinetic effects features. The model combines a stochastic ordinary differential equation for the binding and unbinding of target molecules as well as a diffusion equation for their transport in the liquid. A Brownian-motion based algorithm simulates the diffusion process, which is linked to a stochastic-simulation algorithm for association at and dissociation from the surface. The simulation data show that the shape of the cross section of the sensor yields areas with significantly different target-molecule coverage. Different initial conditions are investigated as well in order to aid rational sensor design. A comparison of the association/hybridization behavior for different receptor densities allows optimization of the functionalization setup depending on the target-molecule density.

  6. Brownian-motion based simulation of stochastic reaction-diffusion systems for affinity based sensors.

    PubMed

    Tulzer, Gerhard; Heitzinger, Clemens

    2016-04-22

    In this work, we develop a 2D algorithm for stochastic reaction-diffusion systems describing the binding and unbinding of target molecules at the surfaces of affinity-based sensors. In particular, we simulate the detection of DNA oligomers using silicon-nanowire field-effect biosensors. Since these devices are uniform along the nanowire, two dimensions are sufficient to capture the kinetic effects features. The model combines a stochastic ordinary differential equation for the binding and unbinding of target molecules as well as a diffusion equation for their transport in the liquid. A Brownian-motion based algorithm simulates the diffusion process, which is linked to a stochastic-simulation algorithm for association at and dissociation from the surface. The simulation data show that the shape of the cross section of the sensor yields areas with significantly different target-molecule coverage. Different initial conditions are investigated as well in order to aid rational sensor design. A comparison of the association/hybridization behavior for different receptor densities allows optimization of the functionalization setup depending on the target-molecule density. PMID:26939610

  7. Theoretical performance assessment and empirical analysis of super-resolution under unknown affine sensor motion.

    PubMed

    Thelen, Brian J; Valenzuela, John R; LeBlanc, Joel W

    2016-04-01

    This paper deals with super-resolution (SR) processing and associated theoretical performance assessment for under-sampled video data collected from a moving imaging platform with unknown motion and assuming a relatively flat scene. This general scenario requires joint estimation of the high-resolution image and the parameters that determine a projective transform that relates the collected frames to one another. A quantitative assessment of the variance in the random error as achieved through a joint-estimation approach (e.g., SR image reconstruction and motion estimation) is carried out via the general framework of M-estimators and asymptotic statistics. This approach provides a performance measure on estimating the fine-resolution scene when there is a lack of perspective information and represents a significant advancement over previous work that considered only the more specific scenario of mis-registration. A succinct overview of the theoretical framework is presented along with some specific results on the approximate random error for the case of unknown translation and affine motions. A comparison is given between the approximated random error and that actually achieved by an M-estimator approach to the joint-estimation problem. These results provide insight on the reduction in SR reconstruction accuracy when jointly estimating unknown inter-frame affine motion. PMID:27140759

  8. Affine Transform to Reform Pixel Coordinates of EOG Signals for Controlling Robot Manipulators Using Gaze Motions

    PubMed Central

    Rusydi, Muhammad Ilhamdi; Sasaki, Minoru; Ito, Satoshi

    2014-01-01

    Biosignals will play an important role in building communication between machines and humans. One of the types of biosignals that is widely used in neuroscience are electrooculography (EOG) signals. An EOG has a linear relationship with eye movement displacement. Experiments were performed to construct a gaze motion tracking method indicated by robot manipulator movements. Three operators looked at 24 target points displayed on a monitor that was 40 cm in front of them. Two channels (Ch1 and Ch2) produced EOG signals for every single eye movement. These signals were converted to pixel units by using the linear relationship between EOG signals and gaze motion distances. The conversion outcomes were actual pixel locations. An affine transform method is proposed to determine the shift of actual pixels to target pixels. This method consisted of sequences of five geometry processes, which are translation-1, rotation, translation-2, shear and dilatation. The accuracy was approximately 0.86° ± 0.67° in the horizontal direction and 0.54° ± 0.34° in the vertical. This system successfully tracked the gaze motions not only in direction, but also in distance. Using this system, three operators could operate a robot manipulator to point at some targets. This result shows that the method is reliable in building communication between humans and machines using EOGs. PMID:24919013

  9. Computational Motion Phantoms and Statistical Models of Respiratory Motion

    NASA Astrophysics Data System (ADS)

    Ehrhardt, Jan; Klinder, Tobias; Lorenz, Cristian

    Breathing motion is not a robust and 100 % reproducible process, and inter- and intra-fractional motion variations form an important problem in radiotherapy of the thorax and upper abdomen. A widespread consensus nowadays exists that it would be useful to use prior knowledge about respiratory organ motion and its variability to improve radiotherapy planning and treatment delivery. This chapter discusses two different approaches to model the variability of respiratory motion. In the first part, we review computational motion phantoms, i.e. computerized anatomical and physiological models. Computational phantoms are excellent tools to simulate and investigate the effects of organ motion in radiation therapy and to gain insight into methods for motion management. The second part of this chapter discusses statistical modeling techniques to describe the breathing motion and its variability in a population of 4D images. Population-based models can be generated from repeatedly acquired 4D images of the same patient (intra-patient models) and from 4D images of different patients (inter-patient models). The generation of those models is explained and possible applications of those models for motion prediction in radiotherapy are exemplified. Computational models of respiratory motion and motion variability have numerous applications in radiation therapy, e.g. to understand motion effects in simulation studies, to develop and evaluate treatment strategies or to introduce prior knowledge into the patient-specific treatment planning.

  10. Affine group formulation of the Standard Model coupled to gravity

    SciTech Connect

    Chou, Ching-Yi; Ita, Eyo; Soo, Chopin

    2014-04-15

    In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant Λ, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant.

  11. Carbohydrate affinity for the glucose-galactose binding protein is regulated by allosteric domain motions.

    PubMed

    Ortega, Gabriel; Castaño, David; Diercks, Tammo; Millet, Oscar

    2012-12-01

    Protein function, structure, and dynamics are intricately correlated, but studies on structure-activity relationships are still only rarely complemented by a detailed analysis of dynamics related to function (functional dynamics). Here, we have applied NMR to investigate the functional dynamics in two homologous periplasmic sugar binding proteins with bidomain composition: Escherichia coli glucose/galactose (GGBP) and ribose (RBP) binding proteins. In contrast to their structural and functional similarity, we observe a remarkable difference in functional dynamics: For RBP, the absence of segmental motions allows only for isolated structural adaptations upon carbohydrate binding in line with an induced fit mechanism; on the other hand, GGBP shows extensive segmental mobility in both apo and holo states, enabling selection of the most favorable conformation upon carbohydrate binding in line with a population shift mechanism. Collective segmental motions are controlled by the hinge composition: by swapping two identified key residues between RBP and GGBP we also interchange their segmental hinge mobility, and the doubly mutated GGBP* no longer experiences changes in conformational entropy upon ligand binding while the complementary RBP* shows the segmental dynamics observed in wild-type GGBP. Most importantly, the segmental interdomain dynamics always increase the apparent substrate affinity and thus, are functional, underscoring the allosteric control that the hinge region exerts on ligand binding. PMID:23148479

  12. Interactions between PTB RRMs induce slow motions and increase RNA binding affinity

    PubMed Central

    Maynard, Caroline M

    2010-01-01

    Polypyrimidine tract binding protein (PTB) participates in a variety of functions in eukaryotic cells, including alternative splicing, mRNA stabilization, and internal ribosomal entry site (IRES) mediated translation initiation. Its mechanism of RNA recognition is determined in part by the novel geometry of its two C-terminal RNA Recognition Motifs (RRM3 and RRM4), which interact with each other to form a stable complex (PTB1:34). This complex itself is unusual among RRMs, suggesting that it performs a specific function for the protein. In order to understand the advantage it provides to PTB, the fundamental properties of PTB1:34 are examined here as a comparative study of the complex and its two constituent RRMs. Both RRM3 and RRM4 adopt folded structures that NMR data show to be similar to their structure in PRB1:34. The RNA binding properties of the domains differ dramatically. The affinity of each separate RRM for polypyrimidine tracts is far weaker than that of PTB1:34, and simply mixing the two RRMs does not create an equivalent binding platform. 15N-NMR relaxation experiments show that PTB1:34 has slow, microsecond motions throughout both RRMs including the interdomain linker. This is in contrast to the individual domains, RRM3 and RRM4, where only a few backbone amides are flexible on this timescale. The slow backbone dynamics of PTB1:34, induced by packing of RRM3 and RRM4, could be essential for high affinity binding to a flexible polypyrimidine tract RNA and also provide entropic compensation for its own formation. PMID:20080103

  13. Students' Mathematical Modeling of Motion

    ERIC Educational Resources Information Center

    Marshall, Jill A.; Carrejo, David J.

    2008-01-01

    We present results of an investigation of university students' development of mathematical models of motion in a physical science course for preservice teachers and graduate students in science and mathematics education. Although some students were familiar with the standard concepts of position, velocity, and acceleration from physics classes,…

  14. Electron affinity of (7)Li calculated with the inclusion of nuclear motion and relativistic corrections.

    PubMed

    Stanke, Monika; Kedziera, Dariusz; Bubin, Sergiy; Adamowicz, Ludwik

    2007-10-01

    Explicitly correlated Gaussian functions have been used to perform very accurate variational calculations for the ground states of (7)Li and (7)Li(-). The nuclear motion has been explicitly included in the calculations (i.e., they have been done without assuming the Born-Oppenheimer (BO) approximation). An approach based on the analytical energy gradient calculated with respect to the Gaussian exponential parameters was employed. This led to a noticeable improvement of the previously determined variational upper bound to the nonrelativistic energy of Li(-). The Li energy obtained in the calculations matches those of the most accurate results obtained with Hylleraas functions. The finite-mass (non-BO) wave functions were used to calculate the alpha(2) relativistic corrections (alpha=1c). With those corrections and the alpha(3) and alpha(4) corrections taken from Pachucki and Komasa [J. Chem. Phys. 125, 204304 (2006)], the electron affinity (EA) of (7)Li was determined. It agrees very well with the most recent experimental EA. PMID:17919011

  15. Molecular modeling of the affinity chromatography of monoclonal antibodies.

    PubMed

    Paloni, Matteo; Cavallotti, Carlo

    2015-01-01

    Molecular modeling is a methodology that offers the possibility of studying complex systems such as protein-ligand complexes from an atomistic point of view, making available information that can be difficultly obtained from experimental studies. Here, a protocol for the construction of molecular models of the interaction between antibodies and ligands that can be used for an affinity chromatography process is presented. The outlined methodology focuses mostly on the description of a procedure that may be adopted to determine the structure and free energy of interaction between the antibody and the affinity ligand. A procedure to extend the proposed methodology to include the effect of the environment (buffer solution, spacer, support matrix) is also briefly outlined. PMID:25749965

  16. Children’s looking preference for biological motion may be related to an affinity for mathematical chaos

    PubMed Central

    Haworth, Joshua L.; Kyvelidou, Anastasia; Fisher, Wayne; Stergiou, Nicholas

    2015-01-01

    Recognition of biological motion is pervasive in early child development. Further, viewing the movement behavior of others is a primary component of a child’s acquisition of complex, robust movement repertoires, through imitation and real-time coordinated action. We theorize that inherent to biological movements are particular qualities of mathematical chaos and complexity. We further posit that this character affords the rich and complex inter-dynamics throughout early motor development. Specifically, we explored whether children’s preference for biological motion may be related to an affinity for mathematical chaos. Cross recurrence quantification analysis (cRQA) was used to investigate the coordination of gaze and posture with various temporal structures (periodic, chaotic, and aperiodic) of the motion of an oscillating visual stimulus. Children appear to competently perceive and respond to chaotic motion, both in rate (cRQA-percent determinism) and duration (cRQA-maxline) of coordination. We interpret this to indicate that children not only recognize chaotic motion structures, but also have a preference for coordination with them. Further, stratification of our sample (by age) uncovers the suggestion that this preference may become refined with age. PMID:25852600

  17. Robust Spectral Clustering Using Statistical Sub-Graph Affinity Model

    PubMed Central

    Eichel, Justin A.; Wong, Alexander; Fieguth, Paul; Clausi, David A.

    2013-01-01

    Spectral clustering methods have been shown to be effective for image segmentation. Unfortunately, the presence of image noise as well as textural characteristics can have a significant negative effect on the segmentation performance. To accommodate for image noise and textural characteristics, this study introduces the concept of sub-graph affinity, where each node in the primary graph is modeled as a sub-graph characterizing the neighborhood surrounding the node. The statistical sub-graph affinity matrix is then constructed based on the statistical relationships between sub-graphs of connected nodes in the primary graph, thus counteracting the uncertainty associated with the image noise and textural characteristics by utilizing more information than traditional spectral clustering methods. Experiments using both synthetic and natural images under various levels of noise contamination demonstrate that the proposed approach can achieve improved segmentation performance when compared to existing spectral clustering methods. PMID:24386111

  18. Animal models in motion sickness research

    NASA Technical Reports Server (NTRS)

    Daunton, Nancy G.

    1990-01-01

    Practical information on candidate animal models for motion sickness research and on methods used to elicit and detect motion sickness in these models is provided. Four good potential models for use in motion sickness experiments include the dog, cat, squirrel monkey, and rat. It is concluded that the appropriate use of the animal models, combined with exploitation of state-of-the-art biomedical techniques, should generate a great step forward in the understanding of motion sickness mechanisms and in the development of efficient and effective approaches to its prevention and treatment in humans.

  19. A free-breathing lung motion model

    NASA Astrophysics Data System (ADS)

    Zhao, Tianyu

    Lung cancer has been the leading cause of cancer deaths for decades in the United States. Although radiotherapy is one of the most effective treatments, side effects from error in delivery of radiation due to organ motion during breathing remain a significant issue. To compensate the breathing motion during the treatment, a free breathing lung motion model, x= x0+αv+betaf, was developed and discussed, where x is the position of a piece of tissue located at reference position x0. α is a parameter which characterizes the motion due to local air filling (motion as a function of tidal volume) and beta is the parameter that accounts for the motion due to the imbalance of dynamical stress distributions during inspiration and exhalation which cause lung motion hysteresis (motion as a function of airflow). The parameters α and beta together provide a quantitative characterization of breathing motion that inherently includes the complex hysteresis interplay. The theoretical foundation of the model was built by investigating the stress distribution inside of a lung and the biomechanical properties of the lung tissues. Accuracy of the model was investigated by using 49 free-breathing patient data sets. Applications of the model in localizing lung cancer, monitoring radiation damage and suppressing artifacts in free-breathing PET images were also discussed. This work supported in part by NIHR01CA096679 and NIHR01CA116712.

  20. Local Structural Alignment of RNA with Affine Gap Model

    NASA Astrophysics Data System (ADS)

    Wong, Thomas K. F.; Cheung, Brenda W. Y.; Lam, T. W.; Yiu, S. M.

    Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

  1. Ground Motion Modeling in the Eastern Caucasus

    NASA Astrophysics Data System (ADS)

    Pitarka, Arben; Gok, Rengin; Yetirmishli, Gurban; Ismayilova, Saida; Mellors, Robert

    2016-05-01

    In this study, we analyzed the performance of a preliminary three-dimensional (3D) velocity model of the Eastern Caucasus covering most of the Azerbaijan. The model was developed in support to long-period ground motion simulations and seismic hazard assessment from regional earthquakes in Azerbaijan. The model's performance was investigated by simulating ground motion from the damaging Mw 5.9, 2012 Zaqatala earthquake, which was well recorded throughout the region by broadband seismic instruments. In our simulations, we use a parallelized finite-difference method of fourth-order accuracy. The comparison between the simulated and recorded ground motion velocity in the modeled period range of 3-20 s shows that in general, the 3D velocity model performs well. Areas in which the model needs improvements are located mainly in the central part of the Kura basin and in the Caspian Sea coastal areas. Comparisons of simulated ground motion using our 3D velocity model and corresponding 1D regional velocity model were used to locate areas with strong 3D wave propagation effects. In areas with complex underground structure, the 1D model fails to produce the observed ground motion amplitude and duration, and spatial extend of ground motion amplification caused by wave propagation effects.

  2. Ground Motion Modeling in the Eastern Caucasus

    NASA Astrophysics Data System (ADS)

    Pitarka, Arben; Gok, Rengin; Yetirmishli, Gurban; Ismayilova, Saida; Mellors, Robert

    2016-08-01

    In this study, we analyzed the performance of a preliminary three-dimensional (3D) velocity model of the Eastern Caucasus covering most of the Azerbaijan. The model was developed in support to long-period ground motion simulations and seismic hazard assessment from regional earthquakes in Azerbaijan. The model's performance was investigated by simulating ground motion from the damaging Mw 5.9, 2012 Zaqatala earthquake, which was well recorded throughout the region by broadband seismic instruments. In our simulations, we use a parallelized finite-difference method of fourth-order accuracy. The comparison between the simulated and recorded ground motion velocity in the modeled period range of 3-20 s shows that in general, the 3D velocity model performs well. Areas in which the model needs improvements are located mainly in the central part of the Kura basin and in the Caspian Sea coastal areas. Comparisons of simulated ground motion using our 3D velocity model and corresponding 1D regional velocity model were used to locate areas with strong 3D wave propagation effects. In areas with complex underground structure, the 1D model fails to produce the observed ground motion amplitude and duration, and spatial extend of ground motion amplification caused by wave propagation effects.

  3. LCD motion blur: modeling, analysis, and algorithm.

    PubMed

    Chan, Stanley H; Nguyen, Truong Q

    2011-08-01

    Liquid crystal display (LCD) devices are well known for their slow responses due to the physical limitations of liquid crystals. Therefore, fast moving objects in a scene are often perceived as blurred. This effect is known as the LCD motion blur. In order to reduce LCD motion blur, an accurate LCD model and an efficient deblurring algorithm are needed. However, existing LCD motion blur models are insufficient to reflect the limitation of human-eye-tracking system. Also, the spatiotemporal equivalence in LCD motion blur models has not been proven directly in the discrete 2-D spatial domain, although it is widely used. There are three main contributions of this paper: modeling, analysis, and algorithm. First, a comprehensive LCD motion blur model is presented, in which human-eye-tracking limits are taken into consideration. Second, a complete analysis of spatiotemporal equivalence is provided and verified using real video sequences. Third, an LCD motion blur reduction algorithm is proposed. The proposed algorithm solves an l(1)-norm regularized least-squares minimization problem using a subgradient projection method. Numerical results show that the proposed algorithm gives higher peak SNR, lower temporal error, and lower spatial error than motion-compensated inverse filtering and Lucy-Richardson deconvolution algorithm, which are two state-of-the-art LCD deblurring algorithms. PMID:21292596

  4. Tending to Change: Toward a Situated Model of Affinity Spaces

    ERIC Educational Resources Information Center

    Bommarito, Dan

    2014-01-01

    The concept of affinity spaces, a theoretical construct used to analyze literate activity from a spatial perspective, has gained popularity among scholars of literacy studies and, particularly, video-game studies. This article seeks to expand current notions of affinity spaces by identifying key assumptions that have limited researchers'…

  5. Biophysical Modeling of Respiratory Organ Motion

    NASA Astrophysics Data System (ADS)

    Werner, René

    Methods to estimate respiratory organ motion can be divided into two groups: biophysical modeling and image registration. In image registration, motion fields are directly extracted from 4D ({D}+{t}) image sequences, often without concerning knowledge about anatomy and physiology in detail. In contrast, biophysical approaches aim at identification of anatomical and physiological aspects of breathing dynamics that are to be modeled. In the context of radiation therapy, biophysical modeling of respiratory organ motion commonly refers to the framework of continuum mechanics and elasticity theory, respectively. Underlying ideas and corresponding boundary value problems of those approaches are described in this chapter, along with a brief comparison to image registration-based motion field estimation.

  6. Modeling the polar motion of Titan

    NASA Astrophysics Data System (ADS)

    Coyette, Alexis; Van Hoolst, Tim; Baland, Rose-Marie; Tokano, Tetsuya

    2016-02-01

    The angular momentum of the atmosphere and of the hydrocarbon lakes of Titan have a large equatorial component that can excite polar motion, a variable orientation of the rotation axis of Titan with respect to its surface. We here use the angular momentum obtained from a General Circulation Model of the atmosphere of Titan and from an Ocean Circulation Model for Titan's polar lakes to model the polar motion of Titan as a function of the interior structure. Besides the gravitational torque exerted by Saturn on Titan's aspherical mass distribution, the rotational model also includes torques arising due to the presence of an ocean under a thin ice shell as well as the influence of the elasticity of the different layers. The Chandler wobble period of a solid and rigid Titan without its atmosphere is about 279 years. The period of the Chandler wobble is mainly influenced by the atmosphere of Titan (-166 years) and the presence of an internal global ocean (+135 to 295 years depending on the internal model) and to a lesser extent by the elastic deformations (+3.7 years). The forced polar motion of a solid and rigid Titan is elliptical with an amplitude of about 50 m and a main period equal to the orbital period of Saturn. It is mainly forced by the atmosphere of Titan while the lakes of Titan are at the origin of a displacement of the mean polar motion, or polar offset. The subsurface ocean can largely increase the polar motion amplitude due to resonant amplification with a wobble free mode of Titan. The amplitudes as well as the main periods of the polar motion depend on whether and which forcing period is close to the period of a free mode. For a thick ice shell, the polar motion mainly has an annual period and an amplitude of about 1 km. For thinner ice shells, the polar motion amplitude can reach several tens of km and shorter periods become dominant. We demonstrate that for thick ice shells, the ice shell rigidity weakly influences the amplitude of the polar motion

  7. Modeling Ground Motions in Eastern Europe

    NASA Astrophysics Data System (ADS)

    Onur, Tuna; Nyst, Marleen

    2010-05-01

    As part of an overall risk modeling effort, we developed empirical models to estimate ground shaking in terms of spectral response due to different types of earthquakes in Eastern Europe. In this presentation, we will focus on the relatively high risk regions such as Vrancea seismic zone in Romania, and high seismic activity regions of Greece and Turkey. Each of these regions presents unique challenges in estimating ground motions. We provide a review of existing research on the estimation of ground motion for intermediate depth Vrancea earthquakes and propose a ground motion model to be used for this region based on spectral response. For Greece and Turkey, we review locally developed ground motion models as well as explore applicability of NGA models developed in the US. Final models that were derived out of this process are presented and discussed. We also provide a discussion of how the present study compares with our earlier models developed for the rest of Europe at the borders of the model regions.

  8. Phase informed model for motion and susceptibility.

    PubMed

    Hutton, Chloe; Andersson, Jesper; Deichmann, Ralf; Weiskopf, Nikolaus

    2013-11-01

    Field inhomogeneities caused by variations in magnetic susceptibility throughout the head lead to geometric distortions, mainly in the phase-encode direction of echo-planar images (EPI). The magnitude and spatial characteristics of the distortions depend on the orientation of the head in the magnetic field and will therefore vary with head movement. A new method is presented, based on a phase informed model for motion and susceptibility (PIMMS), which estimates the change in geometric distortion associated with head motion. This method fits a model of the head motion parameters and scanner hardware characteristics to EPI phase time series. The resulting maps of the model fit parameters are used to correct for susceptibility artifacts in the magnitude images. Results are shown for EPI-based fMRI time-series acquired at 3T, demonstrating that compared with conventional rigid body realignment, PIMMS removes residual variance associated with motion-related distortion effects. Furthermore, PIMMS can lead to a reduction in false negatives compared with the widely accepted approach which uses standard rigid body realignment and includes the head motion parameters in the statistical model. The PIMMS method can be used with any standard EPI sequence for which accurate phase information is available. PMID:22736546

  9. PREDICTING ER BINDING AFFINITY FOR EDC RANKING AND PRIORITIZATION: MODEL II

    EPA Science Inventory

    The training set used to derive a common reactivity pattern (COREPA) model for estrogen receptor (ER) binding affinity in Model I (see Abstract I in this series) was extended to include 47 rat estrogen receptor (rER) relative binding affinity (RBA) measurements in addition to the...

  10. European bioclimatic affinity groups: Data-model comparisons

    NASA Astrophysics Data System (ADS)

    Laurent, J.-M.; François, L.; Bar-Hen, A.; Bel, L.; Cheddadi, R.

    2008-03-01

    Global vegetation models are remarkably effective when considering large areas such as Europe. However, their accuracy at finer scales remains to be tested. In this paper, we validate the simulation of modern potential vegetation by the CARbon Assimilation In the Biosphere (CARAIB) model in Europe. Then, in order to evaluate the simulation of tree group distributions at a finer scale, in France, we present a comparison between observed distributions, distributions reconstructed from palynological data, and model simulated ranges. The results will help to validate past vegetation simulations. For this analysis, we use Bioclimatic Affinity Groups (BAGs), based on vegetation groups' climatic tolerances and requirements. The CARAIB model was adapted to simulate the net primary productivity (NPP), biomass and range of the arboreal BAGs. In Europe, at a 30' latitude/longitude grid scale, simulated NPP of BAGs are used to define classes of vegetation as being present or absent, with a classification rule, based on Kappa statistics. In France, at a 10' lat./long. scale, a second discriminant analysis, based on Classification And Regression Tree (CART), allows for a similar classification with BAG pollen percentages. At each palynological sampling site, we then compared the simulation to the reconstruction from pollen data. With 30' lat./long. resolution, most thresholds that discriminate NPP into absence or presence classes are low, ranging from 1 to 77 g/m 2. Agreement indices between observed and simulated distributions range from 0.4 to 0.83, with broad scale BAG potential patterns and boundaries being accurately simulated by CARAIB. In France, on the 10' lat./long. scale, pollen percentages correctly account for BAG presence/absence despite non-linear pollen-vegetation relationships. Agreement ratios between observed and reconstructed patterns range from 0.53 to 0.95. At the 10' lat./long. scale, the validation of simulated ranges with pollen data is reliable for 9 of

  11. Mathematical model accurately predicts protein release from an affinity-based delivery system.

    PubMed

    Vulic, Katarina; Pakulska, Malgosia M; Sonthalia, Rohit; Ramachandran, Arun; Shoichet, Molly S

    2015-01-10

    Affinity-based controlled release modulates the delivery of protein or small molecule therapeutics through transient dissociation/association. To understand which parameters can be used to tune release, we used a mathematical model based on simple binding kinetics. A comprehensive asymptotic analysis revealed three characteristic regimes for therapeutic release from affinity-based systems. These regimes can be controlled by diffusion or unbinding kinetics, and can exhibit release over either a single stage or two stages. This analysis fundamentally changes the way we think of controlling release from affinity-based systems and thereby explains some of the discrepancies in the literature on which parameters influence affinity-based release. The rate of protein release from affinity-based systems is determined by the balance of diffusion of the therapeutic agent through the hydrogel and the dissociation kinetics of the affinity pair. Equations for tuning protein release rate by altering the strength (KD) of the affinity interaction, the concentration of binding ligand in the system, the rate of dissociation (koff) of the complex, and the hydrogel size and geometry, are provided. We validated our model by collapsing the model simulations and the experimental data from a recently described affinity release system, to a single master curve. Importantly, this mathematical analysis can be applied to any single species affinity-based system to determine the parameters required for a desired release profile. PMID:25449806

  12. Locust Collective Motion and Its Modeling.

    PubMed

    Ariel, Gil; Ayali, Amir

    2015-12-01

    Over the past decade, technological advances in experimental and animal tracking techniques have motivated a renewed theoretical interest in animal collective motion and, in particular, locust swarming. This review offers a comprehensive biological background followed by comparative analysis of recent models of locust collective motion, in particular locust marching, their settings, and underlying assumptions. We describe a wide range of recent modeling and simulation approaches, from discrete agent-based models of self-propelled particles to continuous models of integro-differential equations, aimed at describing and analyzing the fascinating phenomenon of locust collective motion. These modeling efforts have a dual role: The first views locusts as a quintessential example of animal collective motion. As such, they aim at abstraction and coarse-graining, often utilizing the tools of statistical physics. The second, which originates from a more biological perspective, views locust swarming as a scientific problem of its own exceptional merit. The main goal should, thus, be the analysis and prediction of natural swarm dynamics. We discuss the properties of swarm dynamics using the tools of statistical physics, as well as the implications for laboratory experiments and natural swarms. Finally, we stress the importance of a combined-interdisciplinary, biological-theoretical effort in successfully confronting the challenges that locusts pose at both the theoretical and practical levels. PMID:26656851

  13. Locust Collective Motion and Its Modeling

    PubMed Central

    Ariel, Gil; Ayali, Amir

    2015-01-01

    Over the past decade, technological advances in experimental and animal tracking techniques have motivated a renewed theoretical interest in animal collective motion and, in particular, locust swarming. This review offers a comprehensive biological background followed by comparative analysis of recent models of locust collective motion, in particular locust marching, their settings, and underlying assumptions. We describe a wide range of recent modeling and simulation approaches, from discrete agent-based models of self-propelled particles to continuous models of integro-differential equations, aimed at describing and analyzing the fascinating phenomenon of locust collective motion. These modeling efforts have a dual role: The first views locusts as a quintessential example of animal collective motion. As such, they aim at abstraction and coarse-graining, often utilizing the tools of statistical physics. The second, which originates from a more biological perspective, views locust swarming as a scientific problem of its own exceptional merit. The main goal should, thus, be the analysis and prediction of natural swarm dynamics. We discuss the properties of swarm dynamics using the tools of statistical physics, as well as the implications for laboratory experiments and natural swarms. Finally, we stress the importance of a combined-interdisciplinary, biological-theoretical effort in successfully confronting the challenges that locusts pose at both the theoretical and practical levels. PMID:26656851

  14. Ground Motion Prediction Models for Caucasus Region

    NASA Astrophysics Data System (ADS)

    Jorjiashvili, Nato; Godoladze, Tea; Tvaradze, Nino; Tumanova, Nino

    2016-04-01

    Ground motion prediction models (GMPMs) relate ground motion intensity measures to variables describing earthquake source, path, and site effects. Estimation of expected ground motion is a fundamental earthquake hazard assessment. The most commonly used parameter for attenuation relation is peak ground acceleration or spectral acceleration because this parameter gives useful information for Seismic Hazard Assessment. Since 2003 development of Georgian Digital Seismic Network has started. In this study new GMP models are obtained based on new data from Georgian seismic network and also from neighboring countries. Estimation of models is obtained by classical, statistical way, regression analysis. In this study site ground conditions are additionally considered because the same earthquake recorded at the same distance may cause different damage according to ground conditions. Empirical ground-motion prediction models (GMPMs) require adjustment to make them appropriate for site-specific scenarios. However, the process of making such adjustments remains a challenge. This work presents a holistic framework for the development of a peak ground acceleration (PGA) or spectral acceleration (SA) GMPE that is easily adjustable to different seismological conditions and does not suffer from the practical problems associated with adjustments in the response spectral domain.

  15. Mathematical modelling of submarine landslide motion

    NASA Astrophysics Data System (ADS)

    Burminskij, A.

    2012-04-01

    Mathematical modelling of submarine landslide motion The paper presents a mathematical model to calculate dynamic parameters of a submarine landslide. The problem of estimation possible submarine landslides dynamic parameters and run-out distances as well as their effect on submarine structures becomes more and more actual because they can have significant impacts on infrastructure such as the rupture of submarine cables and pipelines, damage to offshore drilling platforms, cause a tsunami. In this paper a landslide is considered as a viscoplastic flow and is described by continuum mechanics equations, averaged over the flow depth. The model takes into account friction at the bottom and at the landslide-water boundary, as well as the involvement of bottom material in motion. A software was created and series of test calculations were performed. Calculations permitted to estimate the contribution of various model coefficients and initial conditions. Motion down inclined bottom was studied both for constant and variable slope angle. Examples of typical distributions of the flow velocity, thickness and density along the landslide body at different stages of motion are given.

  16. Ciliary motion modeling, and dynamic multicilia interactions

    PubMed Central

    Gueron, Shay; Liron, Nadav

    1992-01-01

    This paper presents a rigorous and accurate modeling tool for ciliary motion. The hydrodynamics analysis, originally suggested by Lighthill (1975), has been modified to remove computational problems. This approach is incorporated into a moment-balance model of ciliary motion in place of the previously used hydrodynamic analyses, known as Resistive Force Theory. The method is also developed to include the effect of a plane surface at the base of the cilium, and the effect of the flow fields produced by neighboring cilia. These extensions were not possible with previous work using the Resistive Force Theory hydrodynamics. Performing reliable simulations of a single cilium as well as modeling multicilia interactions is now possible. The result is a general method which could now be used for detailed modeling of the mechanisms for generating ciliary beat patterns and patterns of metachronal interactions in arrays of cilia. A computer animation technique was designed and applied to display the results. PMID:19431847

  17. Model of human visual-motion sensing

    NASA Technical Reports Server (NTRS)

    Watson, A. B.; Ahumada, A. J., Jr.

    1985-01-01

    A model of how humans sense the velocity of moving images is proposed. The model exploits constraints provided by human psychophysics, notably that motion-sensing elements appear tuned for two-dimensional spatial frequency, and by the frequency spectrum of a moving image, namely, that its support lies in the plane in which the temporal frequency equals the dot product of the spatial frequency and the image velocity. The first stage of the model is a set of spatial-frequency-tuned, direction-selective linear sensors. The temporal frequency of the response of each sensor is shown to encode the component of the image velocity in the sensor direction. At the second stage, these components are resolved in order to measure the velocity of image motion at each of a number of spatial locations and spatial frequencies. The model has been applied to several illustrative examples, including apparent motion, coherent gratings, and natural image sequences. The model agrees qualitatively with human perception.

  18. Blind watermark algorithm on 3D motion model based on wavelet transform

    NASA Astrophysics Data System (ADS)

    Qi, Hu; Zhai, Lang

    2013-12-01

    With the continuous development of 3D vision technology, digital watermark technology, as the best choice for copyright protection, has fused with it gradually. This paper proposed a blind watermark plan of 3D motion model based on wavelet transform, and made it loaded into the Vega real-time visual simulation system. Firstly, put 3D model into affine transform, and take the distance from the center of gravity to the vertex of 3D object in order to generate a one-dimensional discrete signal; then make this signal into wavelet transform to change its frequency coefficients and embed watermark, finally generate 3D motion model with watermarking. In fixed affine space, achieve the robustness in translation, revolving and proportion transforms. The results show that this approach has better performances not only in robustness, but also in watermark- invisibility.

  19. Mathematical modelling of animate and intentional motion.

    PubMed Central

    Rittscher, Jens; Blake, Andrew; Hoogs, Anthony; Stein, Gees

    2003-01-01

    Our aim is to enable a machine to observe and interpret the behaviour of others. Mathematical models are employed to describe certain biological motions. The main challenge is to design models that are both tractable and meaningful. In the first part we will describe how computer vision techniques, in particular visual tracking, can be applied to recognize a small vocabulary of human actions in a constrained scenario. Mainly the problems of viewpoint and scale invariance need to be overcome to formalize a general framework. Hence the second part of the article is devoted to the question whether a particular human action should be captured in a single complex model or whether it is more promising to make extensive use of semantic knowledge and a collection of low-level models that encode certain motion primitives. Scene context plays a crucial role if we intend to give a higher-level interpretation rather than a low-level physical description of the observed motion. A semantic knowledge base is used to establish the scene context. This approach consists of three main components: visual analysis, the mapping from vision to language and the search of the semantic database. A small number of robust visual detectors is used to generate a higher-level description of the scene. The approach together with a number of results is presented in the third part of this article. PMID:12689374

  20. Modelling motions within the organ of Corti

    NASA Astrophysics Data System (ADS)

    Ni, Guangjian; Baumgart, Johannes; Elliott, Stephen

    2015-12-01

    Most cochlear models used to describe the basilar membrane vibration along the cochlea are concerned with macromechanics, and often assume that the organ of Corti moves as a single unit, ignoring the individual motion of different components. New experimental technologies provide the opportunity to measure the dynamic behaviour of different components within the organ of Corti, but only for certain types of excitation. It is thus still difficult to directly measure every aspect of cochlear dynamics, particularly for acoustic excitation of the fully active cochlea. The present work studies the dynamic response of a model of the cross-section of the cochlea, at the microscopic level, using the finite element method. The elastic components are modelled with plate elements and the perilymph and endolymph are modelled with inviscid fluid elements. The individual motion of each component within the organ of Corti is calculated with dynamic pressure loading on the basilar membrane and the motions of the experimentally accessible parts are compared with measurements. The reticular lamina moves as a stiff plate, without much bending, and is pivoting around a point close to the region of the inner hair cells, as observed experimentally. The basilar membrane shows a slightly asymmetric mode shape, with maximum displacement occurring between the second-row and the third-row of the outer hair cells. The dynamics responses is also calculated, and compared with experiments, when driven by the outer hair cells. The receptance of the basilar membrane motion and of the deflection of the hair bundles of the outer hair cells is thus obtained, when driven either acoustically or electrically. In this way, the fully active linear response of the basilar membrane to acoustic excitation can be predicted by using a linear superposition of the calculated receptances and a defined gain function for the outer hair cell feedback.

  1. Abnormal behaviors detection using particle motion model

    NASA Astrophysics Data System (ADS)

    Chen, Yutao; Zhang, Hong; Cheng, Feiyang; Yuan, Ding; You, Yuhu

    2015-03-01

    Human abnormal behaviors detection is one of the most challenging tasks in the video surveillance for the public security control. Interaction Energy Potential model is an effective and competitive method published recently to detect abnormal behaviors, but their model of abnormal behaviors is not accurate enough, so it has some limitations. In order to solve this problem, we propose a novel Particle Motion model. Firstly, we extract the foreground to improve the accuracy of interest points detection since the complex background usually degrade the effectiveness of interest points detection largely. Secondly, we detect the interest points using the graphics features. Here, the movement of each human target can be represented by the movements of detected interest points of the target. Then, we track these interest points in videos to record their positions and velocities. In this way, the velocity angles, position angles and distance between each two points can be calculated. Finally, we proposed a Particle Motion model to calculate the eigenvalue of each frame. An adaptive threshold method is proposed to detect abnormal behaviors. Experimental results on the BEHAVE dataset and online videos show that our method could detect fight and robbery events effectively and has a promising performance.

  2. Disorder, pre-stress and non-affinity in polymer 8-chain models

    NASA Astrophysics Data System (ADS)

    Cioroianu, Adrian R.; Spiesz, Ewa M.; Storm, Cornelis

    2016-04-01

    To assess the role of single-chain elasticity, non-affine strain fields and pre-stressed reference states we present and discuss the results of numerical and analytical analyses of a modified 8-chain Arruda-Boyce model for cross-linked polymer networks. This class of models has proved highly successful in modeling the finite-strain response of flexible rubbers. We extend it to include the effects of spatial disorder and the associated non-affinity, and use it to assess the validity of replacing the constituent chain's nonlinear elastic response with equivalent linear, Hookean springs. Surprisingly, we find that even in the regime of linear response, the full polymer model gives very different results from its linearized counterpart, even though none of the chains are stretched beyond their linear regime. We demonstrate that this effect is due to the fact that the polymer models are under considerable pre-stress in their ground state. We show that pre-stress strongly suppresses non-affinity in these unit cell models, resulting in a marked stiffening of the bulk response. Polymer networks with some degree of flexibility are thus intrinsically prestressed, and one effect of such prestresses is to reduce non-affine deformations. Combined, these findings may help explain why fully affine mechanical models, in many cases, predict the bulk mechanical response of disordered polymer networks so well.

  3. Joint PET-MR respiratory motion models for clinical PET motion correction.

    PubMed

    Manber, Richard; Thielemans, Kris; Hutton, Brian F; Wan, Simon; McClelland, Jamie; Barnes, Anna; Arridge, Simon; Ourselin, Sébastien; Atkinson, David

    2016-09-01

    Patient motion due to respiration can lead to artefacts and blurring in positron emission tomography (PET) images, in addition to quantification errors. The integration of PET with magnetic resonance (MR) imaging in PET-MR scanners provides complementary clinical information, and allows the use of high spatial resolution and high contrast MR images to monitor and correct motion-corrupted PET data. In this paper we build on previous work to form a methodology for respiratory motion correction of PET data, and show it can improve PET image quality whilst having minimal impact on clinical PET-MR protocols. We introduce a joint PET-MR motion model, using only 1 min per PET bed position of simultaneously acquired PET and MR data to provide a respiratory motion correspondence model that captures inter-cycle and intra-cycle breathing variations. In the model setup, 2D multi-slice MR provides the dynamic imaging component, and PET data, via low spatial resolution framing and principal component analysis, provides the model surrogate. We evaluate different motion models (1D and 2D linear, and 1D and 2D polynomial) by computing model-fit and model-prediction errors on dynamic MR images on a data set of 45 patients. Finally we apply the motion model methodology to 5 clinical PET-MR oncology patient datasets. Qualitative PET reconstruction improvements and artefact reduction are assessed with visual analysis, and quantitative improvements are calculated using standardised uptake value (SUV(peak) and SUV(max)) changes in avid lesions. We demonstrate the capability of a joint PET-MR motion model to predict respiratory motion by showing significantly improved image quality of PET data acquired before the motion model data. The method can be used to incorporate motion into the reconstruction of any length of PET acquisition, with only 1 min of extra scan time, and with no external hardware required. PMID:27524409

  4. A mechanical model for guided motion of mammalian cells

    NASA Astrophysics Data System (ADS)

    Bitter, P.; Beck, K. L.; Lenz, P.

    2015-12-01

    We introduce a generic, purely mechanical model for environment-sensitive motion of mammalian cells that is applicable to chemotaxis, haptotaxis, and durotaxis as modes of motility. It is able to theoretically explain all relevant experimental observations, in particular, the high efficiency of motion, the behavior on inhomogeneous substrates, and the fixation of the lagging pole during motion. Furthermore, our model predicts that efficiency of motion in following a gradient depends on cell geometry (with more elongated cells being more efficient).

  5. Research on model identification of ultra-precision motion stage

    NASA Astrophysics Data System (ADS)

    Qiang, Sheng; Wang, Bin

    2015-09-01

    Analyzing the structure of precision motion platform, building mathematical model of linear motors and voice coil motors, thereby macro-micro coupling theoretical models and mechanical model are established, which can reflect the combined effect of multiple motors motion characteristics. The unknown parameters of the macro-micro coupling theoretical model are identified by adaptive real-coded genetic algorithm. Validity of the precision motion platform model has been verified by simulations.

  6. An Inexpensive Mechanical Model for Projectile Motion

    ERIC Educational Resources Information Center

    Kagan, David

    2011-01-01

    As experienced physicists, we see the beauty and simplicity of projectile motion. It is merely the superposition of uniform linear motion along the direction of the initial velocity vector and the downward motion due to the constant acceleration of gravity. We see the kinematic equations as just the mathematical machinery to perform the…

  7. Atomic Models for Motional Stark Effects Diagnostics

    SciTech Connect

    Gu, M F; Holcomb, C; Jayakuma, J; Allen, S; Pablant, N A; Burrell, K

    2007-07-26

    We present detailed atomic physics models for motional Stark effects (MSE) diagnostic on magnetic fusion devices. Excitation and ionization cross sections of the hydrogen or deuterium beam traveling in a magnetic field in collisions with electrons, ions, and neutral gas are calculated in the first Born approximation. The density matrices and polarization states of individual Stark-Zeeman components of the Balmer {alpha} line are obtained for both beam into plasma and beam into gas models. A detailed comparison of the model calculations and the MSE polarimetry and spectral intensity measurements obtained at the DIII-D tokamak is carried out. Although our beam into gas models provide a qualitative explanation for the larger {pi}/{sigma} intensity ratios and represent significant improvements over the statistical population models, empirical adjustment factors ranging from 1.0-2.0 must still be applied to individual line intensities to bring the calculations into full agreement with the observations. Nevertheless, we demonstrate that beam into gas measurements can be used successfully as calibration procedures for measuring the magnetic pitch angle through {pi}/{sigma} intensity ratios. The analyses of the filter-scan polarization spectra from the DIII-D MSE polarimetry system indicate unknown channel and time dependent light contaminations in the beam into gas measurements. Such contaminations may be the main reason for the failure of beam into gas calibration on MSE polarimetry systems.

  8. Modelling the motion of particles around choanoflagellates

    NASA Astrophysics Data System (ADS)

    Orme, Belinda; Pettitt, Michala; Otto, Steve; Blake, John

    2001-11-01

    The three-dimensional particle paths due to a helical beat pattern of the flagellum of a sessile choanoflagellate, Salpingoeca Amphoridium (SA), are modelled and compared against experimental observations. The organism's main components are a flagellum and cell body which are situated above a substrate such that the interaction between these entities is crucial in determining the fluid flow around the choanoflagellate. The flow of fluid in the organism's environment can be characterised as Stokes flow and a flow field analogous to one created by the flagellum is generated by a distribution of stokeslets and dipoles along a helical curve. The model describing the flow considers interactions between a slender flagellum, an infinite flat plane (modelling the substrate) and a sphere (modelling the cell body). The use of image systems appropriate to Green's functions for a sphere and plane boundary are described. The computations depict particle paths representing passive tracers from experiments and their motion illustrates overall flow patterns. Figures are presented comparing recorded experimental data with numerically generated results for a number of particle paths. The principal results show good agreement between the experiments and theory.

  9. Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems.

    PubMed

    Fielding, Lee; Rutherford, Samantha; Fletcher, Dan

    2005-06-01

    The usefulness of bovine serum albumin (BSA) as a model protein for testing NMR methods for the study of protein-ligand interactions is discussed. Isothermal titration calorimetry established the binding affinity and stoichiometry of the specific binding site for L-tryptophan, D-tryptophan, naproxen, ibuprofen, salicylic acid and warfarin. The binding affinities of the same ligands determined by NMR methods are universally weaker (larger KD). This is because the NMR methods are susceptible to interference from additional non-specific binding. The L-tryptophan-BSA and naproxen-BSA systems were the best behaved model systems. PMID:15816062

  10. Predicting binding affinities of diverse pharmaceutical chemicals to human serum plasma proteins using QSPR modelling approaches.

    PubMed

    Basant, N; Gupta, S; Singh, K P

    2016-01-01

    The prediction of the plasma protein binding (PPB) affinity of chemicals is of paramount significance in the drug development process. In this study, ensemble machine learning-based QSPR models have been established for a four-category classification and PPB affinity prediction of diverse compounds using a large PPB dataset of 930 compounds and in accordance with the OECD guidelines. The structural diversity of the chemicals was tested by the Tanimoto similarity index. The external predictive power of the developed QSPR models was evaluated through internal and external validations. In the QSPR models, XLogP was the most important descriptor. In the test data, the classification QSPR models rendered an accuracy of >93%, while the regression QSPR models yielded r(2) of >0.920 between the measured and predicted PPB affinities, with the root mean squared error <9.77. Values of statistical coefficients derived for the test data were above their threshold limits, thus put a high confidence in this analysis. The QSPR models in this study performed better than any of the previous studies. The results suggest that the developed QSPR models are reliable for predicting the PPB affinity of structurally diverse chemicals. They can be useful for initial screening of candidate molecules in the drug development process. PMID:26854728

  11. Head Motion Modeling for Human Behavior Analysis in Dyadic Interaction

    PubMed Central

    Xiao, Bo; Georgiou, Panayiotis; Baucom, Brian; Narayanan, Shrikanth S.

    2015-01-01

    This paper presents a computational study of head motion in human interaction, notably of its role in conveying interlocutors’ behavioral characteristics. Head motion is physically complex and carries rich information; current modeling approaches based on visual signals, however, are still limited in their ability to adequately capture these important properties. Guided by the methodology of kinesics, we propose a data driven approach to identify typical head motion patterns. The approach follows the steps of first segmenting motion events, then parametrically representing the motion by linear predictive features, and finally generalizing the motion types using Gaussian mixture models. The proposed approach is experimentally validated using video recordings of communication sessions from real couples involved in a couples therapy study. In particular we use the head motion model to classify binarized expert judgments of the interactants’ specific behavioral characteristics where entrainment in head motion is hypothesized to play a role: Acceptance, Blame, Positive, and Negative behavior. We achieve accuracies in the range of 60% to 70% for the various experimental settings and conditions. In addition, we describe a measure of motion similarity between the interaction partners based on the proposed model. We show that the relative change of head motion similarity during the interaction significantly correlates with the expert judgments of the interactants’ behavioral characteristics. These findings demonstrate the effectiveness of the proposed head motion model, and underscore the promise of analyzing human behavioral characteristics through signal processing methods. PMID:26557047

  12. Vestibular models for design and evaluation of flight simulator motion

    NASA Technical Reports Server (NTRS)

    Bussolari, S. R.; Sullivan, R. B.; Young, L. R.

    1986-01-01

    The use of spatial orientation models in the design and evaluation of control systems for motion-base flight simulators is investigated experimentally. The development of a high-fidelity motion drive controller using an optimal control approach based on human vestibular models is described. The formulation and implementation of the optimal washout system are discussed. The effectiveness of the motion washout system was evaluated by studying the response of six motion washout systems to the NASA/AMES Vertical Motion Simulator for a single dash-quick-stop maneuver. The effects of the motion washout system on pilot performance and simulator acceptability are examined. The data reveal that human spatial orientation models are useful for the design and evaluation of flight simulator motion fidelity.

  13. Modeling of pedestrian motion for recognition

    NASA Astrophysics Data System (ADS)

    Saisan, Payam; Medasani, Swarup; Srinivasa, Narayan; Owechko, Yuri

    2005-03-01

    Good pedestrian classifiers that analyze static images for presence of pedestrians are in existence. However, even a low false positive error rating is sufficient to flood a real system with false warnings. We address the problem of pedestrian motion (gait) modeling and recognition using sequences of images rather than static individual frames, thereby exploiting information in the dynamics. We use two different representations and corresponding distances for gait sequences. In the first a gait is represented as a manifold in a lower dimensional space corresponding to gait images. In the second a gait image sequence is represented as the output of a dynamical system whose underlying driving process is an action like walking or running. We examine distance functions corresponding to these representations. For dynamical systems we formulate distances derived based on parameters of the system taking into account both the structure of the output space and the dynamics within it. Given appearance based models we present results demonstrating the discriminative power of the proposed distances

  14. A diffusion model for picosecond electron bunches from negative electron affinity GaAs photo cathodes

    SciTech Connect

    P. Hartmann; J. Bermuth; D. v. Harrach; J. Hoffmann; S. Kobis; E. Reichert; K. Aulenbacher; J. Schuler; M. Steigerwald

    1998-10-27

    Even though theoretical estimates predict response times for the photo emission process of electrons from a negative electron affinity GaAs photo emitter in excess of hundreds of picoseconds, recent measurements found electron bunch durations of 40 ps or less. This work presents precise measurements of picosecond electron bunches from a negative affinity bulk GaAs photo cathode and develops a model which explains the measured bunch durations as well as the observed bunch shapes. The bunch shape turns out to be independent from the quantum efficiency of the photo emitter.

  15. A simplified motion model for estimating respiratory motion from orbiting views

    NASA Astrophysics Data System (ADS)

    Zeng, Rongping; Fessler, Jeffrey A.; Balter, James M.

    2007-03-01

    We have shown previously that the internal motion caused by a patient's breathing can be estimated from a sequence of slowly rotating 2D cone-beam X-ray projection views and a static prior of of the patient's anatomy. 1, 2 The estimator iteratively updates a parametric 3D motion model so that the modeled projection views of the deformed reference volume best match the measured projection views. Complicated motion models with many degrees of freedom may better describe the real motion, but the optimizations assiciated with them may overfit noise and may be easily trapped by local minima due to a large number of parameters. For the latter problem, we believe it can be solved by offering the optimization algorithm a good starting point within the valley containing the global minimum point. Therefore, we propose to start the motion estimation with a simplified motion model, in which we assume the displacement of each voxel at any time is proportional to the full movement of that voxel from extreme exhale to extreme inhale. We first obtain the full motion by registering two breath-hold CT volumes at end-expiration and end-inspiration. We then estimate a sequence of scalar displacement proportionality parameters. Thus the goal simplifies to finding a motion amplitude signal. This estimation problem can be solved quickly using the exhale reference volume and projection views with coarse (downsampled) resolution, while still providing acceptable estimation accuracy. The estimated simple motion then can be used to initialize a more complicated motion estimator.

  16. Modeling Local Interactions during the Motion of Cyanobacteria

    PubMed Central

    Galante, Amanda; Wisen, Susanne; Bhaya, Devaki; Levy, Doron

    2012-01-01

    Synechocystis sp., a common unicellular freshwater cyanobacterium, has been used as a model organism to study phototaxis, an ability to move in the direction of a light source. This microorganism displays a number of additional characteristics such as delayed motion, surface dependence, and a quasi-random motion, where cells move in a seemingly disordered fashion instead of in the direction of the light source, a global force on the system. These unexplained motions are thought to be modulated by local interactions between cells such as intercellular communication. In this paper, we consider only local interactions of these phototactic cells in order to mathematically model this quasi-random motion. We analyze an experimental data set to illustrate the presence of quasi-random motion and then derive a stochastic dynamic particle system modeling interacting phototactic cells. The simulations of our model are consistent with experimentally observed phototactic motion. PMID:22713858

  17. A dynamic styrofoam-ball model for simulating molecular motion

    NASA Astrophysics Data System (ADS)

    Mak, Se-yuen; Cheung, Derek

    2001-01-01

    In this paper we introduce a simple styrofoam-ball model that can be used for simulating molecular motion in all three states. As the foam balls are driven by a vibrator that is in turn driven by a signal generator, the frequency and the amplitude of vibration can be adjusted independently. Thus, the model is appropriate for simulating molecular motion in the liquid state, which is a combination of vibration and meandering motion.

  18. An Inexpensive Mechanical Model for Projectile Motion

    NASA Astrophysics Data System (ADS)

    Kagan, David

    2011-05-01

    As experienced physicists, we see the beauty and simplicity of projectile motion. It is merely the superposition of uniform linear motion along the direction of the initial velocity vector and the downward motion due to the constant acceleration of gravity. We see the kinematic equations as just the mathematical machinery to perform the calculations. What do our students see? Likely, most see no deeper than the operational understanding needed to use the kinematic equations. Described below is a device (shown in Fig. 1) that illustrates the physicist's view of projectile motion. It can be used as a classroom demonstration or as a project for your students, and it costs less than three dollars to make.

  19. Inter-fraction variations in respiratory motion models

    NASA Astrophysics Data System (ADS)

    McClelland, J. R.; Hughes, S.; Modat, M.; Qureshi, A.; Ahmad, S.; Landau, D. B.; Ourselin, S.; Hawkes, D. J.

    2011-01-01

    Respiratory motion can vary dramatically between the planning stage and the different fractions of radiotherapy treatment. Motion predictions used when constructing the radiotherapy plan may be unsuitable for later fractions of treatment. This paper presents a methodology for constructing patient-specific respiratory motion models and uses these models to evaluate and analyse the inter-fraction variations in the respiratory motion. The internal respiratory motion is determined from the deformable registration of Cine CT data and related to a respiratory surrogate signal derived from 3D skin surface data. Three different models for relating the internal motion to the surrogate signal have been investigated in this work. Data were acquired from six lung cancer patients. Two full datasets were acquired for each patient, one before the course of radiotherapy treatment and one at the end (approximately 6 weeks later). Separate models were built for each dataset. All models could accurately predict the respiratory motion in the same dataset, but had large errors when predicting the motion in the other dataset. Analysis of the inter-fraction variations revealed that most variations were spatially varying base-line shifts, but changes to the anatomy and the motion trajectories were also observed.

  20. Smooth bounce in the affine quantization of a Bianchi I model

    NASA Astrophysics Data System (ADS)

    Bergeron, Hervé; Dapor, Andrea; Gazeau, Jean Pierre; Małkiewicz, Przemysław

    2015-06-01

    We present the affine coherent state quantization of the Bianchi I model. As in our previous paper on quantum theory of Friedmann models, we employ a variable associated with a perfect fluid to play a role of clock. Then we deparametrize the model. A distinctive feature, absent in isotropic models, is an extra nonholonomic constraint, which survives the deparametrization and constrains the range of physical variables. The appearance of the constraint reflects the "amplification" of singularity due to anisotropy. The quantization smoothes the extra constraint and allows quantum contracting trajectories to be smoothly transformed into expanding ones. Making use of an affine coherent state we develop a semiclassical description. Figures are included to illustrate our result.

  1. A depictive neural model for the representation of motion verbs.

    PubMed

    Rao, Sunil; Aleksander, Igor

    2011-11-01

    In this paper, we present a depictive neural model for the representation of motion verb semantics in neural models of visual awareness. The problem of modelling motion verb representation is shown to be one of function application, mapping a set of given input variables defining the moving object and the path of motion to a defined output outcome in the motion recognition context. The particular function-applicative implementation and consequent recognition model design presented are seen as arising from a noun-adjective recognition model enabling the recognition of colour adjectives as applied to a set of shapes representing objects to be recognised. The presence of such a function application scheme and a separately implemented position identification and path labelling scheme are accordingly shown to be the primitives required to enable the design and construction of a composite depictive motion verb recognition scheme. Extensions to the presented design to enable the representation of transitive verbs are also discussed. PMID:21468746

  2. Building Mathematical Models of Simple Harmonic and Damped Motion.

    ERIC Educational Resources Information Center

    Edwards, Thomas

    1995-01-01

    By developing a sequence of mathematical models of harmonic motion, shows that mathematical models are not right or wrong, but instead are better or poorer representations of the problem situation. (MKR)

  3. Modeling correlated motion in filled skutterudites

    NASA Astrophysics Data System (ADS)

    Keiber, Trevor; Bridges, Frank

    2015-10-01

    Recent extended x-ray absorption fine structure (EXAFS) studies suggest that in skutterudites, the nearly square rings (such as As4 in CeFe4As12 ) are quite rigid and may vibrate with low-energy modes in one direction, similar to "rattler" atom vibrations. That work suggests that the motions of the square rings and the rattler atoms are coupled. In addition, for Ln Cu 3Ru4O12 , the second-neighbor pairs about L n have stiffer effective springs than the nearest-neighbor pairs. To investigate these systems, a one-dimensional, four-mass, linear chain spring model is developed to describe the recent experimental results and provide insight about the low-energy vibrations in such systems. Our model solves the resulting coupled network of overlapping weak and strong springs and determines the eigenfrequencies and eigenvectors. The dispersion curves show an acoustic mode, two different low-energy optical rattling modes involving both the rattler and square, and a noninteracting optical mode. Each rattler mode can couple to the acoustic mode, which generates avoided crossings characterized by flattening of the modes; this has important consequences for thermal transport. From these results we calculate atomic correlation functions and the Debye-Waller-like function used in EXAFS σ2 as a function of temperature. These calculations show that for the rattler-neighbor pairs, σ2 is a sum over several modes; it is not the result of a single mode. The inverse slope of σ2(T ) at high T provides a measure of the effective spring constants, and the results show that for small direct spring constants the effective spring constant can be significantly larger than the direct spring constants. The locations of the avoided crossings (between rattler modes and the acoustic mode) in q space can be tuned by the choice of both the rattler and the square atoms. Consequently, it may be possible to further reduce the thermal conductivity using a mixture of nanoparticles, each with avoided

  4. Self-affine and ARX-models zonation of well logging data

    NASA Astrophysics Data System (ADS)

    Shiri, Yousef; Tokhmechi, Behzad; Zarei, Zeinab; Koneshloo, Mohammad

    2012-11-01

    Zonation of time series into models which their parameters are piecewise constant are important and well-studied problems. Geophysical well logging data often show a complex pattern due to their multifractal nature. In a multifractal system, any pieces of it are established by a distinct exponent that can characterize them. This feature has the capability to cluster them. Self-affine zonation by Auto Regressive model with exogenous inputs (ARX) is a new approach which places well logging segments in the clusters which are more self-affine against the other clusters. This approach was performed and compared with a conventional ARX zonation in the well logging data of three different oilfields in southern parts of Iran. The results showed a good accuracy for detecting homogeneous lithological segments and led to a precise interpretation process to update the reservoir architecture.

  5. A simple model for strong ground motions and response spectra

    USGS Publications Warehouse

    Safak, Erdal; Mueller, Charles; Boatwright, John

    1988-01-01

    A simple model for the description of strong ground motions is introduced. The model shows that response spectra can be estimated by using only four parameters of the ground motion, the RMS acceleration, effective duration and two corner frequencies that characterize the effective frequency band of the motion. The model is windowed band-limited white noise, and is developed by studying the properties of two functions, cumulative squared acceleration in the time domain, and cumulative squared amplitude spectrum in the frequency domain. Applying the methods of random vibration theory, the model leads to a simple analytical expression for the response spectra. The accuracy of the model is checked by using the ground motion recordings from the aftershock sequences of two different earthquakes and simulated accelerograms. The results show that the model gives a satisfactory estimate of the response spectra.

  6. Joint model of motion and anatomy for PET image reconstruction

    SciTech Connect

    Qiao Feng; Pan Tinsu; Clark, John W. Jr.; Mawlawi, Osama

    2007-12-15

    Anatomy-based positron emission tomography (PET) image enhancement techniques have been shown to have the potential for improving PET image quality. However, these techniques assume an accurate alignment between the anatomical and the functional images, which is not always valid when imaging the chest due to respiratory motion. In this article, we present a joint model of both motion and anatomical information by integrating a motion-incorporated PET imaging system model with an anatomy-based maximum a posteriori image reconstruction algorithm. The mismatched anatomical information due to motion can thus be effectively utilized through this joint model. A computer simulation and a phantom study were conducted to assess the efficacy of the joint model, whereby motion and anatomical information were either modeled separately or combined. The reconstructed images in each case were compared to corresponding reference images obtained using a quadratic image prior based maximum a posteriori reconstruction algorithm for quantitative accuracy. Results of these studies indicated that while modeling anatomical information or motion alone improved the PET image quantitation accuracy, a larger improvement in accuracy was achieved when using the joint model. In the computer simulation study and using similar image noise levels, the improvement in quantitation accuracy compared to the reference images was 5.3% and 19.8% when using anatomical or motion information alone, respectively, and 35.5% when using the joint model. In the phantom study, these results were 5.6%, 5.8%, and 19.8%, respectively. These results suggest that motion compensation is important in order to effectively utilize anatomical information in chest imaging using PET. The joint motion-anatomy model presented in this paper provides a promising solution to this problem.

  7. Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

    PubMed

    Asti, Lorenzo; Uguzzoni, Guido; Marcatili, Paolo; Pagnani, Andrea

    2016-04-01

    The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire. One of these mechanisms, the affinity maturation process, works in an evolutionary-like fashion: after binding to a foreign molecule, the antibody-producing B-cells exhibit a high-frequency mutation rate in the genome region that codes for the antibody active site. Eventually, cells that produce antibodies with higher affinity for their cognate antigen are selected and clonally expanded. Here, we propose a new statistical approach based on maximum entropy modeling in which a scoring function related to the binding affinity of antibodies against a specific antigen is inferred from a sample of sequences of the immune repertoire of an individual. We use our inference strategy to infer a statistical model on a data set obtained by sequencing a fairly large portion of the immune repertoire of an HIV-1 infected patient. The Pearson correlation coefficient between our scoring function and the IC50 neutralization titer measured on 30 different antibodies of known sequence is as high as 0.77 (p-value 10-6), outperforming other sequence- and structure-based models. PMID:27074145

  8. Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity

    PubMed Central

    Marcatili, Paolo; Pagnani, Andrea

    2016-01-01

    The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire. One of these mechanisms, the affinity maturation process, works in an evolutionary-like fashion: after binding to a foreign molecule, the antibody-producing B-cells exhibit a high-frequency mutation rate in the genome region that codes for the antibody active site. Eventually, cells that produce antibodies with higher affinity for their cognate antigen are selected and clonally expanded. Here, we propose a new statistical approach based on maximum entropy modeling in which a scoring function related to the binding affinity of antibodies against a specific antigen is inferred from a sample of sequences of the immune repertoire of an individual. We use our inference strategy to infer a statistical model on a data set obtained by sequencing a fairly large portion of the immune repertoire of an HIV-1 infected patient. The Pearson correlation coefficient between our scoring function and the IC50 neutralization titer measured on 30 different antibodies of known sequence is as high as 0.77 (p-value 10−6), outperforming other sequence- and structure-based models. PMID:27074145

  9. Ground motion data for International Collider models

    SciTech Connect

    Volk, J.T.; LeBrun, P.; Shiltsev, V.; Singatulin, S.; /Fermilab

    2007-11-01

    The proposed location for the International Linear Collider (ILC) in the Americas region is Fermilab in Batavia Illinois. If built at this location the tunnels would be located in the Galena Platteville shale at a depth of 100 or more meters below the surface. Studies using hydro static water levels and seismometers have been conducted in the MINOS hall and the LaFrange Mine in North Aurora Illinois to determine the level of ground motion. Both these locations are in the Galena Platteville shale and indicate the typical ground motion to be expected for the ILC. The data contains both natural and cultural noise. Coefficients for the ALT law are determined. Seismic measurements at the surface and 100 meters below the surface are presented.

  10. Unsteady aerodynamic modeling for arbitrary motions

    NASA Technical Reports Server (NTRS)

    Edwards, J. W.; Ashley, H.; Breakwell, J. V.

    1977-01-01

    A study is presented on the unsteady aerodynamic loads due to arbitrary motions of a thin wing and their adaptation for the calculation of response and true stability of aeroelastic modes. In an Appendix, the use of Laplace transform techniques and the generalized Theodorsen function for two-dimensional incompressible flow is reviewed. New applications of the same approach are shown also to yield airloads valid for quite general small motions. Numerical results are given for the two-dimensional supersonic case. Previously proposed approximate methods, starting from simple harmonic unsteady theory, are evaluated by comparison with exact results obtained by the present approach. The Laplace inversion integral is employed to separate the loads into 'rational' and 'nonrational' parts, of which only the former are involved in aeroelastic stability of the wing. Among other suggestions for further work, it is explained how existing aerodynamic computer programs may be adapted in a fairly straightforward fashion to deal with arbitrary transients.

  11. On a PCA-based lung motion model

    NASA Astrophysics Data System (ADS)

    Li, Ruijiang; Lewis, John H.; Jia, Xun; Zhao, Tianyu; Liu, Weifeng; Wuenschel, Sara; Lamb, James; Yang, Deshan; Low, Daniel A.; Jiang, Steve B.

    2011-09-01

    Respiration-induced organ motion is one of the major uncertainties in lung cancer radiotherapy and is crucial to be able to accurately model the lung motion. Most work so far has focused on the study of the motion of a single point (usually the tumor center of mass), and much less work has been done to model the motion of the entire lung. Inspired by the work of Zhang et al (2007 Med. Phys. 34 4772-81), we believe that the spatiotemporal relationship of the entire lung motion can be accurately modeled based on principle component analysis (PCA) and then a sparse subset of the entire lung, such as an implanted marker, can be used to drive the motion of the entire lung (including the tumor). The goal of this work is twofold. First, we aim to understand the underlying reason why PCA is effective for modeling lung motion and find the optimal number of PCA coefficients for accurate lung motion modeling. We attempt to address the above important problems both in a theoretical framework and in the context of real clinical data. Second, we propose a new method to derive the entire lung motion using a single internal marker based on the PCA model. The main results of this work are as follows. We derived an important property which reveals the implicit regularization imposed by the PCA model. We then studied the model using two mathematical respiratory phantoms and 11 clinical 4DCT scans for eight lung cancer patients. For the mathematical phantoms with cosine and an even power (2n) of cosine motion, we proved that 2 and 2n PCA coefficients and eigenvectors will completely represent the lung motion, respectively. Moreover, for the cosine phantom, we derived the equivalence conditions for the PCA motion model and the physiological 5D lung motion model (Low et al 2005 Int. J. Radiat. Oncol. Biol. Phys. 63 921-9). For the clinical 4DCT data, we demonstrated the modeling power and generalization performance of the PCA model. The average 3D modeling error using PCA was within 1

  12. A true polar wander model for Neoproterozoic plate motions

    SciTech Connect

    Ripperdan, R.L. )

    1992-01-01

    Recent paleogeographic reconstructions for the interval 750--500 Ma (Neoproterozoic to Late Cambrian) require rapid rates of plate motion and/or rotation around an equatorial Euler pole to accommodate reconstructions for the Early Paleozoic. Motions of this magnitude appear to be very uncommon during the Phanerozoic. A model for plate motions based on the hypothesis that discrete intervals of rapid true polar wander (RTPW) occurred during the Neoproterozoic can account for the paleogeographic changes with minimum amounts of plate motion. The model uses the paleogeographic reconstructions of Hoffman (1991). The following constraints were applied during derivation of the model: (1) relative motions between major continental units were restricted to be combinations of great circle or small circle translations with Euler poles of rotation = spin axis; (2) maximum rates of relative translational plate motion were 0.2 m/yr. Based on these constraints, two separate sets of synthetic plate motion trajectories were determined. The sequence of events in both can be summarized as: (1) A rapid true polar wander event of ca 90[degree] rafting a supercontinent to the spin axis; (2) breakup of the polar supercontinent into two fragments, one with the Congo, West Africa, Amazonia, and Baltica cratons, the other with the Laurentia, East Gondwana, and Kalahari cratons; (3) great circle motion of the blocks towards the equator; (4) small circle motion leading to amalgamation of Gondwana and separation of Laurentia and Baltica. In alternative 1, rifting initiates between East Antarctica and Laurentia and one episode of RTPW is required. Alternative 2 requires two episodes of RTPW; and that rifting occurred first along the eastern margin and later along the western margin of Laurentia. Synthetic plate motion trajectories are compared to existing paleomagnetic and geological data, and implications of the model for paleoclimatic changes during the Neoproterozoic are discussed.

  13. A deformation of quantum affine algebra in squashed Wess-Zumino-Novikov-Witten models

    SciTech Connect

    Kawaguchi, Io; Yoshida, Kentaroh

    2014-06-01

    We proceed to study infinite-dimensional symmetries in two-dimensional squashed Wess-Zumino-Novikov-Witten models at the classical level. The target space is given by squashed S³ and the isometry is SU(2){sub L}×U(1){sub R}. It is known that SU(2){sub L} is enhanced to a couple of Yangians. We reveal here that an infinite-dimensional extension of U(1){sub R} is a deformation of quantum affine algebra, where a new deformation parameter is provided with the coefficient of the Wess-Zumino term. Then we consider the relation between the deformed quantum affine algebra and the pair of Yangians from the viewpoint of the left-right duality of monodromy matrices. The integrable structure is also discussed by computing the r/s-matrices that satisfy the extended classical Yang-Baxter equation. Finally, two degenerate limits are discussed.

  14. Probabilistic approach for predicting periodic orbits in piecewise affine differential models.

    PubMed

    Chaves, Madalena; Farcot, Etienne; Gouzé, Jean-Luc

    2013-06-01

    Piecewise affine models provide a qualitative description of the dynamics of a system, and are often used to study genetic regulatory networks. The state space of a piecewise affine system is partitioned into hyperrectangles, which can be represented as nodes in a directed graph, so that the system's trajectories follow a path in a transition graph. This paper proposes and compares two definitions of probability of transition between two nodes A and B of the graph, based on the volume of the initial conditions on the hyperrectangle A whose trajectories cross to B. The parameters of the system can thus be compared to the observed transitions between two hyperrectangles. This property may become useful to identify sets of parameters for which the system yields a desired periodic orbit with a high probability, or to predict the most likely periodic orbit given a set of parameters, as illustrated by a gene regulatory system composed of two intertwined negative loops. PMID:23054666

  15. Modelling the binding affinity of steroids to zebrafish sex hormone-binding globulin.

    PubMed

    Saxena, A K; Devillers, J; Pery, A R R; Beaudouin, R; Balaramnavar, V M; Ahmed, S

    2014-01-01

    The circulating endogenous steroids are transported in the bloodstream. These are bound to a highly specific sex hormone-binding globulin (SHBG) and in lower affinity to proteins such as the corticosteroid-binding protein and albumin in vertebrates, including fish. It is generally believed that the glycoprotein SHBG protects these steroids from rapid metabolic degradation and thus intervenes in its availability at the target tissues. Endocrine disrupters binding to SHBG affect the normal activity of natural steroids. Since xenobiotics are primarily released in the aquatic environment, there is a need to evaluate the binding affinity of xenosteroid mimics on fish SHBG, especially in zebrafish (Danio rerio), a small freshwater fish originating in India and widely employed in ecotoxicology, toxicology, and genetics. In this context, a zebrafish SHBG (zfSHBG) homology model was developed using the human SHBG (hSHBG) receptor structure as template. It was shown that interactions with amino acids Ser-36, Asp-59 and Thr-54 were important for binding affinity. A ligand-based pharmacophore model was also developed for both zfSHBG and hSHBG inhibitors that differentiated binders from non-binders, but also demonstrated structural requirements for zfSHBG and hSHBG ligands. The study provides insights into the mechanism of action of endocrine disruptors in zebrafish as well as providing a useful tool for identifying anthropogenic compounds inhibiting zfSHBG. PMID:24874994

  16. A kinematic model for Bayesian tracking of cyclic human motion

    NASA Astrophysics Data System (ADS)

    Greif, Thomas; Lienhart, Rainer

    2010-01-01

    We introduce a two-dimensional kinematic model for cyclic motions of humans, which is suitable for the use as temporal prior in any Bayesian tracking framework. This human motion model is solely based on simple kinematic properties: the joint accelerations. Distributions of joint accelerations subject to the cycle progress are learned from training data. We present results obtained by applying the introduced model to the cyclic motion of backstroke swimming in a Kalman filter framework that represents the posterior distribution by a Gaussian. We experimentally evaluate the sensitivity of the motion model with respect to the frequency and noise level of assumed appearance-based pose measurements by simulating various fidelities of the pose measurements using ground truth data.

  17. Constants of motion of the four-particle Calogero model

    SciTech Connect

    Saghatelian, A.

    2012-10-15

    We present the explicit expressions of the complete set of constants of motion of four-particle Calogero model with excluded center of mass, i.e. of the A{sub 3} rational Calogero model. Then we find the constants of motion of its spherical part, defining two-dimensional 12-center spherical oscillator, with the force centers located at the vertexes of cuboctahedron.

  18. Effects of yaw and pitch motion on model attitude measurements

    NASA Technical Reports Server (NTRS)

    Tcheng, Ping; Tripp, John S.; Finley, Tom D.

    1995-01-01

    This report presents a theoretical analysis of the dynamic effects of angular motion in yaw and pitch on model attitude measurements in which inertial sensors were used during wind tunnel tests. A technique is developed to reduce the error caused by these effects. The analysis shows that a 20-to-1 reduction in model attitude measurement error caused by angular motion is possible with this technique.

  19. Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers.

    PubMed

    Martin, Jennifer A; Chushak, Yaroslav; Chávez, Jorge L; Hagen, Joshua A; Kelley-Loughnane, Nancy

    2016-01-01

    Immobilization of nucleic acid aptamer recognition elements selected free in solution onto the surface of biosensor platforms has proven challenging. This study investigated the binding of multiple aptamer/target pairs immobilized on a commercially available microarray as a model system mimicking biosensor applications. The results indicate a minimum distance (linker length) from the surface and thymine nucleobase linker provides reproducible binding across varying conditions. An indirect labeling method, where the target was labeled with a biotin followed by a brief Cy3-streptavidin incubation, provided a higher signal-to-noise ratio and over two orders of magnitude improvement in limit of detection, compared to direct Cy3-protein labeling. We also showed that the affinities of the aptamer/target interaction can change between direct and indirect labeling and conditions to optimize for the highest fluorescence intensity will increase the sensitivity of the assay but will not change the overall affinity. Additionally, some sequences which did not initially bind demonstrated binding when conditions were optimized. These results, in combination with studies demonstrating enhanced binding in nonselection buffers, provided insights into the structure and affinity of aptamers critical for biosensor applications and allowed for generalizations in starting conditions for researchers wishing to investigate aptamers on a microarray surface. PMID:27042344

  20. Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers

    PubMed Central

    Martin, Jennifer A.; Chushak, Yaroslav; Chávez, Jorge L.; Hagen, Joshua A.; Kelley-Loughnane, Nancy

    2016-01-01

    Immobilization of nucleic acid aptamer recognition elements selected free in solution onto the surface of biosensor platforms has proven challenging. This study investigated the binding of multiple aptamer/target pairs immobilized on a commercially available microarray as a model system mimicking biosensor applications. The results indicate a minimum distance (linker length) from the surface and thymine nucleobase linker provides reproducible binding across varying conditions. An indirect labeling method, where the target was labeled with a biotin followed by a brief Cy3-streptavidin incubation, provided a higher signal-to-noise ratio and over two orders of magnitude improvement in limit of detection, compared to direct Cy3-protein labeling. We also showed that the affinities of the aptamer/target interaction can change between direct and indirect labeling and conditions to optimize for the highest fluorescence intensity will increase the sensitivity of the assay but will not change the overall affinity. Additionally, some sequences which did not initially bind demonstrated binding when conditions were optimized. These results, in combination with studies demonstrating enhanced binding in nonselection buffers, provided insights into the structure and affinity of aptamers critical for biosensor applications and allowed for generalizations in starting conditions for researchers wishing to investigate aptamers on a microarray surface. PMID:27042344

  1. On the computation of stress in affine versus nonaffine fibril kinematics within planar collagen network models.

    PubMed

    Pence, Thomas J; Monroe, Ryan J; Wright, Neil T

    2008-08-01

    Some recent analyses modeled the response of collagenous tissues, such as epicardium, using a hypothetical network consisting of interconnected springlike fibers. The fibers in the network were organized such that internal nodes served as the connection point between three such collagen springs. The results for assumed affine and nonaffine deformations are contrasted after a homogeneous deformation at the boundary. Affine deformation provides a stiffer mechanical response than nonaffine deformation. In contrast to nonaffine deformation, affine deformation determines the displacement of internal nodes without imposing detailed force balance, thereby complicating the simplest intuitive notion of stress, one based on free body cuts, at the single node scale. The standard notion of stress may then be recovered via average field theory computations based on large micromesh realizations. An alternative and by all indications complementary viewpoint for the determination of stress in these collagen fiber networks is discussed here, one in which stress is defined using elastic energy storage, a notion which is intuitive at the single node scale. It replaces the average field theory computations by an averaging technique over randomly oriented isolated simple elements. The analytical operations do not require large micromesh realizations, but the tedious nature of the mathematical manipulation is clearly aided by symbolic algebra calculation. For the example case of linear elastic deformation, this results in material stiffnesses that relate the infinitesimal strain and stress. The result that the affine case is stiffer than the nonaffine case is recovered, as would be expected. The energy framework also lends itself to the natural inclusion of changes in mechanical response due to the chemical, electrical, or thermal environment. PMID:18601451

  2. Neurons compute internal models of the physical laws of motion.

    PubMed

    Angelaki, Dora E; Shaikh, Aasef G; Green, Andrea M; Dickman, J David

    2004-07-29

    A critical step in self-motion perception and spatial awareness is the integration of motion cues from multiple sensory organs that individually do not provide an accurate representation of the physical world. One of the best-studied sensory ambiguities is found in visual processing, and arises because of the inherent uncertainty in detecting the motion direction of an untextured contour moving within a small aperture. A similar sensory ambiguity arises in identifying the actual motion associated with linear accelerations sensed by the otolith organs in the inner ear. These internal linear accelerometers respond identically during translational motion (for example, running forward) and gravitational accelerations experienced as we reorient the head relative to gravity (that is, head tilt). Using new stimulus combinations, we identify here cerebellar and brainstem motion-sensitive neurons that compute a solution to the inertial motion detection problem. We show that the firing rates of these populations of neurons reflect the computations necessary to construct an internal model representation of the physical equations of motion. PMID:15282606

  3. Motion.

    ERIC Educational Resources Information Center

    Gerhart, James B.; Nussbaum, Rudi H.

    This monograph was written for the Conference on the New Instructional Materials in Physics held at the University of Washington in summer, 1965. It is intended for use in an introductory course in college physics. It consists of an extensive qualitative discussion of motion followed by a detailed development of the quantitative methods needed to…

  4. Motion.

    ERIC Educational Resources Information Center

    Brand, Judith, Ed.

    2002-01-01

    This issue of Exploratorium Magazine focuses on the topic of motion. Contents include: (1) "First Word" (Zach Tobias); (2) "Cosmic Collisions" (Robert Irion); (3) "The Mobile Cell" (Karen E. Kalumuck); (4) "The Paths of Paths" (Steven Vogel); (5) "Fragments" (Pearl Tesler); (6) "Moving Pictures" (Amy Snyder); (7) "Plants on the Go" (Katharine…

  5. Satellite attitude motion models for capture and retrieval investigations

    NASA Technical Reports Server (NTRS)

    Cochran, John E., Jr.; Lahr, Brian S.

    1986-01-01

    The primary purpose of this research is to provide mathematical models which may be used in the investigation of various aspects of the remote capture and retrieval of uncontrolled satellites. Emphasis has been placed on analytical models; however, to verify analytical solutions, numerical integration must be used. Also, for satellites of certain types, numerical integration may be the only practical or perhaps the only possible method of solution. First, to provide a basis for analytical and numerical work, uncontrolled satellites were categorized using criteria based on: (1) orbital motions, (2) external angular momenta, (3) internal angular momenta, (4) physical characteristics, and (5) the stability of their equilibrium states. Several analytical solutions for the attitude motions of satellite models were compiled, checked, corrected in some minor respects and their short-term prediction capabilities were investigated. Single-rigid-body, dual-spin and multi-rotor configurations are treated. To verify the analytical models and to see how the true motion of a satellite which is acted upon by environmental torques differs from its corresponding torque-free motion, a numerical simulation code was developed. This code contains a relatively general satellite model and models for gravity-gradient and aerodynamic torques. The spacecraft physical model for the code and the equations of motion are given. The two environmental torque models are described.

  6. Model for human use of motion cues in vehicular control

    NASA Technical Reports Server (NTRS)

    Hess, Ronald A.

    1990-01-01

    A feedback model for human use of motion cues in tracking and regulation tasks is offered. The motion cue model is developed as a simple extension of a structural model of the human pilot, although other equivalent dynamic representations of the pilot could be used in place of the structural model. In the structural model,it is hypothesized that proprioceptive cues and an internal representation of the vehicle dynamics allow the human to create compensation characteristics that are appropriate for the dynamics of the particular vehicle being controlled. It is shown that an additional loop closure involving motion feedback can improve the pilot/vehicle dynamics by decreasing high-frequency phase lags in the effective open-loop system transfer function. Data from a roll-attitude tracking/regulation task conducted on a moving base simulator are used to verify the modeling approach.

  7. Spherical shell model description of rotational motion

    SciTech Connect

    Zuker, A.P.; Retamosa, J.; Poves, A.; Caurier, E.

    1995-10-01

    Exact diagonalizations with a realistic interaction show that configurations with four neutrons in a major shell and four protons in another---or the same---major shell, behave systematically as backbending rotors. The dominance of the {ital q}{center_dot}{ital q} component of the interaction is related to an approximate ``quasi-SU3`` symmetry. It is suggested that the onset of rotational motion in the rare earth nuclei is due to the promotion of the eight particle blocks to the major shells above the ones currently filling. Assuming a ``pseudo-SU3`` coupling for the particles in the lower orbits, it is possible to account remarkably well for the observed {ital B}({ital E}2) rates at the beginning of the region.

  8. The Long Decay Model of One-Dimensional Projectile Motion

    ERIC Educational Resources Information Center

    Lattery, Mark Joseph

    2008-01-01

    This article introduces a research study on student model formation and development in introductory mechanics. As a point of entry, I present a detailed analysis of the Long Decay Model of one-dimensional projectile motion. This model has been articulated by Galileo ("in De Motu") and by contemporary students. Implications for instruction are…

  9. Pendulum models of ponytail motion during walking and running

    NASA Astrophysics Data System (ADS)

    Plaut, Raymond H.; Virgin, Lawrence N.

    2013-08-01

    Steady-state motions of a woman's ponytail during level, straight, walking and running are examined. Based on reported data, formulas have been developed for the relationship of the forward speed to the frequencies of vertical and sideways motion of the head, and of the form of that motion. The ponytail is modeled as a compound pendulum or a multi-bar pendulum with 2, 3, or 5 rigid bars. Motions in the vertical plane perpendicular to the direction of progression are analyzed. Rotational springs and dashpots are placed at the joints, and aerodynamic damping (air drag) is included. Attention is focused on the variation of the amplitudes of the bars as the woman's walking speed and then running speed increase. An example of three-dimensional motions of a spherical-pendulum model also is included. Experiments were conducted on a double pendulum with parabolic applied motion at the top. The damping is modeled by rotational friction (i.e., a constant resisting moment at the top and internal joints), and the numerical results agree well with the test data.

  10. A model describing vestibular detection of body sway motion.

    NASA Technical Reports Server (NTRS)

    Nashner, L. M.

    1971-01-01

    An experimental technique was developed which facilitated the formulation of a quantitative model describing vestibular detection of body sway motion in a postural response mode. All cues, except vestibular ones, which gave a subject an indication that he was beginning to sway, were eliminated using a specially designed two-degree-of-freedom platform; body sway was then induced and resulting compensatory responses at the ankle joints measured. Hybrid simulation compared the experimental results with models of the semicircular canals and utricular otolith receptors. Dynamic characteristics of the resulting canal model compared closely with characteristics of models which describe eye movement and subjective responses to body rotational motions. The average threshold level, in the postural response mode, however, was considerably lower. Analysis indicated that the otoliths probably play no role in the initial detection of body sway motion.

  11. Nonlinear force propagation, anisotropic stiffening and non-affine relaxation in a model cytoskeleton

    NASA Astrophysics Data System (ADS)

    Mizuno, Daisuke; Head, David; Ikebe, Emi; Nakamasu, Akiko; Kinoshita, Suguru; Peijuan, Zhang; Ando, Shoji

    2013-03-01

    Forces are generated heterogeneously in living cells and transmitted through cytoskeletal networks that respond highly non-linearly. Here, we carry out high-bandwidth passive microrheology on vimentin networks reconstituted in vitro, and observe the nonlinear mechanical response due to forces propagating from a local source applied by an optical tweezer. Since the applied force is constant, the gel becomes equilibrated and the fluctuation-dissipation theorem can be employed to deduce the viscoelasticity of the local environment from the thermal fluctuations of colloidal probes. Our experiments unequivocally demonstrate the anisotropic stiffening of the cytoskeletal network behind the applied force, with greater stiffening in the parallel direction. Quantitative agreement with an affine continuum model is obtained, but only for the response at certain frequency ~ 10-1000 Hz which separates the high-frequency power law and low-frequency elastic behavior of the network. We argue that the failure of the model at lower frequencies is due to the presence of non-affinity, and observe that zero-frequency changes in particle separation can be fitted when an independently-measured, empirical nonaffinity factor is applied.

  12. The Moon Also Rises: Investigating Celestial Motion Models.

    ERIC Educational Resources Information Center

    Barton, Andrea M.

    2001-01-01

    Introduces a high school science curriculum that embodies inquiry-based genetics, evolution, and astronomy. Presents two astronomy units of scientific modeling. The first activity involves a black box to explain a hidden mechanism's effect on the outflow of water. The second activity involves the development of celestial motion models to explain…

  13. Prediction of Plate Motions and Stresses from Global Dynamic Models

    NASA Astrophysics Data System (ADS)

    Ghosh, A.; Holt, W. E.

    2011-12-01

    Predicting plate motions correctly has been a challenge for global dynamic models. In addition to predicting plate motions, a successful model must also explain the following features: plate rigidity, plate boundary zone deformation, as well as intraplate stress patterns and deformation. In this study we show that, given constraints from shallow lithosphere structure, history of subduction, and first order features from whole mantle tomography, it is possible to achieve a high level of accuracy in predicting plate motions and lithosphere deformation within plate boundary zones. Best-fit dynamic models presently provide an RMS velocity misfit of global surface motions (compared at 63,000 spaced points in the GSRM NNR model [Kreemer et al., 2006]) of order 1 cm/yr. We explore the relative contribution of shallow lithosphere structure vs. whole mantle convection in affecting surface deformation as well as plate motions. We show that shallow lithosphere structure that includes topography and lateral density variations in the lithosphere is an integral part of global force balance. Its inclusion in geodynamic models is essential in order to match observations of surface motions and stresses, particularly within continental zones of deformation. We also argue that stiff slabs may not be as important as has been previously claimed in controlling plate motion and lithosphere deformation. An important result of this study is the calibration of absolute stress magnitudes in the lithosphere, verified through benchmarking using whole mantle convection models. Given additional constraints of the matching of surface motions, we also calibrate the absolute effective lithosphere viscosities. Best-fit models require plates with effective viscosities of order 1023 Pa-s, with plate boundary zones possessing effective viscosities 1-3 orders of magnitude weaker. Given deviatoric stress magnitudes within the lithosphere of order 10 - 60 MPa, our global models predict less than 2 mm

  14. Elements of an improved model of debris‐flow motion

    USGS Publications Warehouse

    Iverson, Richard M.

    2009-01-01

    A new depth‐averaged model of debris‐flow motion describes simultaneous evolution of flow velocity and depth, solid and fluid volume fractions, and pore‐fluid pressure. Non‐hydrostatic pore‐fluid pressure is produced by dilatancy, a state‐dependent property that links the depth‐averaged shear rate and volumetric strain rate of the granular phase. Pore‐pressure changes caused by shearing allow the model to exhibit rate‐dependent flow resistance, despite the fact that the basal shear traction involves only rate‐independent Coulomb friction. An analytical solution of simplified model equations shows that the onset of downslope motion can be accelerated or retarded by pore‐pressure change, contingent on whether dilatancy is positive or negative. A different analytical solution shows that such effects will likely be muted if downslope motion continues long enough, because dilatancy then evolves toward zero, and volume fractions and pore pressure concurrently evolve toward steady states.

  15. Turbulent motion of mass flows. Mathematical modeling

    NASA Astrophysics Data System (ADS)

    Eglit, Margarita; Yakubenko, Alexander; Yakubenko, Tatiana

    2016-04-01

    New mathematical models for unsteady turbulent mass flows, e.g., dense snow avalanches and landslides, are presented. Such models are important since most of large scale flows are turbulent. In addition to turbulence, the two other important points are taken into account: the entrainment of the underlying material by the flow and the nonlinear rheology of moving material. The majority of existing models are based on the depth-averaged equations and the turbulent character of the flow is accounted by inclusion of drag proportional to the velocity squared. In this paper full (not depth-averaged) equations are used. It is assumed that basal entrainment takes place if the bed friction equals the shear strength of the underlying layer (Issler D, M. Pastor Peréz. 2011). The turbulent characteristics of the flow are calculated using a three-parameter differential model (Lushchik et al., 1978). The rheological properties of moving material are modeled by one of the three types of equations: 1) Newtonian fluid with high viscosity, 2) power-law fluid and 3) Bingham fluid. Unsteady turbulent flows down long homogeneous slope are considered. The flow dynamical parameters and entrainment rate behavior in time as well as their dependence on properties of moving and underlying materials are studied numerically. REFERENCES M.E. Eglit and A.E. Yakubenko, 2014. Numerical modeling of slope flows entraining bottom material. Cold Reg. Sci. Technol., 108, 139-148 Margarita E. Eglit and Alexander E. Yakubenko, 2016. The effect of bed material entrainment and non-Newtonian rheology on dynamics of turbulent slope flows. Fluid Dynamics, 51(3) Issler D, M. Pastor Peréz. 2011. Interplay of entrainment and rheology in snow avalanches; a numerical study. Annals of Glaciology, 52(58), 143-147 Lushchik, V.G., Paveliev, A.A. , and Yakubenko, A.E., 1978. Three-parameter model of shear turbulence. Fluid Dynamics, 13, (3), 350-362

  16. Current plate motions. [continental groupings and global modelling

    NASA Technical Reports Server (NTRS)

    Demets, C.; Gordon, R. G.; Argus, D. F.; Stein, S.

    1990-01-01

    A global plate motion model, named NUVEL-1, which describes current plate motions between 12 rigid plates is described, with special attention given to the method, data, and assumptions used. Tectonic implications of the patterns that emerged from the results are discussed. It is shown that wide plate boundary zones can form not only within the continental lithosphere but also within the oceanic lithosphere; e.g., between the Indian and Australian plates and between the North American and South American plates. Results of the model also suggest small but significant diffuse deformation of the oceanic lithosphere, which may be confined to small awkwardly shaped salients of major plates.

  17. Lagrangian speckle model and tissue-motion estimation--theory.

    PubMed

    Maurice, R L; Bertrand, M

    1999-07-01

    It is known that when a tissue is subjected to movements such as rotation, shearing, scaling, etc., changes in speckle patterns that result act as a noise source, often responsible for most of the displacement-estimate variance. From a modeling point of view, these changes can be thought of as resulting from two mechanisms: one is the motion of the speckles and the other, the alterations of their morphology. In this paper, we propose a new tissue-motion estimator to counteract these speckle decorrelation effects. The estimator is based on a Lagrangian description of the speckle motion. This description allows us to follow local characteristics of the speckle field as if they were a material property. This method leads to an analytical description of the decorrelation in a way which enables the derivation of an appropriate inverse filter for speckle restoration. The filter is appropriate for linear geometrical transformation of the scattering function (LT), i.e., a constant-strain region of interest (ROI). As the LT itself is a parameter of the filter, a tissue-motion estimator can be formulated as a nonlinear minimization problem, seeking the best match between the pre-tissue-motion image and a restored-speckle post-motion image. The method is tested, using simulated radio-frequency (RF) images of tissue undergoing axial shear. PMID:10504093

  18. Segmentation in structure from motion: modeling and psychophysics.

    PubMed

    Caudek, C; Rubin, N

    2001-09-01

    Much work has been done on the question of how the visual system extracts the three-dimensional (3D) structure and motion of an object from two-dimensional (2D) motion information, a problem known as 'Structure from Motion', or SFM. Much less is known, however, about the human ability to recover structure and motion when the optic flow field arises from multiple objects, although observations of this ability date as early as Ullman's well-known two-cylinders stimulus [The interpretation of visual motion (1979)]. In the presence of multiple objects, the SFM problem is further aggravated by the need to solve the segmentation problem, i.e. deciding which motion signal belongs to which object. Here, we present a model for how the human visual system solves the combined SFM and segmentation problems, which we term SSFM, concurrently. The model is based on computation of a simple scalar property of the optic flow field known as def, which was previously shown to be used by human observers in SFM. The def values of many triplets of moving dots are computed, and the identification of multiple objects the image is based on detecting multiple peaks in the histogram of def values. In five experiments, we show that human SSFM performance is consistent with the predictions of the model. We compare the predictions of our model to those of other theoretical approaches, in particular those that use a rigidity hypothesis, and discuss the validity of each approach as a model for human SSFM. PMID:11587722

  19. Copper binding to soil fulvic and humic acids: NICA-Donnan modeling and conditional affinity spectra.

    PubMed

    Xu, Jinling; Tan, Wenfeng; Xiong, Juan; Wang, Mingxia; Fang, Linchuan; Koopal, Luuk K

    2016-07-01

    Binding of Cu(II) to soil fulvic acid (JGFA), soil humic acids (JGHA, JLHA), and lignite-based humic acid (PAHA) was investigated through NICA-Donnan modeling and conditional affinity spectrum (CAS). It is to extend the knowledge of copper binding by soil humic substances (HS) both in respect of enlarging the database of metal ion binding to HS and obtaining a good insight into Cu binding to the functional groups of FA and HA by using the NICA-Donnan model to unravel the intrinsic and conditional affinity spectra. Results showed that Cu binding to HS increased with increasing pH and decreasing ionic strength. The amount of Cu bound to the HAs was larger than the amount bound to JGFA. Milne's generic parameters did not provide satisfactory predictions for the present soil HS samples, while material-specific NICA-Donnan model parameters described and predicted Cu binding to the HS well. Both the 'low' and 'high' concentration fitting procedures indicated a substantial bidentate structure of the Cu complexes with HS. By means of CAS underlying NICA isotherm, which was scarcely used, the nature of the binding at different solution conditions for a given sample and the differences in binding mode were illustrated. It was indicated that carboxylic group played an indispensable role in Cu binding to HS in that the carboxylic CAS had stronger conditional affinity than the phenolic distribution due to its large degree of proton dissociation. The fact was especially true for JGFA and JLHA which contain much larger amount of carboxylic groups, and the occupation of phenolic sites by Cu was negligible. Comparable amounts of carboxylic and phenolic groups on PAHA and JGHA, increased the occupation of phenolic type sites by Cu. The binding strength of PAHA-Cu and JGHA-Cu was stronger than that of JGFA-Cu and JLHA-Cu. The presence of phenolic groups increased the chance of forming more stable complexes, such as the salicylate-Cu or catechol-Cu type structures. PMID:27061366

  20. Domain-wall motion in random potential and hysteresis modeling

    SciTech Connect

    Pasquale, M.; Basso, V.; Bertotti, G.; Jiles, D.C.; Bi, Y.

    1998-06-01

    Two different approaches to hysteresis modeling are compared using a common ground based on energy relations, defined in terms of dissipated and stored energy. Using the Preisach model and assuming that magnetization is mainly due to domain-wall motion, one can derive the expression of magnetization along a major loop typical of the Jiles{endash}Atherton model and then extend its validity to cases where mean-field effects and reversible contributions are present. {copyright} {ital 1998 American Institute of Physics.}

  1. Domain-wall motion in random potential and hysteresis modeling

    NASA Astrophysics Data System (ADS)

    Pasquale, M.; Basso, V.; Bertotti, G.; Jiles, D. C.; Bi, Y.

    1998-06-01

    Two different approaches to hysteresis modeling are compared using a common ground based on energy relations, defined in terms of dissipated and stored energy. Using the Preisach model and assuming that magnetization is mainly due to domain-wall motion, one can derive the expression of magnetization along a major loop typical of the Jiles-Atherton model and then extend its validity to cases where mean-field effects and reversible contributions are present.

  2. A high and low noise model for strong motion accelerometers

    NASA Astrophysics Data System (ADS)

    Clinton, J. F.; Cauzzi, C.; Olivieri, M.

    2010-12-01

    We present reference noise models for high-quality strong motion accelerometer installations. We use continuous accelerometer data acquired by the Swiss Seismological Service (SED) since 2006 and other international high-quality accelerometer network data to derive very broadband (50Hz-100s) high and low noise models. The proposed noise models are compared to the Peterson (1993) low and high noise models designed for broadband seismometers; the datalogger self-noise; background noise levels at existing Swiss strong motion stations; and typical earthquake signals recorded in Switzerland and worldwide. The standard strong motion station operated by the SED consists of a Kinemetrics Episensor (2g clip level; flat acceleration response from 200 Hz to DC; <155dB dynamic range) coupled with a 24-bit Nanometrics Taurus datalogger. The proposed noise models are based on power spectral density (PSD) noise levels for each strong motion station computed via PQLX (McNamara and Buland, 2004) from several years of continuous recording. The 'Accelerometer Low Noise Model', ALNM, is dominated by instrument noise from the sensor and datalogger. The 'Accelerometer High Noise Model', AHNM, reflects 1) at high frequencies the acceptable site noise in urban areas, 2) at mid-periods the peak microseismal energy, as determined by the Peterson High Noise Model and 3) at long periods the maximum noise observed from well insulated sensor / datalogger systems placed in vault quality sites. At all frequencies, there is at least one order of magnitude between the ALNM and the AHNM; at high frequencies (> 1Hz) this extends to 2 orders of magnitude. This study provides remarkable confirmation of the capability of modern strong motion accelerometers to record low-amplitude ground motions with seismic observation quality. In particular, an accelerometric station operating at the ALNM is capable of recording the full spectrum of near source earthquakes, out to 100 km, down to M2. Of particular

  3. Brownian motion model with stochastic parameters for asset prices

    NASA Astrophysics Data System (ADS)

    Ching, Soo Huei; Hin, Pooi Ah

    2013-09-01

    The Brownian motion model may not be a completely realistic model for asset prices because in real asset prices the drift μ and volatility σ may change over time. Presently we consider a model in which the parameter x = (μ,σ) is such that its value x (t + Δt) at a short time Δt ahead of the present time t depends on the value of the asset price at time t + Δt as well as the present parameter value x(t) and m-1 other parameter values before time t via a conditional distribution. The Malaysian stock prices are used to compare the performance of the Brownian motion model with fixed parameter with that of the model with stochastic parameter.

  4. The proton-neutron symplectic model of nuclear collective motions

    NASA Astrophysics Data System (ADS)

    Ganev, H. G.

    2016-06-01

    The proton-neutron symplectic model of nuclear collective motion is presented. It is shown that it appears as a natural multi-major-shell extension of the generalized proton- neutron SU(3) scheme which includes rotations with intrinsic vortex as well as monopole, quadrupole and dipole giant resonance vibrational degrees of freedom.

  5. Surrogate-driven deformable motion model for organ motion tracking in particle radiation therapy

    NASA Astrophysics Data System (ADS)

    Fassi, Aurora; Seregni, Matteo; Riboldi, Marco; Cerveri, Pietro; Sarrut, David; Battista Ivaldi, Giovanni; Tabarelli de Fatis, Paola; Liotta, Marco; Baroni, Guido

    2015-02-01

    The aim of this study is the development and experimental testing of a tumor tracking method for particle radiation therapy, providing the daily respiratory dynamics of the patient’s thoraco-abdominal anatomy as a function of an external surface surrogate combined with an a priori motion model. The proposed tracking approach is based on a patient-specific breathing motion model, estimated from the four-dimensional (4D) planning computed tomography (CT) through deformable image registration. The model is adapted to the interfraction baseline variations in the patient’s anatomical configuration. The driving amplitude and phase parameters are obtained intrafractionally from a respiratory surrogate signal derived from the external surface displacement. The developed technique was assessed on a dataset of seven lung cancer patients, who underwent two repeated 4D CT scans. The first 4D CT was used to build the respiratory motion model, which was tested on the second scan. The geometric accuracy in localizing lung lesions, mediated over all breathing phases, ranged between 0.6 and 1.7 mm across all patients. Errors in tracking the surrounding organs at risk, such as lungs, trachea and esophagus, were lower than 1.3 mm on average. The median absolute variation in water equivalent path length (WEL) within the target volume did not exceed 1.9 mm-WEL for simulated particle beams. A significant improvement was achieved compared with error compensation based on standard rigid alignment. The present work can be regarded as a feasibility study for the potential extension of tumor tracking techniques in particle treatments. Differently from current tracking methods applied in conventional radiotherapy, the proposed approach allows for the dynamic localization of all anatomical structures scanned in the planning CT, thus providing complete information on density and WEL variations required for particle beam range adaptation.

  6. Affinity comparison of different THCA synthase to CBGA using modeling computational approaches

    PubMed Central

    Alaoui, Moulay Abdelaziz El; Ibrahimi, Azeddine; Semlali, Oussama; Tarhda, Zineb; Marouane, Melloul; Najwa, Alaoui; Soulaymani, Abdelmajid; Fahime, Elmostafa El

    2014-01-01

    The Δ9-Tetrahydrocannabinol (THCA) is the primary psychoactive compound of Cannabis Sativa. It is produced by Δ1- Tetrahydrocannabinolic acid synthase (THCA) which catalyzes the oxidative cyclization of cannabigerolic acid (CBGA) the precursor of the THCA. In this study, we were interested by the three dimensional structure of THCA synthase protein. Generation of models were done by MODELLER v9.11 and homology modeling with Δ1-tetrahydrocannabinolic acid (THCA) synthase X ray structure (PDB code 3VTE) on the basis of sequences retrieved from GenBank. Procheck, Errat, and Verify 3D tools were used to verify the reliability of the six 3D models obtained, the overall quality factor and the Prosa Z-score were also used to check the quality of the six modeled proteins. The RMSDs for C-alpha atoms, main-chain atoms, side-chain atoms and all atoms between the modeled structures and the corresponding template ranged between 0.290 Å-1.252 Å, reflecting the good quality of the obtained models. Our study of the CBGA-THCA synthase docking demonstrated that the active site pocket was successfully recognized using computational approach. The interaction energy of CBGA computed in ‘fiber types’ proteins ranged between -4.1 95 kcal/mol and -5.95 kcal/mol whereas in the ‘drug type’ was about -7.02 kcal/mol to -7.16 kcal/mol, which maybe indicate the important role played by the interaction energy of CBGA in the determination of the THCA level in Cannabis Sativa L. varieties. Finally, we have proposed an experimental design in order to explore the binding energy source of ligand-enzyme in Cannabis Sativa and the production level of the THCA in the absence of any information regarding the correlation between the enzyme affinity and THCA level production. This report opens the doors to more studies predicting the binding site pocket with accuracy from the perspective of the protein affinity and THCA level produced in Cannabis Sativa. PMID:24516324

  7. Affinity Chromatography.

    ERIC Educational Resources Information Center

    Gray, Gary R.

    1980-01-01

    Presents selected recent advances in immobilization chemistry which have important connections to affinity chromatography. Discusses ligand immobilization and support modification. Cites 51 references. (CS)

  8. A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series

    PubMed Central

    Rapp, Chaya S.; Kalyanaraman, Chakrapani; Schiffmiller, Aviva; Schoenbrun, Esther Leah; Jacobson, Matthew P.

    2011-01-01

    We introduce the “Prime-ligand” method for ranking ligands in congeneric series. The method employs a single scoring function, the OPLS-AA/GBSA molecular mechanics/implicit solvent model, for all stages of sampling and scoring. We evaluate the method using 12 test sets of congeneric series for which experimental binding data is available in the literature, as well as the structure of one member of the series bound to the protein. Ligands are ‘docked’ by superimposing a common stem fragment among the compounds in the series using a crystal complex from the Protein Databank, and sampling the conformational space of the variable region. Our results show good correlation between our predicted rankings and experimental data for cases in which binding affinities differ by at least one order of magnitude. For 11 out of 12 cases, >90% of such ligand pairs could be correctly ranked, while for the remaining case, Factor Xa, 76% of such pairs were correctly ranked. A small number of compounds could not be docked using the current protocol due to the large size of functional groups that could not be accommodated by a rigid receptor. CPU requirements for the method, involving CPU-minutes per ligand, are modest compared with more rigorous methods that use similar force fields, such as free energy perturbation. We also benchmark the scoring function using series of ligand bound to the same protein within the CSAR data set. We demonstrate that energy minimization of ligand in the crystal structures is critical to obtain any correlation with experimentally determined binding affinities. PMID:21780805

  9. Developments in Ground-Motion Modeling in Eastern North America

    NASA Astrophysics Data System (ADS)

    Atkinson, G. M.; Boore, D. M.

    2012-12-01

    Recent well-recorded earthquakes in Eastern North America (ENA) have led us to re-evaluate concepts that have been "standard fare" in the development of ground-motion prediction equations (GMPEs) for ENA for decades, including all published GMPEs that are used in current practice (e.g. Atkinson and Boore, 2011, 2006, 1995; Pezeshk et al., 2011; Campbell, 2003; Toro et al., 1997, etc.). Assumptions common to all ENA GMPEs that may not be true include the following. (1) Typical ENA stress drops, in the context of a Brune model representation of the source spectrum, are in the range of 150-300 bars, with the exception of occasional high-stress events like the 1988 Saguenay earthquake. (2) Attenuation of ground motions can be modeled with a frequency-independent geometric spreading function, either bilinear or trilinear in shape (e.g. Street and Turcotte, 1975; Herrmann and Kijko, 1983; Atkinson and Mereu, 1992; Atkinson, 2004; Boatwright and Seekins, 2011), and an associated frequency-dependent anelastic attenuation term related to the regional Quality factor. The use of a bilinear or trilinear form models the transition from geometric spreading of body waves at close distances to slower surface-wave-type spreading at regional distances. We use ground-motion recordings from recent ENA events to re-examine these basic tenets of GMPE development, in light of constraints on the problem provided at low frequencies by seismic moment, and at high frequencies by stresses inferred from Empirical Greens Function (EGF) analysis. We find strong evidence, in both ground-motion data and from the constraints, that geometric attenuation may be frequency dependent. Moreover, EGF stress drops may be very high (>500 bars) - but they do not lead to particularly large high-frequency ground motions, at least at distances for which we have observations. More complex models of ENA source and attenuation processes appear to be required in order to reconcile our growing ground-motion database

  10. Stabilization control of a hovering model insect: lateral motion

    NASA Astrophysics Data System (ADS)

    Zhang, Yan-Lai; Sun, Mao

    2011-10-01

    Our previous study shows that the lateral disturbance motion of a model drone fly does not have inherent stability (passive stability), because of the existence of an unstable divergence mode. But drone flies are observed to fly stably. Constantly active control must be applied to stabilize the flight. In this study, we investigate the lateral stabilization control of the model drone fly. The method of computational fluid dynamics is used to compute the lateral control derivatives and the techniques of eigenvalue and eigenvector analysis and modal decomposition are used for solving the equations of motion. Controllability analysis shows that although inherently unstable, the lateral disturbance motion is controllable. By feeding back the state variables (i.e. lateral translation velocity, yaw rate, roll rate and roll angle, which can be measured by the sensory system of the insect) to produce anti-symmetrical changes in stroke amplitude and/or in angle of attack between the left and right wings, the motion can be stabilized, explaining why the drone flies can fly stably even if the flight is passively unstable.

  11. Modeling sensory conflict and motion sickness in artificial gravity

    NASA Astrophysics Data System (ADS)

    Elias, Paul Z.; Jarchow, Thomas; Young, Laurence R.

    2008-01-01

    It is necessary to characterize the vestibular response associated with head movements for various centrifuge rotation rates if one is to explore short-radius centrifugation as a viable form of artificial gravity for future spaceflights. An existing motion sickness model was modified to design an adaptation protocol to facilitate head movements at a centrifuge speed of 30 rpm. Modification involved addition of a quantitative sensory conflict model to serve as the input to the motion sickness model. Sensory conflict in this context was based on the dynamics of head movements during centrifugation as well as a previously developed transfer function relating angular accelerations to semicircular canal firing rates. Additionally, an adaptation parameter based on comparison between model predictions and previous experimental results was added. A 3-day incremental adaptation protocol was conducted in which 16 subjects successfully made 30 yaw head movements during rotation at 30 rpm on day 3. Motion sickness results showed good agreement with model predictions and demonstrated the feasibility of adaptation to increasingly high rotation rates.

  12. Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model

    PubMed Central

    Zhang, Yu-Chen; Zhang, Shao-Wu; Liu, Lian; Liu, Hui; Zhang, Lin; Cui, Xiaodong; Huang, Yufei; Meng, Jia

    2015-01-01

    With the development of new sequencing technology, the entire N6-methyl-adenosine (m6A) RNA methylome can now be unbiased profiled with methylated RNA immune-precipitation sequencing technique (MeRIP-Seq), making it possible to detect differential methylation states of RNA between two conditions, for example, between normal and cancerous tissue. However, as an affinity-based method, MeRIP-Seq has yet provided base-pair resolution; that is, a single methylation site determined from MeRIP-Seq data can in practice contain multiple RNA methylation residuals, some of which can be regulated by different enzymes and thus differentially methylated between two conditions. Since existing peak-based methods could not effectively differentiate multiple methylation residuals located within a single methylation site, we propose a hidden Markov model (HMM) based approach to address this issue. Specifically, the detected RNA methylation site is further divided into multiple adjacent small bins and then scanned with higher resolution using a hidden Markov model to model the dependency between spatially adjacent bins for improved accuracy. We tested the proposed algorithm on both simulated data and real data. Result suggests that the proposed algorithm clearly outperforms existing peak-based approach on simulated systems and detects differential methylation regions with higher statistical significance on real dataset. PMID:26301253

  13. 2d Affine XY-Spin Model/4d Gauge Theory Duality and Deconfinement

    SciTech Connect

    Anber, Mohamed M.; Poppitz, Erich; Unsal, Mithat; /SLAC /Stanford U., Phys. Dept. /San Francisco State U.

    2012-08-16

    We introduce a duality between two-dimensional XY-spin models with symmetry-breaking perturbations and certain four-dimensional SU(2) and SU(2) = Z{sub 2} gauge theories, compactified on a small spatial circle R{sup 1,2} x S{sup 1}, and considered at temperatures near the deconfinement transition. In a Euclidean set up, the theory is defined on R{sup 2} x T{sup 2}. Similarly, thermal gauge theories of higher rank are dual to new families of 'affine' XY-spin models with perturbations. For rank two, these are related to models used to describe the melting of a 2d crystal with a triangular lattice. The connection is made through a multi-component electric-magnetic Coulomb gas representation for both systems. Perturbations in the spin system map to topological defects in the gauge theory, such as monopole-instantons or magnetic bions, and the vortices in the spin system map to the electrically charged W-bosons in field theory (or vice versa, depending on the duality frame). The duality permits one to use the two-dimensional technology of spin systems to study the thermal deconfinement and discrete chiral transitions in four-dimensional SU(N{sub c}) gauge theories with n{sub f} {ge} 1 adjoint Weyl fermions.

  14. Development of novel cellular model for affinity studies of histamine H(4) receptor ligands.

    PubMed

    Karcz, Tadeusz; Kieć-Kononowicz, Katarzyna

    2013-01-01

    The G protein-coupled histamine H4 receptor (H4R) is the last member of histamine receptors family discovered so far. Its expression pattern, together with postulated involvement in a wide variety of immunological and inflammatory processes make histamine H4 receptor an interesting target for drug development. Potential H4R ligands may provide an innovative therapies for different immuno-based diseases, including allergy, asthma, pruritus associated with allergy or autoimmune skin conditions, rheumatoid arthritis and pain. However, none of successfully developed selective and potent histamine H4 receptor ligands have been introduced to the market up to date. For that reason there is still a strong demand for pharmacological models to be used in studies on potent H4R ligands. In current work we present the development of novel mammalian cell line, stably expressing human histamine H4 receptor, with use of retroviral transduction approach. Obtained cell line was pharmacologically characterized in radioligand binding studies and its utility for affinity testing of potent receptor ligands was confirmed in comparative studies with the use of relevant insect cells expression model. Obtained results allow for statement that developed cellular model may be successfully employed in search for new compounds active at histamine H4 receptor. PMID:24432340

  15. A discrete impulsive model for random heating and Brownian motion

    NASA Astrophysics Data System (ADS)

    Ramshaw, John D.

    2010-01-01

    The energy of a mechanical system subjected to a random force with zero mean increases irreversibly and diverges with time in the absence of friction or dissipation. This random heating effect is usually encountered in phenomenological theories formulated in terms of stochastic differential equations, the epitome of which is the Langevin equation of Brownian motion. We discuss a simple discrete impulsive model that captures the essence of random heating and Brownian motion. The model may be regarded as a discrete analog of the Langevin equation, although it is developed ab initio. Its analysis requires only simple algebraic manipulations and elementary averaging concepts, but no stochastic differential equations (or even calculus). The irreversibility in the model is shown to be a consequence of a natural causal stochastic condition that is closely analogous to Boltzmann's molecular chaos hypothesis in the kinetic theory of gases. The model provides a simple introduction to several ostensibly more advanced topics, including random heating, molecular chaos, irreversibility, Brownian motion, the Langevin equation, and fluctuation-dissipation theorems.

  16. Quantum Brownian motion model for the stock market

    NASA Astrophysics Data System (ADS)

    Meng, Xiangyi; Zhang, Jian-Wei; Guo, Hong

    2016-06-01

    It is believed by the majority today that the efficient market hypothesis is imperfect because of market irrationality. Using the physical concepts and mathematical structures of quantum mechanics, we construct an econophysical framework for the stock market, based on which we analogously map massive numbers of single stocks into a reservoir consisting of many quantum harmonic oscillators and their stock index into a typical quantum open system-a quantum Brownian particle. In particular, the irrationality of stock transactions is quantitatively considered as the Planck constant within Heisenberg's uncertainty relationship of quantum mechanics in an analogous manner. We analyze real stock data of Shanghai Stock Exchange of China and investigate fat-tail phenomena and non-Markovian behaviors of the stock index with the assistance of the quantum Brownian motion model, thereby interpreting and studying the limitations of the classical Brownian motion model for the efficient market hypothesis from a new perspective of quantum open system dynamics.

  17. Meshless Modeling of Deformable Shapes and their Motion

    PubMed Central

    Adams, Bart; Ovsjanikov, Maks; Wand, Michael; Seidel, Hans-Peter; Guibas, Leonidas J.

    2010-01-01

    We present a new framework for interactive shape deformation modeling and key frame interpolation based on a meshless finite element formulation. Starting from a coarse nodal sampling of an object’s volume, we formulate rigidity and volume preservation constraints that are enforced to yield realistic shape deformations at interactive frame rates. Additionally, by specifying key frame poses of the deforming shape and optimizing the nodal displacements while targeting smooth interpolated motion, our algorithm extends to a motion planning framework for deformable objects. This allows reconstructing smooth and plausible deformable shape trajectories in the presence of possibly moving obstacles. The presented results illustrate that our framework can handle complex shapes at interactive rates and hence is a valuable tool for animators to realistically and efficiently model and interpolate deforming 3D shapes. PMID:24839614

  18. On modeling animal movements using Brownian motion with measurement error.

    PubMed

    Pozdnyakov, Vladimir; Meyer, Thomas; Wang, Yu-Bo; Yan, Jun

    2014-02-01

    Modeling animal movements with Brownian motion (or more generally by a Gaussian process) has a long tradition in ecological studies. The recent Brownian bridge movement model (BBMM), which incorporates measurement errors, has been quickly adopted by ecologists because of its simplicity and tractability. We discuss some nontrivial properties of the discrete-time stochastic process that results from observing a Brownian motion with added normal noise at discrete times. In particular, we demonstrate that the observed sequence of random variables is not Markov. Consequently the expected occupation time between two successively observed locations does not depend on just those two observations; the whole path must be taken into account. Nonetheless, the exact likelihood function of the observed time series remains tractable; it requires only sparse matrix computations. The likelihood-based estimation procedure is described in detail and compared to the BBMM estimation. PMID:24669719

  19. Tumor affinity of radiolabeled peanut agglutinin compared with that of Ga-67 citrate in animal models

    SciTech Connect

    Yokoyama, K.; Aburano, T.; Watanabe, N.; Kawabata, S.; Ishida, H.; Mukai, K.; Tonami, N.; Hisada, K.

    1985-05-01

    Peanut agglutinin (PNA) binds avidly to the immunodominant group of the tumor associated T antigen. The purpose of this study was to evaluate oncodiagnostic potential of radiolabeled PNA in animal models. PNA was labeled with I-125 or I-131 by Iodogen and also with In-111 by cyclic DTPA anhydride. The biological activity of PNA was examined by a hemaglutination titer with a photometer before and after labeling. Animal tumor models used were Lewis Lung Cancer(LLC), B-16 Melanotic Melanoma(MM), Yoshida Sarcoma(YS), Ehrlich Ascites Tumor(EAT and Hepatoma AH109A(HAH). Inflammatory tissue induced by turpentine oil was used as an abscess model. Serial scintigraphic images were obtained following IV injections of 100 ..mu..Ci of I-131 or In-111-DTPA-PNA. The tumor affinity of Ga-67 citrate was studied to compare that of radiolabeled PNA. Tissue biodistribution was studied in EAT bearing mice. All of these tumor models except HAH were clearly visible by radiolabeled PNA without subtraction techniques. In the models of LLC and EAT, PNA showed the better accumulation into the tumor tissue than Ga-67 citrate. In YS and MM, PNA represented almost the same accumulation as Ga-67 citrate. The localization of PNA into abscess tissue wasn't found although Ga-67 citrate markedly accumulated into abscess tissue as well as tumor tissue. The clearance of PNA from tumor was slower than those from any other organs. Tumor to muscle ratio was 5.1 at 48hrs. and tumor to blood ratio increased with time to 2.3 at 96hrs. These results suggested that radiolabeled PNA may have a potential in the detection of tumor.

  20. Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule

    NASA Astrophysics Data System (ADS)

    R. Saeidi, H.; S. Setayandeh, S.; Lohrasebi, A.

    2015-08-01

    Kinesin is a microtubule-associated motor protein which can respond to the external electric field due to its polarity. Using a molecular dynamics simulation method, the effect of such a field on the affinity of kinesin to the αβ-tubulin is investigated in this study. To consider kinesin affinity, the system is exposed to an electric field of 0.03 V/nm with frequency values of 1, 2, …, 9, and 10 GHz. It is found that the applied electric field can change kinesin affinity to the microtubule. These changes could perturb the normal operation of kinesin, such as the processive motility of kinesin on the microtubule.

  1. Constraints on the affinity term for modeling long-term glass dissolution rates

    SciTech Connect

    Bourcier, W.L.; Carroll, S.A.; Phillips, B.L.

    1993-11-01

    Predictions of long-term glass dissolution rates are highly dependent on the form of the affinity term in the rate expression. Analysis of the quantitative effect of saturation state on glass dissolution rate for CSG glass (a simple analog of SRL-165 glass), shows that a simple (1-Q/K) affinity term does not match experimental results. Our data at 100{degree}C show that the data is better fit by an affinity term having the form (1 {minus} (Q/K){sup 1}/{sigma}) where {sigma} = 10.

  2. Excited Protein States of Human Tear Lipocalin for Low- and High-Affinity Ligand Binding Revealed by Functional AB Loop Motion

    PubMed Central

    Gasymov, Oktay K.; Abduragimov, Adil R.; Glasgow, Ben J.

    2010-01-01

    Human tear lipocalin (TL), a prominent member of lipocalin family, exhibits functional and structural promiscuity. The plasticity of loop regions modulates entry to the ligand pocket at the “open” end of the eight-stranded β-barrel. Site directed multi-distance measurements using fluorescence resonance energy transfer between functional loops register two excited protein states for low- and high-affinity ligand binding. At low pH, the longest loop AB adopts the conformation of the low-affinity excited protein state that matches the crystal structure of holo-TL at pH 8. A “crankshaft” like movement is detected for the loop AB in a low pH transition. At pH 7.3 the holo-protein assumes a high-affinity excited protein state, in which the loop AB is more compact (RMS= 3.1Å). In the apo-holo transition, the reporter Trp 28 moves about 4.5 Å that reflects a decrease in distance between Glu27 and Lys108. This interaction fixes the loop AB conformation for the high-affinity mode. No such of movement is detected at low pH, where Glu27 is protonated. Data strongly indicate that the protonation state of Glu27 modulates the conformation of the loop AB for high- and low-affinity binding. PMID:20439130

  3. Excited protein states of human tear lipocalin for low- and high-affinity ligand binding revealed by functional AB loop motion.

    PubMed

    Gasymov, Oktay K; Abduragimov, Adil R; Glasgow, Ben J

    2010-06-01

    Human tear lipocalin (TL), a prominent member of lipocalin family, exhibits functional and structural promiscuity. The plasticity of loop regions modulates entry to the ligand pocket at the "open" end of the eight-stranded beta-barrel. Site-directed multi-distance measurements using fluorescence resonance energy transfer between functional loops register two excited protein states for low- and high-affinity ligand binding. At low pH, the longest loop AB adopts the conformation of the low-affinity excited protein state that matches the crystal structure of holo-TL at pH 8. A "crankshaft" like movement is detected for the loop AB in a low pH transition. At pH 7.3 the holo-protein assumes a high-affinity excited protein state, in which the loop AB is more compact (RMS=3.1A). In the apo-holo transition, the reporter Trp 28 moves about 4.5A that reflects a decrease in distance between Glu27 and Lys108. This interaction fixes the loop AB conformation for the high-affinity mode. No such movement is detected at low pH, where Glu27 is protonated. Data strongly indicate that the protonation state of Glu27 modulates the conformation of the loop AB for high- and low-affinity binding. PMID:20439130

  4. Elements of an improved model of debris-flow motion

    USGS Publications Warehouse

    Iverson, R.M.

    2009-01-01

    A new depth-averaged model of debris-flow motion describes simultaneous evolution of flow velocity and depth, solid and fluid volume fractions, and pore-fluid pressure. Non-hydrostatic pore-fluid pressure is produced by dilatancy, a state-dependent property that links the depth-averaged shear rate and volumetric strain rate of the granular phase. Pore-pressure changes caused by shearing allow the model to exhibit rate-dependent flow resistance, despite the fact that the basal shear traction involves only rate-independent Coulomb friction. An analytical solution of simplified model equations shows that the onset of downslope motion can be accelerated or retarded by pore-pressure change, contingent on whether dilatancy is positive or negative. A different analytical solution shows that such effects will likely be muted if downslope motion continues long enough, because dilatancy then evolves toward zero, and volume fractions and pore pressure concurrently evolve toward steady states. ?? 2009 American Institute of Physics.

  5. Modeling the influence of plate motions on subduction

    NASA Astrophysics Data System (ADS)

    Hillebrand, Bram; Thieulot, Cedric; van den Berg, Arie; Spakman, Wim

    2014-05-01

    Subduction zones are widely studied complex geodynamical systems. Their evolution is influenced by a broad range of parameters such as the age of the plates (both subducting and overriding) as well as their rheology, their nature (oceanic or continental), the presence of a crust and the involved plate motions to name a few. To investigate the importance of these different parameters on the evolution of subduction we have created a series of 2D numerical thermomechanical subduction models. These subduction models are multi-material flow models containing continental and oceanic crusts, a lithosphere and a mantle. We use the sticky air approach to allow for topography build up in the model. In order to model multi-material flow in our Eulerian finite element code of SEPRAN (Segal and Praagman, 2000) we use the well benchmarked level set method (Osher and Sethian, 1988) to track the different materials and their mode of deformation through the model domain. To our knowledge the presented results are the first subduction model results with the level set method. We will present preliminary results of our parametric study focusing mainly on the influence of plate motions on the evolution of subduction. S. Osher and J.A. Sethian. Fronts propagating with curvature-dependent speed: Algorithms based on hamilton-jacobi formulations. JCP 1988 A. Segal and N.P. Praagman. The SEPRAN package. Technical report, 2000 This research is funded by The Netherlands Research Centre for Integrated Solid Earth Science (ISES)

  6. Polar Motion Constraints on Models of the Fortnightly Tide

    NASA Technical Reports Server (NTRS)

    Ray, Richard D.; Egbert, G. D.; Smith, David E. (Technical Monitor)

    2002-01-01

    Estimates of the near-fortnightly Mf ocean tide from Topex/Poseidon satellite altimetry and from numerical solutions to the shallow water equations agree reasonably well, at least in their basin-scale features. For example, both show that the Pacific Ocean tide lags the Atlantic tide by roughly 30 degrees. There are hints of finer scale agreements in the elevation fields, but noise levels are high. In contrast, estimates of Mf currents are only weakly constrained by the TP data, because high-wavenumber Rossby waves (with intense currents) are associated with relatively small perturbations in surface elevation. As a result, a wide range of Mf current fields are consistent with both the TP data and the hydrodynamic equations within a priori plausible misfit bounds. We find that a useful constraint on the Mf currents is provided by independent estimates of the Earth's polar motion. At the Mf period polar motion shows a weak signal (both prograde and retrograde) which must be almost entirely caused by the ocean tide. We have estimated this signal from the SPACE2000 time series, after applying a broad-band correction for atmospheric angular momentum. Although the polar motion estimates have relatively large uncertainties, they are sufficiently precise to fix optimum data weights in a global ocean inverse model of Mf. These weights control the tradeoff between fitting a prior hydrodynamic model of Mf and fitting the relatively noisy T/P measurements of Mf. The predicted polar motion from the final inverse model agrees remarkably well with the Mf polar motion observations. The preferred model is also consistent with noise levels suggested by island gauges, and it is marginally consistent with differences observed by subsetting the altimetry (to the small extent that this is possible). In turn, this new model of the Mf ocean tide allows the ocean component to be removed from Mf estimates of length of day, thus yielding estimates of complex Love numbers less contaminated by

  7. One-degree-of-freedom motion induced by modeled vortex shedding

    NASA Technical Reports Server (NTRS)

    Yates, L. A.; Unal, A.; Szady, M.; Chapman, G. T.

    1989-01-01

    The motion of an elastically supported cylinder forced by a nonlinear, quasi-static, aerodynamic model with the unusual feature of a motion-dependent forcing frequency was studied. Numerical solutions for the motion and the Lyapunov exponents are presented for three forcing amplitudes and two frequencies (1.0 and 1.1 times the Strouhal frequency). Initially, positive Lyapunov exponents occur and the motion can appear chaotic. After thousands of characteristic times, the motion changes to a motion (verified analytically) that is periodic and damped. This periodic, damped motion was not observed experimentally, thus raising questions concerning the modeling.

  8. Energetics of ligand-receptor binding affinity on endothelial cells: An in vitro model.

    PubMed

    Fotticchia, Iolanda; Guarnieri, Daniela; Fotticchia, Teresa; Falanga, Andrea Patrizia; Vecchione, Raffaele; Giancola, Concetta; Netti, Paolo Antonio

    2016-08-01

    Targeted therapies represent a challenge in modern medicine. In this contest, we propose a rapid and reliable methodology based on Isothermal Titration Calorimetry (ITC) coupled with confluent cell layers cultured around biocompatible templating microparticles to quantify the number of overexpressing receptors on cell membrane and study the energetics of receptor-ligand binding in near-physiological conditions. In the in vitro model here proposed we used the bEnd3 cell line as brain endothelial cells to mimic the blood brain barrier (BBB) cultured on dextran microbeads ranging from 67μm to 80μm in size (Cytodex) and the primary human umbilical vein cells (HUVEC) for comparison. The revealed affinity between transferrin (Tf) and transferrin receptor (TfR) in both systems is very high, Kd values are in the order of nM. Conversely, the value of TfRs/cell reveals a 100-fold increase in the number of TfRs per bEnd3 cells compared to HUVEC cells. The presented methodology can represent a novel and helpful strategy to identify targets, to address drug design and selectively deliver therapeutics that can cross biological barriers such as the blood brain barrier. PMID:27100851

  9. Binding Affinity Effects on Physical Characteristics of a Model Phase-Separated Protein Droplet

    NASA Astrophysics Data System (ADS)

    Chuang, Sara; Banani, Salman; Rosen, Michael; Brangwynne, Clifford

    2015-03-01

    Non-membrane bound organelles are associated with a range of biological functions. Several of these structures exhibit liquid-like properties, and may represent droplets of phase-separated RNA and/or proteins. These structures are often enriched in multi-valent molecules, however little is known about the interactions driving the assembly, properties, and function. Here, we address this question using a model multi-valent protein system consisting of repeats of Small Ubiquitin-like Modifier (SUMO) protein and a SUMO-interacting motif (SIM). These proteins undergo phase separation into liquid-like droplets. We combine microrheology and quantitative microscopy to determine affect of binding affinity on the viscosity, density and surface tension of these droplets. We also use fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and partitioning experiments to probe the structure and dynamics within these droplets. Our results shed light on how inter-molecular interactions manifests in droplet properties, and lay the groundwork for a comprehensive biophysical picture of intracellular RNA/protein organelles.

  10. Monolayers of a Model Anesthetic-Binding Membrane Protein: Formation, Characterization, and Halothane-Binding Affinity

    PubMed Central

    Churbanova, Inna Y.; Tronin, Andrey; Strzalka, Joseph; Gog, Thomas; Kuzmenko, Ivan; Johansson, Jonas S.; Blasie, J. Kent

    2006-01-01

    hbAP0 is a model membrane protein designed to possess an anesthetic-binding cavity in its hydrophilic domain and a cation channel in its hydrophobic domain. Grazing incidence x-ray diffraction shows that hbAP0 forms four-helix bundles that are vectorially oriented within Langmuir monolayers at the air-water interface. Single monolayers of hbAP0 on alkylated solid substrates would provide an optimal system for detailed structural and dynamical studies of anesthetic-peptide interaction via x-ray and neutron scattering and polarized spectroscopic techniques. Langmuir-Blodgett and Langmuir-Schaeffer deposition and self-assembly techniques were used to form single monolayer films of the vectorially oriented peptide hbAP0 via both chemisorption and physisorption onto suitably alkylated solid substrates. The films were characterized by ultraviolet absorption, ellipsometry, circular dichroism, and polarized Fourier transform infrared spectroscopy. The α-helical secondary structure of the peptide was retained in the films. Under certain conditions, the average orientation of the helical axis was inclined relative to the plane of the substrate, approaching perpendicular in some cases. The halothane-binding affinity of the vectorially oriented hbAP0 peptide in the single monolayers, with the volatile anesthetic introduced into the moist vapor environment of the monolayer, was found to be similar to that for the detergent-solubilized peptide. PMID:16473900

  11. Synthetic cannabinoids: In silico prediction of the cannabinoid receptor 1 affinity by a quantitative structure-activity relationship model.

    PubMed

    Paulke, Alexander; Proschak, Ewgenij; Sommer, Kai; Achenbach, Janosch; Wunder, Cora; Toennes, Stefan W

    2016-03-14

    The number of new synthetic psychoactive compounds increase steadily. Among the group of these psychoactive compounds, the synthetic cannabinoids (SCBs) are most popular and serve as a substitute of herbal cannabis. More than 600 of these substances already exist. For some SCBs the in vitro cannabinoid receptor 1 (CB1) affinity is known, but for the majority it is unknown. A quantitative structure-activity relationship (QSAR) model was developed, which allows the determination of the SCBs affinity to CB1 (expressed as binding constant (Ki)) without reference substances. The chemically advance template search descriptor was used for vector representation of the compound structures. The similarity between two molecules was calculated using the Feature-Pair Distribution Similarity. The Ki values were calculated using the Inverse Distance Weighting method. The prediction model was validated using a cross validation procedure. The predicted Ki values of some new SCBs were in a range between 20 (considerably higher affinity to CB1 than THC) to 468 (considerably lower affinity to CB1 than THC). The present QSAR model can serve as a simple, fast and cheap tool to get a first hint of the biological activity of new synthetic cannabinoids or of other new psychoactive compounds. PMID:26795018

  12. Mobility and dynamics modeling for unmanned ground vehicle motion planning

    NASA Astrophysics Data System (ADS)

    Witus, Gary

    1999-07-01

    This paper presents an approach to modeling unmanned ground vehicle (UGV) mobility performance and vehicle dynamics for evaluating the feasibility and cost of alternative motion plans. Feasibility constraints include power, traction, and roll stability limits. Sensor stabilization performance is considered in a system-level constraint requiring that the obstacle detection distance exceed the stopping distance. Mission time and power requirements are inputs to a multi- attribute cost function for planning under uncertainty. The modeling approach combines a theoretical first-principles mathematical model with an empirical knowledge-based model. The first-principles model predicts performance in an idealized deterministic environment. On-board vehicle dynamics control, for dynamic load balancing and traction management, legitimize some of the simplifying assumptions. The knowledge- based model uses historical relationships to predict the mean and variance of total system performance accounting for the contributions of unplanned reactive behaviors, local terrain variations, and vehicle response transients.

  13. Fractional-order variational optical flow model for motion estimation.

    PubMed

    Chen, Dali; Sheng, Hu; Chen, YangQuan; Xue, Dingyü

    2013-05-13

    A new class of fractional-order variational optical flow models, which generalizes the differential of optical flow from integer order to fractional order, is proposed for motion estimation in this paper. The corresponding Euler-Lagrange equations are derived by solving a typical fractional variational problem, and the numerical implementation based on the Grünwald-Letnikov fractional derivative definition is proposed to solve these complicated fractional partial differential equations. Theoretical analysis reveals that the proposed fractional-order variational optical flow model is the generalization of the typical Horn and Schunck (first-order) variational optical flow model and the second-order variational optical flow model, which provides a new idea for us to study the optical flow model and has an important theoretical implication in optical flow model research. The experiments demonstrate the validity of the generalization of differential order. PMID:23547225

  14. PET Motion Compensation for Radiation Therapy Using a CT-Based Mid-Position Motion Model: Methodology and Clinical Evaluation

    SciTech Connect

    Kruis, Matthijs F.; Kamer, Jeroen B. van de; Houweling, Antonetta C.; Sonke, Jan-Jakob; Belderbos, José S.A.; Herk, Marcel van

    2013-10-01

    Purpose: Four-dimensional positron emission tomography (4D PET) imaging of the thorax produces sharper images with reduced motion artifacts. Current radiation therapy planning systems, however, do not facilitate 4D plan optimization. When images are acquired in a 2-minute time slot, the signal-to-noise ratio of each 4D frame is low, compromising image quality. The purpose of this study was to implement and evaluate the construction of mid-position 3D PET scans, with motion compensated using a 4D computed tomography (CT)-derived motion model. Methods and Materials: All voxels of 4D PET were registered to the time-averaged position by using a motion model derived from the 4D CT frames. After the registration the scans were summed, resulting in a motion-compensated 3D mid-position PET scan. The method was tested with a phantom dataset as well as data from 27 lung cancer patients. Results: PET motion compensation using a CT-based motion model improved image quality of both phantoms and patients in terms of increased maximum SUV (SUV{sub max}) values and decreased apparent volumes. In homogenous phantom data, a strong relationship was found between the amplitude-to-diameter ratio and the effects of the method. In heterogeneous patient data, the effect correlated better with the motion amplitude. In case of large amplitudes, motion compensation may increase SUV{sub max} up to 25% and reduce the diameter of the 50% SUV{sub max} volume by 10%. Conclusions: 4D CT-based motion-compensated mid-position PET scans provide improved quantitative data in terms of uptake values and volumes at the time-averaged position, thereby facilitating more accurate radiation therapy treatment planning of pulmonary lesions.

  15. Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation.

    PubMed

    Frederick, Kendra King; Sharp, Kim A; Warischalk, Nicholas; Wand, A Joshua

    2008-09-25

    NMR spin relaxation retains a central role in the characterization of the fast internal motion of proteins and their complexes. Knowledge of the distribution and amplitude of the motion of amino acid side chains is critical for the interpretation of the dynamical proxy for the residual conformational entropy of proteins, which can potentially significantly contribute to the entropy of protein function. A popular treatment of NMR relaxation phenomena in macromolecules dissolved in liquids is the so-called model-free approach of Lipari and Szabo. The robustness of the mode-free approach has recently been strongly criticized and the remarkable range and structural context of the internal motion of proteins, characterized by such NMR relaxation techniques, attributed to artifacts arising from the model-free treatment, particularly with respect to the symmetry of the underlying motion. We develop an objective quantification of both spatial and temporal asymmetry of motion and re-examine the foundation of the model-free treatment. Concerns regarding the robustness of the model-free approach to asymmetric motion appear to be generally unwarranted. The generalized order parameter is robustly recovered. The sensitivity of the model-free treatment to asymmetric motion is restricted to the effective correlation time, which is by definition a normalized quantity and not a true time constant and therefore of much less interest in this context. With renewed confidence in the model-free approach, we then examine the microscopic distribution of side chain motion in the complex between calcium-saturated calmodulin and the calmodulin-binding domain of the endothelial nitric oxide synthase. Deuterium relaxation is used to characterize the motion of methyl groups in the complex. A remarkable range of Lipari-Szabo model-free generalized order parameters are seen with little correlation with basic structural parameters such as the depth of burial. These results are contrasted with the

  16. A mathematical model for efficient estimation of aircraft motions

    NASA Technical Reports Server (NTRS)

    Bach, R. E., Jr.

    1983-01-01

    In the usual formulation of the aircraft state-estimation problem, motions along a flight trajectory are represented by a plant consisting of nonlinear state and measurement models. Problem solution using this formulation requires that both state- and measurement-dependent Jacobian matrices be evaluated along any trajectory. In this paper it is shown that a set of state variables can be chosen to realize a linear state model of very simple form, such that all nonlinearities appear in the measurement model. The potential advantage of the new formulation is computational: the Jacobian matrix corresponding to a linear state model is constant, a feature that should outweigh the fact that the measurement model is more complicated than in the conventinal formulation. To compare the modeling methods, aircraft motions from typical flight-test and accident data were estimated, using each formulation with the same off-line (smoothing) algorithm. The results of these experiments, reported in the paper, demonstrate clearly the computational superiority of the linear state-variable formulation. The procedure advocated here may be extended to other nonlinear estimation problems, including on-line (filtering) applications.

  17. Modelling the emergence of coordinated collective motion by minimizing dissatisfaction.

    PubMed

    Quera, Vicenç; Beltran, Francesc S; Gimeno, Elisabet

    2016-01-01

    Coordinated collective motion (CCM) has been recently studied using agent-based simulations by applying three behavioural rules: repulsion, attraction and alignment. But these rules are so similar to the expected group behaviour that it can hardly be labelled emergent. We developed an agent-based model that produces CCM using a set of low-level dyadic interaction rules. The agents change their positions with regard to other agents in order to minimize their own dissatisfaction with their inter-individual distances. To test the emergence of CCM, several simulation experiments were performed. The results show that the agents were able to achieve CCM after a few thousand time steps, and that the bigger the area perceived by them, the more coordinated and cohesive the group motion became. An increased memory span and capacity to remember other agents' identities improved cohesion and coordination. The relationship with biological referents is discussed. PMID:26626359

  18. Deformable models with sparsity constraints for cardiac motion analysis.

    PubMed

    Yu, Yang; Zhang, Shaoting; Li, Kang; Metaxas, Dimitris; Axel, Leon

    2014-08-01

    Deformable models integrate bottom-up information derived from image appearance cues and top-down priori knowledge of the shape. They have been widely used with success in medical image analysis. One limitation of traditional deformable models is that the information extracted from the image data may contain gross errors, which adversely affect the deformation accuracy. To alleviate this issue, we introduce a new family of deformable models that are inspired from the compressed sensing, a technique for accurate signal reconstruction by harnessing some sparseness priors. In this paper, we employ sparsity constraints to handle the outliers or gross errors, and integrate them seamlessly with deformable models. The proposed new formulation is applied to the analysis of cardiac motion using tagged magnetic resonance imaging (tMRI), where the automated tagging line tracking results are very noisy due to the poor image quality. Our new deformable models track the heart motion robustly, and the resulting strains are consistent with those calculated from manual labels. PMID:24721617

  19. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site

    PubMed Central

    Boyce, Sarah E.; Mobley, David L.; Rocklin, Gabriel; Graves, Alan P.

    2009-01-01

    We present a combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute binding free energies. These were blind tests performed prospectively on 13 diverse, previously untested candidate ligand molecules. We predicted that eight compounds would bind to the cavity and five would not; 11 of 13 predictions were correct at this level. The RMS error to the measurable absolute binding energies was 1.8 kcal/mol. In addition, we computed relative binding free energies for six phenol derivatives starting from two known ligands: phenol and catechol. The average RMS error in the relative free energy prediction was 2.5 (phenol) and 1.1 (catechol) kcal/mol. To understand these results at atomic resolution, we obtained x-ray co-complex structures for nine of the diverse ligands and for all six phenol analogs. The average RMSD of the predicted pose to the experiment was 2.0Å (diverse set), 1.8Å (phenol derived predictions) and 1.2Å (catechol derived predictions). We found that to predict accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site. Unanticipated binding modes, multiple ligand binding, and protein conformational change all proved challenging for the free energy methods. We believe these results can help guide future improvements in physics-based absolute binding free energy methods. PMID:19782087

  20. Modeling the Nonlinear Motion of the Rat Central Airways.

    PubMed

    Ibrahim, G; Rona, A; Hainsworth, S V

    2016-01-01

    Advances in volumetric medical imaging techniques allowed the subject-specific modeling of the bronchial flow through the first few generations of the central airways using computational fluid dynamics (CFD). However, a reliable CFD prediction of the bronchial flow requires modeling of the inhomogeneous deformation of the central airways during breathing. This paper addresses this issue by introducing two models of the central airways motion. The first model utilizes a node-to-node mapping between the discretized geometries of the central airways generated from a number of successive computed tomography (CT) images acquired dynamically (without breath hold) over the breathing cycle of two Sprague-Dawley rats. The second model uses a node-to-node mapping between only two discretized airway geometries generated from the CT images acquired at end-exhale and at end-inhale along with the ventilator measurement of the lung volume change. The advantage of this second model is that it uses just one pair of CT images, which more readily complies with the radiation dosage restrictions for humans. Three-dimensional computer aided design geometries of the central airways generated from the dynamic-CT images were used as benchmarks to validate the output from the two models at sampled time-points over the breathing cycle. The central airway geometries deformed by the first model showed good agreement to the benchmark geometries within a tolerance of 4%. The central airway geometry deformed by the second model better approximated the benchmark geometries than previous approaches that used a linear or harmonic motion model. PMID:26592166

  1. Age Dependent Absolute Plate and Plume Motion Modeling

    NASA Astrophysics Data System (ADS)

    Heaton, D. E.; Koppers, A. A. P.

    2015-12-01

    Current absolute plate motion (APM) models from 80 - 0 Ma are constrained by the location of mantle plume related hotspot seamounts, in particular those of the Hawaiian-Emperor and Louisville seamount trails. Originally the 'fixed' hotspot hypothesis was developed to explain past plate motion based on linear age progressive intra-plate volcanism. However, now that 'moving' hotspots are accepted, it is becoming clear that APM models need to be corrected for individual plume motion vectors. For older seamount trails that were active between roughly 50 and 80 Ma the APM models that use 'fixed' hotspots overestimate the measured age progression in those trails, while APM models corrected for 'moving' hotspots underestimate those age progressions. These mismatches are due to both a lack of reliable ages in the older portions of both the Hawaii and Louisville seamount trails and insufficient APM modeling constraints from other seamount trails in the Pacific Basin. Seamounts are difficult to sample and analyze because many are hydrothermally altered and have low potassium concentrations. New 40Ar/39Ar Age results from International Ocean Drilling Project (IODP) Expedition 330 Sites U1372 (n=18), U1375 (n=3), U1376 (n=15) and U1377 (n=7) aid in constraining the oldest end of the Louisville Seamount trail. A significant observation in this study is that the age range recovered in the drill cores match the range of ages that were acquired on dredging cruises at the same seamounts (e.g. Koppers et al., 2011). This is important for determining the inception age of a seamount. The sections recovered from IODP EXP 330 are in-situ volcanoclastic breccia and lava flows. Comparing the seismic interpretations of Louisville guyots (Contreras-Reyes et al., 2010), Holes U1372, U1373 and U1374 penetrated the extrusive and volcanoclastic sections of the seamount. The ages obtained are consistent over stratigraphic intervals >100-450 m thick, providing evidence that these seamounts

  2. A Pelvic Phantom for Modeling Internal Organ Motions

    SciTech Connect

    Kovacs, Peter; Sebestyen, Zsolt; Farkas, Robert; Bellyei, Szabolcs; Szigeti, Andras; Liposits, Gabor; Hideghety, Katalin; Derczy, Katalin; Mangel, Laszlo

    2011-10-01

    A pelvic phantom was developed for use in testing image-guided radiation therapy (IGRT) and adaptive applications in radiation therapy (ART) with simulating the anterior-posterior internal organ motions during prostate radiotherapy. Measurements could be done with an ionization chamber (IC) in the simulated prostate. The rectum was simulated by air-equivalent material (AEM). The volume superior to the IC placement was considered as the bladder. The extension of AEM volume could be varied. The vertical position of the IC placement could be shifted by {+-}1 cm to simulate the prostate motion parallel to the changes in bladder volume. The reality of the simulation was inspected. Three-millimeter-slice-increment computed tomography (CT) scans were taken for irradiation planning. The structure set was adapted to the phantom from a treated patient. Planning target volume was delineated according to the RTOG 0126 study. IMRT and 3D conformal radiation therapy (3D-CRT) plans were made. Prostate motion and rectum volume changes were simulated in the phantom. IC displacement was corrected by phantom shifting. The delivered dose was measured with IC in 7 cases using intensity-modulated radiation therapy (IMRT) and 3D-CRT fractions, and single square-shaped beams: anteroposterior (AP), posteroanterior (PA), and lateral (LAT). Variations from the calculated doses were slightly below 1% at IMRT and around 1% at 3D-CRT; below 4.5% at square AP beam; up to 9% at square PA beam; and around 0.5% at square LAT beam. Other authors have already shown that by using planning systems and ultrasonic and cone beam CT guidance, correction of organ motions in a real patient during prostate cancer IGRT does not have a significant dosimetric effect. The inspection of our phantom-as described here-ended with similar results. Our team suggested that our model is sufficiently realistic and can be used for IGRT and ART testing.

  3. A pelvic phantom for modeling internal organ motions.

    PubMed

    Kovács, Péter; Sebestyén, Zsolt; Farkas, Róbert; Bellyei, Szabolcs; Szigeti, András; Liposits, Gábor; Hideghéty, Katalin; Dérczy, Katalin; Mangel, László

    2011-01-01

    A pelvic phantom was developed for use in testing image-guided radiation therapy (IGRT) and adaptive applications in radiation therapy (ART) with simulating the anterior-posterior internal organ motions during prostate radiotherapy. Measurements could be done with an ionization chamber (IC) in the simulated prostate. The rectum was simulated by air-equivalent material (AEM). The volume superior to the IC placement was considered as the bladder. The extension of AEM volume could be varied. The vertical position of the IC placement could be shifted by ± 1 cm to simulate the prostate motion parallel to the changes in bladder volume. The reality of the simulation was inspected. Three-millimeter-slice-increment computed tomography (CT) scans were taken for irradiation planning. The structure set was adapted to the phantom from a treated patient. Planning target volume was delineated according to the RTOG 0126 study. IMRT and 3D conformal radiation therapy (3D-CRT) plans were made. Prostate motion and rectum volume changes were simulated in the phantom. IC displacement was corrected by phantom shifting. The delivered dose was measured with IC in 7 cases using intensity-modulated radiation therapy (IMRT) and 3D-CRT fractions, and single square-shaped beams: anteroposterior (AP), posteroanterior (PA), and lateral (LAT). Variations from the calculated doses were slightly below 1% at IMRT and around 1% at 3D-CRT; below 4.5% at square AP beam; up to 9% at square PA beam; and around 0.5% at square LAT beam. Other authors have already shown that by using planning systems and ultrasonic and cone beam CT guidance, correction of organ motions in a real patient during prostate cancer IGRT does not have a significant dosimetric effect. The inspection of our phantom--as described here-ended with similar results. Our team suggested that our model is sufficiently realistic and can be used for IGRT and ART testing. PMID:20561777

  4. Sparse deformable models with application to cardiac motion analysis.

    PubMed

    Yu, Yang; Zhang, Shaoting; Huang, Junzhou; Metaxas, Dimitris; Axel, Leon

    2013-01-01

    Deformable models have been widely used with success in medical image analysis. They combine bottom-up information derived from image appearance cues, with top-down shape-based constraints within a physics-based formulation. However, in many real world problems the observations extracted from the image data often contain gross errors, which adversely affect the deformation accuracy. To alleviate this issue, we introduce a new family of deformable models that are inspired from compressed sensing, a technique for efficiently reconstructing a signal based on its sparseness in some domain. In this problem, we employ sparsity to represent the outliers or gross errors, and combine it seamlessly with deformable models. The proposed new formulation is applied to the analysis of cardiac motion, using tagged magnetic resonance imaging (tMRI), where the automated tagging line tracking results are very noisy due to the poor image quality. Our new deformable models track the heart motion robustly, and the resulting strains are consistent with those calculated from manual labels. PMID:24683970

  5. Models of subjective response to in-flight motion data

    NASA Technical Reports Server (NTRS)

    Rudrapatna, A. N.; Jacobson, I. D.

    1973-01-01

    Mathematical relationships between subjective comfort and environmental variables in an air transportation system are investigated. As a first step in model building, only the motion variables are incorporated and sensitivities are obtained using stepwise multiple regression analysis. The data for these models have been collected from commercial passenger flights. Two models are considered. In the first, subjective comfort is assumed to depend on rms values of the six-degrees-of-freedom accelerations. The second assumes a Rustenburg type human response function in obtaining frequency weighted rms accelerations, which are used in a linear model. The form of the human response function is examined and the results yield a human response weighting function for different degrees of freedom.

  6. Model and parametric uncertainty in source-based kinematic models of earthquake ground motion

    USGS Publications Warehouse

    Hartzell, Stephen; Frankel, Arthur; Liu, Pengcheng; Zeng, Yuehua; Rahman, Shariftur

    2011-01-01

    Four independent ground-motion simulation codes are used to model the strong ground motion for three earthquakes: 1994 Mw 6.7 Northridge, 1989 Mw 6.9 Loma Prieta, and 1999 Mw 7.5 Izmit. These 12 sets of synthetics are used to make estimates of the variability in ground-motion predictions. In addition, ground-motion predictions over a grid of sites are used to estimate parametric uncertainty for changes in rupture velocity. We find that the combined model uncertainty and random variability of the simulations is in the same range as the variability of regional empirical ground-motion data sets. The majority of the standard deviations lie between 0.5 and 0.7 natural-log units for response spectra and 0.5 and 0.8 for Fourier spectra. The estimate of model epistemic uncertainty, based on the different model predictions, lies between 0.2 and 0.4, which is about one-half of the estimates for the standard deviation of the combined model uncertainty and random variability. Parametric uncertainty, based on variation of just the average rupture velocity, is shown to be consistent in amplitude with previous estimates, showing percentage changes in ground motion from 50% to 300% when rupture velocity changes from 2.5 to 2.9 km/s. In addition, there is some evidence that mean biases can be reduced by averaging ground-motion estimates from different methods.

  7. Diffusion modelling of metamorphic layered coronas with stability criterion and consideration of affinity

    NASA Astrophysics Data System (ADS)

    Ashworth, J. R.; Sheplev, V. S.

    1997-09-01

    Layered coronas between two reactant minerals can, in many cases, be attributed to diffusion-controlled growth with local equilibrium. This paper clarifies and unifies the previous approaches of various authors to the simplest form of modelling, which uses no assumed values for thermochemical quantities. A realistic overall reaction must be estimated from measured overall proportions of minerals and their major element compositions. Modelling is not restricted to a particular number of components S, relative to the number of phases Φ. IfΦ > S + 1, the overall reaction is a combination of simultaneous reactions. The stepwise method, solving for the local reaction at each boundary in turn, is extended to allow for recurrence of a mineral (its presence in two parts of the layer structure separated by a gap). The equations are also given in matrix form. A thermodynamic stability criterion is derived, determining which layer sequence is truly stable if several are computable from the same inputs. A layer structure satisfying the stability criterion has greater growth rate (and greater rate of entropy production) than the other computable layer sequences. This criterion of greatest entropy production is distinct from Prigogine's theorem of minimum entropy production, which distinguishes the stationary or quasi-stationary state from other states of the same layer sequence. The criterion leads to modification of previous results for coronas comprising hornblende, spinel, and orthopyroxene between olivine (Ol) and plagioclase (Pl). The outcome supports the previous inference that Si, and particularly Al, commonly behave as immobile relative to other cation-forming major elements. The affinity (-ΔG) of a corona-forming reaction is estimated, using previous estimates of diffusion coefficient and the duration t of reaction, together with a new model quantity (-ΔG) *. For an example of the Ol + Pl reaction, a rough calculation gives (-ΔG) > 1.7RT (per mole of P1 consumed

  8. A Fully Nonlinear, Dynamically Consistent Numerical Model for Solid-Body Ship Motion. I. Ship Motion with Fixed Heading

    NASA Technical Reports Server (NTRS)

    Lin, Ray-Quing; Kuang, Weijia

    2011-01-01

    In this paper, we describe the details of our numerical model for simulating ship solidbody motion in a given environment. In this model, the fully nonlinear dynamical equations governing the time-varying solid-body ship motion under the forces arising from ship wave interactions are solved with given initial conditions. The net force and moment (torque) on the ship body are directly calculated via integration of the hydrodynamic pressure over the wetted surface and the buoyancy effect from the underwater volume of the actual ship hull with a hybrid finite-difference/finite-element method. Neither empirical nor free parametrization is introduced in this model, i.e. no a priori experimental data are needed for modelling. This model is benchmarked with many experiments of various ship hulls for heave, roll and pitch motion. In addition to the benchmark cases, numerical experiments are also carried out for strongly nonlinear ship motion with a fixed heading. These new cases demonstrate clearly the importance of nonlinearities in ship motion modelling.

  9. A geodetic plate motion and Global Strain Rate Model

    NASA Astrophysics Data System (ADS)

    Kreemer, Corné; Blewitt, Geoffrey; Klein, Elliot C.

    2014-10-01

    present a new global model of plate motions and strain rates in plate boundary zones constrained by horizontal geodetic velocities. This Global Strain Rate Model (GSRM v.2.1) is a vast improvement over its predecessor both in terms of amount of data input as in an increase in spatial model resolution by factor of ˜2.5 in areas with dense data coverage. We determined 6739 velocities from time series of (mostly) continuous GPS measurements; i.e., by far the largest global velocity solution to date. We transformed 15,772 velocities from 233 (mostly) published studies onto our core solution to obtain 22,511 velocities in the same reference frame. Care is taken to not use velocities from stations (or time periods) that are affected by transient phenomena; i.e., this data set consists of velocities best representing the interseismic plate velocity. About 14% of the Earth is allowed to deform in 145,086 deforming grid cells (0.25° longitude by 0.2° latitude in dimension). The remainder of the Earth's surface is modeled as rigid spherical caps representing 50 tectonic plates. For 36 plates we present new GPS-derived angular velocities. For all the plates that can be compared with the most recent geologic plate motion model, we find that the difference in angular velocity is significant. The rigid-body rotations are used as boundary conditions in the strain rate calculations. The strain rate field is modeled using the Haines and Holt method, which uses splines to obtain an self-consistent interpolated velocity gradient tensor field, from which strain rates, vorticity rates, and expected velocities are derived. We also present expected faulting orientations in areas with significant vorticity, and update the no-net rotation reference frame associated with our global velocity gradient field. Finally, we present a global map of recurrence times for Mw=7.5 characteristic earthquakes.

  10. Fuzzy controller design for passive continuous-time affine T-S fuzzy models with relaxed stability conditions.

    PubMed

    Chang, Wen-Jer; Ku, Cheung-Chieh; Huang, Pei-Hwa; Chang, Wei

    2009-07-01

    In order to design a fuzzy controller for complex nonlinear systems, the work of this paper deals with developing the relaxed stability conditions for continuous-time affine Takagi-Sugeno (T-S) fuzzy models. By applying the passivity theory and Lyapunov theory, the relaxed stability conditions are derived to guarantee the stability and passivity property of closed-loop systems. Based on these relaxed stability conditions, the synthesis of fuzzy controller design problem for passive continuous-time affine T-S fuzzy models can be easily solved via the Optimal Convex Programming Algorithm (OCPA) and Linear Matrix Inequality (LMI) technique. At last, a simulation example for the fuzzy control of a nonlinear synchronous generator system is presented to manifest the applications and effectiveness of proposed fuzzy controller design approach. PMID:19389667

  11. New Ground Motion Prediction Models for Caucasus Region

    NASA Astrophysics Data System (ADS)

    Jorjiashvili, N.

    2012-12-01

    The Caucasus is a region of numerous natural hazards and ensuing disasters. Analysis of the losses due to past disasters indicates the those most catastrophic in the region have historically been due to strong earthquakes. Estimation of expected ground motion is a fundamental earthquake hazard assessment. The most commonly used parameter for attenuation relation is peak ground acceleration because this parameter gives useful information for Seismic Hazard Assessment. Because of this, many peak ground acceleration attenuation relations have been developed by different authors. Besides, a few attenuation relations were developed for Caucasus region: Ambraseys et al. (1996,2005) which were based on entire European region and they were not focused locally on Caucasus Region; Smit et.al. (2000) that was based on a small amount of acceleration data that really is not enough. Since 2003 construction of Georgian Digital Seismic Network has started with the help of number of International organizations, Projects and Private companies. The works conducted involved scientific as well as organizational activities: Resolving technical problems concerning communication and data transmission. Thus, today we have a possibility to get real time data and make scientific research based on digital seismic data. Generally, ground motion and damage are influenced by the magnitude of the earthquake, the distance from the seismic source to site, the local ground conditions and the characteristics of buildings. Estimation of expected ground motion is a fundamental earthquake hazard assessment. This is the reason why this topic is emphasized in this study. In this study new GMP models are obtained based on new data from Georgian seismic network and also from neighboring countries. Estimation of models are obtained by classical, statistical way, regression analysis. Also site ground conditions are considered because the same earthquake recorded at the same distance may cause different damage

  12. Affinity of Aporphines for the Human 5-HT2A Receptor: Insights from Homology Modeling and Molecular Docking Studies

    PubMed Central

    Pecic, Stevan; Makkar, Pooja; Chaudhary, Sandeep; Reddy, Boojala V.; Navarro, Hernan A.; Harding, Wayne W.

    2010-01-01

    Analogs of nantenine were docked into a modeled structure of the human 5-HT2A receptor using ICM Pro, GLIDE and GOLD docking methods. The resultant docking scores were used to correlate with observed in vitro apparent affinity (Ke) data. The GOLD docking algorithm when used with a homology model of 5-HT2A, based on a bovine rhodopsin template and built by the program MODELLER, gives results which are most in agreement with the in vitro results. Further analysis of the docking poses among members of a C1 alkyl series of nantenine analogs, indicate that they bind to the receptor in a similar orientation, but differently than nantenine. Besides an important interaction between the protonated nitrogen of the C1 alkyl analogs and residue Asp155, we identified Ser242, Phe234 and Gly238 as key residues responsible for the affinity of these compounds for the 5-HT2A receptor. Specifically, the ability of some of these analogs to establish a H-bond with Ser242 and hydrophobic interactions with Phe234 and Gly238 appears to explain their enhanced affinity as compared to nantenine. PMID:20621490

  13. Fast-coding robust motion estimation model in a GPU

    NASA Astrophysics Data System (ADS)

    García, Carlos; Botella, Guillermo; de Sande, Francisco; Prieto-Matias, Manuel

    2015-02-01

    Nowadays vision systems are used with countless purposes. Moreover, the motion estimation is a discipline that allow to extract relevant information as pattern segmentation, 3D structure or tracking objects. However, the real-time requirements in most applications has limited its consolidation, considering the adoption of high performance systems to meet response times. With the emergence of so-called highly parallel devices known as accelerators this gap has narrowed. Two extreme endpoints in the spectrum of most common accelerators are Field Programmable Gate Array (FPGA) and Graphics Processing Systems (GPU), which usually offer higher performance rates than general propose processors. Moreover, the use of GPUs as accelerators involves the efficient exploitation of any parallelism in the target application. This task is not easy because performance rates are affected by many aspects that programmers should overcome. In this paper, we evaluate OpenACC standard, a programming model with directives which favors porting any code to a GPU in the context of motion estimation application. The results confirm that this programming paradigm is suitable for this image processing applications achieving a very satisfactory acceleration in convolution based problems as in the well-known Lucas & Kanade method.

  14. Mixed-model QSAR at the glucocorticoid receptor: predicting the binding mode and affinity of psychotropic drugs.

    PubMed

    Spreafico, Morena; Ernst, Beat; Lill, Markus A; Smiesko, Martin; Vedani, Angelo

    2009-01-01

    The glucocorticoid receptor (GR) is a member of the nuclear receptor superfamily that affects immune response, development, and metabolism in target tissues. Glucocorticoids are widely used to treat diverse pathophysiological conditions, but their clinical applicability is limited by side effects. A prediction of the binding affinity toward the GR would be beneficial for identifying glucocorticoid-mediated adverse effects triggered by drugs or chemicals. By identifying the binding mode to the GR using flexible docking (software Yeti) and quantifying the binding affinity through multidimensional QSAR (software Quasar), we validated a model family based on 110 compounds, representing four different chemical classes. The correlation with the experimental data (cross-validated r(2)=0.702; predictive r(2)=0.719) suggests that our approach is suited for predicting the binding affinity of related compounds toward the GR. After challenging the model by a series of scramble tests, a consensus approach (software Raptor), and a prediction set, it was incorporated into our VirtualToxLab and used to simulate and quantify the interaction of 24 psychotropic drugs with the GR. PMID:19009570

  15. Towards Analytic Solutions of Step-Wise Safe Switching for Known Affine-Linear Models

    SciTech Connect

    Koumboulis, Fotis N.; Tzamtzi, Maria P.

    2008-09-17

    In the present work we establish conditions which guarantee safe transitions for the closed-loop system produced by the application of the Step-Wise Safe Switching control approach to an affine linear system when the nonlinear description of the plant is known. These conditions are based on the local Input to State Stability (ISS) properties of the nonlinear system around the plant's nominal operating points.

  16. Statistical modeling of ground motion relations for seismic hazard analysis

    NASA Astrophysics Data System (ADS)

    Raschke, Mathias

    2013-10-01

    We introduce a new approach for ground motion relations (GMR) in the probabilistic seismic hazard analysis (PSHA), being influenced by the extreme value theory of mathematical statistics. Therein, we understand a GMR as a random function. We derive mathematically the principle of area equivalence, wherein two alternative GMRs have an equivalent influence on the hazard if these GMRs have equivalent area functions. This includes local biases. An interpretation of the difference between these GMRs (an actual and a modeled one) as a random component leads to a general overestimation of residual variance and hazard. Beside this, we discuss important aspects of classical approaches and discover discrepancies with the state of the art of stochastics and statistics (model selection and significance, test of distribution assumptions, extreme value statistics). We criticize especially the assumption of logarithmic normally distributed residuals of maxima like the peak ground acceleration (PGA). The natural distribution of its individual random component (equivalent to exp( ɛ 0) of Joyner and Boore, Bull Seism Soc Am 83(2):469-487, 1993) is the generalized extreme value. We show by numerical researches that the actual distribution can be hidden and a wrong distribution assumption can influence the PSHA negatively as the negligence of area equivalence does. Finally, we suggest an estimation concept for GMRs of PSHA with a regression-free variance estimation of the individual random component. We demonstrate the advantages of event-specific GMRs by analyzing data sets from the PEER strong motion database and estimate event-specific GMRs. Therein, the majority of the best models base on an anisotropic point source approach. The residual variance of logarithmized PGA is significantly smaller than in previous models. We validate the estimations for the event with the largest sample by empirical area functions, which indicate the appropriate modeling of the GMR by an anisotropic

  17. Lumped mass modeling of overburden motion during explosive blasting

    SciTech Connect

    Schamaun, J. T.

    1981-02-01

    The in situ extraction of oil from most oil shale beds is highly dependent upon explosive fracturing and rubbling of rock in a controlled and predictable manner. Besides the rubbling requirement, it is also important that the surrounding rock remain competent to minimize fluid leakage during processing. For rubbling concepts in which the overburden is explosively lifted to provide the required void in an oil shale zone, an engineering lumped mass model has been devised to describe the motion of the overburden. The model simulates the overburden as an array of interacting lumped masses which are loaded from below with a time-dependent force to approximate the explosive load. Correlation with experimental data obtained from field blasting operations shows that this model will provide an adequate approximation of overburden behavior. The basic features of the model are described in the report along with the correlations with field data. Results from several parametric studies are also presented which were used to aid in blast design. This lumped mass model can be extended to include other parameters and has potential for the study of other related blasting situations.

  18. SU-E-J-186: Using 4DCT-Based Motion Modeling to Predict Motion and Duty Cycle On Successive Days of Gated Radiotherapy

    SciTech Connect

    Myronakis, M; Cai, W; Dhou, S; Cifter, F; Lewis, J

    2015-06-15

    Purpose: To determine if 4DCT-based motion modeling and external surrogate motion measured during treatment simulation can enhance prediction of residual tumor motion and duty cycle during treatment delivery. Methods: This experiment was conducted using simultaneously recorded tumor and external surrogate motion acquired over multiple fractions of lung cancer radiotherapy. These breathing traces were combined with the XCAT phantom to simulate CT images. Data from the first day was used to estimate the residual tumor motion and duty cycle both directly from the 4DCT (the current clinical standard), and from external-surrogate based motion modeling. The accuracy of these estimated residual tumor motions and duty cycles are evaluated by comparing to the measured internal/external motions from other treatment days. Results: All calculations were done for 25% and 50% duty cycles. The results indicated that duty cycle derived from 4DCT information alone is not enough to accurately predict duty cycles during treatment. Residual tumor motion was determined from the recorded data and compared with the estimated residual tumor motion from 4DCT. Relative differences in residual tumor motion varied from −30% to 55%, suggesting that more information is required to properly predict residual tumor motion. Compared to estimations made from 4DCT, in three out of four patients examined, the 30 seconds of motion modeling data was able to predict the duty cycle with better accuracy than 4DCT. No improvement was observed in prediction of residual tumor motion for this dataset. Conclusion: Motion modeling during simulation has the potential to enhance 4DCT and provide more information about target motion, duty cycles, and delivered dose. Based on these four patients, 30 seconds of motion modeling data produced improve duty cycle estimations but showed no measurable improvement in residual tumor motion prediction. More patient data is needed to verify this Result. I would like to

  19. On entropy weak solutions of Hughes' model for pedestrian motion

    NASA Astrophysics Data System (ADS)

    El-Khatib, Nader; Goatin, Paola; Rosini, Massimiliano D.

    2013-04-01

    We consider a generalized version of Hughes' macroscopic model for crowd motion in the one-dimensional case. It consists in a scalar conservation law accounting for the conservation of the number of pedestrians, coupled with an eikonal equation giving the direction of the flux depending on pedestrian density. As a result of this non-trivial coupling, we have to deal with a conservation law with space-time discontinuous flux, whose discontinuity depends non-locally on the density itself. We propose a definition of entropy weak solution, which allows us to recover a maximum principle. Moreover, we study the structure of the solutions to Riemann-type problems, and we construct them explicitly for small times, depending on the choice of the running cost in the eikonal equation. In particular, aiming at the optimization of the evacuation time, we propose a strategy that is optimal in the case of high densities. All results are illustrated by numerical simulations.

  20. Models for motion-based video indexing and retrieval.

    PubMed

    Dağtaş, S; Al-Khatib, W; Ghafoor, A; Kashyap, R L

    2000-01-01

    With the rapid proliferation of multimedia applications that require video data management, it is becoming more desirable to provide proper video data indexing techniques capable of representing the rich semantics in video data. In real-time applications, the need for efficient query processing is another reason for the use of such techniques. We present models that use the object motion information in order to characterize the events to allow subsequent retrieval. Algorithms for different spatiotemporal search cases in terms of spatial and temporal translation and scale invariance have been developed using various signal and image processing techniques. We have developed a prototype video search engine, PICTURESQUE (pictorial information and content transformation unified retrieval engine for spatiotemporal queries) to verify the proposed methods. Development of such technology will enable true multimedia search engines that will enable indexing and searching of the digital video data based on its true content. PMID:18255375

  1. A Generalized Brownian Motion Model for Turbulent Relative Particle Dispersion

    NASA Astrophysics Data System (ADS)

    Shivamoggi, Bhimsen

    2015-11-01

    A generalized Brownian motion model has been applied to the turbulent relative particle dispersion problem (Shivamoggi). The fluctuating pressure forces acting on a fluid particle are taken to follow an Uhlenbeck-Ornstein process while it appears plausible to take their correlation time to have a power-law dependence on the flow Reynolds number Re. This ansatz provides an insight into the result that the Richardson-Obukhov scaling holds only in the infinite-Re limit and disappears otherwise. It provides a determination of the Richardson-Obukhov constant g as a function of Re, with an asymptotic constant value in the infinite-Re limit. This ansatz is further shown to be in quantitative agreement, in the small-Re limit, with the Batchelor-Townsend ansatz for the rate of change of the mean square interparticle separation in 3D FDT. My thanks to The Netherlands Organization for Scientific Research for Support.

  2. Optimal dividends in the Brownian motion risk model with interest

    NASA Astrophysics Data System (ADS)

    Fang, Ying; Wu, Rong

    2009-07-01

    In this paper, we consider a Brownian motion risk model, and in addition, the surplus earns investment income at a constant force of interest. The objective is to find a dividend policy so as to maximize the expected discounted value of dividend payments. It is well known that optimality is achieved by using a barrier strategy for unrestricted dividend rate. However, ultimate ruin of the company is certain if a barrier strategy is applied. In many circumstances this is not desirable. This consideration leads us to impose a restriction on the dividend stream. We assume that dividends are paid to the shareholders according to admissible strategies whose dividend rate is bounded by a constant. Under this additional constraint, we show that the optimal dividend strategy is formed by a threshold strategy.

  3. Early breakup of Gondwana: constraints from global plate motion models

    NASA Astrophysics Data System (ADS)

    Seton, Maria; Zahirovic, Sabin; Williams, Simon; Whittaker, Joanne; Gibbons, Ana; Muller, Dietmar; Brune, Sascha; Heine, Christian

    2015-04-01

    Supercontinent break-up and amalgamation is a fundamental Earth cycle, contributing to long-term sea-level fluctuations, species diversity and extinction events, long-term greenhouse-icehouse cycles and changes in the long-wavelength density structure of the mantle. The most recent and best-constrained example involves the fragmentation of Gondwana, starting with rifting between Africa/Madagascar and Antarctica in the Early Jurassic and ending with the separation of the Lord Howe microcontinental blocks east of Australia in the Late Cretaceous. Although the first order configuration of Gondwana within modern reconstructions appears similar to that first proposed by Wegener a century ago, recent studies utilising a wealth of new geophysical and geological data provide a much more detailed picture of relative plate motions both during rifting and subsequent seafloor spreading. We present our latest global plate motion model that includes extensive, new regional analyses. These include: South Atlantic rifting, which started at 150 Ma and propagated into cratonic Africa by 145 Ma (Heine et al., 2013); rifting and early seafloor spreading between Australia, India and Antarctica, which reconciles the fit between Broken Ridge-Kergulean Plateau and the eastern Tasman region (Whittaker et al., 2013); rifting of continental material from northeastern Gondwana and its accretion onto Eurasia and SE Asia including a new model of microcontinent formation and early seafloor spreading in the eastern Indian Ocean (Gibbons et al., 2012; 2013; in review; Williams et al., 2013; Zahirovic et al., 2014); and a new model for the isolation of Zealandia east of Australia, with rifting initiating at 100 Ma until the start of seafloor spreading in the Tasman Sea at ~85 Ma (Williams et al., in prep). Using these reconstructions within the open-source GPlates software, accompanied by a set of evolving plates and plate boundaries, we can explore the factors that govern the behavior of plate

  4. Digital resolver for helicopter model blade motion analysis

    NASA Technical Reports Server (NTRS)

    Daniels, T. S.; Berry, J. D.; Park, S.

    1992-01-01

    The paper reports the development and initial testing of a digital resolver to replace existing analog signal processing instrumentation. Radiometers, mounted directly on one of the fully articulated blades, are electrically connected through a slip ring to analog signal processing circuitry. The measured signals are periodic with azimuth angle and are resolved into harmonic components, with 0 deg over the tail. The periodic nature of the helicopter blade motion restricts the frequency content of each flapping and yaw signal to the fundamental and harmonics of the rotor rotational frequency. A minicomputer is employed to collect these data and then plot them graphically in real time. With this and other information generated by the instrumentation, a helicopter test pilot can then adjust the helicopter model's controls to achieve the desired aerodynamic test conditions.

  5. A model for the pilot's use of motion cues in roll-axis tracking tasks

    NASA Technical Reports Server (NTRS)

    Levison, W. H.; Junker, A. M.

    1977-01-01

    Simulated target-following and disturbance-regulation tasks were explored with subjects using visual-only and combined visual and motion cues. The effects of motion cues on task performance and pilot response behavior were appreciably different for the two task configurations and were consistent with data reported in earlier studies for similar task configurations. The optimal-control model for pilot/vehicle systems provided a task-independent framework for accounting for the pilot's use of motion cues. Specifically, the availability of motion cues was modeled by augmenting the set of perceptual variables to include position, rate, acceleration, and accleration-rate of the motion simulator, and results were consistent with the hypothesis of attention-sharing between visual and motion variables. This straightforward informational model allowed accurate model predictions of the effects of motion cues on a variety of response measures for both the target-following and disturbance-regulation tasks.

  6. Cytoplasm dynamics and cell motion: two-phase flow models.

    PubMed

    Alt, W; Dembo, M

    1999-03-01

    The motion of amoeboid cells is characterized by cytoplasmic streaming and by membrane protrusions and retractions which occur even in the absence of interactions with a substratum. Cell translocation requires, in addition, a transmission mechanism wherein the power produced by the cytoplasmic engine is applied to the substratum in a highly controlled fashion through specific adhesion proteins. Here we present a simple mechano-chemical model that tries to capture the physical essence of these complex biomolecular processes. Our model is based on the continuum equations for a viscous and reactive two-phase fluid model with moving boundaries, and on force balance equations that average the stochastic interactions between actin polymers and membrane proteins. In this paper we present a new derivation and analysis of these equations based on minimization of a power functional. This derivation also leads to a clear formulation and classification of the kinds of boundary conditions that should be specified at free surfaces and at the sites of interaction of the cell and the substratum. Numerical simulations of a one-dimensional lamella reveal that even this extremely simplified model is capable of producing several typical features of cell motility. These include periodic 'ruffle' formation, protrusion-retraction cycles, centripetal flow and cell-substratum traction forces. PMID:10204394

  7. Mathematical models of polymer solutions motion and their symmetries

    NASA Astrophysics Data System (ADS)

    Bozhkov, Yu. D.; Pukhnachev, V. V.; Pukhnacheva, T. P.

    2015-10-01

    We consider three mathematical models describing motion of aqueous polymer solutions. All of them are derived from equations of Maxwell type viscoelastic medium at small relaxation time. Distinction consists in the choice of time derivative in the rheological constitutive law. Namely, we can choose (a) connective, (b) partial or (c) objective derivative of the strain tensor in time. We found widest symmetry groups admitted by each of these models. Systems (a) and (c) admit the extended Galilei group containing four arbitrary functions of time while the group admitted by system (b) is rather poor. Wide classes of exact solutions are obtained and their behaviors are analyzed if the relaxation viscosity tends to zero. Asymptotic expansion in this solution's parameter describing the flow near a critical point in planar and axially symmetric cases is derived. Analogs of the classical Hagen-Poiseuille and Nusselt solutions are studied too. We found difference in the pressure distribution between solutions calculated on the base of model (c) and two other models.

  8. Deciphering the Crowd: Modeling and Identification of Pedestrian Group Motion

    PubMed Central

    Yücel, Zeynep; Zanlungo, Francesco; Ikeda, Tetsushi; Miyashita, Takahiro; Hagita, Norihiro

    2013-01-01

    Associating attributes to pedestrians in a crowd is relevant for various areas like surveillance, customer profiling and service providing. The attributes of interest greatly depend on the application domain and might involve such social relations as friends or family as well as the hierarchy of the group including the leader or subordinates. Nevertheless, the complex social setting inherently complicates this task. We attack this problem by exploiting the small group structures in the crowd. The relations among individuals and their peers within a social group are reliable indicators of social attributes. To that end, this paper identifies social groups based on explicit motion models integrated through a hypothesis testing scheme. We develop two models relating positional and directional relations. A pair of pedestrians is identified as belonging to the same group or not by utilizing the two models in parallel, which defines a compound hypothesis testing scheme. By testing the proposed approach on three datasets with different environmental properties and group characteristics, it is demonstrated that we achieve an identification accuracy of 87% to 99%. The contribution of this study lies in its definition of positional and directional relation models, its description of compound evaluations, and the resolution of ambiguities with our proposed uncertainty measure based on the local and global indicators of group relation. PMID:23344382

  9. The use of vestibular models for design and evaluation of flight simulator motion

    NASA Technical Reports Server (NTRS)

    Bussolari, Steven R.; Young, Laurence R.; Lee, Alfred T.

    1989-01-01

    Quantitative models for the dynamics of the human vestibular system are applied to the design and evaluation of flight simulator platform motion. An optimal simulator motion control algorithm is generated to minimize the vector difference between perceived spatial orientation estimated in flight and in simulation. The motion controller has been implemented on the Vertical Motion Simulator at NASA Ames Research Center and evaluated experimentally through measurement of pilot performance and subjective rating during VTOL aircraft simulation. In general, pilot performance in a longitudinal tracking task (formation flight) did not appear to be sensitive to variations in platform motion condition as long as motion was present. However, pilot assessment of motion fidelity by means of a rating scale designed for this purpose, were sensitive to motion controller design. Platform motion generated with the optimal motion controller was found to be generally equivalent to that generated by conventional linear crossfeed washout. The vestibular models are used to evaluate the motion fidelity of transport category aircraft (Boeing 727) simulation in a pilot performance and simulator acceptability study at the Man-Vehicle Systems Research Facility at NASA Ames Research Center. Eighteen airline pilots, currently flying B-727, were given a series of flight scenarios in the simulator under various conditions of simulator motion. The scenarios were chosen to reflect the flight maneuvers that these pilots might expect to be given during a routine pilot proficiency check. Pilot performance and subjective rating of simulator fidelity was relatively insensitive to the motion condition, despite large differences in the amplitude of motion provided. This lack of sensitivity may be explained by means of the vestibular models, which predict little difference in the modeled motion sensations of the pilots when different motion conditions are imposed.

  10. Ridge-spotting: A new test for Pacific absolute plate motion models

    NASA Astrophysics Data System (ADS)

    Wessel, Paul; Müller, R. Dietmar

    2016-06-01

    Relative plate motions provide high-resolution descriptions of motions of plates relative to other plates. Yet geodynamically, motions of plates relative to the mantle are required since such motions can be attributed to forces (e.g., slab pull and ridge push) acting upon the plates. Various reference frames have been proposed, such as the hot spot reference frame, to link plate motions to a mantle framework. Unfortunately, both accuracy and precision of absolute plate motion models lag behind those of relative plate motion models. Consequently, it is paramount to use relative plate motions in improving our understanding of absolute plate motions. A new technique called "ridge-spotting" combines absolute and relative plate motions and examines the viability of proposed absolute plate motion models. We test the method on six published Pacific absolute plate motions models, including fixed and moving hot spot models as well as a geodynamically derived model. Ridge-spotting reconstructs the Pacific-Farallon and Pacific-Antarctica ridge systems over the last 80 Myr. All six absolute plate motion models predict large amounts of northward migration and monotonic clockwise rotation for the Pacific-Farallon ridge. A geodynamic implication of our ridge migration predictions is that the suggestion that the Pacific-Farallon ridge may have been pinned by a large mantle upwelling is not supported. Unexpected or erratic ridge behaviors may be tied to limitations in the models themselves or (for Indo-Atlantic models) discrepancies in the plate circuits used to project models into the Pacific realm. Ridge-spotting is promising and will be extended to include more plates and other ocean basins.

  11. Modeling closure of circular wounds through coordinated collective motion

    NASA Astrophysics Data System (ADS)

    Li, David S.; Zimmermann, Juliane; Levine, Herbert

    2016-02-01

    Wound healing enables tissues to restore their original states, and is achieved through collective cell migration into the wound space, contraction of the wound edge via an actomyosin filament ‘purse-string,’ as well as cell division. Recently, experimental techniques have been developed to create wounds with various regular morphologies in epithelial monolayers, and these experiments of circular closed-contour wounds support coordinated lamellipodial cell crawling as the predominant driver of gap closure. Through utilizing a particle-based mechanical tissue simulation, exhibiting long-range coordination of cell motility, we computationally model these closed-contour experiments with a high level of agreement between experimentally observed and simulated wound closure dynamics and tissue velocity profiles. We also determine the sensitivity of wound closure time in the model to changes in cell motility force and division rate. Our simulation results confirm that circular wounds can close due to collective cell migration without the necessity for a purse-string mechanism or for cell division, and show that the alignment mechanism of cellular motility force with velocity, leading to collective motion in the model, may speed up wound closure.

  12. Modeling closure of circular wounds through coordinated collective motion.

    PubMed

    Li, David S; Zimmermann, Juliane; Levine, Herbert

    2016-02-01

    Wound healing enables tissues to restore their original states, and is achieved through collective cell migration into the wound space, contraction of the wound edge via an actomyosin filament 'purse-string,' as well as cell division. Recently, experimental techniques have been developed to create wounds with various regular morphologies in epithelial monolayers, and these experiments of circular closed-contour wounds support coordinated lamellipodial cell crawling as the predominant driver of gap closure. Through utilizing a particle-based mechanical tissue simulation, exhibiting long-range coordination of cell motility, we computationally model these closed-contour experiments with a high level of agreement between experimentally observed and simulated wound closure dynamics and tissue velocity profiles. We also determine the sensitivity of wound closure time in the model to changes in cell motility force and division rate. Our simulation results confirm that circular wounds can close due to collective cell migration without the necessity for a purse-string mechanism or for cell division, and show that the alignment mechanism of cellular motility force with velocity, leading to collective motion in the model, may speed up wound closure. PMID:26871883

  13. Micro air vehicle motion tracking and aerodynamic modeling

    NASA Astrophysics Data System (ADS)

    Uhlig, Daniel V.

    exhibited quasi-steady effects caused by small variations in the angle of attack. The quasi-steady effects, or small unsteady effects, caused variations in the aerodynamic characteristics (particularly incrementing the lift curve), and the magnitude of the influence depended on the angle-of-attack rate. In addition to nominal gliding flight, MAVs in general are capable of flying over a wide flight envelope including agile maneuvers such as perching, hovering, deep stall and maneuvering in confined spaces. From the captured motion trajectories, the aerodynamic characteristics during the numerous unsteady flights were gathered without the complexity required for unsteady wind tunnel tests. Experimental results for the MAVs show large flight envelopes that included high angles of attack (on the order of 90 deg) and high angular rates, and the aerodynamic coefficients had dynamic stall hysteresis loops and large values. From the large number of unsteady high angle-of-attack flights, an aerodynamic modeling method was developed and refined for unsteady MAV flight at high angles of attack. The method was based on a separation parameter that depended on the time history of the angle of attack and angle-of-attack rate. The separation parameter accounted for the time lag inherit in the longitudinal characteristics during dynamic maneuvers. The method was applied to three MAVs and showed general agreement with unsteady experimental results and with nominal gliding flight results. The flight tests with the MAVs indicate that modern motion tracking systems are capable of capturing the flight trajectories, and the captured trajectories can be used to determine the aerodynamic characteristics. From the captured trajectories, low Reynolds number MAV flight is explored in both nominal gliding flight and unsteady high angle-of-attack flight. Building on the experimental results, a modeling method for the longitudinal characteristics is developed that is applicable to the full flight

  14. Affinity of HIV-1 antibody 2G12 with monosaccharides: a theoretical study based on explicit and implicit water models.

    PubMed

    Koyama, Yuka; Ueno-Noto, Kaori; Takano, Keiko

    2014-04-01

    In order to develop potential ligands to HIV-1 antibody 2G12 toward HIV-1 vaccine, binding mechanisms of the antibody 2G12 with the glycan ligand of D-mannose and D-fructose were theoretically examined. D-Fructose, whose molecular structure is slightly different from D-mannose, has experimentally shown to have stronger binding affinity to the antibody than that of D-mannose. To clarify the nature of D-fructose's higher binding affinity over D-mannose, we studied interaction between the monosaccharides and the antibody using ab initio fragment molecular orbital (FMO) method considering solvation effect as implicit model (FMO-PCM) as well as explicit water model. The calculated binding free energies of the glycans were qualitatively well consistent with the experimentally reported order of their affinities with the antibody 2G12. In addition, the FMO-PCM calculation elucidated the advantages of D-fructose over D-mannose in the solvation energy as well as the entropic contribution term obtained by MD simulations. The effects of explicit water molecules observed in the X-ray crystal structure were also scrutinized by means of FMO methods. Significant pair interaction energies among D-fructose, amino acids, and water molecules were uncovered, which indicated contributions from the water molecules to the strong binding ability of D-fructose to the antibody 2G12. These FMO calculation results of explicit water model as well as implicit water model indicated that the strong binding of D-fructose over D-mannose was due to the solvation effects on the D-fructose interaction energy. PMID:24583603

  15. Ground-motion modeling of Hayward fault scenario earthquakes, part II: Simulation of long-period and broadband ground motions

    USGS Publications Warehouse

    Aagaard, Brad T.; Graves, Robert W.; Rodgers, Arthur; Brocher, Thomas M.; Simpson, Robert W.; Dreger, Douglas; Petersson, N. Anders; Larsen, Shawn C.; Ma, Shuo; Jachens, Robert C.

    2010-01-01

    We simulate long-period (T>1.0–2.0 s) and broadband (T>0.1 s) ground motions for 39 scenario earthquakes (Mw 6.7–7.2) involving the Hayward, Calaveras, and Rodgers Creek faults. For rupture on the Hayward fault, we consider the effects of creep on coseismic slip using two different approaches, both of which reduce the ground motions, compared with neglecting the influence of creep. Nevertheless, the scenario earthquakes generate strong shaking throughout the San Francisco Bay area, with about 50% of the urban area experiencing modified Mercalli intensity VII or greater for the magnitude 7.0 scenario events. Long-period simulations of the 2007 Mw 4.18 Oakland earthquake and the 2007 Mw 5.45 Alum Rock earthquake show that the U.S. Geological Survey’s Bay Area Velocity Model version 08.3.0 permits simulation of the amplitude and duration of shaking throughout the San Francisco Bay area for Hayward fault earthquakes, with the greatest accuracy in the Santa Clara Valley (San Jose area). The ground motions for the suite of scenarios exhibit a strong sensitivity to the rupture length (or magnitude), hypocenter (or rupture directivity), and slip distribution. The ground motions display a much weaker sensitivity to the rise time and rupture speed. Peak velocities, peak accelerations, and spectral accelerations from the synthetic broadband ground motions are, on average, slightly higher than the Next Generation Attenuation (NGA) ground-motion prediction equations. We attribute much of this difference to the seismic velocity structure in the San Francisco Bay area and how the NGA models account for basin amplification; the NGA relations may underpredict amplification in shallow sedimentary basins. The simulations also suggest that the Spudich and Chiou (2008) directivity corrections to the NGA relations could be improved by increasing the areal extent of rupture directivity with period.

  16. Analytic model for surface ground motion with spall induced by underground nuclear tests

    SciTech Connect

    MacQueen, D.H.

    1982-04-01

    This report provides a detailed presentation and critique of a model used to characterize the surface ground motion following a contained, spalling underground nuclear explosion intended for calculation of the resulting atmospheric acoustic pulse. Some examples of its use are included. Some discussion of the general approach of ground motion model parameter extraction, not dependent on the specific model, is also presented.

  17. Demonstrating Circular Motion with a Model Satellite/Earth System

    ERIC Educational Resources Information Center

    Whittaker, Jeff

    2008-01-01

    A number of interesting demonstrations of circular and satellite motion have been described in this journal. This paper presents a variation of a centripetal force apparatus found in G.D. Freier and F.J. Anderson's "A Demonstration Handbook for Physics," which has been modified in order to demonstrate both centripetal force and satellite motion.…

  18. Hamiltonian model of capture into mean motion resonance

    NASA Astrophysics Data System (ADS)

    Mustill, Alexander J.; Wyatt, Mark C.

    2011-11-01

    Mean motion resonances are a common feature of both our own Solar System and of extrasolar planetary systems. Bodies can be trapped in resonance when their orbital semi-major axes change, for instance when they migrate through a protoplanetary disc. We use a Hamiltonian model to thoroughly investigate the capture behaviour for first and second order resonances. Using this method, all resonances of the same order can be described by one equation, with applications to specific resonances by appropriate scaling. We focus on the limit where one body is a massless test particle and the other a massive planet. We quantify how the the probability of capture into a resonance depends on the relative migration rate of the planet and particle, and the particle's eccentricity. Resonant capture fails for high migration rates, and has decreasing probability for higher eccentricities, although for certain migration rates, capture probability peaks at a finite eccentricity. We also calculate libration amplitudes and the offset of the libration centres for captured particles, and the change in eccentricity if capture does not occur. Libration amplitudes are higher for larger initial eccentricity. The model allows for a complete description of a particle's behaviour as it successively encounters several resonances. The model is applicable to many scenarios, including (i) Planet migration through gas discs trapping other planets or planetesimals in resonances; (ii) Planet migration through a debris disc; (iii) Dust migration through PR drag. The Hamiltonian model will allow quick interpretation of the resonant properties of extrasolar planets and Kuiper Belt Objects, and will allow synthetic images of debris disc structures to be quickly generated, which will be useful for predicting and interpreting disc images made with ALMA, Darwin/TPF or similar missions. Full details can be found in Mustill & Wyatt (2011).

  19. Towards the chemometric dissection of peptide--HLA-A*0201 binding affinity: comparison of local and global QSAR models.

    PubMed

    Doytchinova, Irini A; Walshe, Valerie; Borrow, Persephone; Flower, Darren R

    2005-03-01

    The affinities of 177 nonameric peptides binding to the HLA-A*0201 molecule were measured using a FACS-based MHC stabilisation assay and analysed using chemometrics. Their structures were described by global and local descriptors, QSAR models were derived by genetic algorithm, stepwise regression and PLS. The global molecular descriptors included molecular connectivity chi indices, kappa shape indices, E-state indices, molecular properties like molecular weight and log P, and three-dimensional descriptors like polarizability, surface area and volume. The local descriptors were of two types. The first used a binary string to indicate the presence of each amino acid type at each position of the peptide. The second was also position-dependent but used five z-scales to describe the main physicochemical properties of the amino acids forming the peptides. The models were developed using a representative training set of 131 peptides and validated using an independent test set of 46 peptides. It was found that the global descriptors could not explain the variance in the training set nor predict the affinities of the test set accurately. Both types of local descriptors gave QSAR models with better explained variance and predictive ability. The results suggest that, in their interactions with the MHC molecule, the peptide acts as a complicated ensemble of multiple amino acids mutually potentiating each other. PMID:16059672

  20. Validation and modeling of earthquake strong ground motion using a composite source model

    NASA Astrophysics Data System (ADS)

    Zeng, Y.

    2001-12-01

    Zeng et al. (1994) have proposed a composite source model for synthetic strong ground motion prediction. In that model, the source is taken as a superposition of circular subevents with a constant stress drop. The number of subevents and their radius follows a power law distribution equivalent to the Gutenberg and Richter's magnitude-frequency relation for seismicity. The heterogeneous nature of the composite source model is characterized by its maximum subevent size and subevent stress drop. As rupture propagates through each subevent, it radiates a Brune's pulse or a Sato and Hirasawa's circular crack pulse. The method has been proved to be successful in generating realistic strong motion seismograms in comparison with observations from earthquakes in California, eastern US, Guerrero of Mexico, Turkey and India. The model has since been improved by including scattering waves from small scale heterogeneity structure of the earth, site specific ground motion prediction using weak motion site amplification, and nonlinear soil response using geotechnical engineering models. Last year, I have introduced an asymmetric circular rupture to improve the subevent source radiation and to provide a consistent rupture model between overall fault rupture process and its subevents. In this study, I revisit the Landers, Loma Prieta, Northridge, Imperial Valley and Kobe earthquakes using the improved source model. The results show that the improved subevent ruptures provide an improved effect of rupture directivity compared to our previous studies. Additional validation includes comparison of synthetic strong ground motions to the observed ground accelerations from the Chi-Chi, Taiwan and Izmit, Turkey earthquakes. Since the method has evolved considerably when it was first proposed, I will also compare results between each major modification of the model and demonstrate its backward compatibility to any of its early simulation procedures.

  1. Ground motion modeling of Hayward fault scenario earthquakes II:Simulation of long-period and broadband ground motions

    SciTech Connect

    Aagaard, B T; Graves, R W; Rodgers, A; Brocher, T M; Simpson, R W; Dreger, D; Petersson, N A; Larsen, S C; Ma, S; Jachens, R C

    2009-11-04

    We simulate long-period (T > 1.0-2.0 s) and broadband (T > 0.1 s) ground motions for 39 scenarios earthquakes (Mw 6.7-7.2) involving the Hayward, Calaveras, and Rodgers Creek faults. For rupture on the Hayward fault we consider the effects of creep on coseismic slip using two different approaches, both of which reduce the ground motions compared with neglecting the influence of creep. Nevertheless, the scenario earthquakes generate strong shaking throughout the San Francisco Bay area with about 50% of the urban area experiencing MMI VII or greater for the magnitude 7.0 scenario events. Long-period simulations of the 2007 Mw 4.18 Oakland and 2007 Mw 4.5 Alum Rock earthquakes show that the USGS Bay Area Velocity Model version 08.3.0 permits simulation of the amplitude and duration of shaking throughout the San Francisco Bay area, with the greatest accuracy in the Santa Clara Valley (San Jose area). The ground motions exhibit a strong sensitivity to the rupture length (or magnitude), hypocenter (or rupture directivity), and slip distribution. The ground motions display a much weaker sensitivity to the rise time and rupture speed. Peak velocities, peak accelerations, and spectral accelerations from the synthetic broadband ground motions are, on average, slightly higher than the Next Generation Attenuation (NGA) ground-motion prediction equations. We attribute at least some of this difference to the relatively narrow width of the Hayward fault ruptures. The simulations suggest that the Spudich and Chiou (2008) directivity corrections to the NGA relations could be improved by including a dependence on the rupture speed and increasing the areal extent of rupture directivity with period. The simulations also indicate that the NGA relations may under-predict amplification in shallow sedimentary basins.

  2. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods

    SciTech Connect

    Politi, Regina; Rusyn, Ivan; Tropsha, Alexander

    2014-10-01

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R{sup 2} = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R{sup 2} = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables

  3. Facial motion parameter estimation and error criteria in model-based image coding

    NASA Astrophysics Data System (ADS)

    Liu, Yunhai; Yu, Lu; Yao, Qingdong

    2000-04-01

    Model-based image coding has been given extensive attention due to its high subject image quality and low bit-rates. But the estimation of object motion parameter is still a difficult problem, and there is not a proper error criteria for the quality assessment that are consistent with visual properties. This paper presents an algorithm of the facial motion parameter estimation based on feature point correspondence and gives the motion parameter error criteria. The facial motion model comprises of three parts. The first part is the global 3-D rigid motion of the head, the second part is non-rigid translation motion in jaw area, and the third part consists of local non-rigid expression motion in eyes and mouth areas. The feature points are automatically selected by a function of edges, brightness and end-node outside the blocks of eyes and mouth. The numbers of feature point are adjusted adaptively. The jaw translation motion is tracked by the changes of the feature point position of jaw. The areas of non-rigid expression motion can be rebuilt by using block-pasting method. The estimation approach of motion parameter error based on the quality of reconstructed image is suggested, and area error function and the error function of contour transition-turn rate are used to be quality criteria. The criteria reflect the image geometric distortion caused by the error of estimated motion parameters properly.

  4. Demonstrating Circular Motion with a Model Satellite/Earth System

    NASA Astrophysics Data System (ADS)

    Whittaker, Jeff

    2008-04-01

    A number of interesting demonstrations of circular and satellite motion have been described in this journal.1-4 This paper presents a variation of a centripetal force apparatus found in G.D. Freier and F.J. Anderson's A Demonstration Handbook for Physics,5 which has been modified in order to demonstrate both centripetal force and satellite motion. Nice discussions of satellite motion may be found in a number of textbooks.6-8 The following is a description of how to construct the apparatus and some suggested experiments.

  5. ANFIS modeling for prediction of particle motions in fluid flows

    NASA Astrophysics Data System (ADS)

    Safdari, Arman; Kim, Kyung Chun

    2015-11-01

    Accurate dynamic analysis of parcel of solid particles driven in fluid flow system is of interest for many natural and industrial applications such as sedimentation process, study of cloud particles in atmosphere, etc. In this paper, numerical modeling of solid particles in incompressible flow using Eulerian-Lagrangian approach is carried out to investigate the dynamic behavior of particles in different flow conditions; channel and cavity flow. Although modern computers have been well developed, the high computational time and costs for this kind of problems are still demanded. The Lattice Boltzmann Method (LBM) is used to simulate fluid flows and combined with the Lagrangian approach to predict the motion of particles in the range of masses. Some particles are selected, and subjected to Adaptive-network-based fuzzy inference system (ANFIS) to predict the trajectory of moving solid particles. Using a hybrid learning procedure from computational particle movement, the ANFIS can construct an input-output mapping based on fuzzy if-then rules and stipulated computational fluid dynamics prediction pairs. The obtained results from ANFIS algorithm is validated and compared with the set of benchmark data provided based on point-like approach coupled with the LBM method.

  6. A generalized Brownian motion model for turbulent relative particle dispersion

    NASA Astrophysics Data System (ADS)

    Shivamoggi, B. K.

    2016-08-01

    There is speculation that the difficulty in obtaining an extended range with Richardson-Obukhov scaling in both laboratory experiments and numerical simulations is due to the finiteness of the flow Reynolds number Re in these situations. In this paper, a generalized Brownian motion model has been applied to describe the relative particle dispersion problem in more realistic turbulent flows and to shed some light on this issue. The fluctuating pressure forces acting on a fluid particle are taken to be a colored noise and follow a stationary process and are described by the Uhlenbeck-Ornstein model while it appears plausible to take their correlation time to have a power-law dependence on Re, thus introducing a bridge between the Lagrangian quantities and the Eulerian parameters for this problem. This ansatz is in qualitative agreement with the possibility of a connection speculated earlier by Corrsin [26] between the white-noise representation for the fluctuating pressure forces and the large-Re assumption in the Kolmogorov [4] theory for the 3D fully developed turbulence (FDT) as well as a similar argument of Monin and Yaglom [23] and a similar result of Sawford [13] and Borgas and Sawford [24]. It also provides an insight into the result that the Richardson-Obukhov scaling holds only in the infinite-Re limit and disappears otherwise. This ansatz further provides a determination of the Richardson-Obukhov constant g as a function of Re, with an asymptotic constant value in the infinite-Re limit. It is shown to lead to full agreement, in the small-Re limit as well, with the Batchelor-Townsend [27] scaling for the rate of change of the mean square interparticle separation in 3D FDT, hence validating its soundness further.

  7. Unsteady aerodynamic modeling for arbitrary motions. [for active control techniques

    NASA Technical Reports Server (NTRS)

    Edwards, J. W.

    1977-01-01

    Results indicating that unsteady aerodynamic loads derived under the assumption of simple harmonic motions executed by airfoil or wing can be extended to arbitrary motions are summarized. The generalized Theodorsen (1953) function referable to loads due to simple harmonic oscillations of a wing section in incompressible flow, the Laplace inversion integral for unsteady aerodynamic loads, calculations of root loci of aeroelastic loads, and analysis of generalized compressible transient airloads are discussed.

  8. Mathematical model for the simulation of Dynamic Docking Test System (DDST) active table motion

    NASA Technical Reports Server (NTRS)

    Gates, R. M.; Graves, D. L.

    1974-01-01

    The mathematical model developed to describe the three-dimensional motion of the dynamic docking test system active table is described. The active table is modeled as a rigid body supported by six flexible hydraulic actuators which produce the commanded table motions.

  9. Analytic signal phase-based myocardial motion estimation in tagged MRI sequences by a bilinear model and motion compensation.

    PubMed

    Wang, Liang; Basarab, Adrian; Girard, Patrick R; Croisille, Pierre; Clarysse, Patrick; Delachartre, Philippe

    2015-08-01

    Different mathematical tools, such as multidimensional analytic signals, allow for the calculation of 2D spatial phases of real-value images. The motion estimation method proposed in this paper is based on two spatial phases of the 2D analytic signal applied to cardiac sequences. By combining the information of these phases issued from analytic signals of two successive frames, we propose an analytical estimator for 2D local displacements. To improve the accuracy of the motion estimation, a local bilinear deformation model is used within an iterative estimation scheme. The main advantages of our method are: (1) The phase-based method allows the displacement to be estimated with subpixel accuracy and is robust to image intensity variation in time; (2) Preliminary filtering is not required due to the bilinear model. The proposed algorithm, integrating phase-based optical flow motion estimation and the combination of global motion compensation with local bilinear transform, allows spatio-temporal cardiac motion analysis, e.g. strain and dense trajectory estimation over the cardiac cycle. Results from 7 realistic simulated tagged magnetic resonance imaging (MRI) sequences show that our method is more accurate compared with state-of-the-art method for cardiac motion analysis and with another differential approach from the literature. The motion estimation errors (end point error) of the proposed method are reduced by about 33% compared with that of the two methods. In our work, the frame-to-frame displacements are further accumulated in time, to allow for the calculation of myocardial Lagrangian cardiac strains and point trajectories. Indeed, from the estimated trajectories in time on 11 in vivo data sets (9 patients and 2 healthy volunteers), the shape of myocardial point trajectories belonging to pathological regions are clearly reduced in magnitude compared with the ones from normal regions. Myocardial point trajectories, estimated from our phase-based analytic

  10. Testing the Double Corner Source Spectral Model for Long- and Short-Period Ground Motion Simulations

    NASA Astrophysics Data System (ADS)

    Miyake, H.; Koketsu, K.

    2010-12-01

    The omega-squared source model with a single corner frequency is widely used in the earthquake source analyses and ground motion simulations. Recent studies show that the Brune stress drop of subduction-zone earthquakes is almost half of that for crustal earthquakes for a given magnitude. On the other hand, the empirical attenuation relations and spectral analyses of seismic source and ground motions support the fact that subduction-zone earthquakes provide 1-2 times of the short-period source spectral level for crustal earthquakes. To link long- and short-period source characteristics is a crucial issue to perform broadband ground motion simulations. This discrepancy may lead the source modeling with double corner frequencies [e.g., Atkinson, 1993]. We modeled the lower corner frequency corresponding to the size of asperities generating for long-period (> 2-5 s) ground motions by the deterministic approach and the higher corner frequency corresponding to the size of strong motion generation area for short-period ground motions by the semi-empirical approach. We propose that the double corner source spectral model is expressed as a frequency-dependent source model consists of either the asperities in a long-period range or the strong motion generation area in a short-period range and the surrounding background area inside the total rupture area. The characterized source model has been the potential to reproduce fairly well the rupture directivity pulses seen in the observed ground motions. We explore the applicability of the double corner source spectral model to broadband ground motion simulations for the 1978 Mw 7.6 Miyagi-oki and 2003 Mw 8.3 Tokachi-oki earthquakes along the Japan Trench. For both cases, the double corner source spectral model, where the size and stress drop for strong motion generation areas are respectively half and double of those for asperities, worked well to reproduce ground motion time histories and seismic intensity distribution.

  11. Numerical modeling of on-orbit propellant motion resulting from an impulsive acceleration

    NASA Technical Reports Server (NTRS)

    Aydelott, John C.; Mjolsness, Raymond C.; Torrey, Martin D.; Hochstein, John I.

    1987-01-01

    In-space docking and separation maneuvers of spacecraft that have large fluid mass fractions may cause undesirable spacecraft motion in response to the impulsive-acceleration-induced fluid motion. An example of this potential low gravity fluid management problem arose during the development of the shuttle/Centaur vehicle. Experimentally verified numerical modeling techniques were developed to establish the propellant dynamics, and subsequent vehicle motion, associated with the separation of the Centaur vehicle from the shuttle orbiter cargo bay. Although the shuttle/Centaur development activity was suspended, the numerical modeling techniques are available to predict on-orbit liquid motion resulting from impulsive accelerations for other missions and spacecraft.

  12. Evaluating Effectiveness of Modeling Motion System Feedback in the Enhanced Hess Structural Model of the Human Operator

    NASA Technical Reports Server (NTRS)

    Zaychik, Kirill; Cardullo, Frank; George, Gary; Kelly, Lon C.

    2009-01-01

    In order to use the Hess Structural Model to predict the need for certain cueing systems, George and Cardullo significantly expanded it by adding motion feedback to the model and incorporating models of the motion system dynamics, motion cueing algorithm and a vestibular system. This paper proposes a methodology to evaluate effectiveness of these innovations by performing a comparison analysis of the model performance with and without the expanded motion feedback. The proposed methodology is composed of two stages. The first stage involves fine-tuning parameters of the original Hess structural model in order to match the actual control behavior recorded during the experiments at NASA Visual Motion Simulator (VMS) facility. The parameter tuning procedure utilizes a new automated parameter identification technique, which was developed at the Man-Machine Systems Lab at SUNY Binghamton. In the second stage of the proposed methodology, an expanded motion feedback is added to the structural model. The resulting performance of the model is then compared to that of the original one. As proposed by Hess, metrics to evaluate the performance of the models include comparison against the crossover models standards imposed on the crossover frequency and phase margin of the overall man-machine system. Preliminary results indicate the advantage of having the model of the motion system and motion cueing incorporated into the model of the human operator. It is also demonstrated that the crossover frequency and the phase margin of the expanded model are well within the limits imposed by the crossover model.

  13. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure based modeling methods

    PubMed Central

    Politi, Regina; Rusyn, Ivan; Tropsha, Alexander

    2016-01-01

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure-Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R2=0.55 and CCR=0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R2=0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. PMID:25058446

  14. Hydrological excitation of polar motion by different variables of the GLDAS models

    NASA Astrophysics Data System (ADS)

    Wińska, Małgorzata; Nastula, Jolanta

    Continental hydrological loading, by land water, snow, and ice, is an element that is strongly needed for a full understanding of the excitation of polar motion. In this study we compute different estimations of hydrological excitation functions of polar motion (Hydrological Angular Momentum - HAM) using various variables from the Global Land Data Assimilation System (GLDAS) models of land hydrosphere. The main aim of this study is to show the influence of different variables for example: total evapotranspiration, runoff, snowmelt, soil moisture to polar motion excitations in annual and short term scale. In our consideration we employ several realizations of the GLDAS model as: GLDAS Common Land Model (CLM), GLDAS Mosaic Model, GLDAS National Centers for Environmental Prediction/Oregon State University/Air Force/Hydrologic Research Lab Model (Noah), GLDAS Variable Infiltration Capacity (VIC) Model. Hydrological excitation functions of polar motion, both global and regional, are determined by using selected variables of these GLDAS realizations. First we compare a timing, spectra and phase diagrams of different regional and global HAMs with each other. Next, we estimate, the hydrological signal in geodetically observed polar motion excitation by subtracting the atmospheric -- AAM (pressure + wind) and oceanic -- OAM (bottom pressure + currents) contributions. Finally, the hydrological excitations are compared to these hydrological signal in observed polar motion excitation series. The results help us understand which variables of considered hydrological models are the most important for the polar motion excitation and how well we can close polar motion excitation budget in the seasonal and inter-annual spectral ranges.

  15. An affine continuum mechanical model for cross-linked F-actin networks with compliant linker proteins.

    PubMed

    Holzapfel, Gerhard A; Unterberger, Michael J; Ogden, Ray W

    2014-10-01

    Cross-linked actin networks are important building blocks of the cytoskeleton. In order to gain deeper insight into the interpretation of experimental data on actin networks, adequate models are required. In this paper we introduce an affine constitutive network model for cross-linked F-actin networks based on nonlinear continuum mechanics, and specialize it in order to reproduce the experimental behavior of in vitro reconstituted model networks. The model is based on the elastic properties of single filaments embedded in an isotropic matrix such that the overall properties of the composite are described by a free-energy function. In particular, we are able to obtain the experimentally determined shear and normal stress responses of cross-linked actin networks typically observed in rheometer tests. In the present study an extensive analysis is performed by applying the proposed model network to a simple shear deformation. The single filament model is then extended by incorporating the compliance of cross-linker proteins and further extended by including viscoelasticity. All that is needed for the finite element implementation is the constitutive model for the filaments, the linkers and the matrix, and the associated elasticity tensor in either the Lagrangian or Eulerian formulation. The model facilitates parameter studies of experimental setups such as micropipette aspiration experiments and we present such studies to illustrate the efficacy of this modeling approach. PMID:25043658

  16. Robust fuzzy output feedback controller for affine nonlinear systems via T-S fuzzy bilinear model: CSTR benchmark.

    PubMed

    Hamdy, M; Hamdan, I

    2015-07-01

    In this paper, a robust H∞ fuzzy output feedback controller is designed for a class of affine nonlinear systems with disturbance via Takagi-Sugeno (T-S) fuzzy bilinear model. The parallel distributed compensation (PDC) technique is utilized to design a fuzzy controller. The stability conditions of the overall closed loop T-S fuzzy bilinear model are formulated in terms of Lyapunov function via linear matrix inequality (LMI). The control law is robustified by H∞ sense to attenuate external disturbance. Moreover, the desired controller gains can be obtained by solving a set of LMI. A continuous stirred tank reactor (CSTR), which is a benchmark problem in nonlinear process control, is discussed in detail to verify the effectiveness of the proposed approach with a comparative study. PMID:25765955

  17. Ground motion modeling of the 1906 San Francisco earthquake II: Ground motion estimates for the 1906 earthquake and scenario events

    SciTech Connect

    Aagaard, B; Brocher, T; Dreger, D; Frankel, A; Graves, R; Harmsen, S; Hartzell, S; Larsen, S; McCandless, K; Nilsson, S; Petersson, N A; Rodgers, A; Sjogreen, B; Tkalcic, H; Zoback, M L

    2007-02-09

    We estimate the ground motions produced by the 1906 San Francisco earthquake making use of the recently developed Song et al. (2008) source model that combines the available geodetic and seismic observations and recently constructed 3D geologic and seismic velocity models. Our estimates of the ground motions for the 1906 earthquake are consistent across five ground-motion modeling groups employing different wave propagation codes and simulation domains. The simulations successfully reproduce the main features of the Boatwright and Bundock (2005) ShakeMap, but tend to over predict the intensity of shaking by 0.1-0.5 modified Mercalli intensity (MMI) units. Velocity waveforms at sites throughout the San Francisco Bay Area exhibit characteristics consistent with rupture directivity, local geologic conditions (e.g., sedimentary basins), and the large size of the event (e.g., durations of strong shaking lasting tens of seconds). We also compute ground motions for seven hypothetical scenarios rupturing the same extent of the northern San Andreas fault, considering three additional hypocenters and an additional, random distribution of slip. Rupture directivity exerts the strongest influence on the variations in shaking, although sedimentary basins do consistently contribute to the response in some locations, such as Santa Rosa, Livermore, and San Jose. These scenarios suggest that future large earthquakes on the northern San Andreas fault may subject the current San Francisco Bay urban area to stronger shaking than a repeat of the 1906 earthquake. Ruptures propagating southward towards San Francisco appear to expose more of the urban area to a given intensity level than do ruptures propagating northward.

  18. Whole-Motion Model of Perception during Forward- and Backward-Facing Centrifuge Runs

    PubMed Central

    Holly, Jan E.; Vrublevskis, Arturs; Carlson, Lindsay E.

    2009-01-01

    Illusory perceptions of motion and orientation arise during human centrifuge runs without vision. Asymmetries have been found between acceleration and deceleration, and between forward-facing and backward-facing runs. Perceived roll tilt has been studied extensively during upright fixed-carriage centrifuge runs, and other components have been studied to a lesser extent. Certain, but not all, perceptual asymmetries in acceleration-vs-deceleration and forward-vs-backward motion can be explained by existing analyses. The immediate acceleration-deceleration roll-tilt asymmetry can be explained by the three-dimensional physics of the external stimulus; in addition, longer-term data has been modeled in a standard way using physiological time constants. However, the standard modeling approach is shown in the present research to predict forward-vs-backward-facing symmetry in perceived roll tilt, contradicting experimental data, and to predict perceived sideways motion, rather than forward or backward motion, around a curve. The present work develops a different whole-motion-based model taking into account the three-dimensional form of perceived motion and orientation. This model predicts perceived forward or backward motion around a curve, and predicts additional asymmetries such as the forward-backward difference in roll tilt. This model is based upon many of the same principles as the standard model, but includes an additional concept of familiarity of motions as a whole. PMID:19208962

  19. Minimal Assumptions Comprehensive Electrostatic Model for Mitotic Motions

    NASA Astrophysics Data System (ADS)

    Gagliardi, L. John

    2003-03-01

    Primitive biological cells had to divide using very few biological mechanisms. This work proposes physicochemical mechanisms based on nanoscale electrostatics which explain and unify the basic motions during mitosis: (1) assembly of the asters, (2) motion of asters to poles, (3) chromosome attachment, (4) separation of sister chromatids, (5) prometaphase monovalent attachment motions, (6) chromosome congression to the cell equator, (7) metaphase oscillations, and (8) anaphase A poleward chromosome motion. In the cytosol of cells, electrostatic fields are subject to strong attenuation by ionic screening. However, the presence of microtubules within cells changes the situation completely. Microtubule dimer subunits are electric dipolar structures, and can act as intermediaries which extend the reach of the electrostatic interaction over cellular distances. Experimental studies have shown that intracellular pH rises to a peak at mitosis, and decreases through cytokinesis. This result, in conjunction with the electric dipole nature of microtubule subunits is sufficient to explain the dynamics of the above events and motions, including their timing and sequencing. The physicochemical methods utilized by primitive eukaryotic cells could provide important clues regarding our understanding of cell division in modern eukaryotic cells.

  20. Failure of the three compartment model to describe the pharmacokinetics in brain of a high affinity substituted benzamide.

    PubMed

    Votaw, J R; Kessler, R M; de Paulis, T

    1993-11-01

    The applicability of using the standard 3-compartment model to describe the neuropharmacokinetics of a high affinity substituted benzamide was investigated. We performed the following experiments using the [18F]-5-(3-fluoropropyl) analog of epidepride ([18F]5-FPrEpid), a potent dopamine D2 receptor antagonist: constant left ventricular infusion, first-pass clearance, varying ligand specific activity, and displacing bound ligand with varying amounts of unlabelled ligand. Taken together, the information from these experiments rigorously tests the standard 3-compartment model. The obtained data and predictions from the model of the kinetic behavior of the ligand are inconsistent. The measured and model predicted dissociation rate (measured koff = 0.065 min-1, model prediction koff = 0.007 min-1) and the equilibrium dissociation constant (measured KD = 0.14 nM, model prediction KD = 2.2 nM) differ by an order of magnitude. Furthermore, the model cannot be used to accurately estimate the receptor density. We postulate that the synapse geometry and physical relationship between receptors are necessary components of a model that describes the pharmacokinetics of [18F]5-FPrEpid. PMID:8278896

  1. Motion analysis study on sensitivity of finite element model of the cervical spine to geometry.

    PubMed

    Zafarparandeh, Iman; Erbulut, Deniz U; Ozer, Ali F

    2016-07-01

    Numerous finite element models of the cervical spine have been proposed, with exact geometry or with symmetric approximation in the geometry. However, few researches have investigated the sensitivity of predicted motion responses to the geometry of the cervical spine. The goal of this study was to evaluate the effect of symmetric assumption on the predicted motion by finite element model of the cervical spine. We developed two finite element models of the cervical spine C2-C7. One model was based on the exact geometry of the cervical spine (asymmetric model), whereas the other was symmetric (symmetric model) about the mid-sagittal plane. The predicted range of motion of both models-main and coupled motions-was compared with published experimental data for all motion planes under a full range of loads. The maximum differences between the asymmetric model and symmetric model predictions for the principal motion were 31%, 78%, and 126% for flexion-extension, right-left lateral bending, and right-left axial rotation, respectively. For flexion-extension and lateral bending, the minimum difference was 0%, whereas it was 2% for axial rotation. The maximum coupled motions predicted by the symmetric model were 1.5° axial rotation and 3.6° lateral bending, under applied lateral bending and axial rotation, respectively. Those coupled motions predicted by the asymmetric model were 1.6° axial rotation and 4° lateral bending, under applied lateral bending and axial rotation, respectively. In general, the predicted motion response of the cervical spine by the symmetric model was in the acceptable range and nonlinearity of the moment-rotation curve for the cervical spine was properly predicted. PMID:27107032

  2. Modeling Functional Motions of Biological Systems by Customized Natural Moves.

    PubMed

    Demharter, Samuel; Knapp, Bernhard; Deane, Charlotte M; Minary, Peter

    2016-08-23

    Simulating the functional motions of biomolecular systems requires large computational resources. We introduce a computationally inexpensive protocol for the systematic testing of hypotheses regarding the dynamic behavior of proteins and nucleic acids. The protocol is based on natural move Monte Carlo, a highly efficient conformational sampling method with built-in customization capabilities that allows researchers to design and perform a large number of simulations to investigate functional motions in biological systems. We demonstrate the use of this protocol on both a protein and a DNA case study. Firstly, we investigate the plasticity of a class II major histocompatibility complex in the absence of a bound peptide. Secondly, we study the effects of the epigenetic mark 5-hydroxymethyl on cytosine on the structure of the Dickerson-Drew dodecamer. We show how our customized natural moves protocol can be used to investigate causal relationships of functional motions in biological systems. PMID:27558715

  3. A general model for the perception of space and motion.

    PubMed

    Wade, N J; Swanston, M T

    1996-01-01

    The perception of space and motion involves successive transformations of signals with respect to different reference systems. The visual input is coded in terms of retinal coordinates. The retinocentric values from each eye require to be unified, and to be combined with signals for eye position and movement. This egocentric reference provides a signal for the angular size, motion, or orientation of the stimulus with respect to the observer. The egocentric signals are transformed to a coordinate system that is three-dimensional-the geocentric frame of reference. Further transformations can occur at earlier levels owing to patterncentric interactions within the visual field. When the geocentric signal corresponds to the physical dimensions of space and motion, this is referred to as perceptual constancy. PMID:8733147

  4. Scatter to volume registration for model-free respiratory motion estimation from dynamic MRIs.

    PubMed

    Miao, S; Wang, Z J; Pan, L; Butler, J; Moran, G; Liao, R

    2016-09-01

    Respiratory motion is one major complicating factor in many image acquisition applications and image-guided interventions. Existing respiratory motion estimation and compensation methods typically rely on breathing motion models learned from certain training data, and therefore may not be able to effectively handle intra-subject and/or inter-subject variations of respiratory motion. In this paper, we propose a respiratory motion compensation framework that directly recovers motion fields from sparsely spaced and efficiently acquired dynamic 2-D MRIs without using a learned respiratory motion model. We present a scatter-to-volume deformable registration algorithm to register dynamic 2-D MRIs with a static 3-D MRI to recover dense deformation fields. Practical considerations and approximations are provided to solve the scatter-to-volume registration problem efficiently. The performance of the proposed method was investigated on both synthetic and real MRI datasets, and the results showed significant improvements over the state-of-art respiratory motion modeling methods. We also demonstrated a potential application of the proposed method on MRI-based motion corrected PET imaging using hybrid PET/MRI. PMID:27180910

  5. Center of gravity motions and ankle joint stiffness control in upright undisturbed stance modeled through a fractional Brownian motion framework.

    PubMed

    Rougier, P; Caron, O

    2000-12-01

    The authors modeled the center of gravity vertical projection (CG(v)) and the difference, CP - CG(v), which, combined, constitute the center of pressure (CP) trajectory, as fractional Brownian motion in order to investigate their relative contributions and their spatiotemporal articulation. The results demonstrated that CG(v) and CP - CG(v) motions are both endowed in complementary fashion with strong stochastic and part-deterministic behaviors. In addition, if the temporal coordinates remain similar for all 3 trajectories by definition, the switch between the successive control mechanisms appears for shorter displacements for CP - CG(v) and CG(v) than for CP trajectories. Results deduced from both input (CG(v)) and muscular stiffness (CP - CG(v)) thus provide insight into the way the central nervous system regulates stance control and in particular how CG and CP - CG are controlled. PMID:11114233

  6. Nonlocal contour dynamics model for chemical front motion

    NASA Astrophysics Data System (ADS)

    Petrich, Dean M.; Goldstein, Raymond E.

    1994-02-01

    Pattern formation exhibited by a two-dimensional reaction-diffusion system in the fast inhibitor limit is considered for the point of view of interface motion. A dissipative nonlocal equation of motion for the boundary between high and low concentrations of the slow species is derived heuristically. Under these dynamics, a compact domain of high concentration may develop into a space-filling labyrinthine structure in which nearby fronts repel. Similar patterns have been observed recently by Lee, McCormick, Ouyang, and Swinney in a reacting chemical system.

  7. TU-F-17A-03: An Analytical Respiratory Perturbation Model for Lung Motion Prediction

    SciTech Connect

    Li, G; Yuan, A; Wei, J

    2014-06-15

    Purpose: Breathing irregularity is common, causing unreliable prediction in tumor motion for correlation-based surrogates. Both tidal volume (TV) and breathing pattern (BP=ΔVthorax/TV, where TV=ΔVthorax+ΔVabdomen) affect lung motion in anterior-posterior and superior-inferior directions. We developed a novel respiratory motion perturbation (RMP) model in analytical form to account for changes in TV and BP in motion prediction from simulation to treatment. Methods: The RMP model is an analytical function of patient-specific anatomic and physiologic parameters. It contains a base-motion trajectory d(x,y,z) derived from a 4-dimensional computed tomography (4DCT) at simulation and a perturbation term Δd(ΔTV,ΔBP) accounting for deviation at treatment from simulation. The perturbation is dependent on tumor-specific location and patient-specific anatomy. Eleven patients with simulation and treatment 4DCT images were used to assess the RMP method in motion prediction from 4DCT1 to 4DCT2, and vice versa. For each patient, ten motion trajectories of corresponding points in the lower lobes were measured in both 4DCTs: one served as the base-motion trajectory and the other as the ground truth for comparison. In total, 220 motion trajectory predictions were assessed. The motion discrepancy between two 4DCTs for each patient served as a control. An established 5D motion model was used for comparison. Results: The average absolute error of RMP model prediction in superior-inferior direction is 1.6±1.8 mm, similar to 1.7±1.6 mm from the 5D model (p=0.98). Some uncertainty is associated with limited spatial resolution (2.5mm slice thickness) and temporal resolution (10-phases). Non-corrected motion discrepancy between two 4DCTs is 2.6±2.7mm, with the maximum of ±20mm, and correction is necessary (p=0.01). Conclusion: The analytical motion model predicts lung motion with accuracy similar to the 5D model. The analytical model is based on physical relationships, requires no

  8. Robust velocity computation from a biologically motivated model of motion perception

    PubMed Central

    Johnston, A.; McOwan, P. W.; Benton, C. P.

    1999-01-01

    Current computational models of motion processing in the primate motion pathway do not cope well with image sequences in which a moving pattern is superimposed upon a static texture. The use of non-linear operations and the need for contrast normalization in motion models mean that the separation of the influences of moving and static patterns on the motion computation is not trivial. Therefore, the response to the superposition of static and moving patterns provides an important means of testing various computational strategies. Here we describe a computational model of motion processing in the visual cortex, one of the advantages of which is that it is highly resistant to interference from static patterns.

  9. Modelling the Projectile Motion of a Cricket Ball.

    ERIC Educational Resources Information Center

    Coutis, Peter

    1998-01-01

    Presents the equations of motion governing the trajectory of a cricket ball subject to a linear drag force. Uses a perturbation expansion technique to solve the resulting trajectory equation for the range of a cricket ball struck into the outfield. (Author/ASK)

  10. Comparison of Nonlinear Model Results Using Modified Recorded and Synthetic Ground Motions

    SciTech Connect

    Robert E. Spears; J. Kevin Wilkins

    2011-11-01

    A study has been performed that compares results of nonlinear model runs using two sets of earthquake ground motion time histories that have been modified to fit the same design response spectra. The time histories include applicable modified recorded earthquake ground motion time histories and synthetic ground motion time histories. The modified recorded earthquake ground motion time histories are modified from time history records that are selected based on consistent magnitude and distance. The synthetic ground motion time histories are generated using appropriate Fourier amplitude spectrums, Arias intensity, and drift correction. All of the time history modification is performed using the same algorithm to fit the design response spectra. The study provides data to demonstrate that properly managed synthetic ground motion time histories are reasonable for use in nonlinear seismic analysis.

  11. Estimating Internal Respiratory Motion from Respiratory Surrogate Signals Using Correspondence Models

    NASA Astrophysics Data System (ADS)

    McClelland, Jamie

    It is often difficult or impossible to directly monitor the respiratory motion of the tumour and other internal anatomy during RT treatment. Implanted markers can be used, but this involves an invasive procedure and has a number of other associated risks and problems. An alternative option is to use a correspondence model. This models the relationship between a respiratory surrogate signal(s), such as spirometry or the displacement of the skin surface, and the motion of the internal anatomy. Such a model allows the internal motion to be estimated from the surrogate signal(s), which can be easily monitored during RT treatment. The correspondence model is constructed prior to RT treatment. Imaging data is simultaneously acquired with the surrogate signal(s), and the internal motion is measured from the imaging data, e.g. using deformable image registration. A correspondence model is then fit relating the internal motion to the surrogate signal(s). This can then be used during treatment to estimate the internal motion from the surrogate signal(s). This chapter reviews the most popular correspondence models that have been used in the literature, as well as the different surrogate signals, types of imaging data used to measure the internal motion, and fitting methods used to fit the correspondence model to the data.

  12. Basic simple modeling of balloting motion of railgun projectiles. Technical report

    SciTech Connect

    Chu, S.H.

    1991-07-01

    This is the second of three basic reports dealing with the in-bore balloting motion of a projectile launched in an electromagnetic railgun. The first report addressed axial projectile motion without cocking and was titled A Basic Single Model of In-bore Motion of Railgun Projectiles. Understanding the inbore motion of a projectile is important to its design and its ability to hit a target with some effectiveness. Analysis of in-bore motion is a complicated problem since many parameters are involved and the interacting relationships between them must be determined. To make the problem easier to understand, it was analyzed on several levels beginning with the basic simple model which computed only the axial motion and followed by more complicated models in the upper analysis levels that included as many lateral forces and gun tube vibration effects as possible. This report deals with the second basic or zero level of balloting analysis. A basic simple model considering only the effect of the propulsion force, the friction force of the armature, and the clearance between the projectile and the barrel is presented. The computation of the axial projectile motion with a certain cocking angle is the goal of this analysis. Equations of motion are derived and solved. A sample computation with available data is performed and the results plotted to give a clearer understanding of balloting action.

  13. SU-E-J-163: A Biomechanical Lung Model for Respiratory Motion Study

    SciTech Connect

    Liu, X; Belcher, AH; Grelewicz, Z; Wiersma, RD

    2015-06-15

    Purpose: This work presents a biomechanical model to investigate the complex respiratory motion for the lung tumor tracking in radiosurgery by computer simulation. Methods: The models include networked massspring-dampers to describe the tumor motion, different types of surrogate signals, and the force generated by the diaphragm. Each mass-springdamper has the same mechanical structure and each model can have different numbers of mass-spring-dampers. Both linear and nonlinear stiffness parameters were considered, and the damping ratio was tuned in a range so that the tumor motion was over-damped (no natural tumor oscillation occurs without force from the diaphragm). The simulation was run by using ODE45 (ordinary differential equations by Runge-Kutta method) in MATLAB, and all time courses of motions and inputs (force) were generated and compared. Results: The curvature of the motion time courses around their peaks was sensitive to the damping ratio. Therefore, the damping ratio can be determined based on the clinical data of a high sampling rate. The peak values of different signals and the time the peaks occurred were compared, and it was found that the diaphragm force had a time lead over the tumor motion, and the lead time (0.1–0.4 seconds) depended on the distance between the tumor and the diaphragm. Conclusion: We reported a model based analysis approach for the spatial and temporal relation between the motion of the lung tumor and the surrogate signals. Due to the phase lead of the diaphragm in comparing with the lung tumor motion, the measurement of diaphragm motion (or its electromyography signal) can be used as a beam gating signal in radiosurgery, and it can also be an additional surrogate signal for better tumor motion tracking. The research is funded by the American Cancer Society (ACS) grant. The grant name is: Frameless SRS Based on Robotic Head Motion Cancellation. The grant number is: RSG-13-313-01-CCE.

  14. Modeling Long-Period Ground Motions for Marmara Region

    NASA Astrophysics Data System (ADS)

    Demircioglu, M.; Sesetyan, K.; Erdik, M.; Durukal, E.

    2007-12-01

    As a consequence of the change of paradigm in earthquake resistant design stronger design earthquakes now control the seismic design of important structures. These stronger earthquakes include the effects of near-field pulses, fault-normal motions, and near-field deep soil site motions. As a consequence, there is a strong need for the development of robust and reliable techniques for the assessment of long period earthquake ground motions especially for near field conditions. To provide an example to the assessment of long period ground motion a comparative study has been carried out for the Marmara Region, Turkey. The probabilistic earthquake hazard has been investigated using PEER-NGA (2007) and older generation attenuation relationships for PGA and SA (0.2s, 1s, 2s, 4s, 6s, 8s and 10s) corresponding to 50, 10 and 2 percent probabilities of exceedance in 50 years. PGA values were used to obtain the EuroCode whereas, SA(0.2s and 1s) were used to obtain the NEHRP (2003) based response spectra. SA (0.2s, 1s, 2s, 4s, 6s, 8s and 10s) values were used to plot the equi-hazard spectrum. Furthermore associated hazard deaggregation has been conducted for several selected sites to obtain rational estimates of the deterministic long period spectral accelerations and the deterministic spectral shapes. Comparison of the findings indicate significant variation of long period spectral accelerations. The accuracy of seismic design spectra given in current codes is not sufficient at these periods. There is also a need to develop guidelines for the selection of design basis ground motion for long period or highly nonlinear (softening) structure.

  15. Embodied learning of a generative neural model for biological motion perception and inference

    PubMed Central

    Schrodt, Fabian; Layher, Georg; Neumann, Heiko; Butz, Martin V.

    2015-01-01

    Although an action observation network and mirror neurons for understanding the actions and intentions of others have been under deep, interdisciplinary consideration over recent years, it remains largely unknown how the brain manages to map visually perceived biological motion of others onto its own motor system. This paper shows how such a mapping may be established, even if the biologically motion is visually perceived from a new vantage point. We introduce a learning artificial neural network model and evaluate it on full body motion tracking recordings. The model implements an embodied, predictive inference approach. It first learns to correlate and segment multimodal sensory streams of own bodily motion. In doing so, it becomes able to anticipate motion progression, to complete missing modal information, and to self-generate learned motion sequences. When biological motion of another person is observed, this self-knowledge is utilized to recognize similar motion patterns and predict their progress. Due to the relative encodings, the model shows strong robustness in recognition despite observing rather large varieties of body morphology and posture dynamics. By additionally equipping the model with the capability to rotate its visual frame of reference, it is able to deduce the visual perspective onto the observed person, establishing full consistency to the embodied self-motion encodings by means of active inference. In further support of its neuro-cognitive plausibility, we also model typical bistable perceptions when crucial depth information is missing. In sum, the introduced neural model proposes a solution to the problem of how the human brain may establish correspondence between observed bodily motion and its own motor system, thus offering a mechanism that supports the development of mirror neurons. PMID:26217215

  16. Architecture in motion: A model for music composition

    NASA Astrophysics Data System (ADS)

    Variego, Jorge Elias

    2011-12-01

    Speculations regarding the relationship between music and architecture go back to the very origins of these disciplines. Throughout history, these links have always reaffirmed that music and architecture are analogous art forms that only diverge in their object of study. In the 1 st c. BCE Vitruvius conceived Architecture as "one of the most inclusive and universal human activities" where the architect should be educated in all the arts, having a vast knowledge in history, music and philosophy. In the 18th c., the German thinker Johann Wolfgang von Goethe, described Architecture as "frozen music". More recently, in the 20th c., Iannis Xenakis studied the similar structuring principles between Music and Architecture creating his own "models" of musical composition based on mathematical principles and geometric constructions. The goal of this document is to propose a compositional method that will function as a translator between the acoustical properties of a room and music, to facilitate the creation of musical works that will not only happen within an enclosed space but will also intentionally interact with the space. Acoustical measurements of rooms such as reverberation time, frequency response and volume will be measured and systematically organized in correspondence with orchestrational parameters. The musical compositions created after the proposed model are evocative of the spaces on which they are based. They are meant to be performed in any space, not exclusively in the one where the acoustical measurements were obtained. The visual component of architectural design is disregarded; the room is considered a musical instrument, with its particular sound qualities and resonances. Compositions using the proposed model will not result as sonified shapes, they will be musical works literally "tuned" to a specific space. This Architecture in motion is an attempt to adopt scientific research to the service of a creative activity and to let the aural properties of

  17. Low oxygen affinity in reptilian hemoglobin D: prediction of residue interactions in Geochelone carbonaria HbD by homology modeling.

    PubMed

    Lutfullah, Ghosia; Khalil, Hilal Shahid; Amin, Farhat; Azhar, Noreen

    2008-04-01

    The homology model of hemoglobin D from Geochelone carbonaria, the red-footed tortoise was predicted using the 3D structure coordinates of Geochelone gigantea hemoglobin D as the template. The model was built using the program, MODELLER (8v1) and evaluated with PROCHECK and PROSA. The present study features an in-depth analysis of the 3D model and its conformational changes brought about with variations in its environment. These structural changes are correlated with its ability to adapt to different environmental constraints enabling the organism to better suit to its natural habitat. The model shows additional contacts between amino acid pairs of alpha-119 and beta-55, alpha-35 and beta-124, alpha-103 and beta-112, alpha-115 and beta-116, alpha-120 and beta-52, alpha-120 and beta-55, alpha-36 and beta-127 which are not found in human hemoglobin. It is predicted that these contacts may result in T-state stabilization thus lowering oxygen affinity. Furthermore, decrease in the interaction of phosphate heteroatoms with the amino acid residues of G. carbonaria Hb was also predicted in this study. PMID:18085430

  18. Modeling Taylor dispersion injections: determination of kinetic/affinity interaction constants and diffusion coefficients in label-free biosensing.

    PubMed

    Quinn, John G

    2012-02-15

    A new method based on Taylor dispersion has been developed that enables an analyte gradient to be titrated over a ligand-coated surface for kinetic/affinity analysis of interactions from a minimal number of injections. Taylor dispersion injections generate concentration ranges in excess of four orders of magnitude and enable the analyte diffusion coefficient to be reliably estimated as a fitted parameter when fitting binding interaction models. A numerical model based on finite element analysis, Monte Carlo simulations, and statistical profiling were used to compare the Taylor dispersion method with standard fixed concentration injections in terms of parameter correlation, linearity of parameter error space, and global versus local model fitting. A dramatic decrease in parameter correlations was observed for TDi curves relative to curves from standard fixed concentration injections when surface saturation was achieved. In FCI the binding progress is recorded with respect to injection time, whereas in TDi the second time dependency encoded in the analyte gradient increases resolving power. This greatly lowers the dependence of all parameters on each other and on experimental interferences. When model parameters were fitted locally, the performance of TDis remained comparable to global model fitting, whereas fixed concentration binding response curves yielded unreliable parameter estimates. PMID:22197421

  19. Left ventricle motion modeling and analysis by adaptive-size physically based models

    NASA Astrophysics Data System (ADS)

    Huang, Wen-Chen; Goldgof, Dmitry B.

    1992-06-01

    This paper presents a new physically based modeling method which employs adaptive-size meshes to model left ventricle (LV) shape and track its motion during cardiac cycle. The mesh size increases or decreases dynamically during surface reconstruction process to locate nodes near surface areas of interest and to minimize the fitting error. Further, presented with multiple 3-D data frames, the mesh size varies as the LV undergoes nonrigid motion. Simulation results illustrate the performance and accuracy of the proposed algorithm. Then, the algorithm is applied to the volumetric temporal cardiac data. The LV data was acquired by the 3-D computed tomography scanner. It was provided by Dr. Eric Hoffman at University of Pennsylvania Medical school and consists of 16 volumetric (128 by 128 by 118) images taken through the heart cycle.

  20. A finite state model for respiratory motion analysis in image guided radiation therapy

    NASA Astrophysics Data System (ADS)

    Wu, Huanmei; Sharp, Gregory C.; Salzberg, Betty; Kaeli, David; Shirato, Hiroki; Jiang, Steve B.

    2004-12-01

    Effective image guided radiation treatment of a moving tumour requires adequate information on respiratory motion characteristics. For margin expansion, beam tracking and respiratory gating, the tumour motion must be quantified for pretreatment planning and monitored on-line. We propose a finite state model for respiratory motion analysis that captures our natural understanding of breathing stages. In this model, a regular breathing cycle is represented by three line segments, exhale, end-of-exhale and inhale, while abnormal breathing is represented by an irregular breathing state. In addition, we describe an on-line implementation of this model in one dimension. We found this model can accurately characterize a wide variety of patient breathing patterns. This model was used to describe the respiratory motion for 23 patients with peak-to-peak motion greater than 7 mm. The average root mean square error over all patients was less than 1 mm and no patient has an error worse than 1.5 mm. Our model provides a convenient tool to quantify respiratory motion characteristics, such as patterns of frequency changes and amplitude changes, and can be applied to internal or external motion, including internal tumour position, abdominal surface, diaphragm, spirometry and other surrogates.

  1. A discriminative model of motion and cross ratio for view-invariant action recognition.

    PubMed

    Huang, Kaiqi; Zhang, Yeying; Tan, Tieniu

    2012-04-01

    Action recognition is very important for many applications such as video surveillance, human-computer interaction, and so on; view-invariant action recognition is hot and difficult as well in this field. In this paper, a new discriminative model is proposed for video-based view-invariant action recognition. In the discriminative model, motion pattern and view invariants are perfectly fused together to make a better combination of invariance and distinctiveness. We address a series of issues, including interest point detection in image sequence, motion feature extraction and description, and view-invariant calculation. First, motion detection is used to extract motion information from videos, which is much more efficient than traditional background modeling and tracking-based methods. Second, as for feature representation, we exact variety of statistical information from motion and view-invariant feature based on cross ratio. Last, in the action modeling, we apply a discriminative probabilistic model-hidden conditional random field to model motion patterns and view invariants, by which we could fuse the statistics of motion and projective invariability of cross ratio in one framework. Experimental results demonstrate that our method can improve the ability to distinguish different categories of actions with high robustness to view change in real circumstances. PMID:22438508

  2. A trade-off analysis design tool. Aircraft interior noise-motion/passenger satisfaction model

    NASA Technical Reports Server (NTRS)

    Jacobson, I. D.

    1977-01-01

    A design tool was developed to enhance aircraft passenger satisfaction. The effect of aircraft interior motion and noise on passenger comfort and satisfaction was modelled. Effects of individual aircraft noise sources were accounted for, and the impact of noise on passenger activities and noise levels to safeguard passenger hearing were investigated. The motion noise effect models provide a means for tradeoff analyses between noise and motion variables, and also provide a framework for optimizing noise reduction among noise sources. Data for the models were collected onboard commercial aircraft flights and specially scheduled tests.

  3. Characterization of free breathing patterns with 5D lung motion model

    SciTech Connect

    Zhao Tianyu; Lu Wei; Yang Deshan; Mutic, Sasa; Noel, Camille E.; Parikh, Parag J.; Bradley, Jeffrey D.; Low, Daniel A.

    2009-11-15

    Purpose: To determine the quiet respiration breathing motion model parameters for lung cancer and nonlung cancer patients. Methods: 49 free breathing patient 4DCT image datasets (25 scans, cine mode) were collected with simultaneous quantitative spirometry. A cross-correlation registration technique was employed to track the lung tissue motion between scans. The registration results were applied to a lung motion model: X-vector=X-vector{sub 0}+{alpha}-vector{beta}-vector f, where X-vector is the position of a piece of tissue located at reference position X-vector{sub 0} during a reference breathing phase (zero tidal volume v, zero airflow f). {alpha}-vector is a parameter that characterizes the motion due to air filling (motion as a function of tidal volume v) and {beta}-vector is the parameter that accounts for the motion due to the imbalance of dynamical stress distributions during inspiration and exhalation that causes lung motion hysteresis (motion as a function of airflow f). The parameters {alpha}-vector and {beta}-vector together provide a quantitative characterization of breathing motion that inherently includes the complex hysteresis interplay. The {alpha}-vector and {beta}-vector distributions were examined for each patient to determine overall general patterns and interpatient pattern variations. Results: For 44 patients, the greatest values of |{alpha}-vector| were observed in the inferior and posterior lungs. For the rest of the patients, |{alpha}-vector| reached its maximum in the anterior lung in three patients and the lateral lung in two patients. The hysteresis motion {beta}-vector had greater variability, but for the majority of patients, |{beta}-vector| was largest in the lateral lungs. Conclusions: This is the first report of the three-dimensional breathing motion model parameters for a large cohort of patients. The model has the potential for noninvasively predicting lung motion. The majority of patients exhibited similar |{alpha}-vector| maps

  4. Model-based risk assessment for motion effects in 3D radiotherapy of lung tumors

    NASA Astrophysics Data System (ADS)

    Werner, René; Ehrhardt, Jan; Schmidt-Richberg, Alexander; Handels, Heinz

    2012-02-01

    Although 4D CT imaging becomes available in an increasing number of radiotherapy facilities, 3D imaging and planning is still standard in current clinical practice. In particular for lung tumors, respiratory motion is a known source of uncertainty and should be accounted for during radiotherapy planning - which is difficult by using only a 3D planning CT. In this contribution, we propose applying a statistical lung motion model to predict patients' motion patterns and to estimate dosimetric motion effects in lung tumor radiotherapy if only 3D images are available. Being generated based on 4D CT images of patients with unimpaired lung motion, the model tends to overestimate lung tumor motion. It therefore promises conservative risk assessment regarding tumor dose coverage. This is exemplarily evaluated using treatment plans of lung tumor patients with different tumor motion patterns and for two treatment modalities (conventional 3D conformal radiotherapy and step-&- shoot intensity modulated radiotherapy). For the test cases, 4D CT images are available. Thus, also a standard registration-based 4D dose calculation is performed, which serves as reference to judge plausibility of the modelbased 4D dose calculation. It will be shown that, if combined with an additional simple patient-specific breathing surrogate measurement (here: spirometry), the model-based dose calculation provides reasonable risk assessment of respiratory motion effects.

  5. Autoregressive model based algorithm for correcting motion and serially correlated errors in fNIRS

    PubMed Central

    Barker, Jeffrey W.; Aarabi, Ardalan; Huppert, Theodore J.

    2013-01-01

    Systemic physiology and motion-induced artifacts represent two major sources of confounding noise in functional near infrared spectroscopy (fNIRS) imaging that can reduce the performance of analyses and inflate false positive rates (i.e., type I errors) of detecting evoked hemodynamic responses. In this work, we demonstrated a general algorithm for solving the general linear model (GLM) for both deconvolution (finite impulse response) and canonical regression models based on designing optimal pre-whitening filters using autoregressive models and employing iteratively reweighted least squares. We evaluated the performance of the new method by performing receiver operating characteristic (ROC) analyses using synthetic data, in which serial correlations, motion artifacts, and evoked responses were controlled via simulations, as well as using experimental data from children (3–5 years old) as a source baseline physiological noise and motion artifacts. The new method outperformed ordinary least squares (OLS) with no motion correction, wavelet based motion correction, or spline interpolation based motion correction in the presence of physiological and motion related noise. In the experimental data, false positive rates were as high as 37% when the estimated p-value was 0.05 for the OLS methods. The false positive rate was reduced to 5–9% with the proposed method. Overall, the method improves control of type I errors and increases performance when motion artifacts are present. PMID:24009999

  6. Mathematical Model of the Firefly Luciferase Complementation Assay Reveals a Non-Linear Relationship between the Detected Luminescence and the Affinity of the Protein Pair Being Analyzed.

    PubMed

    Dale, Renee; Ohmuro-Matsuyama, Yuki; Ueda, Hiroshi; Kato, Naohiro

    2016-01-01

    The firefly luciferase complementation assay is widely used as a bioluminescent reporter technology to detect protein-protein interactions in vitro, in cellulo, and in vivo. Upon the interaction of a protein pair, complemented firefly luciferase emits light through the adenylation and oxidation of its substrate, luciferin. Although it has been suggested that kinetics of light production in the firefly luciferase complementation assay is different from that in full length luciferase, the mechanism behind this is still not understood. To quantitatively understand the different kinetics and how changes in affinity of a protein pair affect the light emission in the assay, a mathematical model of the in vitro firefly luciferase complementation assay was constructed. Analysis of the model finds that the change in kinetics is caused by rapid dissociation of the protein pair, low adenylation rate of luciferin, and increased affinity of adenylated luciferin to the enzyme. The model suggests that the affinity of the protein pair has an exponential relationship with the light detected in the assay. This relationship causes the change of affinity in a protein pair to be underestimated. This study underlines the importance of understanding the molecular mechanism of the firefly luciferase complementation assay in order to analyze protein pair affinities quantitatively. PMID:26886551

  7. Mathematical Model of the Firefly Luciferase Complementation Assay Reveals a Non-Linear Relationship between the Detected Luminescence and the Affinity of the Protein Pair Being Analyzed

    PubMed Central

    Dale, Renee; Ohmuro-Matsuyama, Yuki; Ueda, Hiroshi; Kato, Naohiro

    2016-01-01

    The firefly luciferase complementation assay is widely used as a bioluminescent reporter technology to detect protein-protein interactions in vitro, in cellulo, and in vivo. Upon the interaction of a protein pair, complemented firefly luciferase emits light through the adenylation and oxidation of its substrate, luciferin. Although it has been suggested that kinetics of light production in the firefly luciferase complementation assay is different from that in full length luciferase, the mechanism behind this is still not understood. To quantitatively understand the different kinetics and how changes in affinity of a protein pair affect the light emission in the assay, a mathematical model of the in vitro firefly luciferase complementation assay was constructed. Analysis of the model finds that the change in kinetics is caused by rapid dissociation of the protein pair, low adenylation rate of luciferin, and increased affinity of adenylated luciferin to the enzyme. The model suggests that the affinity of the protein pair has an exponential relationship with the light detected in the assay. This relationship causes the change of affinity in a protein pair to be underestimated. This study underlines the importance of understanding the molecular mechanism of the firefly luciferase complementation assay in order to analyze protein pair affinities quantitatively. PMID:26886551

  8. Use of the optimal control model in the design of motion cue experiments

    NASA Technical Reports Server (NTRS)

    Junker, A. M.; Levison, W. H.

    1977-01-01

    An experiment is presented in which the effects of roll motions on human operator performance were investigated. The motion cues considered were the result of commanded vehicle motion and vehicle disturbances. An optimal control pilot-vehicle model was used in the design of the experiment and to predict system performance prior to executing the experiment. The model predictions and experimental results are compared. Seventy-eight per cent of the model predictions are within one standard deviation of the means of the experimental results. The high correlation between model predictions and system performance indicate the usefulness of the predictive model for experimental design and for prediction of pilot performance influenced by motion cues.

  9. Stochastic point-source modeling of ground motions in the Cascadia region

    USGS Publications Warehouse

    Atkinson, G.M.; Boore, D.M.

    1997-01-01

    A stochastic model is used to develop preliminary ground motion relations for the Cascadia region for rock sites. The model parameters are derived from empirical analyses of seismographic data from the Cascadia region. The model is based on a Brune point-source characterized by a stress parameter of 50 bars. The model predictions are compared to ground-motion data from the Cascadia region and to data from large earthquakes in other subduction zones. The point-source simulations match the observations from moderate events (M 100 km). The discrepancy at large magnitudes suggests further work on modeling finite-fault effects and regional attenuation is warranted. In the meantime, the preliminary equations are satisfactory for predicting motions from events of M < 7 and provide conservative estimates of motions from larger events at distances less than 100 km.

  10. Research on motion model for the hypersonic boost-glide aircraft

    NASA Astrophysics Data System (ADS)

    Xu, Shenda; Wu, Jing; Wang, Xueying

    2015-11-01

    A motion model for the hypersonic boost-glide aircraft(HBG) was proposed in this paper, which also analyzed the precision of model through simulation. Firstly the trajectory of HBG was analyzed, and a scheme which divide the trajectory into two parts then build the motion model on each part. Secondly a restrained model of boosting stage and a restrained model of J2 perturbation were established, and set up the observe model. Finally the analysis of simulation results show the feasible and high-accuracy of the model, and raise a expectation for intensive research.

  11. Multilayer Joint Gait-Pose Manifolds for Human Gait Motion Modeling.

    PubMed

    Ding, Meng; Fan, Guolian

    2015-11-01

    We present new multilayer joint gait-pose manifolds (multilayer JGPMs) for complex human gait motion modeling, where three latent variables are defined jointly in a low-dimensional manifold to represent a variety of body configurations. Specifically, the pose variable (along the pose manifold) denotes a specific stage in a walking cycle; the gait variable (along the gait manifold) represents different walking styles; and the linear scale variable characterizes the maximum stride in a walking cycle. We discuss two kinds of topological priors for coupling the pose and gait manifolds, i.e., cylindrical and toroidal, to examine their effectiveness and suitability for motion modeling. We resort to a topologically-constrained Gaussian process (GP) latent variable model to learn the multilayer JGPMs where two new techniques are introduced to facilitate model learning under limited training data. First is training data diversification that creates a set of simulated motion data with different strides. Second is the topology-aware local learning to speed up model learning by taking advantage of the local topological structure. The experimental results on the Carnegie Mellon University motion capture data demonstrate the advantages of our proposed multilayer models over several existing GP-based motion models in terms of the overall performance of human gait motion modeling. PMID:25532201

  12. Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Walters, Rodney R.

    1985-01-01

    Supports, affinity ligands, immobilization, elution methods, and a number of applications are among the topics considered in this discussion of affinity chromatography. An outline of the basic principles of affinity chromatography is included. (JN)

  13. Stochastic Modeling and Simulation of Near-Fault Ground Motions for Performance-Based Earthquake Engineering

    NASA Astrophysics Data System (ADS)

    Dabaghi, Mayssa Nabil

    A comprehensive parameterized stochastic model of near-fault ground motions in two orthogonal horizontal directions is developed. The proposed model uniquely combines several existing and new sub-models to represent major characteristics of recorded near-fault ground motions. These characteristics include near-fault effects of directivity and fling step; temporal and spectral non-stationarity; intensity, duration and frequency content characteristics; directionality of components, as well as the natural variability of motions for a given earthquake and site scenario. By fitting the model to a database of recorded near-fault ground motions with known earthquake source and site characteristics, empirical "observations" of the model parameters are obtained. These observations are used to develop predictive equations for the model parameters in terms of a small number of earthquake source and site characteristics. Functional forms for the predictive equations that are consistent with seismological theory are employed. A site-based simulation procedure that employs the proposed stochastic model and predictive equations is developed to generate synthetic near-fault ground motions at a site. The procedure is formulated in terms of information about the earthquake design scenario that is normally available to a design engineer. Not all near-fault ground motions contain a forward directivity pulse, even when the conditions for such a pulse are favorable. The proposed procedure produces pulselike and non-pulselike motions in the same proportions as they naturally occur among recorded near-fault ground motions for a given design scenario. The proposed models and simulation procedure are validated by several means. Synthetic ground motion time series with fitted parameter values are compared with the corresponding recorded motions. The proposed empirical predictive relations are compared to similar relations available in the literature. The overall simulation procedure is

  14. Hydrological excitation of polar motion by different variables from the GLDAS model

    NASA Astrophysics Data System (ADS)

    Wińska, Małgorzata; Nastula, Jolanta; Salstein, David

    2015-04-01

    Continental hydrological loading, by land water, snow, and ice, is an element that is strongly needed for a full understanding of the excitation of polar motion. In this study we compute different estimations of hydrological excitation functions of polar motion (Hydrological Angular Momentum - HAM) using various variables from the Global Land Data Assimilation System (GLDAS) model of the land-based hydrosphere. The main aim of this study is to show the influence of variables from different hydrological processes, including for example: total evapotranspiration, runoff, snowmelt, soil moisture to polar motion excitations in seasonal timescale. Hydrological excitation functions of polar motion, both global and regional, are determined by using selected variables of these GLDAS realizations. First we compare the timing, spectra and phase diagrams of different regional and global HAMs with each other. Next, we estimate, the hydrological signal in geodetically-observed polar motion excitation as a residual by subtracting the atmospheric - AAM (pressure + wind) and oceanic - OAM (bottom pressure + currents) contributions. Finally, the hydrological excitations are compared to these hydrological signal from the observed polar motion excitation series residuals. The results help us understand the relative importance for polar motion excitation of the individual variables from different hydrological processes, based on hydrological modeling. This method can allows us to estimate how well the polar motion excitation budget in the seasonal spectral ranges can be closed.

  15. Large Tanker Motion Model Identification Using Generalized Ellipsoidal Basis Function-Based Fuzzy Neural Networks.

    PubMed

    Wang, Ning; Er, Meng Joo; Han, Min

    2015-12-01

    In this paper, the motion dynamics of a large tanker is modeled by the generalized ellipsoidal function-based fuzzy neural network (GEBF-FNN). The reference model of tanker motion dynamics in the form of nonlinear difference equations is established to generate training data samples for the GEBF-FNN algorithm which begins with no hidden neuron. In the sequel, fuzzy rules associated with the GEBF-FNN-based model can be online self-constructed by generation criteria and parameter estimation, and can dynamically capture essential motion dynamics of the large tanker with high prediction accuracy. Simulation studies and comprehensive comparisons are conducted on typical zig-zag maneuvers with moderate and extreme steering, and demonstrate that the GEBF-FNN-based model of tanker motion dynamics achieves superior performance in terms of both approximation and prediction. PMID:25561605

  16. A heuristic mathematical model for the dynamics of sensory conflict and motion sickness

    NASA Technical Reports Server (NTRS)

    Oman, C. M.

    1980-01-01

    The etiology of motion sickness is explained in terms of a qualitatively formulated sensory conflict hypothesis. By consideration of the information processing task faced by the central nervous system in estimating body spatial orientation and in controlling active body movement using an internal model referenced control strategy, a mathematical model for sensory conflict generation is developed. The model postulates a major dynamic functional role for sensory conflict signals in movement control, as well as in sensory-motor adaptation. It accounts for the role of active movement in creating motion sickness symptoms in some experimental circumstances, and in alleviating them in others. The relationship between motion sickness produced by sensory rearrangement and that resulting from external motion disturbances is explicitly defined. A nonlinear conflict averaging model is proposed which describes dynamic aspects of experimentally observed subjective discomfort sensation, and suggests resulting behaviors.

  17. A heuristic mathematical model for the dynamics of sensory conflict and motion sickness

    NASA Technical Reports Server (NTRS)

    Oman, C. M.

    1982-01-01

    The etiology of motion sickness is now usually explained in terms of a qualitatively formulated sensory conflict hypothesis. By consideration of the information processing task faced by the central nervous system in estimating body spatial orientation and in controlling active body movement using an internal model referenced control strategy, a mathematical model for sensory conflict generation is developed. The model postulates a major dynamic functional role for sensory conflict signals in movement control, as well as in sensory motor adaptation. It accounts for the role of active movement in creating motion sickness symptoms in some experimental circumstances, and in alleviating them in others. The relationship between motion sickness produced by sensory rearrangement and that resulting from external motion disturbances is explicitly defined. A nonlinear conflict averaging model describes dynamic aspects of experimentally observed subjective discomfort sensation, and suggests resulting behavior.

  18. A multiloop approach to modeling motion sensor responses. [pilot sensory feedback control in compensatory tracking

    NASA Technical Reports Server (NTRS)

    Junker, A. M.; Repperger, D. W.; Neff, J. A.

    1975-01-01

    By using a least squares identification algorithm, a multiloop approach is taken to effectively model the response characteristics of the motion sensors. The inputs to the model include the possible sources of information provided to the human via his motion sensing system. One input models the response of the angular acceleration sensors (second derivative of position) and the second input models the response of the linear sensors (sine of position). The third input is the visual display error provided to the human in the closed loop tracking experiment. Data from a roll axis tracking simulation were analyzed. The major source of pilot lead under the motion mode of operation is discussed for control of plants in which motion information improved performance and in which there was no improvement in performance.

  19. No-net-rotation model of current plate velocities incorporating plate motion model NUVEL-1

    NASA Technical Reports Server (NTRS)

    Argus, Donald F.; Gordon, Richard G.

    1991-01-01

    NNR-NUVEL1 is presented which is a model of plate velocities relative to the unique reference frame defined by requiring no-net-rotation of the lithosphere while constraining relative plate velocities to equal those in global plate motion model NUVEL-1 (DeMets et al., 1990). In NNR-NUVEL1, the Pacific plate rotates in a right-handed sense relative to the no-net-rotation reference frame at 0.67 deg/m.y. about 63 deg S, 107 deg E. At Hawaii the Pacific plate moves relative to the no-net-rotation reference frame at 70 mm/yr, which is 25 mm/yr slower than the Pacific plate moves relative to the hotspots. Differences between NNR-NUVEL1 and HS2-NUVEL1 are described. The no-net-rotation reference frame differs significantly from the hotspot reference frame. If the difference between reference frames is caused by motion of the hotspots relative to a mean-mantle reference frame, then hotspots beneath the Pacific plate move with coherent motion towards the east-southeast. Alternatively, the difference between reference frames can show that the uniform drag, no-net-torque reference frame, which is kinematically equivalent to the no-net-rotation reference frame, is based on a dynamically incorrect premise.

  20. Mixed-model QSAR at the human mineralocorticoid receptor: predicting binding mode and affinity of anabolic steroids.

    PubMed

    Peristera, Ourania; Spreafico, Morena; Smiesko, Martin; Ernst, Beat; Vedani, Angelo

    2009-09-28

    We present a computational study on the human mineralocorticoid receptor (hMR) that is based on multi-dimensional quantitative structure-activity relationships (mQSAR). Therein, we identified the binding mode of 48 steroid and non-steroid homologues by flexible docking to the crystal structure (software Yeti) and quantified it using 6D-QSAR (software Quasar). The receptor surrogate, evolved using a genetic algorithm, converged at a cross-validated r2 of 0.810, and yielded a predictive r2 of 0.661. The model was challenged by a series of scramble tests and by consensus scoring (software Raptor: r2=0.844, predictive r(2)=0.620). The model was then employed to predict the binding affinity of 26 anabolic steroids, demonstrating to which extent they might disrupt the endocrine system via binding to the hMR. The model for the hMR was added to the VirtualToxLab, a technology developed by the Biographics Laboratory 3R, allows the identification of the endocrine-disrupting potential of drugs, chemicals and natural products in silico. PMID:19523507

  1. From the affinity constant to the half-saturation index: understanding conventional modeling concepts in novel wastewater treatment processes.

    PubMed

    Arnaldos, Marina; Amerlinck, Youri; Rehman, Usman; Maere, Thomas; Van Hoey, Stijn; Naessens, Wouter; Nopens, Ingmar

    2015-03-01

    The "affinity constant" (KS) concept is applied in wastewater treatment models to incorporate the effect of substrate limitation on process performance. As an increasing number of wastewater treatment processes rely on low substrate concentrations, a proper understanding of these so-called constants is critical in order to soundly model and evaluate emerging treatment systems. In this paper, an in-depth analysis of the KS concept has been carried out, focusing on the different physical and biological phenomena that affect its observed value. By structuring the factors influencing half-saturation indices (newly proposed nomenclature) into advectional, diffusional and biological, light has been shed onto some of the apparent inconsistencies present in the literature. Particularly, the importance of non-ideal mixing as a source of variability between observed KS values in different systems has been illustrated. Additionally, discussion on the differences existent between substrates that affect half-saturation indices has been carried out; it has been shown that the observed KS for some substrates will reflect transport or biological limitations more than others. Finally, potential modeling strategies that could alleviate the shortcomings of the KS concept have been provided. These could be of special importance when considering the evaluation and design of emerging wastewater treatment processes. PMID:25576693

  2. Fast Modeling of Binding Affinities by Means of Superposing Significant Interaction Rules (SSIR) Method.

    PubMed

    Besalú, Emili

    2016-01-01

    The Superposing Significant Interaction Rules (SSIR) method is described. It is a general combinatorial and symbolic procedure able to rank compounds belonging to combinatorial analogue series. The procedure generates structure-activity relationship (SAR) models and also serves as an inverse SAR tool. The method is fast and can deal with large databases. SSIR operates from statistical significances calculated from the available library of compounds and according to the previously attached molecular labels of interest or non-interest. The required symbolic codification allows dealing with almost any combinatorial data set, even in a confidential manner, if desired. The application example categorizes molecules as binding or non-binding, and consensus ranking SAR models are generated from training and two distinct cross-validation methods: leave-one-out and balanced leave-two-out (BL2O), the latter being suited for the treatment of binary properties. PMID:27240346

  3. Fast Modeling of Binding Affinities by Means of Superposing Significant Interaction Rules (SSIR) Method

    PubMed Central

    Besalú, Emili

    2016-01-01

    The Superposing Significant Interaction Rules (SSIR) method is described. It is a general combinatorial and symbolic procedure able to rank compounds belonging to combinatorial analogue series. The procedure generates structure-activity relationship (SAR) models and also serves as an inverse SAR tool. The method is fast and can deal with large databases. SSIR operates from statistical significances calculated from the available library of compounds and according to the previously attached molecular labels of interest or non-interest. The required symbolic codification allows dealing with almost any combinatorial data set, even in a confidential manner, if desired. The application example categorizes molecules as binding or non-binding, and consensus ranking SAR models are generated from training and two distinct cross-validation methods: leave-one-out and balanced leave-two-out (BL2O), the latter being suited for the treatment of binary properties. PMID:27240346

  4. Modelling of Motion of Bodies Near Triangular Lagrangian Points

    NASA Astrophysics Data System (ADS)

    Bobrov, O. A.

    In this paper, we consider a system of three bodies connected by gravity, two of which are of comparable mass (the Sun and Jupiter), and the third is negligible and it is located in one of the triangular Lagrange points (restricted 3 - body problem). We used the equations of motion in a planar coordinate system that rotates together with massive bodies. Several programs have been written in the programming environment Pascal ABC, in order to build the trajectory of a small body, to indicate the osculating orbit around a massive body, to display equipotential surfaces.

  5. Construction and evaluation of an integrated dynamical model of visual motion perception.

    PubMed

    Tlapale, Émilien; Dosher, Barbara Anne; Lu, Zhong-Lin

    2015-07-01

    Although numerous models describe the individual neural mechanisms that may be involved in the perception of visual motion, few of them have been constructed to take arbitrary stimuli and map them to a motion percept. Here, we propose an integrated dynamical motion model (IDM), which is sufficiently general to handle diverse moving stimuli, yet sufficiently precise to account for a wide-ranging set of empirical observations made on a family of random dot kinematograms. In particular, we constructed models of the cortical areas involved in motion detection, motion integration and perceptual decision. We analyzed their parameters through dynamical simulations and numerical continuation to constrain their proper ranges. Then, empirical data from a family of random dot kinematograms experiments with systematically varying direction distribution, presentation duration and stimulus size, were used to evaluate our model and estimate corresponding model parameters. The resulting model provides an excellent account of a demanding set of parametrically varied behavioral effects on motion perception, providing both quantitative and qualitative elements of evaluation. PMID:25897511

  6. Construction and evaluation of an integrated dynamical model of visual motion perception

    PubMed Central

    Dosher, Barbara Anne; Lu, Zhong-Lin

    2015-01-01

    Although numerous models describe the individual neural mechanisms that may be involved in the perception of visual motion, few of them have been constructed to take arbitrary stimuli and map them to a motion percept. Here, we propose an integrated dynamical motion model (IDM), which is sufficiently general to handle diverse moving stimuli, yet sufficiently precise to account for a wide-ranging set of empirical observations made on a family of random dot kinematograms. In particular, we constructed models of the cortical areas involved in motion detection, motion integration and perceptual decision. We analyzed their parameters through dynamical simulations and numerical continuation to constrain their proper ranges. Then, empirical data from a family of random dot kinematograms experiments with systematically varying direction distribution, presentation duration and stimulus size, were used to evaluate our model and estimate corresponding model parameters. The resulting model provides an excellent account of a demanding set of parametrically varied behavioral effects on motion perception, providing both quantitative and qualitative elements of evaluation. PMID:25897511

  7. Cardiac Motion Analysis Using High-Speed Video Images in a Rat Model for Myocardial Infarction

    NASA Astrophysics Data System (ADS)

    Ishii, Idaku; Okuda, Toshikazu; Nie, Yuman; Takaki, Takeshi; Orito, Kensuke; Tanaka, Akane; Matsuda, Hiroshi

    In this study, we performed a cardiac motion analysis by using 1000-frames per second (fps) stereo images to capture the three-dimensional motion of small color markers in a rat heart. This method of recording cardiac motion could quantify the rate of change in the myocardial area, which indicated localized myocardial activity of rhythmic expansion and contraction. We analyzed the three-dimensional motion distributions in a rat model for myocardial infarction, in which the heart rate was 4 times/s or more. In the analysis, we spatiotemporally quantified the characteristic cardiac motion in ischemic heart diseases and found that infarction due to ischemia in the rat heart was spread around the left ventricle.

  8. Cardiac motion compensation and resolution modeling in simultaneous PET-MR: a cardiac lesion detection study

    NASA Astrophysics Data System (ADS)

    Petibon, Y.; Ouyang, J.; Zhu, X.; Huang, C.; Reese, T. G.; Chun, S. Y.; Li, Q.; El Fakhri, G.

    2013-04-01

    Cardiac motion and partial volume effects (PVE) are two of the main causes of image degradation in cardiac PET. Motion generates artifacts and blurring while PVE lead to erroneous myocardial activity measurements. Newly available simultaneous PET-MR scanners offer new possibilities in cardiac imaging as MRI can assess wall contractility while collecting PET perfusion data. In this perspective, we develop a list-mode iterative reconstruction framework incorporating both tagged-MR derived non-rigid myocardial wall motion and position dependent detector point spread function (PSF) directly into the PET system matrix. In this manner, our algorithm performs both motion ‘deblurring’ and PSF deconvolution while reconstructing images with all available PET counts. The proposed methods are evaluated in a beating non-rigid cardiac phantom whose hot myocardial compartment contains small transmural and non-transmural cold defects. In order to accelerate imaging time, we investigate collecting full and half k-space tagged MR data to obtain tagged volumes that are registered using non-rigid B-spline registration to yield wall motion information. Our experimental results show that tagged-MR based motion correction yielded an improvement in defect/myocardium contrast recovery of 34-206% as compared to motion uncorrected studies. Likewise, lesion detectability improved by respectively 115-136% and 62-235% with MR-based motion compensation as compared to gating and no motion correction and made it possible to distinguish non-transmural from transmural defects, which has clinical significance given the inherent limitations of current single modality imaging in identifying the amount of residual ischemia. The incorporation of PSF modeling within the framework of MR-based motion compensation significantly improved defect/myocardium contrast recovery (5.1-8.5%, p < 0.01) and defect detectability (39-56%, p < 0.01). No statistical difference was found in PET contrast and lesion

  9. A heuristic mathematical model for the dynamics of sensory conflict and motion sickness

    NASA Technical Reports Server (NTRS)

    Oman, C. M.

    1982-01-01

    By consideration of the information processing task faced by the central nervous system in estimating body spatial orientation and in controlling active body movement using an internal model referenced control strategy, a mathematical model for sensory conflict generation is developed. The model postulates a major dynamic functional role for sensory conflict signals in movement control, as well as in sensory-motor adaptation. It accounts for the role of active movement in creating motion sickness symptoms in some experimental circumstance, and in alleviating them in others. The relationship between motion sickness produced by sensory rearrangement and that resulting from external motion disturbances is explicitly defined. A nonlinear conflict averaging model is proposed which describes dynamic aspects of experimentally observed subjective discomfort sensation, and suggests resulting behaviours. The model admits several possibilities for adaptive mechanisms which do not involve internal model updating. Further systematic efforts to experimentally refine and validate the model are indicated.

  10. Joint motion model for local stereo video-matching method

    NASA Astrophysics Data System (ADS)

    Zhang, Jinglin; Bai, Cong; Nezan, Jean-Francois; Cousin, Jean-Gabriel

    2015-12-01

    As one branch of stereo matching, video stereo matching becomes more and more significant in computer vision applications. The conventional stereo matching methods for static images would cause flicker-frames and worse matching results. We propose a joint motion-based square step (JMSS) method for stereo video matching. The motion vector is introduced as one component in the support region building for the raw cost aggregation. Then we aggregate the raw cost along two directions in the support region. Finally, the winner-take-all strategy determines the best disparity under our hypothesis. Experimental results show that the JMSS method not only outperforms other state-of-the-art stereo matching methods on test sequences with abundant movements, but also performs well in some real-world scenes with fixed and moving stereo cameras, respectively, in particular under some extreme conditions of real stereo visions. Additionally, the proposed JMSS method can be implemented in real time, which is superior to other state-of-the-art methods. The time efficiency is also a very important consideration in our algorithm design.

  11. On-chip visual perception of motion: a bio-inspired connectionist model on FPGA.

    PubMed

    Torres-Huitzil, César; Girau, Bernard; Castellanos-Sánchez, Claudio

    2005-01-01

    Visual motion provides useful information to understand the dynamics of a scene to allow intelligent systems interact with their environment. Motion computation is usually restricted by real time requirements that need the design and implementation of specific hardware architectures. In this paper, the design of hardware architecture for a bio-inspired neural model for motion estimation is presented. The motion estimation is based on a strongly localized bio-inspired connectionist model with a particular adaptation of spatio-temporal Gabor-like filtering. The architecture is constituted by three main modules that perform spatial, temporal, and excitatory-inhibitory connectionist processing. The biomimetic architecture is modeled, simulated and validated in VHDL. The synthesis results on a Field Programmable Gate Array (FPGA) device show the potential achievement of real-time performance at an affordable silicon area. PMID:16102939

  12. Pilot/vehicle model analysis of visual and motion cue requirements in flight simulation

    NASA Technical Reports Server (NTRS)

    Lancraft, R.; Zacharias, G.; Baron, S.

    1981-01-01

    The optimal control model for pilot/vehicle analysis is used to explore the effects of a CGI visual system and motion system dynamics on helicopter hover simulation fidelity. This is accomplished by expanding the perceptual aspects of the model to include motion sensing and by relating CGI parameters to information processing parameters of the model. Simulator fidelity is examined by comparing predicted performance and workload for flight with that predicted for various simulator configuration. The results of the analysis suggest that simulator deficiencies or a reasonable nature (by current standards) can result in substantial performance and/or workload infidelity. Both CGI and motion system effects are significant for this task. There is also a distinct interaction between the two sources of pilot cues. In particular, the presence of motion reduces the sensitivity to CGI limitations.

  13. New analogues of epiboxidine incorporating the 4,5-dihydroisoxazole nucleus: synthesis, binding affinity at neuronal nicotinic acetylcholine receptors, and molecular modeling investigations.

    PubMed

    Dallanoce, Clelia; Magrone, Pietro; Bazza, Paola; Grazioso, Giovanni; Rizzi, Luca; Riganti, Loredana; Gotti, Cecilia; Clementi, Francesco; Frydenvang, Karla; De Amici, Marco

    2009-02-01

    A group of novel 4,5-dihydro-3-methylisoxazolyl derivatives, structurally related to epiboxidine (=(1R,4S,6S)-6-(3-methylisoxazol-5-yl)-7-azabicyclo[2.2.1]heptane), was prepared via 1,3-dipolar cycloaddition of acetonitrile oxide to different olefins. Target compounds 1a and 1b, 2a and 2b, 3, 4, and 5 were tested for affinity at neuronal nicotinic heteromeric (alpha4beta2) and homomeric (alpha7) acetylcholine receptors. Notably, diastereoisomers 1a and 1b were characterized by a massive drop of the affinity at the alpha4beta2 subtypes (K(i) values spanning the range 4.3-126 microM), when compared with that of epiboxidine (K(i)=0.6 nM). Therefore, the replacement of the 3-methylisoxazole ring of epiboxidine with the 4,5-dihydro-3-methylisoxazole nucleus is detrimental for the affinity at alpha4beta2 receptors. A comparable lack of affinity/selectivity for the two nAChR subtypes under study was evidenced for the remaining epiboxidine-related dihydroisoxazole derivatives 2a and 2b, and 3-5. Diastereoisomers 1a and 1b, and spirocyclic derivative 3 were docked into molecular models of the receptor subtypes under study, and their binding mode was compared with that of reference ligands endowed with high binding affinity. PMID:19235154

  14. Neural network-based motion control of an underactuated wheeled inverted pendulum model.

    PubMed

    Yang, Chenguang; Li, Zhijun; Cui, Rongxin; Xu, Bugong

    2014-11-01

    In this paper, automatic motion control is investigated for one of wheeled inverted pendulum (WIP) models, which have been widely applied for modeling of a large range of two wheeled modern vehicles. First, the underactuated WIP model is decomposed into a fully actuated second order subsystem Σa consisting of planar movement of vehicle forward and yaw angular motions, and a nonactuated first order subsystem Σb of pendulum motion. Due to the unknown dynamics of subsystem Σa and the universal approximation ability of neural network (NN), an adaptive NN scheme has been employed for motion control of subsystem Σa . The model reference approach has been used whereas the reference model is optimized by the finite time linear quadratic regulation technique. The pendulum motion in the passive subsystem Σb is indirectly controlled using the dynamic coupling with planar forward motion of subsystem Σa , such that satisfactory tracking of a set pendulum tilt angle can be guaranteed. Rigours theoretic analysis has been established, and simulation studies have been performed to demonstrate the developed method. PMID:25330424

  15. A space-variant model for motion interpretation across the visual field.

    PubMed

    Chessa, Manuela; Maiello, Guido; Bex, Peter J; Solari, Fabio

    2016-01-01

    We implement a neural model for the estimation of the focus of radial motion (FRM) at different retinal locations and assess the model by comparing its results with respect to the precision with which human observers can estimate the FRM in naturalistic motion stimuli. The model describes the deep hierarchy of the first stages of the dorsal visual pathway and is space variant, since it takes into account the retino-cortical transformation of the primate visual system through log-polar mapping. The log-polar transform of the retinal image is the input to the cortical motion-estimation stage, where optic flow is computed by a three-layer neural population. The sensitivity to complex motion patterns that has been found in area MST is modeled through a population of adaptive templates. The first-order description of cortical optic flow is derived from the responses of the adaptive templates. Information about self-motion (e.g., direction of heading) is estimated by combining the first-order descriptors computed in the cortical domain. The model's performance at FRM estimation as a function of retinal eccentricity neatly maps onto data from human observers. By employing equivalent-noise analysis we observe that loss in FRM accuracy for both model and human observers is attributable to a decrease in the efficiency with which motion information is pooled with increasing retinal eccentricity in the visual field. The decrease in sampling efficiency is thus attributable to receptive-field size increases with increasing retinal eccentricity, which are in turn driven by the lossy log-polar mapping that projects the retinal image onto primary visual areas. We further show that the model is able to estimate direction of heading in real-world scenes, thus validating the model's potential application to neuromimetic robotic architectures. More broadly, we provide a framework in which to model complex motion integration across the visual field in real-world scenes. PMID:27580091

  16. Synthesis, structure-affinity relationships, and molecular modeling studies of novel pyrazolo[3,4-c]quinoline derivatives as adenosine receptor antagonists.

    PubMed

    Lenzi, Ombretta; Colotta, Vittoria; Catarzi, Daniela; Varano, Flavia; Squarcialupi, Lucia; Filacchioni, Guido; Varani, Katia; Vincenzi, Fabrizio; Borea, Pier Andrea; Dal Ben, Diego; Lambertucci, Catia; Cristalli, Gloria

    2011-06-15

    This paper reports the study of new 2-phenyl- and 2-methylpyrazolo[3,4-c]quinolin-4-ones (series A) and 4-amines (series B), designed as adenosine receptor (AR) antagonists. The synthesized compounds bear at the 6-position various groups, with different lipophilicity and steric hindrance, that were thought to increase human A(1) and A(2A) AR affinities and selectivities, with respect to those of the parent 6-unsubstituted compounds. In series A, this modification was not tolerated since it reduced AR affinity, while in series B it shifted the binding towards the hA(1) subtype. To rationalize the observed structure-affinity relationships, molecular docking studies at A(2A)AR-based homology models of the A(1) and A(3) ARs and at the A(2A)AR crystal structure were carried out. PMID:21616671

  17. Investigating a Model of Commonsense Thinking about Causes of Motion with 7 to 16-year-old Pupils.

    ERIC Educational Resources Information Center

    Whitelock, Denise

    1991-01-01

    The testing of a formal causal model of thinking about motion is described using a matching-pairs paper-and-pencil task. Subjects were asked to distinguish between examples of stereotypical motions by the similarity or difference of causes of pairs of motions. The results suggest that responses can be predicted by the model with the addition of an…

  18. Vesicular stomatitis virus polymerase's strong affinity to its template suggests exotic transcription models.

    PubMed

    Tang, Xiaolin; Bendjennat, Mourad; Saffarian, Saveez

    2014-12-01

    Vesicular stomatitis virus (VSV) is the prototype for negative sense non segmented (NNS) RNA viruses which include potent human and animal pathogens such as Rabies, Ebola and measles. The polymerases of NNS RNA viruses only initiate transcription at or near the 3' end of their genome template. We measured the dissociation constant of VSV polymerases from their whole genome template to be 20 pM. Given this low dissociation constant, initiation and sustainability of transcription becomes nontrivial. To explore possible mechanisms, we simulated the first hour of transcription using Monte Carlo methods and show that a one-time initial dissociation of all polymerases during entry is not sufficient to sustain transcription. We further show that efficient transcription requires a sliding mechanism for non-transcribing polymerases and can be realized with different polymerase-polymerase interactions and distinct template topologies. In conclusion, we highlight a model in which collisions between transcribing and sliding non-transcribing polymerases result in release of the non-transcribing polymerases allowing for redistribution of polymerases between separate templates during transcription and suggest specific experiments to further test these mechanisms. PMID:25501005

  19. Distance-dependent Ground motion variability from source models of the 1992 Landers earthquake and synthetic rupture models.

    NASA Astrophysics Data System (ADS)

    Vyas, J. C.; Mai, P. M.; Galis, M.

    2014-12-01

    We investigate near field ground motion variability due to five different kinematic rupture models for 1992 Landers earthquake. The ground motion simulations are accomplished by solving the elasto-dynamic equations of motion using a generalized finite-difference method (Ely et al., 2008). Simulated waveforms are calibrated against near-field strong-motion recordings. We then analyze a large data-set of ground-motions from 2000 sites, binned with respect to distance and azimuth to compute mean and standard deviation of peak ground velocity (PGV). We consider 1D-velocity structures as used in the source inversions, and honor the geometrical complexity due to fault segmentation. Our simulations reveal that ground motion variability is reduced as the distance from the fault increases. Variability in the kinematic sources has considerable impact on the resulting shaking variability, although the five source models considered are derived by inversion of seismic and/or geodetic data. Simulated mean PGV and its standard deviation are comparable to empirical estimates using the ground-motion prediction equation (GMPE) of Boore and Atkinson (2008). In addition, we find that intra-event ground motion variability is large in fault-parallel and small in fault-normal direction. We also compare our simulations with and without Spudich and Chiou (2008) directivity corrections, applied to Boore and Atkinson (2008), which shows that slip heterogeneity controls near-field ground-motion variability. We further investigate the effect of slip heterogeneity by considering eleven (ten heterogeneous and one uniform) synthetic rupture models. Heterogeneous slip models are generated following the algorithm of Mai and Beroza (2002) for different correlation lengths and Hurst exponents. We then examine synthetic seismograms calculated at 1500 stations for the eleven rupture models, confirming that the distance decay of ground motion variability is due to slip heterogeneity.

  20. Analytical approach to calculation of response spectra from seismological models of ground motion

    USGS Publications Warehouse

    Safak, Erdal

    1988-01-01

    An analytical approach to calculate response spectra from seismological models of ground motion is presented. Seismological models have three major advantages over empirical models: (1) they help in an understanding of the physics of earthquake mechanisms, (2) they can be used to predict ground motions for future earthquakes and (3) they can be extrapolated to cases where there are no data available. As shown with this study, these models also present a convenient form for the calculation of response spectra, by using the methods of random vibration theory, for a given magnitude and site conditions. The first part of the paper reviews the past models for ground motion description, and introduces the available seismological models. Then, the random vibration equations for the spectral response are presented. The nonstationarity, spectral bandwidth and the correlation of the peaks are considered in the calculation of the peak response.

  1. Observing and modeling long-period tidal variations in polar motion

    NASA Astrophysics Data System (ADS)

    Gross, R. S.; Dickman, S. R.

    2011-10-01

    By exchanging angular momentum with the solid Earth, ocean tides cause the Earth's rotation to change. While hydrodynamic tide models have been used to study the effect of ocean tides on polar motion, it is shown here that none of the published models can fully account for the observed variations. An empirical ocean tide model is therefore determined by fitting periodic terms at the tidal frequencies to polar motion excitation observations spanning 1980.0-2010.4 from which atmospheric and non-tidal oceanic effects were removed. While the empirical ocean tide model does fully account for all of the observed tidal power, tests indicate that the model may not have completely converged. So better models of the effects of ocean tides on polar motion are still needed, both dynamical and empirical.

  2. Observing and Modeling Long-Period Tidal Variations in Polar Motion

    NASA Technical Reports Server (NTRS)

    Gross, Richard S.; Dickman, S. R.

    2011-01-01

    By exchanging angular momentum with the solid Earth, ocean tides cause the Earth's rotation to change. While hydrodynamic tide models have been used to study the effect of ocean tides on polar motion, it is shown here that none of the published models can fully account for the observed variations. An empirical ocean tide model is therefore determined by fitting periodic terms at the tidal frequencies to polar motion excitation observations, from which atmospheric and non-tidal oceanic effects were removed. While the empirical ocean tide model does fully account for allof the observed tidal power, tests indicate that the model may not have completely converged. So better models of the effects of ocean tides on polar motion are still needed, both dynamical and empirical.

  3. Identifying and modeling motion primitives for the hydromedusae Sarsia tubulosa and Aequorea victoria.

    PubMed

    Sledge, Isaac; Krieg, Michael; Lipinski, Doug; Mohseni, Kamran

    2015-12-01

    The movements of organisms can be thought of as aggregations of motion primitives: motion segments containing one or more significant actions. Here, we present a means to identify and characterize motion primitives from recorded movement data. We address these problems by assuming that the motion sequences can be characterized as a series of dynamical-system-based pattern generators. By adopting a nonparametric, Bayesian formalism for learning and simplifying these pattern generators, we arrive at a purely data-driven model to automatically identify breakpoints in the movement sequences. We apply this model to swimming sequences from two hydromedusa. The first hydromedusa is the prolate Sarsia tubulosa, for which we obtain five motion primitives that correspond to bell cavity pressurization, jet formation, jetting, cavity fluid refill, and coasting. The second hydromedusa is the oblate Aequorea victoria, for which we obtain five motion primitives that correspond to bell compression, vortex separation, cavity fluid refill, vortex formation, and coasting. Our experimental results indicate that the breakpoints between primitives are correlated with transitions in the bell geometry, vortex formation and shedding, and changes in derived dynamical quantities. These dynamics quantities include terms like pressure, power, drag, and thrust. Such findings suggest that dynamics information is inherently present in the observed motions. PMID:26495992

  4. 4D cone-beam CT reconstruction using multi-organ meshes for sliding motion modeling.

    PubMed

    Zhong, Zichun; Gu, Xuejun; Mao, Weihua; Wang, Jing

    2016-02-01

    A simultaneous motion estimation and image reconstruction (SMEIR) strategy was proposed for 4D cone-beam CT (4D-CBCT) reconstruction and showed excellent results in both phantom and lung cancer patient studies. In the original SMEIR algorithm, the deformation vector field (DVF) was defined on voxel grid and estimated by enforcing a global smoothness regularization term on the motion fields. The objective of this work is to improve the computation efficiency and motion estimation accuracy of SMEIR for 4D-CBCT through developing a multi-organ meshing model. Feature-based adaptive meshes were generated to reduce the number of unknowns in the DVF estimation and accurately capture the organ shapes and motion. Additionally, the discontinuity in the motion fields between different organs during respiration was explicitly considered in the multi-organ mesh model. This will help with the accurate visualization and motion estimation of the tumor on the organ boundaries in 4D-CBCT. To further improve the computational efficiency, a GPU-based parallel implementation was designed. The performance of the proposed algorithm was evaluated on a synthetic sliding motion phantom, a 4D NCAT phantom, and four lung cancer patients. The proposed multi-organ mesh based strategy outperformed the conventional Feldkamp-Davis-Kress, iterative total variation minimization, original SMEIR and single meshing method based on both qualitative and quantitative evaluations. PMID:26758496

  5. 4D cone-beam CT reconstruction using multi-organ meshes for sliding motion modeling

    NASA Astrophysics Data System (ADS)

    Zhong, Zichun; Gu, Xuejun; Mao, Weihua; Wang, Jing

    2016-02-01

    A simultaneous motion estimation and image reconstruction (SMEIR) strategy was proposed for 4D cone-beam CT (4D-CBCT) reconstruction and showed excellent results in both phantom and lung cancer patient studies. In the original SMEIR algorithm, the deformation vector field (DVF) was defined on voxel grid and estimated by enforcing a global smoothness regularization term on the motion fields. The objective of this work is to improve the computation efficiency and motion estimation accuracy of SMEIR for 4D-CBCT through developing a multi-organ meshing model. Feature-based adaptive meshes were generated to reduce the number of unknowns in the DVF estimation and accurately capture the organ shapes and motion. Additionally, the discontinuity in the motion fields between different organs during respiration was explicitly considered in the multi-organ mesh model. This will help with the accurate visualization and motion estimation of the tumor on the organ boundaries in 4D-CBCT. To further improve the computational efficiency, a GPU-based parallel implementation was designed. The performance of the proposed algorithm was evaluated on a synthetic sliding motion phantom, a 4D NCAT phantom, and four lung cancer patients. The proposed multi-organ mesh based strategy outperformed the conventional Feldkamp-Davis-Kress, iterative total variation minimization, original SMEIR and single meshing method based on both qualitative and quantitative evaluations.

  6. Development of a novel experimental model to investigate radiobiological implications of respiratory motion in advanced radiotherapy

    NASA Astrophysics Data System (ADS)

    Cole, Aidan J.; McGarry, Conor K.; Butterworth, Karl T.; Prise, Kevin M.; O'Sullivan, Joe M.; Hounsell, Alan R.

    2012-11-01

    Respiratory motion introduces complex spatio-temporal variations in the dosimetry of radiotherapy. There is a paucity of literature investigating the radiobiological consequences of intrafraction motion and concerns regarding the impact of movement when applied to cancer cell lines in vitro exist. We have addressed this by developing a novel model which accurately replicates respiratory motion under experimental conditions to allow clinically relevant irradiation of cell lines. A bespoke phantom and motor driven moving platform was adapted to accommodate flasks containing medium and cells in order to replicate respiratory motion using varying frequencies and amplitude settings. To study this effect on cell survival in vitro, dose response curves were determined for human lung cancer cell lines H1299 and H460 exposed to a uniform 6 MV radiation field under moving or stationary conditions. Cell survival curves showed no significant difference between irradiation at different dose points for these cell lines in the presence or absence of motion. These data indicate that motion of unshielded cells in vitro does not affect cell survival in the presence of uniform irradiation. This model provides a novel research platform to investigate the radiobiological consequences of respiratory motion in radiotherapy.

  7. Stability, metabolism and transport of D-Asp(OBzl)-Ala--a model prodrug with affinity for the oligopeptide transporter.

    PubMed

    Steffansen, B; Lepist, E I; Taub, M E; Larsen, B D; Frokjaer, S; Lennernäs, H

    1999-04-01

    The model prodrug D-Asp(OBzl)-Ala has previously been shown to have affinity and to be transported by the oligopeptide transporter PepT1 expressed in Caco-2 cells. The main objective of the present study was to investigate the aqueous stability of D-Asp(OBzl)-Ala and its in vitro metabolism in different gastrointestinal media arising from rats and humans, as well as in human plasma. The second major aim of the study was to evaluate our previous study in Caco-2 cell culture, by determining the effective intestinal permeability (Peff) of D-Asp(OBzl)-Ala in situ using the single-pass rat perfusion model. The aqueous stability studies show water, general buffer, as well as specific acid and base catalysis of D-Asp(OBzl)-Ala. The degradation of the model prodrug was independent of ionic strength. The half-lives in rat jejunal fluid and homogenate were >3 h. In human gastric and intestinal fluids, the half-lives were >3 h and 2.3+/-0. 03 h, respectively. Using the rat single-pass perfusion technique, the effective jejunal permeability (Peff) of D-Asp(OBzl)-Ala was determined to be high (1.29+/-0.5.10-4 cm/s). The 32 times higher Peff value found in the perfusion model compared to Caco-2 cells is most likely due to a higher functional expression of the oligopeptide transporter. Rat jejuna Peff was reduced by approximately 50% in the presence of well known oligopeptide transporter substrates, such as Gly-Sar and cephalexin. It may be that D-Asp(OBzl)-Ala is primarily absorbed intact by the rat jejunal oligopeptide transporter, since the stability in the intestinal homogenate and fluids was rather high (t1/2>2.3 h). PMID:10072480

  8. Human motion recognition based on features and models selected HMM

    NASA Astrophysics Data System (ADS)

    Lu, Haixiang; Zhou, Hongjun

    2015-03-01

    This paper research on the motion recognition based on HMM with Kinect. Kinect provides skeletal data consist of 3D body joints with its lower price and convenience. In this work, several methods are used to determine the optimal subset of features among Cartesian coordinates, distance to hip center, velocity, angle and angular velocity, in order to improve the recognition rate. K-means is used for vector quantization and HMM is used as recognition method. HMM is an effective signal processing method which contains time calibration, provides a learning mechanism and recognition ability. Cluster numbers of K-means, structure and state numbers of HMM are optimized as well. The proposed methods are applied to the MSR Action3D dataset. Results show that the proposed methods obtain better recognition accuracy than the state of the art methods.

  9. 3D fluoroscopic image estimation using patient-specific 4DCBCT-based motion models

    PubMed Central

    Dhou, Salam; Hurwitz, Martina; Mishra, Pankaj; Cai, Weixing; Rottmann, Joerg; Li, Ruijiang; Williams, Christopher; Wagar, Matthew; Berbeco, Ross; Ionascu, Dan; Lewis, John H.

    2015-01-01

    3D fluoroscopic images represent volumetric patient anatomy during treatment with high spatial and temporal resolution. 3D fluoroscopic images estimated using motion models built using 4DCT images, taken days or weeks prior to treatment, do not reliably represent patient anatomy during treatment. In this study we develop and perform initial evaluation of techniques to develop patient-specific motion models from 4D cone-beam CT (4DCBCT) images, taken immediately before treatment, and use these models to estimate 3D fluoroscopic images based on 2D kV projections captured during treatment. We evaluate the accuracy of 3D fluoroscopic images by comparing to ground truth digital and physical phantom images. The performance of 4DCBCT- and 4DCT- based motion models are compared in simulated clinical situations representing tumor baseline shift or initial patient positioning errors. The results of this study demonstrate the ability for 4DCBCT imaging to generate motion models that can account for changes that cannot be accounted for with 4DCT-based motion models. When simulating tumor baseline shift and patient positioning errors of up to 5 mm, the average tumor localization error and the 95th percentile error in six datasets were 1.20 and 2.2 mm, respectively, for 4DCBCT-based motion models. 4DCT-based motion models applied to the same six datasets resulted in average tumor localization error and the 95th percentile error of 4.18 and 5.4 mm, respectively. Analysis of voxel-wise intensity differences was also conducted for all experiments. In summary, this study demonstrates the feasibility of 4DCBCT-based 3D fluoroscopic image generation in digital and physical phantoms, and shows the potential advantage of 4DCBCT-based 3D fluoroscopic image estimation when there are changes in anatomy between the time of 4DCT imaging and the time of treatment delivery. PMID:25905722

  10. 3D fluoroscopic image estimation using patient-specific 4DCBCT-based motion models

    NASA Astrophysics Data System (ADS)

    Dhou, S.; Hurwitz, M.; Mishra, P.; Cai, W.; Rottmann, J.; Li, R.; Williams, C.; Wagar, M.; Berbeco, R.; Ionascu, D.; Lewis, J. H.

    2015-05-01

    3D fluoroscopic images represent volumetric patient anatomy during treatment with high spatial and temporal resolution. 3D fluoroscopic images estimated using motion models built using 4DCT images, taken days or weeks prior to treatment, do not reliably represent patient anatomy during treatment. In this study we developed and performed initial evaluation of techniques to develop patient-specific motion models from 4D cone-beam CT (4DCBCT) images, taken immediately before treatment, and used these models to estimate 3D fluoroscopic images based on 2D kV projections captured during treatment. We evaluate the accuracy of 3D fluoroscopic images by comparison to ground truth digital and physical phantom images. The performance of 4DCBCT-based and 4DCT-based motion models are compared in simulated clinical situations representing tumor baseline shift or initial patient positioning errors. The results of this study demonstrate the ability for 4DCBCT imaging to generate motion models that can account for changes that cannot be accounted for with 4DCT-based motion models. When simulating tumor baseline shift and patient positioning errors of up to 5 mm, the average tumor localization error and the 95th percentile error in six datasets were 1.20 and 2.2 mm, respectively, for 4DCBCT-based motion models. 4DCT-based motion models applied to the same six datasets resulted in average tumor localization error and the 95th percentile error of 4.18 and 5.4 mm, respectively. Analysis of voxel-wise intensity differences was also conducted for all experiments. In summary, this study demonstrates the feasibility of 4DCBCT-based 3D fluoroscopic image generation in digital and physical phantoms and shows the potential advantage of 4DCBCT-based 3D fluoroscopic image estimation when there are changes in anatomy between the time of 4DCT imaging and the time of treatment delivery.

  11. Couch-based motion compensation: modelling, simulation and real-time experiments.

    PubMed

    Haas, Olivier C L; Skworcow, Piotr; Paluszczyszyn, Daniel; Sahih, Abdelhamid; Ruta, Mariusz; Mills, John A

    2012-09-21

    The paper presents a couch-based active motion compensation strategy evaluated in simulation and validated experimentally using both a research and a clinical Elekta Precise Table™. The control strategy combines a Kalman filter to predict the surrogate motion used as a reference by a linear model predictive controller with the control action calculation based on estimated position and velocity feedback provided by an observer as well as predicted couch position and velocity using a linearized state space model. An inversion technique is used to compensate for the dead-zone nonlinearity. New generic couch models are presented and applied to model the Elekta Precise Table™ dynamics and nonlinearities including dead zone. Couch deflection was measured for different manufacturers and found to be up to 25 mm. A feed-forward approach is proposed to compensate for such couch deflection. Simultaneous motion compensation for longitudinal, lateral and vertical motions was evaluated using arbitrary trajectories generated from sensors or loaded from files. Tracking errors were between 0.5 and 2 mm RMS. A dosimetric evaluation of the motion compensation was done using a sinusoidal waveform. No notable differences were observed between films obtained for a fixed- or motion-compensated target. Further dosimetric improvement could be made by combining gating, based on tracking error together with beam on/off time, and PSS compensation. PMID:22951301

  12. Applying Model Analysis to a Resource-Based Analysis of the Force and Motion Conceptual Evaluation

    ERIC Educational Resources Information Center

    Smith, Trevor I.; Wittmann, Michael C.; Carter, Tom

    2014-01-01

    Previously, we analyzed the Force and Motion Conceptual Evaluation in terms of a resources-based model that allows for clustering of questions so as to provide useful information on how students correctly or incorrectly reason about physics. In this paper, we apply model analysis to show that the associated model plots provide more information…

  13. Kinematic model for the space-variant image motion of star sensors under dynamical conditions

    NASA Astrophysics Data System (ADS)

    Liu, Chao-Shan; Hu, Lai-Hong; Liu, Guang-Bin; Yang, Bo; Li, Ai-Jun

    2015-06-01

    A kinematic description of a star spot in the focal plane is presented for star sensors under dynamical conditions, which involves all necessary parameters such as the image motion, velocity, and attitude parameters of the vehicle. Stars at different locations of the focal plane correspond to the slightly different orientation and extent of motion blur, which characterize the space-variant point spread function. Finally, the image motion, the energy distribution, and centroid extraction are numerically investigated using the kinematic model under dynamic conditions. A centroid error of eight successive iterations <0.002 pixel is used as the termination criterion for the Richardson-Lucy deconvolution algorithm. The kinematic model of a star sensor is useful for evaluating the compensation algorithms of motion-blurred images.

  14. Nuclear quadrupole resonance lineshape analysis for different motional models: Stochastic Liouville approach

    NASA Astrophysics Data System (ADS)

    Kruk, D.; Earle, K. A.; Mielczarek, A.; Kubica, A.; Milewska, A.; Moscicki, J.

    2011-12-01

    A general theory of lineshapes in nuclear quadrupole resonance (NQR), based on the stochastic Liouville equation, is presented. The description is valid for arbitrary motional conditions (particularly beyond the valid range of perturbation approaches) and interaction strengths. It can be applied to the computation of NQR spectra for any spin quantum number and for any applied magnetic field. The treatment presented here is an adaptation of the "Swedish slow motion theory," [T. Nilsson and J. Kowalewski, J. Magn. Reson. 146, 345 (2000), 10.1006/jmre.2000.2125] originally formulated for paramagnetic systems, to NQR spectral analysis. The description is formulated for simple (Brownian) diffusion, free diffusion, and jump diffusion models. The two latter models account for molecular cooperativity effects in dense systems (such as liquids of high viscosity or molecular glasses). The sensitivity of NQR slow motion spectra to the mechanism of the motional processes modulating the nuclear quadrupole interaction is discussed.

  15. Key elements of regional seismic velocity models for long period ground motion simulations

    USGS Publications Warehouse

    Brocher, T.M.

    2008-01-01

    Regional 3-D seismic velocity models used for broadband strong motion simulations must include compressional-wave velocity (Vp), shear-wave velocity (Vs), intrinsic attenuation (Qp, Qs), and density. Vs and Qs are the most important of these parameters because the strongest ground motions are generated chiefly by shear- and surface-wave arrivals. Because Vp data are more common than Vs data, many researchers first develop a Vp model and convert it to a Vs model. I describe recent empirical relations between Vs, Vp, Qs, Qp, and density that allow velocity models to be rapidly and accurately calculated. ?? Springer Science+Business Media B.V. 2007.

  16. Lung tumor motion prediction during lung brachytherapy using finite element model

    NASA Astrophysics Data System (ADS)

    Shirzadi, Zahra; Sadeghi Naini, Ali; Samani, Abbas

    2012-02-01

    A biomechanical model is proposed to predict deflated lung tumor motion caused by diaphragm respiratory motion. This model can be very useful for targeting the tumor in tumor ablative procedures such as lung brachytherapy. To minimize motion within the target lung, these procedures are performed while the lung is deflated. However, significant amount of tissue deformation still occurs during respiration due to the diaphragm contact forces. In the absence of effective realtime image guidance, biomechanical models can be used to estimate tumor motion as a function of diaphragm's position. To develop this model, Finite Element Method (FEM) was employed. To demonstrate the concept, we conducted an animal study of an ex-vivo porcine deflated lung with a tumor phantom. The lung was deformed by compressing a diaphragm mimicking cylinder against it. Before compression, 3D-CT image of this lung was acquired, which was segmented and turned into FE mesh. The lung tissue was modeled as hyperelastic material with a contact loading to calculate the lung deformation and tumor motion during respiration. To validate the results from FE model, the motion of a small area on the surface close to the tumor was tracked while the lung was being loaded by the cylinder. Good agreement was demonstrated between the experiment results and simulation results. Furthermore, the impact of tissue hyperelastic parameters uncertainties in the FE model was investigated. For this purpose, we performed in-silico simulations with different hyperelastic parameters. This study demonstrated that the FEM was accurate and robust for tumor motion prediction.

  17. Safe motion planning for mobile agents: A model of reactive planning for multiple mobile agents

    SciTech Connect

    Fujimura, Kikuo.

    1990-01-01

    The problem of motion planning for multiple mobile agents is studied. Each planning agent independently plans its own action based on its map which contains a limited information about the environment. In an environment where more than one mobile agent interacts, the motions of the robots are uncertain and dynamic. A model for reactive agents is described and simulation results are presented to show their behavior patterns. 18 refs., 2 figs.

  18. Tsunami simulation using submarine displacement calculated from simulation of ground motion due to seismic source model

    NASA Astrophysics Data System (ADS)

    Akiyama, S.; Kawaji, K.; Fujihara, S.

    2013-12-01

    Since fault fracturing due to an earthquake can simultaneously cause ground motion and tsunami, it is appropriate to evaluate the ground motion and the tsunami by single fault model. However, several source models are used independently in the ground motion simulation or the tsunami simulation, because of difficulty in evaluating both phenomena simultaneously. Many source models for the 2011 off the Pacific coast of Tohoku Earthquake are proposed from the inversion analyses of seismic observations or from those of tsunami observations. Most of these models show the similar features, which large amount of slip is located at the shallower part of fault area near the Japan Trench. This indicates that the ground motion and the tsunami can be evaluated by the single source model. Therefore, we examine the possibility of the tsunami prediction, using the fault model estimated from seismic observation records. In this study, we try to carry out the tsunami simulation using the displacement field of oceanic crustal movements, which is calculated from the ground motion simulation of the 2011 off the Pacific coast of Tohoku Earthquake. We use two fault models by Yoshida et al. (2011), which are based on both the teleseismic body wave and on the strong ground motion records. Although there is the common feature in those fault models, the amount of slip near the Japan trench is lager in the fault model from the strong ground motion records than in that from the teleseismic body wave. First, the large-scale ground motion simulations applying those fault models used by the voxel type finite element method are performed for the whole eastern Japan. The synthetic waveforms computed from the simulations are generally consistent with the observation records of K-NET (Kinoshita (1998)) and KiK-net stations (Aoi et al. (2000)), deployed by the National Research Institute for Earth Science and Disaster Prevention (NIED). Next, the tsunami simulations are performed by the finite

  19. Plate motion

    SciTech Connect

    Gordon, R.G. )

    1991-01-01

    The motion of tectonic plates on the earth is characterized in a critical review of U.S. research from the period 1987-1990. Topics addressed include the NUVEL-1 global model of current plate motions, diffuse plate boundaries and the oceanic lithosphere, the relation between plate motions and distributed deformations, accelerations and the steadiness of plate motions, the distribution of current Pacific-North America motion across western North America and its margin, plate reconstructions and their uncertainties, hotspots, and plate dynamics. A comprehensive bibliography is provided. 126 refs.

  20. Global motions of the nuclear pore complex: insights from elastic network models.

    PubMed

    Lezon, Timothy R; Sali, Andrej; Bahar, Ivet

    2009-09-01

    The nuclear pore complex (NPC) is the gate to the nucleus. Recent determination of the configuration of proteins in the yeast NPC at approximately 5 nm resolution permits us to study the NPC global dynamics using coarse-grained structural models. We investigate these large-scale motions by using an extended elastic network model (ENM) formalism applied to several coarse-grained representations of the NPC. Two types of collective motions (global modes) are predicted by the ENMs to be intrinsically favored by the NPC architecture: global bending and extension/contraction from circular to elliptical shapes. These motions are shown to be robust against tested variations in the representation of the NPC, and are largely captured by a simple model of a toroid with axially varying mass density. We demonstrate that spoke multiplicity significantly affects the accessible number of symmetric low-energy modes of motion; the NPC-like toroidal structures composed of 8 spokes have access to highly cooperative symmetric motions that are inaccessible to toroids composed of 7 or 9 spokes. The analysis reveals modes of motion that may facilitate macromolecular transport through the NPC, consistent with previous experimental observations. PMID:19730674

  1. Coronary arteries motion modeling on 2D x-ray images

    NASA Astrophysics Data System (ADS)

    Gao, Yang; Sundar, Hari

    2012-02-01

    During interventional procedures, 3D imaging modalities like CT and MRI are not commonly used due to interference with the surgery and radiation exposure concerns. Therefore, real-time information is usually limited and building models of cardiac motion are difficult. In such case, vessel motion modeling based on 2-D angiography images become indispensable. Due to issues with existing vessel segmentation algorithms and the lack of contrast in occluded vessels, manual segmentation of certain branches is usually necessary. In addition, such occluded branches are the most important vessels during coronary interventions and obtaining motion models for these can greatly help in reducing the procedure time and radiation exposure. Segmenting different cardiac phases independently does not guarantee temporal consistency and is not efficient for occluded branches required manual segmentation. In this paper, we propose a coronary motion modeling system which extracts the coronary tree for every cardiac phase, maintaining the segmentation by tracking the coronary tree during the cardiac cycle. It is able to map every frame to the specific cardiac phase, thereby inferring the shape information of the coronary arteries using the model corresponding to its phase. Our experiments show that our motion modeling system can achieve promising results with real-time performance.

  2. Ab initio modeling of the motional Stark effect on MAST

    SciTech Connect

    De Bock, M. F. M.; Conway, N. J.; Walsh, M. J.; Carolan, P. G.; Hawkes, N. C.

    2008-10-15

    A multichord motional Stark effect (MSE) system has recently been built on the MAST tokamak. In MAST the {pi} and {sigma} lines of the MSE spectrum overlap due to the low magnetic field typical for present day spherical tokamaks. Also, the field curvature results in a large change in the pitch angle over the observation volume. The measured polarization angle does not relate to one local pitch angle but to an integration over all pitch angles in the observation volume. The velocity distribution of the neutral beam further complicates the measurement. To take into account volume effects and velocity distribution, an ab initio code was written that simulates the MSE spectrum on MAST. The code is modular and can easily be adjusted for other tokamaks. The code returns the intensity, polarized fraction, and polarization angle as a function of wavelength. Results of the code are presented, showing the effect on depolarization and wavelength dependence of the polarization angle. The code is used to optimize the design and calibration of the MSE diagnostic.

  3. Sensitivity of tumor motion simulation accuracy to lung biomechanical modeling approaches and parameters

    NASA Astrophysics Data System (ADS)

    Nasehi Tehrani, Joubin; Yang, Yin; Werner, Rene; Lu, Wei; Low, Daniel; Guo, Xiaohu; Wang, Jing

    2015-11-01

    Finite element analysis (FEA)-based biomechanical modeling can be used to predict lung respiratory motion. In this technique, elastic models and biomechanical parameters are two important factors that determine modeling accuracy. We systematically evaluated the effects of lung and lung tumor biomechanical modeling approaches and related parameters to improve the accuracy of motion simulation of lung tumor center of mass (TCM) displacements. Experiments were conducted with four-dimensional computed tomography (4D-CT). A Quasi-Newton FEA was performed to simulate lung and related tumor displacements between end-expiration (phase 50%) and other respiration phases (0%, 10%, 20%, 30%, and 40%). Both linear isotropic and non-linear hyperelastic materials, including the neo-Hookean compressible and uncoupled Mooney-Rivlin models, were used to create a finite element model (FEM) of lung and tumors. Lung surface displacement vector fields (SDVFs) were obtained by registering the 50% phase CT to other respiration phases, using the non-rigid demons registration algorithm. The obtained SDVFs were used as lung surface displacement boundary conditions in FEM. The sensitivity of TCM displacement to lung and tumor biomechanical parameters was assessed in eight patients for all three models. Patient-specific optimal parameters were estimated by minimizing the TCM motion simulation errors between phase 50% and phase 0%. The uncoupled Mooney-Rivlin material model showed the highest TCM motion simulation accuracy. The average TCM motion simulation absolute errors for the Mooney-Rivlin material model along left-right, anterior-posterior, and superior-inferior directions were 0.80 mm, 0.86 mm, and 1.51 mm, respectively. The proposed strategy provides a reliable method to estimate patient-specific biomechanical parameters in FEM for lung tumor motion simulation.

  4. Sensitivity of tumor motion simulation accuracy to lung biomechanical modeling approaches and parameters.

    PubMed

    Tehrani, Joubin Nasehi; Yang, Yin; Werner, Rene; Lu, Wei; Low, Daniel; Guo, Xiaohu; Wang, Jing

    2015-11-21

    Finite element analysis (FEA)-based biomechanical modeling can be used to predict lung respiratory motion. In this technique, elastic models and biomechanical parameters are two important factors that determine modeling accuracy. We systematically evaluated the effects of lung and lung tumor biomechanical modeling approaches and related parameters to improve the accuracy of motion simulation of lung tumor center of mass (TCM) displacements. Experiments were conducted with four-dimensional computed tomography (4D-CT). A Quasi-Newton FEA was performed to simulate lung and related tumor displacements between end-expiration (phase 50%) and other respiration phases (0%, 10%, 20%, 30%, and 40%). Both linear isotropic and non-linear hyperelastic materials, including the neo-Hookean compressible and uncoupled Mooney-Rivlin models, were used to create a finite element model (FEM) of lung and tumors. Lung surface displacement vector fields (SDVFs) were obtained by registering the 50% phase CT to other respiration phases, using the non-rigid demons registration algorithm. The obtained SDVFs were used as lung surface displacement boundary conditions in FEM. The sensitivity of TCM displacement to lung and tumor biomechanical parameters was assessed in eight patients for all three models. Patient-specific optimal parameters were estimated by minimizing the TCM motion simulation errors between phase 50% and phase 0%. The uncoupled Mooney-Rivlin material model showed the highest TCM motion simulation accuracy. The average TCM motion simulation absolute errors for the Mooney-Rivlin material model along left-right, anterior-posterior, and superior-inferior directions were 0.80 mm, 0.86 mm, and 1.51 mm, respectively. The proposed strategy provides a reliable method to estimate patient-specific biomechanical parameters in FEM for lung tumor motion simulation. PMID:26531324

  5. Toward a computational theory for motion understanding: The expert animators model

    NASA Technical Reports Server (NTRS)

    Mohamed, Ahmed S.; Armstrong, William W.

    1988-01-01

    Artificial intelligence researchers claim to understand some aspect of human intelligence when their model is able to emulate it. In the context of computer graphics, the ability to go from motion representation to convincing animation should accordingly be treated not simply as a trick for computer graphics programmers but as important epistemological and methodological goal. In this paper we investigate a unifying model for animating a group of articulated bodies such as humans and robots in a three-dimensional environment. The proposed model is considered in the framework of knowledge representation and processing, with special reference to motion knowledge. The model is meant to help setting the basis for a computational theory for motion understanding applied to articulated bodies.

  6. Local harmonic motion monitoring of focused ultrasound surgery--a simulation model.

    PubMed

    Heikkilä, Janne; Curiel, Laura; Hynynen, Kullervo

    2010-01-01

    In this paper, a computational model for localized harmonic motion (LHM) imaging-based monitoring of high-intensity focused ultrasound surgery (FUS) is presented. The LHM technique is based on a focused, time-varying ultrasound radiation force excitation, which induces local oscillatory motions at the focal region. These vibrations are tracked, using pulse-echo imaging, and then, used to estimate the mechanical properties of the sonication region. LHM is feasible for FUS monitoring because changes in the material properties during the coagulation process affect the measured displacements. The presented model includes separate models to simulate acoustic sonication fields, sonication-induced temperature elevation and mechanical motion, and pulse-echo imaging of the induced motions. These 3-D simulation models are based on Rayleigh-Sommerfield integral, finite element, and spatial impulse response methods. Simulated-tissue temperature elevation and mechanical motion were compared with previously published in vivo measurements. Finally, the simulation model was used to simulate coagulation and LHM monitoring, as would occur with multiple, neighbouring sonication locations covering a large tumor. PMID:19822463

  7. Elastic network models capture the motions apparent within ensembles of RNA structures

    PubMed Central

    Zimmermann, Michael T.; Jernigan, Robert L.

    2014-01-01

    The role of structure and dynamics in mechanisms for RNA becomes increasingly important. Computational approaches using simple dynamics models have been successful at predicting the motions of proteins and are often applied to ribonucleo-protein complexes but have not been thoroughly tested for well-packed nucleic acid structures. In order to characterize a true set of motions, we investigate the apparent motions from 16 ensembles of experimentally determined RNA structures. These indicate a relatively limited set of motions that are captured by a small set of principal components (PCs). These limited motions closely resemble the motions computed from low frequency normal modes from elastic network models (ENMs), either at atomic or coarse-grained resolution. Various ENM model types, parameters, and structure representations are tested here against the experimental RNA structural ensembles, exposing differences between models for proteins and for folded RNAs. Differences in performance are seen, depending on the structure alignment algorithm used to generate PCs, modulating the apparent utility of ENMs but not significantly impacting their ability to generate functional motions. The loss of dynamical information upon coarse-graining is somewhat larger for RNAs than for globular proteins, indicating, perhaps, the lower cooperativity of the less densely packed RNA. However, the RNA structures show less sensitivity to the elastic network model parameters than do proteins. These findings further demonstrate the utility of ENMs and the appropriateness of their application to well-packed RNA-only structures, justifying their use for studying the dynamics of ribonucleo-proteins, such as the ribosome and regulatory RNAs. PMID:24759093

  8. Onset of collective motion in locusts is captured by a minimal model

    NASA Astrophysics Data System (ADS)

    Dyson, Louise; Yates, Christian A.; Buhl, Jerome; McKane, Alan J.

    2015-11-01

    We present a minimal model to describe the onset of collective motion seen when a population of locusts are placed in an annular arena. At low densities motion is disordered, while at high densities locusts march in a common direction, which may reverse during the experiment. The data are well captured by an individual-based model, in which demographic noise leads to the observed density-dependent effects. By fitting the model parameters to equation-free coefficients, we give a quantitative comparison, showing time series, stationary distributions, and the mean switching times between states.

  9. Onset of collective motion in locusts is captured by a minimal model.

    PubMed

    Dyson, Louise; Yates, Christian A; Buhl, Jerome; McKane, Alan J

    2015-11-01

    We present a minimal model to describe the onset of collective motion seen when a population of locusts are placed in an annular arena. At low densities motion is disordered, while at high densities locusts march in a common direction, which may reverse during the experiment. The data are well captured by an individual-based model, in which demographic noise leads to the observed density-dependent effects. By fitting the model parameters to equation-free coefficients, we give a quantitative comparison, showing time series, stationary distributions, and the mean switching times between states. PMID:26651724

  10. A patient specific 4D MRI liver motion model based on sparse imaging and registration

    NASA Astrophysics Data System (ADS)

    Noorda, Y. H.; Bartels, L. W.; van Stralen, Marijn; Pluim, J. P. W.

    2013-03-01

    Introduction: Image-guided minimally invasive procedures are becoming increasingly popular. Currently, High-Intensity Focused Ultrasound (HIFU) treatment of lesions in mobile organs, such as the liver, is in development. A requirement for such treatment is automatic motion tracking, such that the position of the lesion can be followed in real time. We propose a 4D liver motion model, which can be used during planning of this procedure. During treatment, the model can serve as a motion predictor. In a similar fashion, this model could be used for radiotherapy treatment of the liver. Method: The model is built by acquiring 2D dynamic sagittal MRI data at six locations in the liver. By registering these dynamics to a 3D MRI liver image, 2D deformation fields are obtained at every location. The 2D fields are ordered according to the position of the liver at that specific time point, such that liver motion during an average breathing period can be simulated. This way, a sparse deformation field is created over time. This deformation field is finally interpolated over the entire volume, yielding a 4D motion model. Results: The accuracy of the model is evaluated by comparing unseen slices to the slice predicted by the model at that specific location and phase in the breathing cycle. The mean Dice coefficient of the liver regions was 0.90. The mean misalignment of the vessels was 1.9 mm. Conclusion: The model is able to predict patient specific deformations of the liver and can predict regular motion accurately.

  11. Modeling and measurement of the motion of the DIII-D vacuum vessel during vertical instabilities

    SciTech Connect

    Reis, E.; Blevins, R.D.; Jensen, T.H.; Luxon, J.L.; Petersen, P.I.; Strait, E.J.

    1991-11-01

    The motions of the D3-D vacuum vessel during vertical instabilities of elongated plasmas have been measured and studied over the past five years. The currents flowing in the vessel wall and the plasma scrapeoff layer were also measured and correlated to a physics model. These results provide a time history load distribution on the vessel which were input to a dynamic analysis for correlation to the measured motions. The structural model of the vessel using the loads developed from the measured vessel currents showed that the calculated displacement history correlated well with the measured values. The dynamic analysis provides a good estimate of the stresses and the maximum allowable deflection of the vessel. In addition, the vessel motions produce acoustic emissions at 21 Hertz that are sufficiently loud to be felt as well as heard by the D3-D operators. Time history measurements of the sounds were correlated to the vessel displacements. An analytical model of an oscillating sphere provided a reasonable correlation to the amplitude of the measured sounds. The correlation of the theoretical and measured vessel currents, the dynamic measurements and analysis, and the acoustic measurements and analysis show that: (1) The physics model can predict vessel forces for selected values of plasma resistivity. The model also predicts poloidal and toroidal wall currents which agree with measured values; (2) The force-time history from the above model, used in conjunction with an axisymmetric structural model of the vessel, predicts vessel motions which agree well with measured values; (3) The above results, input to a simple acoustic model predicts the magnitude of sounds emitted from the vessel during disruptions which agree with acoustic measurements; (4) Correlation of measured vessel motions with structural analysis shows that a maximum vertical motion of the vessel up to 0.24 in will not overstress the vessel or its supports. 11 refs., 10 figs., 1 tab.

  12. Viscoelastic model based force control for soft tissue interaction and its application in physiological motion compensation.

    PubMed

    Moreira, Pedro; Zemiti, Nabil; Liu, Chao; Poignet, Philippe

    2014-09-01

    Controlling the interaction between robots and living soft tissues has become an important issue as the number of robotic systems inside the operating room increases. Many researches have been done on force control to help surgeons during medical procedures, such as physiological motion compensation and tele-operation systems with haptic feedback. In order to increase the performance of such controllers, this work presents a novel force control scheme using Active Observer (AOB) based on a viscoelastic interaction model. The control scheme has shown to be stable through theoretical analysis and its performance was evaluated by in vitro experiments. In order to evaluate how the force control scheme behaves under the presence of physiological motion, experiments considering breathing and beating heart disturbances are presented. The proposed control scheme presented a stable behavior in both static and moving environment. The viscoelastic AOB presented a compensation ratio of 87% for the breathing motion and 79% for the beating heart motion. PMID:24612709

  13. Ranking of several ground-motion models for seismic hazard analysis in Iran

    NASA Astrophysics Data System (ADS)

    Ghasemi, H.; Zare, M.; Fukushima, Y.

    2008-09-01

    In this study, six attenuation relationships are classified with respect to the ranking scheme proposed by Scherbaum et al (2004 Bull. Seismol. Soc. Am. 94 1-22). First, the strong motions recorded during the 2002 Avaj, 2003 Bam, 2004 Kojour and 2006 Silakhor earthquakes are consistently processed. Then the normalized residual sets are determined for each selected ground-motion model, considering the strong-motion records chosen. The main advantage of these records is that corresponding information about the causative fault plane has been well studied for the selected events. Such information is used to estimate several control parameters which are essential inputs for attenuation relations. The selected relations (Zare et al (1999 Soil Dyn. Earthq. Eng. 18 101-23) Fukushima et al (2003 J. Earthq. Eng. 7 573-98) Sinaeian (2006 PhD Thesis International Institute of Earthquake Engineering and Seismology, Tehran, Iran); Boore and Atkinson (2007 PEER, Report 2007/01); Campbell and Bozorgnia (2007 PEER, Report 2007/02); and Chiou and Youngs (2006 PEER Interim Report for USGS Review)) have been deemed suitable for predicting peak ground-motion amplitudes in the Iranian plateau. Several graphical techniques and goodness-of-fit measures are also applied for statistical distribution analysis of the normalized residual sets. Such analysis reveals ground-motion models, developed using Iranian strong-motion records as the most appropriate ones in the Iranian context. The results of the present study are applicable in seismic hazard assessment projects in Iran.

  14. Simulation of Wave Motion Using a Lattice Gas Model

    NASA Astrophysics Data System (ADS)

    Buick, J.; Easson, W.; Greated, C.

    1996-02-01

    The lattice gas model for simulating two-phase flow, proposed by Appert and Zaleski, has been modified by the introduction of gravitational interactions and the new model has been used to simulate standing wave patterns on the free surface of a fluid. The results compare well with linear theory.

  15. Flap motion of helicopter rotors with novel, dynamic stall model

    NASA Astrophysics Data System (ADS)

    Han, Wei; Liu, Jie; Liu, Chun; Chen, Lei; Su, Xichao; Zhao, Peng

    2016-07-01

    In this paper, a nonlinear flapping equation for large inflow angles and flap angles is established by analyzing the aerodynamics of helicopter blade elements. In order to obtain a generalized flap equation, the Snel stall model was first applied to determine the lift coefficient of the helicopter rotor. A simulation experiment for specific airfoils was then conducted to verify the effectiveness of the Snel stall model as it applies to helicopters. Results show that the model requires no extraneous parameters compared to the traditional stall model and is highly accurate and practically applicable. Based on the model, the relationship between the flapping angle and the angle of attack was analyzed, as well as the advance ratio under the dynamic stall state.

  16. Two-stage model of African absolute motion during the last 30 million years

    NASA Astrophysics Data System (ADS)

    Pollitz, Fred F.

    1991-07-01

    The absolute motion of Africa (relative to the hotspots) for the past 30 My is modeled with two Euler vectors, with a change occurring at 6 Ma. Because of the high sensitivity of African absolute motions to errors in the absolute motions of the North America and Pacific plates, both the pre-6 Ma and post-6 Ma African absolute motions are determined simultaneously with North America and Pacific absolute motions for various epochs. Geologic data from the northern Atlantic and hotspot tracks from the African plate are used to augment previous data sets for the North America and Pacific plates. The difference between the pre-6 Ma and post-6 Ma absolute plate motions may be represented as a counterclockwise rotation about a pole at 48 °S, 84 °E, with angular velocity 0.085 °/My. This change is supported by geologic evidence along a large portion of the African plate boundary, including the Red Sea and Gulf of Aden spreading systems, the Alpine deformation zone, and the central and southern mid-Atlantic Ridge. Although the change is modeled as one abrupt transition at 6 Ma, it was most likely a gradual change spanning the period 8-4 Ma. As a likely mechanism for the change, we favor strong asthenospheric return flow from the Afar hotspot towards the southwest; this could produce the uniform southwesterly shift in absolute motion which we have inferred as well as provide a mechanism for the opening of the East African Rift. Comparing the absolute motions of the North America and Pacific plates with earlier estimates, the pole positions are revised by up to 5° and the angular velocities are decreased by 10-20%.

  17. The application of the sinusoidal model to lung cancer patient respiratory motion

    SciTech Connect

    George, R.; Vedam, S.S.; Chung, T.D.; Ramakrishnan, V.; Keall, P.J.

    2005-09-15

    Accurate modeling of the respiratory cycle is important to account for the effect of organ motion on dose calculation for lung cancer patients. The aim of this study is to evaluate the accuracy of a respiratory model for lung cancer patients. Lujan et al. [Med. Phys. 26(5), 715-720 (1999)] proposed a model, which became widely used, to describe organ motion due to respiration. This model assumes that the parameters do not vary between and within breathing cycles. In this study, first, the correlation of respiratory motion traces with the model f(t) as a function of the parameter n(n=1,2,3) was undertaken for each breathing cycle from 331 four-minute respiratory traces acquired from 24 lung cancer patients using three breathing types: free breathing, audio instruction, and audio-visual biofeedback. Because cos{sup 2} and cos{sup 4} had similar correlation coefficients, and cos{sup 2} and cos{sup 1} have a trigonometric relationship, for simplicity, the cos{sup 1} value was consequently used for further analysis in which the variations in mean position (z{sub 0}), amplitude of motion (b) and period ({tau}) with and without biofeedback or instructions were investigated. For all breathing types, the parameter values, mean position (z{sub 0}), amplitude of motion (b), and period ({tau}) exhibited significant cycle-to-cycle variations. Audio-visual biofeedback showed the least variations for all three parameters (z{sub 0}, b, and {tau}). It was found that mean position (z{sub 0}) could be approximated with a normal distribution, and the amplitude of motion (b) and period ({tau}) could be approximated with log normal distributions. The overall probability density function (pdf) of f(t) for each of the three breathing types was fitted with three models: normal, bimodal, and the pdf of a simple harmonic oscillator. It was found that the normal and the bimodal models represented the overall respiratory motion pdfs with correlation values from 0.95 to 0.99, whereas the range

  18. Strong ground-motion prediction from Stochastic-dynamic source models

    USGS Publications Warehouse

    Guatteri, Mariagiovanna; Mai, P.M.; Beroza, G.C.; Boatwright, J.

    2003-01-01

    In the absence of sufficient data in the very near source, predictions of the intensity and variability of ground motions from future large earthquakes depend strongly on our ability to develop realistic models of the earthquake source. In this article we simulate near-fault strong ground motion using dynamic source models. We use a boundary integral method to simulate dynamic rupture of earthquakes by specifying dynamic source parameters (fracture energy and stress drop) as spatial random fields. We choose these quantities such that they are consistent with the statistical properties of slip heterogeneity found in finite-source models of past earthquakes. From these rupture models we compute theoretical strong-motion seismograms up to a frequency of 2 Hz for several realizations of a scenario strike-slip Mw 7.0 earthquake and compare empirical response spectra, spectra obtained from our dynamic models, and spectra determined from corresponding kinematic simulations. We find that spatial and temporal variations in slip, slip rise time, and rupture propagation consistent with dynamic rupture models exert a strong influence on near-source ground motion. Our results lead to a feasible approach to specify the variability in the rupture time distribution in kinematic models through a generalization of Andrews' (1976) result relating rupture speed to apparent fracture energy, stress drop, and crack length to 3D dynamic models. This suggests that a simplified representation of dynamic rupture may be obtained to approximate the effects of dynamic rupture without having to do full dynamic simulations.

  19. Transverse momentum dependent distribution functions in a covariant parton model approach with quark orbital motion

    SciTech Connect

    Efremov, A. V.; Teryaev, O. V.; Schweitzer, P.; Zavada, P.

    2009-07-01

    Transverse parton momentum dependent distribution functions (TMDs) of the nucleon are studied in a covariant model, which describes the intrinsic motion of partons in terms of a covariant momentum distribution. The consistency of the approach is demonstrated, and model relations among TMDs are studied. As a by-product it is shown how the approach allows to formulate the nonrelativistic limit.

  20. REPRESENTATION OF ATMOSPHERIC MOTION IN MODELS OF REGIONAL-SCALE AIR POLLUTION

    EPA Science Inventory

    A method is developed for generating ensembles of wind fields for use in regional scale (1000 km) models of transport and diffusion. The underlying objective is a methodology for representing atmospheric motion in applied air pollution models that permits explicit treatment of th...

  1. Theoretical models of flux pinning and flux motion in high-{Tc} superconducting oxides

    SciTech Connect

    Welch, D.O.

    1991-12-31

    Various issues involved in the development of phenomenological models of flux pinning and motion in high-{Tc} oxides are discussed. A simplified model is presented for the critical current density and is used to examine the question of whether flux flow results from an instability due to plasticity of the flux-line array or from pin breaking.

  2. Theoretical models of flux pinning and flux motion in high- Tc superconducting oxides

    SciTech Connect

    Welch, D.O.

    1991-01-01

    Various issues involved in the development of phenomenological models of flux pinning and motion in high-{Tc} oxides are discussed. A simplified model is presented for the critical current density and is used to examine the question of whether flux flow results from an instability due to plasticity of the flux-line array or from pin breaking.

  3. ROTATING MOTIONS AND MODELING OF THE ERUPTING SOLAR POLAR-CROWN PROMINENCE ON 2010 DECEMBER 6

    SciTech Connect

    Su, Yingna; Van Ballegooijen, Adriaan

    2013-02-10

    A large polar-crown prominence composed of different segments spanning nearly the entire solar disk erupted on 2010 December 6. Prior to the eruption, the filament in the active region part split into two layers: a lower layer and an elevated layer. The eruption occurs in several episodes. Around 14:12 UT, the lower layer of the active region filament breaks apart: One part ejects toward the west, while the other part ejects toward the east, which leads to the explosive eruption of the eastern quiescent filament. During the early rise phase, part of the quiescent filament sheet displays strong rolling motion (observed by STEREO-B) in the clockwise direction (viewed from east to west) around the filament axis. This rolling motion appears to start from the border of the active region, then propagates toward the east. The Atmospheric Imaging Assembly (AIA) observes another type of rotating motion: In some other parts of the erupting quiescent prominence, the vertical threads turn horizontal, then turn upside down. The elevated active region filament does not erupt until 18:00 UT, when the erupting quiescent filament has already reached a very large height. We develop two simplified three-dimensional models that qualitatively reproduce the observed rolling and rotating motions. The prominence in the models is assumed to consist of a collection of discrete blobs that are tied to particular field lines of a helical flux rope. The observed rolling motion is reproduced by continuous twist injection into the flux rope in Model 1 from the active region side. Asymmetric reconnection induced by the asymmetric distribution of the magnetic fields on the two sides of the filament may cause the observed rolling motion. The rotating motion of the prominence threads observed by AIA is consistent with the removal of the field line dips in Model 2 from the top down during the eruption.

  4. Rapid D-Affine Biventricular Cardiac Function with Polar Prediction

    PubMed Central

    Gilbert, Kathleen; Cowan, Brett; Suinesiaputra, Avan; Occleshaw, Christopher; Young, Alistair

    2014-01-01

    Although many solutions have been proposed for left ventricular functional analysis of the heart, right and left (bi-) ventricular function has been problematic due to the complex geometry and large motions. Biventricular function is particularly important in congenital heart disease, the most common type of birth defects. We describe a rapid interactive analysis tool for biventricular function which incorporates 1) a 3D+ time finite element model of biventricular geometry, 2) a fast prediction step which estimates an initial geometry in a polar coordinate system, and 3) a Cartesian update which penalizes deviations from affine transformations (D-Affine) from a prior. Solution times were very rapid, enabling interaction in real time using guide point modeling. The method was applied to 13 patients with congenital heart disease and compared with the clinical gold standard of manual tracing. Results between the methods showed good correlation (R2 > 0.9) and good precision (volume<17ml; mass<11g) for both chambers. PMID:25485422

  5. A patient-specific respiratory model of anatomical motion for radiation treatment planning

    SciTech Connect

    Zhang Qinghui; Pevsner, Alex; Hertanto, Agung; Hu Yuchi; Rosenzweig, Kenneth E.; Ling, C. Clifton; Mageras, Gig S

    2007-12-15

    The modeling of respiratory motion is important for a more accurate understanding and accounting of its effect on dose to cancers in the thorax and abdomen by radiotherapy. We have developed a model of respiration-induced organ motion in the thorax without the commonly adopted assumption of repeatable breath cycles. The model describes the motion of a volume of interest within the patient based on a reference three-dimensional (3D) image (at end expiration) and the diaphragm positions at different time points. The input data are respiration-correlated CT (RCCT) images of patients treated for non-small- cell lung cancer, consisting of 3D images, including the diaphragm positions, at ten phases of the respiratory cycle. A deformable image registration algorithm calculates the deformation field that maps each 3D image to the reference 3D image. A principal component analysis is performed to parameterize the 3D deformation field in terms of the diaphragm motion. We show that the first two principal components are adequate to accurately and completely describe the organ motion in the data of four patients. Artifacts in the RCCT images that commonly occur at the mid-respiration states are reduced in the model-generated images. Further validation of the model is demonstrated in the successful application of the parameterized 3D deformation field to RCCT data of the same patient but acquired several days later. We have developed a method for predicting respiration-induced organ motion in patients that has potential for improving the accuracy of dose calculation in radiotherapy. Possible limitations of the model are cases where the correlation between lung tumor and diaphragm position is less reliable such as superiorly situated tumors and interfraction changes in tumor-diaphragm correlation. The limited number of clinical cases examined suggests, but does not confirm, the model's applicability to a wide range of patients.

  6. Validation of attenuation models for ground motion applications in central and eastern North America

    DOE PAGESBeta

    Pasyanos, Michael E.

    2015-11-01

    Recently developed attenuation models are incorporated into standard one-dimensional (1-D) ground motion prediction equations (GMPEs), effectively making them two-dimensional (2-D) and eliminating the need to create different GMPEs for an increasing number of sub-regions. The model is tested against a data set of over 10,000 recordings from 81 earthquakes in North America. The use of attenuation models in GMPEs improves our ability to fit observed ground motions and should be incorporated into future national hazard maps. The improvement is most significant at higher frequencies and longer distances which have a greater number of wave cycles. This has implications for themore » rare high-magnitude earthquakes, which produce potentially damaging ground motions over wide areas, and drive the seismic hazards. Furthermore, the attenuation models can be created using weak ground motions, they could be developed for regions of low seismicity where empirical recordings of ground motions are uncommon and do not span the full range of magnitudes and distances.« less

  7. Moving object detection using dynamic motion modelling from UAV aerial images.

    PubMed

    Saif, A F M Saifuddin; Prabuwono, Anton Satria; Mahayuddin, Zainal Rasyid

    2014-01-01

    Motion analysis based moving object detection from UAV aerial image is still an unsolved issue due to inconsideration of proper motion estimation. Existing moving object detection approaches from UAV aerial images did not deal with motion based pixel intensity measurement to detect moving object robustly. Besides current research on moving object detection from UAV aerial images mostly depends on either frame difference or segmentation approach separately. There are two main purposes for this research: firstly to develop a new motion model called DMM (dynamic motion model) and secondly to apply the proposed segmentation approach SUED (segmentation using edge based dilation) using frame difference embedded together with DMM model. The proposed DMM model provides effective search windows based on the highest pixel intensity to segment only specific area for moving object rather than searching the whole area of the frame using SUED. At each stage of the proposed scheme, experimental fusion of the DMM and SUED produces extracted moving objects faithfully. Experimental result reveals that the proposed DMM and SUED have successfully demonstrated the validity of the proposed methodology. PMID:24892103

  8. Building motion models of lung tumours from cone-beam CT for radiotherapy applications.

    PubMed

    Martin, James; McClelland, Jamie; Yip, Connie; Thomas, Christopher; Hartill, Clare; Ahmad, Shahreen; O'Brien, Richard; Meir, Ivan; Landau, David; Hawkes, David

    2013-03-21

    A method is presented to build a surrogate-driven motion model of a lung tumour from a cone-beam CT scan, which does not require markers. By monitoring an external surrogate in real time, it is envisaged that the motion model be used to drive gated or tracked treatments. The motion model would be built immediately before each fraction of treatment and can account for inter-fraction variation. The method could also provide a better assessment of tumour shape and motion prior to delivery of each fraction of stereotactic ablative radiotherapy. The two-step method involves enhancing the tumour region in the projections, and then fitting the surrogate-driven motion model. On simulated data, the mean absolute error was reduced to 1 mm. For patient data, errors were determined by comparing estimated and clinically identified tumour positions in the projections, scaled to mm at the isocentre. Averaged over all used scans, the mean absolute error was under 2.5 mm in superior-inferior and transverse directions. PMID:23442367

  9. Validation of attenuation models for ground motion applications in central and eastern North America

    SciTech Connect

    Pasyanos, Michael E.

    2015-11-01

    Recently developed attenuation models are incorporated into standard one-dimensional (1-D) ground motion prediction equations (GMPEs), effectively making them two-dimensional (2-D) and eliminating the need to create different GMPEs for an increasing number of sub-regions. The model is tested against a data set of over 10,000 recordings from 81 earthquakes in North America. The use of attenuation models in GMPEs improves our ability to fit observed ground motions and should be incorporated into future national hazard maps. The improvement is most significant at higher frequencies and longer distances which have a greater number of wave cycles. This has implications for the rare high-magnitude earthquakes, which produce potentially damaging ground motions over wide areas, and drive the seismic hazards. Furthermore, the attenuation models can be created using weak ground motions, they could be developed for regions of low seismicity where empirical recordings of ground motions are uncommon and do not span the full range of magnitudes and distances.

  10. Hidden Markov Modeling for Weigh-In-Motion Estimation

    SciTech Connect

    Abercrombie, Robert K; Ferragut, Erik M; Boone, Shane

    2012-01-01

    This paper describes a hidden Markov model to assist in the weight measurement error that arises from complex vehicle oscillations of a system of discrete masses. Present reduction of oscillations is by a smooth, flat, level approach and constant, slow speed in a straight line. The model uses this inherent variability to assist in determining the true total weight and individual axle weights of a vehicle. The weight distribution dynamics of a generic moving vehicle were simulated. The model estimation converged to within 1% of the true mass for simulated data. The computational demands of this method, while much greater than simple averages, took only seconds to run on a desktop computer.

  11. Multi-modal gesture recognition using integrated model of motion, audio and video

    NASA Astrophysics Data System (ADS)

    Goutsu, Yusuke; Kobayashi, Takaki; Obara, Junya; Kusajima, Ikuo; Takeichi, Kazunari; Takano, Wataru; Nakamura, Yoshihiko

    2015-07-01

    Gesture recognition is used in many practical applications such as human-robot interaction, medical rehabilitation and sign language. With increasing motion sensor development, multiple data sources have become available, which leads to the rise of multi-modal gesture recognition. Since our previous approach to gesture recognition depends on a unimodal system, it is difficult to classify similar motion patterns. In order to solve this problem, a novel approach which integrates motion, audio and video models is proposed by using dataset captured by Kinect. The proposed system can recognize observed gestures by using three models. Recognition results of three models are integrated by using the proposed framework and the output becomes the final result. The motion and audio models are learned by using Hidden Markov Model. Random Forest which is the video classifier is used to learn the video model. In the experiments to test the performances of the proposed system, the motion and audio models most suitable for gesture recognition are chosen by varying feature vectors and learning methods. Additionally, the unimodal and multi-modal models are compared with respect to recognition accuracy. All the experiments are conducted on dataset provided by the competition organizer of MMGRC, which is a workshop for Multi-Modal Gesture Recognition Challenge. The comparison results show that the multi-modal model composed of three models scores the highest recognition rate. This improvement of recognition accuracy means that the complementary relationship among three models improves the accuracy of gesture recognition. The proposed system provides the application technology to understand human actions of daily life more precisely.

  12. Statistical mechanics models for motion and force planning

    NASA Technical Reports Server (NTRS)

    Rodriguez, G.

    1990-01-01

    The models of statistical mechanics provide an alternative to the methods of classical mechanics more traditionally used in robotics. They have a potential to: improve analysis of object collisions; handle kinematic and dynamic contact interactions within the same frmework; and reduce the need for perfect deterministic world model information. The statistical mechanics models characterize the state of the system as a probability density function (p.d.f.) whose time evolution is governed by a partial differential equation subject to boundary and initial conditions. The boundary conditions when rigid objects collide reflect the conservation of momentum. The models are being developed to embedd in remote semi-autonomous systems with a need to reason and interact with a multiobject environment.

  13. Mineralogy of new Antarctic achondrites with affinity to Lodran and a model of their evolution in an asteroid

    NASA Technical Reports Server (NTRS)

    Takeda, Hiroshi; Mori, Hiroshi; Hiroi, Takahiro; Saito, Jun

    1994-01-01

    We studied five new Antartic achondrites, MacAlpine Hills (MAC) 88177, Yamato (Y)74357, Y75274, Y791491 and Elephant Moraine (EET)84302 by mineralogical techniques to gain a better understanding of the mineral assemblages of a group of meteorites with an affinity to Lodran (stony-iron meteorite) and their formation processes. This group is being called lodranites. These meteorites contain major coarse-grained orthopyroxene (Opx) and olivine as in Lodran and variable amounts of FeNi metal and troilite etc. MAC88177 has more augite and less FeNi than Lodran; Y74357 has more olivine and contains minor augite; Y791491 contains in addition plagioclase. EET84302 has an Acapulco-like chondritic mineral assembladge and is enriched in FeNi metal and plagioclase, but one part is enriched in Opx and chromite. The EET84302 and MAC88177 Opx crystals have dusty cores as in Acapulco. EET84302 and Y75274 are more Mg-rich than other members of the lodranite group, and Y74357 is intermediate. Since these meteorites all have coarse-grained textures, similar major mineral assemblages, variable amounts of augite, plagioclase, FeNi metal, chromite and olivine, we suggest that they are related and are linked to a parent body with modified chondritic compositions. The variability of the abundances of these minerals are in line with a proposed model of the surface mineral assemblages of the S asteroids. The mineral assemblages can best be explained by differing degrees of loss or movements of lower temperature partial melts and recrystallization, and reduction. A portion of EET84302 rich in metal and plagioclase may represent a type of component removed from the lodranite group meteorites. Y791058 and Caddo County, which were studied for comparison, are plagioclase-rich silicate inclusions in IAB iron meteorites and may have been derived by similar process but in a different body.

  14. Tensegrity applied to modelling the motion of viruses

    NASA Astrophysics Data System (ADS)

    Simona-Mariana, Cretu; Gabriela-Catalina, Brinzan

    2011-02-01

    A considerable number of viruses' structures have been discovered and more are expected to be identified. Different viruses' symmetries can be observed at the nanoscale level. The mechanical models of some viruses realised by scientists are described in this paper, none of which has taken into consideration the internal deformation of subsystems. The authors' models for some viruses' elements are introduced, with rigid and flexible links, which reproduce the movements of viruses including internal deformations of the subunits.

  15. Kinematic source models for long-period ground motion simulations of megathrust earthquakes: validation against ground motion data for the 2003 Tokachi-oki earthquake

    NASA Astrophysics Data System (ADS)

    Iwaki, Asako; Maeda, Takahiro; Morikawa, Nobuyuki; Aoi, Shin; Fujiwara, Hiroyuki

    2016-06-01

    In this study, a method for simulating the ground motion of megathrust earthquakes at periods of approximately 2 s and longer was validated by using the characterized source model combined with multi-scale spatial heterogeneity. Source models for the M W 8.3, 2003 Tokachi-oki earthquake were constructed, and ground motion simulations were conducted to test their performance. First, a characterized source model was generated based on a source model obtained from waveform inversion analysis. Then, multi-scale heterogeneity was added to the spatial distribution of several source parameters to yield a heterogeneous source model. An investigation of the Fourier spectra and 5 % damped velocity response spectra of the simulated and observed ground motions demonstrated that adding multi-scale heterogeneity to the spatial distributions of the slip, rupture velocity, and rake angle of the characterized source model is an effective method for constructing a source model that explains the ground motion at periods of 2-20 s. It was also revealed how the complexity of the parameters affects the resulting ground motion. The complexity of the rupture velocity had the largest influence among the three parameters.

  16. Bounding Ground Motions for Hayward Fault Scenario Earthquakes Using Suites of Stochastic Rupture Models

    NASA Astrophysics Data System (ADS)

    Rodgers, A. J.; Xie, X.; Petersson, A.

    2007-12-01

    The next major earthquake in the San Francisco Bay area is likely to occur on the Hayward-Rodgers Creek Fault system. Attention on the southern Hayward section is appropriate given the upcoming 140th anniversary of the 1868 M 7 rupture coinciding with the estimated recurrence interval. This presentation will describe ground motion simulations for large (M > 6.5) earthquakes on the Hayward Fault using a recently developed elastic finite difference code and high-performance computers at Lawrence Livermore National Laboratory. Our code easily reads the recent USGS 3D seismic velocity model of the Bay Area developed in 2005 and used for simulations of the 1906 San Francisco and 1989 Loma Prieta earthquakes. Previous work has shown that the USGS model performs very well when used to model intermediate period (4-33 seconds) ground motions from moderate (M ~ 4-5) earthquakes (Rodgers et al., 2008). Ground motions for large earthquakes are strongly controlled by the hypocenter location, spatial distribution of slip, rise time and directivity effects. These are factors that are impossible to predict in advance of a large earthquake and lead to large epistemic uncertainties in ground motion estimates for scenario earthquakes. To bound this uncertainty, we are performing suites of simulations of scenario events on the Hayward Fault using stochastic rupture models following the method of Liu et al. (Bull. Seism. Soc. Am., 96, 2118-2130, 2006). These rupture models have spatially variable slip, rupture velocity, rise time and rake constrained by characterization of inferred finite fault ruptures and expert opinion. Computed ground motions show variability due to the variability in rupture models and can be used to estimate the average and spread of ground motion measures at any particular site. This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No.W-7405-Eng-48. This is

  17. A Novel Humanized GLP-1 Receptor Model Enables Both Affinity Purification and Cre-LoxP Deletion of the Receptor

    PubMed Central

    Jun, Lucy S.; Showalter, Aaron D.; Ali, Nosher; Dai, Feihan; Ma, Wenzhen; Coskun, Tamer; Ficorilli, James V.; Wheeler, Michael B.; Michael, M. Dodson; Sloop, Kyle W.

    2014-01-01

    Class B G protein-coupled receptors (GPCRs) are important regulators of endocrine physiology, and peptide-based therapeutics targeting some of these receptors have proven effective at treating disorders such as hypercalcemia, osteoporosis, and type 2 diabetes mellitus (T2DM). As next generation efforts attempt to develop novel non-peptide, orally available molecules for these GPCRs, new animal models expressing human receptor orthologs may be required because small molecule ligands make fewer receptor contacts, and thus, the impact of amino acid differences across species may be substantially greater. The objective of this report was to generate and characterize a new mouse model of the human glucagon-like peptide-1 receptor (hGLP-1R), a class B GPCR for which established peptide therapeutics exist for the treatment of T2DM. hGLP-1R knock-in mice express the receptor from the murine Glp-1r locus. Glucose tolerance tests and gastric emptying studies show hGLP-1R mice and their wild-type littermates display similar physiological responses for glucose metabolism, insulin secretion, and gastric transit, and treatment with the GLP-1R agonist, exendin-4, elicits similar responses in both groups. Further, ex vivo assays show insulin secretion from humanized islets is glucose-dependent and enhanced by GLP-1R agonists. To enable additional utility, the targeting construct of the knock-in line was engineered to contain both flanking LoxP sites and a C-terminal FLAG epitope. Anti-FLAG affinity purification shows strong expression of hGLP-1R in islets, lung, and stomach. We crossed the hGLP-1R line with Rosa26Cre mice and generated global Glp-1r−/− animals. Immunohistochemistry of pancreas from humanized and knock-out mice identified a human GLP-1R-specific antibody that detects the GLP-1R in human pancreas as well as in the pancreas of hGLP-1r knock-in mice. This new hGLP-1R model will allow tissue-specific deletion of the GLP-1R, purification of potential GLP-1R partner

  18. The chaotic atom model via a fractal approximation of motion

    NASA Astrophysics Data System (ADS)

    Agop, M.; Nica, P.; Gurlui, S.; Focsa, C.; Magop, D.; Borsos, Z.

    2011-10-01

    A new model of the atom is built based on a complete and detailed nonlinear dynamics analysis (complete time series, Poincaré sections, complete phase space, Lyapunov exponents, bifurcation diagrams and fractal analysis), through the correlation of the chaotic-stochastic model with a fractal one. Some specific mechanisms that ensure the atom functionality are proposed: gun, chaotic gun and multi-gun effects for the excited states (the classical analogue of quantum absorption) and the fractalization of the trajectories for the stationary states (a natural way of introducing the quantification).

  19. Flocking and Turning: a New Model for Self-organized Collective Motion

    NASA Astrophysics Data System (ADS)

    Cavagna, Andrea; Del Castello, Lorenzo; Giardina, Irene; Grigera, Tomas; Jelic, Asja; Melillo, Stefania; Mora, Thierry; Parisi, Leonardo; Silvestri, Edmondo; Viale, Massimiliano; Walczak, Aleksandra M.

    2015-02-01

    Birds in a flock move in a correlated way, resulting in large polarization of velocities. A good understanding of this collective behavior exists for linear motion of the flock. Yet observing actual birds, the center of mass of the group often turns giving rise to more complicated dynamics, still keeping strong polarization of the flock. Here we propose novel dynamical equations for the collective motion of polarized animal groups that account for correlated turning including solely social forces. We exploit rotational symmetries and conservation laws of the problem to formulate a theory in terms of generalized coordinates of motion for the velocity directions akin to a Hamiltonian formulation for rotations. We explicitly derive the correspondence between this formulation and the dynamics of the individual velocities, thus obtaining a new model of collective motion. In the appropriate overdamped limit we recover the well-known Vicsek model, which dissipates rotational information and does not allow for polarized turns. Although the new model has its most vivid success in describing turning groups, its dynamics is intrinsically different from previous ones in a wide dynamical regime, while reducing to the hydrodynamic description of Toner and Tu at very large length-scales. The derived framework is therefore general and it may describe the collective motion of any strongly polarized active matter system.

  20. Robot body self-modeling algorithm: a collision-free motion planning approach for humanoids.

    PubMed

    Leylavi Shoushtari, Ali

    2016-01-01

    Motion planning for humanoid robots is one of the critical issues due to the high redundancy and theoretical and technical considerations e.g. stability, motion feasibility and collision avoidance. The strategies which central nervous system employs to plan, signal and control the human movements are a source of inspiration to deal with the mentioned problems. Self-modeling is a concept inspired by body self-awareness in human. In this research it is integrated in an optimal motion planning framework in order to detect and avoid collision of the manipulated object with the humanoid body during performing a dynamic task. Twelve parametric functions are designed as self-models to determine the boundary of humanoid's body. Later, the boundaries which mathematically defined by the self-models are employed to calculate the safe region for box to avoid the collision with the robot. Four different objective functions are employed in motion simulation to validate the robustness of algorithm under different dynamics. The results also confirm the collision avoidance, reality and stability of the predicted motion. PMID:27186507

  1. ARMA models for earthquake ground motions. Seismic safety margins research program

    SciTech Connect

    Chang, M. K.; Kwiatkowski, J. W.; Nau, R. F.; Oliver, R. M.; Pister, K. S.

    1981-02-01

    Four major California earthquake records were analyzed by use of a class of discrete linear time-domain processes commonly referred to as ARMA (Autoregressive/Moving-Average) models. It was possible to analyze these different earthquakes, identify the order of the appropriate ARMA model(s), estimate parameters, and test the residuals generated by these models. It was also possible to show the connections, similarities, and differences between the traditional continuous models (with parameter estimates based on spectral analyses) and the discrete models with parameters estimated by various maximum-likelihood techniques applied to digitized acceleration data in the time domain. The methodology proposed is suitable for simulating earthquake ground motions in the time domain, and appears to be easily adapted to serve as inputs for nonlinear discrete time models of structural motions. 60 references, 19 figures, 9 tables.

  2. Rheological Models in the Time-Domain Modeling of Seismic Motion

    NASA Astrophysics Data System (ADS)

    Moczo, P.; Kristek, J.

    2004-12-01

    The time-domain stress-strain relation in a viscoelastic medium has a form of the convolutory integral which is numerically intractable. This was the reason for the oversimplified models of attenuation in the time-domain seismic wave propagation and earthquake motion modeling. In their pioneering work, Day and Minster (1984) showed the way how to convert the integral into numerically tractable differential form in the case of a general viscoelastic modulus. In response to the work by Day and Minster, Emmerich and Korn (1987) suggested using the rheology of their generalized Maxwell body (GMB) while Carcione et al. (1988) suggested using the generalized Zener body (GZB). The viscoelastic moduli of both rheological models have a form of the rational function and thus the differential form of the stress-strain relation is rather easy to obtain. After the papers by Emmerich and Korn and Carcione et al. numerical modelers decided either for the GMB or GZB rheology and developed 'non-communicating' algorithms. In the many following papers the authors using the GMB never commented the GZB rheology and the corresponding algorithms, and the authors using the GZB never related their methods to the GMB rheology and algorithms. We analyze and compare both rheologies and the corresponding incorporations of the realistic attenuation into the time-domain computations. We then focus on the most recent staggered-grid finite-difference modeling, mainly on accounting for the material heterogeneity in the viscoelastic media, and the computational efficiency of the finite-difference algorithms.

  3. Visuovestibular perception of self-motion modeled as a dynamic optimization process.

    PubMed

    Reymond, Gilles; Droulez, Jacques; Kemeny, Andras

    2002-10-01

    This article describes a computational model for the sensory perception of self-motion, considered as a compromise between sensory information and physical coherence constraints. This compromise is realized by a dynamic optimization process minimizing a set of cost functions. Measure constraints are expressed as quadratic errors between motion estimates and corresponding sensory signals, using internal models of sensor transfer functions. Coherence constraints are expressed as quadratic errors between motion estimates, and their prediction is based on internal models of the physical laws governing the corresponding physical stimuli. This general scheme leads to a straightforward representation of fundamental sensory interactions (fusion of visual and canal rotational inputs, identification of the gravity component from the otolithic input, otolithic contribution to the perception of rotations, and influence of vection on the subjective vertical). The model is tuned and assessed using a range of well-known psychophysical results, including off-vertical axis rotations and centrifuge experiments. The ability of the model to predict and help analyze new situations is illustrated by a study of the vestibular contributions to self-motion perception during automobile driving and during acceleration cueing in driving simulators. The extendable structure of the model allows for further developments and applications, by using other cost functions representing additional sensory interactions. PMID:12386745

  4. Direct Visuo-Haptic 4D Volume Rendering Using Respiratory Motion Models.

    PubMed

    Fortmeier, Dirk; Wilms, Matthias; Mastmeyer, Andre; Handels, Heinz

    2015-01-01

    This article presents methods for direct visuo-haptic 4D volume rendering of virtual patient models under respiratory motion. Breathing models are computed based on patient-specific 4D CT image data sequences. Virtual patient models are visualized in real-time by ray casting based rendering of a reference CT image warped by a time-variant displacement field, which is computed using the motion models at run-time. Furthermore, haptic interaction with the animated virtual patient models is provided by using the displacements computed at high rendering rates to translate the position of the haptic device into the space of the reference CT image. This concept is applied to virtual palpation and the haptic simulation of insertion of a virtual bendable needle. To this aim, different motion models that are applicable in real-time are presented and the methods are integrated into a needle puncture training simulation framework, which can be used for simulated biopsy or vessel puncture in the liver. To confirm real-time applicability, a performance analysis of the resulting framework is given. It is shown that the presented methods achieve mean update rates around 2,000 Hz for haptic simulation and interactive frame rates for volume rendering and thus are well suited for visuo-haptic rendering of virtual patients under respiratory motion. PMID:26087498

  5. Multi-level model for 2D human motion analysis and description

    NASA Astrophysics Data System (ADS)

    Foures, Thomas; Joly, Philippe

    2003-01-01

    This paper deals with the proposition of a model for human motion analysis in a video. Its main caracteristic is to adapt itself automatically to the current resolution, the actual quality of the picture, or the level of precision required by a given application, due to its possible decomposition into several hierarchical levels. The model is region-based to address some analysis processing needs. The top level of the model is only defined with 5 ribbons, which can be cut into sub-ribbons regarding to a given (or an expected) level of details. Matching process between model and current picture consists in the comparison of extracted subject shape with a graphical rendering of the model built on the base of some computed parameters. The comparison is processed by using a chamfer matching algorithm. In our developments, we intend to realize a platform of interaction between a dancer and tools synthetizing abstract motion pictures and music in the conditions of a real-time dialogue between a human and a computer. In consequence, we use this model in a perspective of motion description instead of motion recognition: no a priori gestures are supposed to be recognized as far as no a priori application is specially targeted. The resulting description will be made following a Description Scheme compliant with the movement notation called "Labanotation".

  6. RNase One Gene Isolation, Expression, and Affinity Purification Models Research Experimental Progression and Culminates with Guided Inquiry-Based Experiments

    ERIC Educational Resources Information Center

    Bailey, Cheryl P.

    2009-01-01

    This new biochemistry laboratory course moves through a progression of experiments that generates a platform for guided inquiry-based experiments. RNase One gene is isolated from prokaryotic genomic DNA, expressed as a tagged protein, affinity purified, and tested for activity and substrate specificity. Student pairs present detailed explanations…

  7. A comparative study of lectin affinity based plant n-glycoproteome profiling using tomato fruit as a model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lectin affinity chromatography (LAC) can provide a valuable front-end enrichment strategy for the study of N-glycoproteins and has been used to characterize a broad range eukaryotic N-glycoproteomes. Moreover, studies with mammalian systems have suggested that the use of multiple lectins with differ...

  8. Cardiac motion compensation and resolution modeling in simultaneous PET-MR: a cardiac lesion detection study

    PubMed Central

    Petibon, Y; Ouyang, J; Zhu, X; Huang, C; Reese, T G; Chun, S Y; Li, Q; El Fakhri, G

    2013-01-01

    Cardiac motion and Partial Volume Effects (PVE) are two of the main causes of image degradation in cardiac PET. Motion generates artifacts and blurring while PVE lead to erroneous myocardial activity measurements. Newly available simultaneous PET-MR scanners offer new possibilities in cardiac imaging as MRI can assess wall contractility while collecting PET perfusion data. In this perspective, we develop a list-mode iterative reconstruction framework incorporating both tagged-MR derived non-rigid myocardial wall motion and position dependent detector Point Spread Function (PSF) directly into the PET system matrix. In this manner, our algorithm performs both motion “deblurring” and PSF deconvolution while reconstructing images with all available PET counts. The proposed methods are evaluated in a beating non-rigid cardiac phantom whose hot myocardial compartment contains small transmural and non-transmural cold defects. In order to accelerate imaging time, we investigate collecting full and half k-space tagged MR data to obtain tagged volumes that are registered using non-rigid B-spline registration to yield wall motion information. Our experimental results show that tagged-MR based motion correction yielded an improvement in defect/myocardium contrast recovery of 34-206% as compared to motion uncorrected studies. Likewise, lesion detectability improved by respectively 115-136% and 62-235% with MR-based motion compensation as compared to gating and no motion correction and made it possible to distinguish non-transmural from transmural defects, which has clinical significance given inherent limitations of current single modality imaging in identifying the amount of residual ischemia. The incorporation of PSF modeling within the framework of MR-based motion compensation significantly improved defect/myocardium contrast recovery (5.1-8.5%, p<0.01) and defect detectability (39-56%, p<0.01). No statistical difference was found in PET contrast and lesion detectability

  9. Generation of a mixture model ground-motion prediction equation for Northern Chile

    NASA Astrophysics Data System (ADS)

    Haendel, A.; Kuehn, N. M.; Scherbaum, F.

    2012-12-01

    In probabilistic seismic hazard analysis (PSHA) empirically derived ground motion prediction equations (GMPEs) are usually applied to estimate the ground motion at a site of interest as a function of source, path and site related predictor variables. Because GMPEs are derived from limited datasets they are not expected to give entirely accurate estimates or to reflect the whole range of possible future ground motion, thus giving rise to epistemic uncertainty in the hazard estimates. This is especially true for regions without an indigenous GMPE where foreign models have to be applied. The choice of appropriate GMPEs can then dominate the overall uncertainty in hazard assessments. In order to quantify this uncertainty, the set of ground motion models used in a modern PSHA has to capture (in SSHAC language) the center, body, and range of the possible ground motion at the site of interest. This was traditionally done within a logic tree framework in which existing (or only slightly modified) GMPEs occupy the branches of the tree and the branch weights describe the degree-of-belief of the analyst in their applicability. This approach invites the problem to combine GMPEs of very different quality and hence to potentially overestimate epistemic uncertainty. Some recent hazard analysis have therefore resorted to using a small number of high quality GMPEs as backbone models from which the full distribution of GMPEs for the logic tree (to capture the full range of possible ground motion uncertainty) where subsequently generated by scaling (in a general sense). In the present study, a new approach is proposed to determine an optimized backbone model as weighted components of a mixture model. In doing so, each GMPE is assumed to reflect the generation mechanism (e. g. in terms of stress drop, propagation properties, etc.) for at least a fraction of possible ground motions in the area of interest. The combination of different models into a mixture model (which is learned from

  10. Fully-deformable patient motion models from cone-beam CT for radiotherapy applications

    NASA Astrophysics Data System (ADS)

    Martin, J.; McClelland, J.; Yip, C.; Thomas, C.; Hartill, C.; Ahmad, S.; Meir, I.; Landau, D.; Hawkes, D.

    2014-03-01

    We propose a method to build a fully deformable motion model directly from cone-beam CT (CBCT) projections. This allows inter-fraction variations in the respiratory motion to be accounted for. It is envisaged that the model be used to track the tumour, and monitor organs at risk (OAR), during gated or tracked radiotherapy (RT) treatment of lung cancer. The method is tested on CBCT projections from a simulated phantom in two cases. The simulations are generated from a patient respiratory trace and associated CBCT scanner geometry. Without and with motion correction, l2 norm maximum errors were reduced from 24.5 to 0.698 mm in case 1, and 20.0 to 0.101 mm in case 2, respectively.

  11. A Comparative Study of Lectin Affinity Based Plant N-Glycoproteome Profiling Using Tomato Fruit as a Model*

    PubMed Central

    Ruiz-May, Eliel; Hucko, Simon; Howe, Kevin J.; Zhang, Sheng; Sherwood, Robert W.; Thannhauser, Theodore W.; Rose, Jocelyn K. C.

    2014-01-01

    Lectin affinity chromatography (LAC) can provide a valuable front-end enrichment strategy for the study of N-glycoproteins and has been used to characterize a broad range eukaryotic N-glycoproteomes. Moreover, studies with mammalian systems have suggested that the use of multiple lectins with different affinities can be particularly effective. A multi-lectin approach has also been reported to provide a significant benefit for the analysis of plant N-glycoproteins; however, it has yet to be determined whether certain lectins, or combinations of lectins are optimal for plant N-glycoproteome profiling; or whether specific lectins show preferential association with particular N-glycosylation sites or N-glycan structures. We describe here a comparative study of three mannose-binding lectins, concanavalin A, snowdrop lectin, and lentil lectin, to profile the N-glycoproteome of mature green stage tomato (Solanum lycopersicum) fruit pericarp. Through coupling lectin affinity chromatography with a shotgun proteomics strategy, we identified 448 putative N-glycoproteins, whereas a parallel lectin affinity chromatography plus hydrophilic interaction chromatography analysis revealed 318 putative N-glycosylation sites on 230 N-glycoproteins, of which 100 overlapped with the shotgun analysis, as well as 17 N-glycan structures. The use of multiple lectins substantially increased N-glycoproteome coverage and although there were no discernible differences in the structures of N-glycans, or the charge, isoelectric point (pI) or hydrophobicity of the glycopeptides that differentially bound to each lectin, differences were observed in the amino acid frequency at the −1 and +1 subsites of the N-glycosylation sites. We also demonstrated an alternative and complementary in planta recombinant expression strategy, followed by affinity MS analysis, to identify the putative N-glycan structures of glycoproteins whose abundance is too low to be readily determined by a shotgun approach, and

  12. Image-driven, model-based 3D abdominal motion estimation for MR-guided radiotherapy

    NASA Astrophysics Data System (ADS)

    Stemkens, Bjorn; Tijssen, Rob H. N.; de Senneville, Baudouin Denis; Lagendijk, Jan J. W.; van den Berg, Cornelis A. T.

    2016-07-01

    Respiratory motion introduces substantial uncertainties in abdominal radiotherapy for which traditionally large margins are used. The MR-Linac will open up the opportunity to acquire high resolution MR images just prior to radiation and during treatment. However, volumetric MRI time series are not able to characterize 3D tumor and organ-at-risk motion with sufficient temporal resolution. In this study we propose a method to estimate 3D deformation vector fields (DVFs) with high spatial and temporal resolution based on fast 2D imaging and a subject-specific motion model based on respiratory correlated MRI. In a pre-beam phase, a retrospectively sorted 4D-MRI is acquired, from which the motion is parameterized using a principal component analysis. This motion model is used in combination with fast 2D cine-MR images, which are acquired during radiation, to generate full field-of-view 3D DVFs with a temporal resolution of 476 ms. The geometrical accuracies of the input data (4D-MRI and 2D multi-slice acquisitions) and the fitting procedure were determined using an MR-compatible motion phantom and found to be 1.0–1.5 mm on average. The framework was tested on seven healthy volunteers for both the pancreas and the kidney. The calculated motion was independently validated using one of the 2D slices, with an average error of 1.45 mm. The calculated 3D DVFs can be used retrospectively for treatment simulations, plan evaluations, or to determine the accumulated dose for both the tumor and organs-at-risk on a subject-specific basis in MR-guided radiotherapy.

  13. Image-driven, model-based 3D abdominal motion estimation for MR-guided radiotherapy.

    PubMed

    Stemkens, Bjorn; Tijssen, Rob H N; de Senneville, Baudouin Denis; Lagendijk, Jan J W; van den Berg, Cornelis A T

    2016-07-21

    Respiratory motion introduces substantial uncertainties in abdominal radiotherapy for which traditionally large margins are used. The MR-Linac will open up the opportunity to acquire high resolution MR images just prior to radiation and during treatment. However, volumetric MRI time series are not able to characterize 3D tumor and organ-at-risk motion with sufficient temporal resolution. In this study we propose a method to estimate 3D deformation vector fields (DVFs) with high spatial and temporal resolution based on fast 2D imaging and a subject-specific motion model based on respiratory correlated MRI. In a pre-beam phase, a retrospectively sorted 4D-MRI is acquired, from which the motion is parameterized using a principal component analysis. This motion model is used in combination with fast 2D cine-MR images, which are acquired during radiation, to generate full field-of-view 3D DVFs with a temporal resolution of 476 ms. The geometrical accuracies of the input data (4D-MRI and 2D multi-slice acquisitions) and the fitting procedure were determined using an MR-compatible motion phantom and found to be 1.0-1.5 mm on average. The framework was tested on seven healthy volunteers for both the pancreas and the kidney. The calculated motion was independently validated using one of the 2D slices, with an average error of 1.45 mm. The calculated 3D DVFs can be used retrospectively for treatment simulations, plan evaluations, or to determine the accumulated dose for both the tumor and organs-at-risk on a subject-specific basis in MR-guided radiotherapy. PMID:27362636

  14. Pitching motion control of a butterfly-like 3D flapping wing-body model

    NASA Astrophysics Data System (ADS)

    Suzuki, Kosuke; Minami, Keisuke; Inamuro, Takaji

    2014-11-01

    Free flights and a pitching motion control of a butterfly-like flapping wing-body model are numerically investigated by using an immersed boundary-lattice Boltzmann method. The model flaps downward for generating the lift force and backward for generating the thrust force. Although the model can go upward against the gravity by the generated lift force, the model generates the nose-up torque, consequently gets off-balance. In this study, we discuss a way to control the pitching motion by flexing the body of the wing-body model like an actual butterfly. The body of the model is composed of two straight rigid rod connected by a rotary actuator. It is found that the pitching angle is suppressed in the range of +/-5° by using the proportional-plus-integral-plus-derivative (PID) control for the input torque of the rotary actuator.

  15. Template CoMFA Generates Single 3D-QSAR Models that, for Twelve of Twelve Biological Targets, Predict All ChEMBL-Tabulated Affinities

    PubMed Central

    Cramer, Richard D.

    2015-01-01

    The possible applicability of the new template CoMFA methodology to the prediction of unknown biological affinities was explored. For twelve selected targets, all ChEMBL binding affinities were used as training and/or prediction sets, making these 3D-QSAR models the most structurally diverse and among the largest ever. For six of the targets, X-ray crystallographic structures provided the aligned templates required as input (BACE, cdk1, chk2, carbonic anhydrase-II, factor Xa, PTP1B). For all targets including the other six (hERG, cyp3A4 binding, endocrine receptor, COX2, D2, and GABAa), six modeling protocols applied to only three familiar ligands provided six alternate sets of aligned templates. The statistical qualities of the six or seven models thus resulting for each individual target were remarkably similar. Also, perhaps unexpectedly, the standard deviations of the errors of cross-validation predictions accompanying model derivations were indistinguishable from the standard deviations of the errors of truly prospective predictions. These standard deviations of prediction ranged from 0.70 to 1.14 log units and averaged 0.89 (8x in concentration units) over the twelve targets, representing an average reduction of almost 50% in uncertainty, compared to the null hypothesis of “predicting” an unknown affinity to be the average of known affinities. These errors of prediction are similar to those from Tanimoto coefficients of fragment occurrence frequencies, the predominant approach to side effect prediction, which template CoMFA can augment by identifying additional active structural classes, by improving Tanimoto-only predictions, by yielding quantitative predictions of potency, and by providing interpretable guidance for avoiding or enhancing any specific target response. PMID:26065424

  16. Medical prevention of space motion sickness—animal model of therapeutic effect of a new medicine on motion sickness

    NASA Astrophysics Data System (ADS)

    Yang, T. D.; Pei, J. S.; Yang, S. L.; Liu, Z. Q.; Sun, R. L.

    Space motion sickness (MS) is one of the most important problems in the field of space medicine. In order to prevent space MS, a new medicine, PMPA, has been prepared by means of synthesizing in our laboratory. The purposes of this study were to set up animal models of PMPA against MS, and to observe its effects on anti-MS, and to prove its function of antagonism to choline. Eight cats, forty rabbits and two hundred and ten rats were selected as animal subjects. The parallel swing stimulus, a method causing the reversal syndromes and tests of anti-choline function were used in our experiments. The results are as follows: (1) The score of MS symptoms in cats with PMPA or scopolamine (SCOP) is significantly lower than that in cats with placebo (p<0.01), while the incidences of efficiency and prevention of PMPA (87.5%, 75%) are higher than those of SCOP (75.0%, 50%) in cats. (2) PMPA of 1.6 mg/kg or 0.8 mg/kg could antagonize the reversal syndromes and repress reversal rotation significantly in rabbits like SCOP in comparison with placebo (p<0.01). (3) PMPA could inhibit tremor evoked by oxotremorine or by nicotine-procaine in rats like SCOP, and play an important role in the antagonism to central M-choline and N-choline receptors. The animal experiments demonstrate that PMPA is an effective medicine against MS with antagonism function to choline.

  17. Generalized Laplacian eigenmaps for modeling and tracking human motions.

    PubMed

    Martinez-del-Rincon, Jesus; Lewandowski, Michal; Nebel, Jean-Christophe; Makris, Dimitrios

    2014-09-01

    This paper presents generalized Laplacian eigenmaps, a novel dimensionality reduction approach designed to address stylistic variations in time series. It generates compact and coherent continuous spaces whose geometry is data-driven. This paper also introduces graph-based particle filter, a novel methodology conceived for efficient tracking in low dimensional space derived from a spectral dimensionality reduction method. Its strengths are a propagation scheme, which facilitates the prediction in time and style, and a noise model coherent with the manifold, which prevents divergence, and increases robustness. Experiments show that a combination of both techniques achieves state-of-the-art performance for human pose tracking in underconstrained scenarios. PMID:25137692

  18. Position Estimation of an Epicardial Crawling Robot on the Beating Heart by Modeling of Physiological Motion

    PubMed Central

    Wood, Nathan A.; del Agua, Diego Moral; Zenati, Marco A.; Riviere, Cameron N.

    2012-01-01

    HeartLander, a small mobile robot designed to provide treatments to the surface of the beating heart, overcomes a major difficulty of minimally invasive cardiac surgery, providing a stable operating platform. This is achieved inherently in the way the robot adheres to and crawls over the surface of the heart. This mode of operation does not require physiological motion compensation to provide this stable environment; however, modeling of physiological motion is advantageous in providing more accurate position estimation as well as synchronization of motion to the physiological cycles. The work presented uses an Extended Kalman Filter framework to estimate parameters of non-stationary Fourier series models of the motion of the heart due to the respiratory and cardiac cycles as well as the position of the robot as it moves over the surface of the heart. The proposed method is demonstrated in the laboratory with HeartLander operating on a physiological motion simulator. Improved performance is demonstrated in comparison to the filtering methods previously used with HeartLander. The use of detected physiological cycle phases to synchronize locomotion of HeartLander is also described. PMID:23066511

  19. Modeling Visual, Vestibular and Oculomotor Interactions in Self-Motion Estimation

    NASA Technical Reports Server (NTRS)

    Perrone, John

    1997-01-01

    A computational model of human self-motion perception has been developed in collaboration with Dr. Leland S. Stone at NASA Ames Research Center. The research included in the grant proposal sought to extend the utility of this model so that it could be used for explaining and predicting human performance in a greater variety of aerospace applications. This extension has been achieved along with physiological validation of the basic operation of the model.

  20. Meeting Review: Diffuse X-Ray Scattering to Model Protein Motions

    PubMed Central

    Wall, Michael E.; Adams, Paul D.; Fraser, James S.; Sautter, Nicholas K.

    2014-01-01

    Problems in biology increasingly need models of protein flexibility to understand and control protein function. At the same time, as they improve, crystallographic methods are marching closer to the limits of what can be learned from Bragg data in isolation. It is thus inevitable that mainstream protein crystallography will turn to diffuse scattering to model protein motions and improve crystallographic models. The time is ripe to make it happen. PMID:24507780

  1. A cyclic model for particle motion in the pulmonary acinus

    NASA Astrophysics Data System (ADS)

    Haber, S.; Tsuda, A.

    2006-11-01

    A simplified model for the pulmonary alveolus that imitates the rhythmical expansion of the alveolus and the periodic shear flow in the adjacent airway is explored. The model consists of two eccentric cylinders and incompressible fluid that occupies the gap between them. The two cylinders undergo a simultaneous rhythmical expansion and contraction (mimicking the alveolus expansion) while the inner cylinder performs a periodic rotation about its axis (inducing shear flow mimicking airway ductal flow). An analytical solution is obtained for the creeping flow induced by the simultaneously expanding cylinders. It is shown that above a certain critical value of rotation to expansion velocity ratio, the flow exhibits characteristic features such as a saddle point and closed streamlines about a centre, similar to those existing inside a single alveolus during inhalation and exhalation. Poincaré maps of the trajectories of fluid particles demonstrate that, under various flow conditions, chaotic trajectories may exist, provided that expansion and rotation are slightly out of phase. This is similar to normal breathing conditions where the periodic expansion of the alveolus and the tidal flow (i.e. shear flow above the mouth of the alveolus) may be slightly out of phase. A novel definition of overall convective mixing efficiency is also suggested that inherently discounts reversible processes that do not contribute to mixing. It is demonstrated that two different convective mechanisms, related to the irreversibility of exhalation and inhalation and the onset of chaos, govern mixing efficiency in lung alveoli.

  2. 4DCBCT-based motion modeling and 3D fluoroscopic image generation for lung cancer radiotherapy

    NASA Astrophysics Data System (ADS)

    Dhou, Salam; Hurwitz, Martina; Mishra, Pankaj; Berbeco, Ross; Lewis, John

    2015-03-01

    A method is developed to build patient-specific motion models based on 4DCBCT images taken at treatment time and use them to generate 3D time-varying images (referred to as 3D fluoroscopic images). Motion models are built by applying Principal Component Analysis (PCA) on the displacement vector fields (DVFs) estimated by performing deformable image registration on each phase of 4DCBCT relative to a reference phase. The resulting PCA coefficients are optimized iteratively by comparing 2D projections captured at treatment time with projections estimated using the motion model. The optimized coefficients are used to generate 3D fluoroscopic images. The method is evaluated using anthropomorphic physical and digital phantoms reproducing real patient trajectories. For physical phantom datasets, the average tumor localization error (TLE) and (95th percentile) in two datasets were 0.95 (2.2) mm. For digital phantoms assuming superior image quality of 4DCT and no anatomic or positioning disparities between 4DCT and treatment time, the average TLE and the image intensity error (IIE) in six datasets were smaller using 4DCT-based motion models. When simulating positioning disparities and tumor baseline shifts at treatment time compared to planning 4DCT, the average TLE (95th percentile) and IIE were 4.2 (5.4) mm and 0.15 using 4DCT-based models, while they were 1.2 (2.2) mm and 0.10 using 4DCBCT-based ones, respectively. 4DCBCT-based models were shown to perform better when there are positioning and tumor baseline shift uncertainties at treatment time. Thus, generating 3D fluoroscopic images based on 4DCBCT-based motion models can capture both inter- and intra- fraction anatomical changes during treatment.

  3. Modelling the interactions between grain, hydraulics, and local topography to understand the impact on incipient motion

    NASA Astrophysics Data System (ADS)

    von Boetticher, Albrecht; Turowski, Jens M.

    2013-04-01

    Sediment transport plays the key role in the forming fluvial systems, and it has become a major issue for the management and operation of hydropower plants and shipping channels as well as for the understanding of flooding hazards. The interactions between grain, hydraulics, and local topography are complicated, and it is difficult to quantify them in the laboratory, in the field, or in simple theoretical models based on two-dimensional force balances. In many theoretical models of incipient motion, grains are assumed to have simple geometrical shapes (usually spheres), despite the fact that in the real world grain shapes can vary from platy to elongated to symmetrical, and from angular to rounded. In addition, grain shape may influence protrusion and angle of repose for a grain sitting in the same pocket, and both local grain environment and grain shape in turn influence the local flow field around the grain, and thus the forces acting on it. In this project a numerical model will be developed that is capable of resolving the interaction between the grain and the flow. The model will be used to study the influence of the grain environment and grain shape on initiation of motion. The aims of the project are three-fold. First, we want to develop a numerical model that is adapted to and can efficiently deal with the specific problems occurring in the study of initiation of bedload sediment motion in streams. Second, we want to identify which of the parameters describing grain shape and local topography (e.g., protrusion, angle of repose, grain angularity) dominantly influence the initiation of motion of an individual grain. Third, we want to clarify when and where simple analytical approximations of the sort that have been used in many previous models are applicable. In three tasks we will develop the model, validate it against laboratory and field data, and perform a number of systematic numerical experiments to better understand incipient motion.

  4. Modelling of the Seismic Ground Motion in Barquisimeto and Cabudare cities

    NASA Astrophysics Data System (ADS)

    Alvarado, L.; Alvarez, L.; Rocabado, V.; Schmitz, M.; Granado, C.; Rendon, H.

    2007-05-01

    A 2D modeling of the seismic response is obtained using modeling techniques that allow the computation of synthetic seismograms, corresponding to two different seismic source models. The application of the modal summation technique, extended to laterally heterogeneous structural models, to the area of Barquisimeto and Cabudare allows us to create synthetic seismograms that can be used for the study of the local response along of four profiles The calculation has been made by a hybrid method: Modal summation in the regional anelastic mode (1D) where the source is located, and the finite difference in the local sedimentary structure (2D). The realistic modeling of ground motion is a very important base of knowledge for the preparation of ground shaking scenarios, as well as for the assessment of ground motion parameters for seismic microzonation.

  5. Student Teachers' Levels of Understanding and Model of Understanding about Newton's Laws of Motion

    ERIC Educational Resources Information Center

    Saglam-Arslan, Aysegul; Devecioglu, Yasemin

    2010-01-01

    This study was conducted to determine the level of student teachers' understandings of Newton's laws of motion and relating these levels to identify student teachers' models of understanding. An achievement test composed of two parts comprising 12 open ended questions was constructed and given to 45 pre-service classroom teachers. The first part…

  6. From deep TLS validation to ensembles of atomic models built from elemental motions

    DOE PAGESBeta

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; Fraser, James S.; Adams, Paul D.

    2015-07-28

    The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy severalmore » conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.« less

  7. From deep TLS validation to ensembles of atomic models built from elemental motions

    SciTech Connect

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; Fraser, James S.; Adams, Paul D.

    2015-07-28

    The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.

  8. An Interactive Computer Model for Improved Student Understanding of Random Particle Motion and Osmosis

    ERIC Educational Resources Information Center

    Kottonau, Johannes

    2011-01-01

    Effectively teaching the concepts of osmosis to college-level students is a major obstacle in biological education. Therefore, a novel computer model is presented that allows students to observe the random nature of particle motion simultaneously with the seemingly directed net flow of water across a semipermeable membrane during osmotic…

  9. From deep TLS validation to ensembles of atomic models built from elemental motions

    SciTech Connect

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; Fraser, James S.; Adams, Paul D.

    2015-07-28

    Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.

  10. Effects of Teaching One and Two Dimensional Motion Units through Mathematical Modeling

    ERIC Educational Resources Information Center

    Baskan, Zeynep; Alev, Nedim

    2013-01-01

    The aim of this study is to investigate the effect of physics lessons that are taught through mathematical modelling on conceptual understanding and operational achievements of prospective science teachers in one and two dimensional motions. Through a quasi-experimental design "operational achievement test" (OAT) and "conceptual…

  11. Modeling, system identification, and control for slosh-free motion of an open container of liquid

    SciTech Connect

    Feddema, J.; Baty, R.; Dykhuizen, R.; Dohrmann, C.; Parker, G.; Robinett, R.; Romero, V.; Schmitt, D.

    1996-04-01

    This report discusses work performed under a Cooperative Research And Development Agreement (CRADA) with Corning, Inc., to analyze and test various techniques for controlling the motion of a high speed robotic arm carrying an open container of viscous liquid, in this case, molten glass. A computer model was generated to estimate the modes of oscillation of the liquid based on the shape of the container and the viscosity of the liquid. This fluid model was experimentally verified and tuned based on experimental data from a capacitive sensor on the side of the container. A model of the robot dynamics was also developed and verified through experimental tests on a Fanuc S-800 robot arm. These two models were used to estimate the overall modes of oscillation of an open container of liquid being carried by a robot arm. Using the estimated modes, inverse dynamic control techniques were used to determine a motion profile which would eliminate waves on the liquid`s surface. Experimental tests showed that residual surface waves in an open container of water at the end of motion were reduced by over 95% and that in-motion surface waves were reduced by over 75%.

  12. Self-noise models of five commercial strong-motion accelerometers

    USGS Publications Warehouse

    Ringler, Adam; Evans, John R.; Hutt, Charles R.

    2015-01-01

    To better characterize the noise of a number of commonly deployed accelerometers in a standardized way, we conducted noise measurements on five different models of strong‐motion accelerometers. Our study was limited to traditional accelerometers (Fig. 1) and is in no way exhaustive.

  13. A margin model to account for respiration-induced tumour motion and its variability

    NASA Astrophysics Data System (ADS)

    Coolens, Catherine; Webb, Steve; Shirato, H.; Nishioka, K.; Evans, Phil M.

    2008-08-01

    In order to reduce the sensitivity of radiotherapy treatments to organ motion, compensation methods are being investigated such as gating of treatment delivery, tracking of tumour position, 4D scanning and planning of the treatment, etc. An outstanding problem that would occur with all these methods is the assumption that breathing motion is reproducible throughout the planning and delivery process of treatment. This is obviously not a realistic assumption and is one that will introduce errors. A dynamic internal margin model (DIM) is presented that is designed to follow the tumour trajectory and account for the variability in respiratory motion. The model statistically describes the variation of the breathing cycle over time, i.e. the uncertainty in motion amplitude and phase reproducibility, in a polar coordinate system from which margins can be derived. This allows accounting for an additional gating window parameter for gated treatment delivery as well as minimizing the area of normal tissue irradiated. The model was illustrated with abdominal motion for a patient with liver cancer and tested with internal 3D lung tumour trajectories. The results confirm that the respiratory phases around exhale are most reproducible and have the smallest variation in motion amplitude and phase (approximately 2 mm). More importantly, the margin area covering normal tissue is significantly reduced by using trajectory-specific margins (as opposed to conventional margins) as the angular component is by far the largest contributor to the margin area. The statistical approach to margin calculation, in addition, offers the possibility for advanced online verification and updating of breathing variation as more data become available.

  14. A synthetic GMPE based on deterministic simulated ground motion data obtained from dynamic rupture models

    NASA Astrophysics Data System (ADS)

    Dalguer, L. A.; Baumann, C.; Cauzzi, C.

    2013-12-01

    Empirical ground motion prediction in the very near-field and for large magnitudes is often based on extrapolation of ground motion prediction equations (GMPEs) outside the range where they are well constrained by recorded data. With empirical GMPEs it is also difficult to capture source-dominated ground motion patterns, such as the effects of velocity pulses induced by subshear and supershear rupture directivity, buried and surface-rupturing, hanging-wall and foot-wall, weak shallow layers, complex geometry faults and stress drop. A way to cope at least in part with these shortcomings is to augment the calibration datasets with synthetic ground motions. To this aim, physics-based dynamic rupture models - where the physical bases involved in the fault rupture are explicitly considered - appear to be a suitable approach to produce synthetic ground motions. In this contribution, we first perform an assessment of a database of synthetic ground motions generated by a suite of dynamic rupture simulations to verify compatibility of the peak ground amplitudes with current GMPEs. The synthetic data-set is composed by 360 earthquake scenarios with moment magnitudes in the range of 5.5-7, for three mechanisms of faulting (reverse, normal and strike-slip) and for both buried faults and surface rupturing faults. Second, we parameterise the synthetic dataset through a GMPE. For this purpose, we identify the basic functional forms by analyzing the variation of the synthetic peak ground motions and spectral ordinates as a function of different explanatory variables related to the earthquake source characteristics, in order to account for some of the source effects listed above. We argue that this study provides basic guidelines for the developments of future GMPEs including data from physics-based numerical simulations.

  15. On the coupling between fluid flow and mesh motion in the modelling of fluid structure interaction

    NASA Astrophysics Data System (ADS)

    Dettmer, Wulf G.; Perić, Djordje

    2008-12-01

    Partitioned Newton type solution strategies for the strongly coupled system of equations arising in the computational modelling of fluid solid interaction require the evaluation of various coupling terms. An essential part of all ALE type solution strategies is the fluid mesh motion. In this paper, we investigate the effect of the terms which couple the fluid flow with the fluid mesh motion on the convergence behaviour of the overall solution procedure. We show that the computational efficiency of the simulation of many fluid solid interaction processes, including fluid flow through flexible pipes, can be increased significantly if some of these coupling terms are calculated exactly.

  16. The sacroiliac spine - computer simulation of motion and modeling of the ligaments.

    PubMed

    Buford, William L; Moulton, D L; Gugala, Z; Lindsey, R W

    2010-01-01

    Using an interactive, 3D, kinematic simulation of the human skeleton, the motion of the sacro-iliac (SI) joint is modeled based upon descriptions available in the literature. The major ligaments are added to the simulation data structure using deformable cubic B-spline curve paths. Ligament strains were generated and studied in response to the motion simulations. Results improve our understanding of sacro-iliac kinematics and highlight the importance of further studies to elucidate pathological as well as normal SI joint and ligament function. PMID:21095806

  17. Microscopic theory of Brownian motion revisited: The Rayleigh model

    NASA Astrophysics Data System (ADS)

    Kim, Changho; Karniadakis, George Em

    2013-03-01

    We investigate three force autocorrelation functions , , and and the friction coefficient γ for the Rayleigh model (a massive particle in an ideal gas) by analytic methods and molecular-dynamics (MD) simulations. Here, F and F+ are the total force and the Mori fluctuating force, respectively, whereas F0 is the force on the Brownian particle under the frozen dynamics, where the Brownian particle is held fixed and the solvent particles move under the external potential due to the presence of the Brownian particle. By using ensemble averaging and the ray representation approach, we obtain two expressions for in terms of the one-particle trajectory and corresponding expressions for γ by the time integration of these expressions. Performing MD simulations of the near-Brownian-limit (NBL) regime, we investigate the convergence of and and compare them with . We show that for a purely repulsive potential between the Brownian particle and a solvent particle, both expressions for produce in the NBL regime. On the other hand, for a potential containing an attractive component, the ray representation expression produces only the contribution of the nontrapped solvent particles. However, we show that the net contribution of the trapped particles to γ disappears, and hence we confirm that both the ensemble-averaged expression and the ray representation expression for γ are valid even if the potential contains an attractive component. We also obtain a closed-form expression of γ for the square-well potential. Finally, we discuss theoretical and practical aspects for the evaluation of and γ.

  18. Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions.

    PubMed

    Kang, Yu; Gohlke, Ulrich; Engström, Olof; Hamark, Christoffer; Scheidt, Tom; Kunstmann, Sonja; Heinemann, Udo; Widmalm, Göran; Santer, Mark; Barbirz, Stefanie

    2016-07-27

    Understanding interactions of bacterial surface polysaccharides with receptor protein scaffolds is important for the development of antibiotic therapies. The corresponding protein recognition domains frequently form low-affinity complexes with polysaccharides that are difficult to address with experimental techniques due to the conformational flexibility of the polysaccharide. In this work, we studied the tailspike protein (TSP) of the bacteriophage Sf6. Sf6TSP binds and hydrolyzes the high-rhamnose, serotype Y O-antigen polysaccharide of the Gram-negative bacterium Shigella flexneri (S. flexneri) as a first step of bacteriophage infection. Spectroscopic analyses and enzymatic cleavage assays confirmed that Sf6TSP binds long stretches of this polysaccharide. Crystal structure analysis and saturation transfer difference (STD) NMR spectroscopy using an enhanced method to interpret the data permitted the detailed description of affinity contributions and flexibility in an Sf6TSP-octasaccharide complex. Dodecasaccharide fragments corresponding to three repeating units of the O-antigen in complex with Sf6TSP were studied computationally by molecular dynamics simulations. They showed that distortion away from the low-energy solution conformation found in the octasaccharide complex is necessary for ligand binding. This is in agreement with a weak-affinity functional polysaccharide-protein contact that facilitates correct placement and thus hydrolysis of the polysaccharide close to the catalytic residues. Our simulations stress that the flexibility of glycan epitopes together with a small number of specific protein contacts provide the driving force for Sf6TSP-polysaccharide complex formation in an overall weak-affinity interaction system. PMID:27045683

  19. Self-affine surface morphology of plastically deformed metals.

    PubMed

    Zaiser, Michael; Grasset, Frederic Madani; Koutsos, Vasileios; Aifantis, Elias C

    2004-11-01

    We analyze the surface morphology of metals after plastic deformation over a range of scales from 10 nm to 2 mm using atomic force microscopy and scanning white-light interferometry. We demonstrate that an initially smooth surface during deformation develops self-affine roughness over almost 4 orders of magnitude in scale. The Hurst exponent H of one-dimensional surface profiles initially decreases with increasing strain and then stabilizes at H approximately 0.75. We show that the profiles can be mathematically modeled as graphs of a fractional Brownian motion. Our findings can be understood in terms of a fractal distribution of plastic strain within the deformed samples. PMID:15600851

  20. Software package for modeling spin-orbit motion in storage rings

    NASA Astrophysics Data System (ADS)

    Zyuzin, D. V.

    2015-12-01

    A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 106-109 particles in a beam during 109 turns in an accelerator (about 1012-1015 integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin-orbit dynamics.

  1. Software package for modeling spin–orbit motion in storage rings

    SciTech Connect

    Zyuzin, D. V.

    2015-12-15

    A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 10{sup 6}–10{sup 9} particles in a beam during 10{sup 9} turns in an accelerator (about 10{sup 12}–10{sup 15} integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin–orbit dynamics.

  2. A ``Spring-mass'' model of tethered satellite systems: properties of planar periodic motions

    NASA Astrophysics Data System (ADS)

    Sidorenko, Vladislav V.; Celletti, Alessandra

    2010-06-01

    This paper is devoted to the dynamics in a central gravity field of two point masses connected by a massless tether (the so called “spring-mass” model of tethered satellite systems). Only the motions with straight strained tether are studied, while the case of “slack” tether is not considered. It is assumed that the distance between the point masses is substantially smaller than the distance between the system’s center of mass and the field center. This assumption allows us to treat the motion of the center of mass as an unperturbed Keplerian one, so to focus our study on attitude dynamics. A particular attention is given to the family of planar periodic motions in which the center of mass moves on an elliptic orbit, and the point masses never leave the orbital plane. If the eccentricity tends to zero, the corresponding family admits as a limit case the relative equilibrium in which the tether is elongated along the line joining the center of mass with the field center. We study the bifurcations and the stability of these planar periodic motions with respect to in-plane and out-of-plane perturbations. Our results show that the stable motions take place if the eccentricity of the orbit is sufficiently small.

  3. Ampicillin/penicillin-binding protein interactions as a model drug-target system to optimize affinity pull-down and mass spectrometric strategies for target and pathway identification.

    PubMed

    von Rechenberg, Moritz; Blake, Brian Kelly; Ho, Yew-Seng J; Zhen, Yuejun; Chepanoske, Cindy Lou; Richardson, Bonnie E; Xu, Nafei; Kery, Vladimir

    2005-05-01

    The identification and validation of the targets of active compounds identified in cell-based assays is an important step in preclinical drug development. New analytical approaches that combine drug affinity pull-down assays with mass spectrometry (MS) could lead to the identification of new targets and druggable pathways. In this work, we investigate a drug-target system consisting of ampicillin- and penicillin-binding proteins (PBPs) to evaluate and compare different amino-reactive resins for the immobilization of the affinity compound and mass spectrometric methods to identify proteins from drug affinity pull-down assays. First, ampicillin was immobilized onto various amino-reactive resins, which were compared in the ampicillin-PBP model with respect to their nonspecific binding of proteins from an Escherichia coli membrane extract. Dynal M-270 magnetic beads were chosen to further study the system as a model for capturing and identifying the targets of ampicillin, PBPs that were specifically and covalently bound to the immobilized ampicillin. The PBPs were identified, after in situ digestion of proteins bound to ampicillin directly on the beads, by using either one-dimensional (1-D) or two-dimensional (2-D) liquid chromatography (LC) separation techniques followed by tandem mass spectrometry (MS/MS) analysis. Alternatively, an elution with N-lauroylsarcosine (sarcosyl) from the ampicillin beads followed by in situ digestion and 2-D LC-MS/MS analysis identified proteins potentially interacting noncovalently with the PBPs or the ampicillin. The in situ approach required only little time, resources, and sample for the analysis. The combination of drug affinity pull-down assays with in situ digestion and 2-D LC-MS/MS analysis is a useful tool in obtaining complex information about a primary drug target as well as its protein interactors. PMID:15761956

  4. Angular Motion Estimation Using Dynamic Models in a Gyro-Free Inertial Measurement Unit

    PubMed Central

    Edwan, Ezzaldeen; Knedlik, Stefan; Loffeld, Otmar

    2012-01-01

    In this paper, we summarize the results of using dynamic models borrowed from tracking theory in describing the time evolution of the state vector to have an estimate of the angular motion in a gyro-free inertial measurement unit (GF-IMU). The GF-IMU is a special type inertial measurement unit (IMU) that uses only a set of accelerometers in inferring the angular motion. Using distributed accelerometers, we get an angular information vector (AIV) composed of angular acceleration and quadratic angular velocity terms. We use a Kalman filter approach to estimate the angular velocity vector since it is not expressed explicitly within the AIV. The bias parameters inherent in the accelerometers measurements' produce a biased AIV and hence the AIV bias parameters are estimated within an augmented state vector. Using dynamic models, the appended bias parameters of the AIV become observable and hence we can have unbiased angular motion estimate. Moreover, a good model is required to extract the maximum amount of information from the observation. Observability analysis is done to determine the conditions for having an observable state space model. For higher grades of accelerometers and under relatively higher sampling frequency, the error of accelerometer measurements is dominated by the noise error. Consequently, simulations are conducted on two models, one has bias parameters appended in the state space model and the other is a reduced model without bias parameters. PMID:22778586

  5. Subject-specific four-dimensional liver motion modeling based on registration of dynamic MRI.

    PubMed

    Noorda, Yolanda H; Bartels, Lambertus W; Viergever, Max A; Pluim, Josien P W

    2016-01-01

    Magnetic resonance-guided high intensity focused ultrasound treatment of the liver is a promising noninvasive technique for ablation of liver lesions. For the technique to be used in clinical practice, however, the issue of liver motion needs to be addressed. A subject-specific four-dimensional liver motion model is presented that is created based on registration of dynamically acquired magnetic resonance data. This model can be used for predicting the tumor motion trajectory for treatment planning and to indicate the tumor position for treatment guidance. The performance of the model was evaluated on a dynamic scan series that was not used to build the model. The method achieved an average Dice coefficient of 0.93 between the predicted and actual liver profiles and an average vessel misalignment of 3.0 mm. The model performed robustly, with a small variation in the results per subject. The results demonstrate the potential of the model to be used for MRI-guided treatment of liver lesions. Furthermore, the model can possibly be applied in other image-guided therapies, for instance radiotherapy of the liver. PMID:27493981

  6. Empirical predictive model for the vmax/ amax ratio of strong ground motions using genetic programming

    NASA Astrophysics Data System (ADS)

    Jafarian, Yaser; Kermani, Elnaz; Baziar, Mohammad H.

    2010-12-01

    Earthquake-induced deformation of structures is strongly influenced by the frequency content of input motion. Nevertheless, state-of-the-practice studies commonly use the intensity measures such as peak ground acceleration ( PGA), which are not frequency dependent. The vmax/ amax ratio of strong ground motions can be used in seismic hazard studies as a parameter that captures the influence of frequency content. In the present study, genetic programming (GP) is employed to develop a new empirical predictive equation for the vmax/ amax ratio of the shallow crustal strong ground motions recorded at free field sites. The proposed model is a function of earthquake magnitude, closest distance from source to site ( Rclstd), faulting mechanism, and average shear wave velocity over the top 30 m of site ( Vs30 ). A wide-ranging database of strong ground motion released by Pacific Earthquake Engineering Research Center (PEER) was utilized. It is demonstrated that residuals of the final equation show insignificant bias against the variations of the predictive parameters. The results indicate that vmax/ amax increases through increasing earthquake magnitude and source-to-site distance while magnitude dependency is considerably more than distance dependency. In addition, the proposed model predicts higher vmax/ amax ratio at softer sites that possess higher fundamental periods. Consequently, as an instance for the application of the proposed model, its reasonable performance in liquefaction potential assessment of sands and silty sands is presented.

  7. Wave motion on the surface of the human tympanic membrane: Holographic measurement and modeling analysis

    PubMed Central

    Cheng, Jeffrey Tao; Hamade, Mohamad; Merchant, Saumil N.; Rosowski, John J.; Harrington, Ellery; Furlong, Cosme

    2013-01-01

    Sound-induced motions of the surface of the tympanic membrane (TM) were measured using stroboscopic holography in cadaveric human temporal bones at frequencies between 0.2 and 18 kHz. The results are consistent with the combination of standing-wave-like modal motions and traveling-wave-like motions on the TM surface. The holographic techniques also quantified sound-induced displacements of the umbo of the malleus, as well as volume velocity of the TM. These measurements were combined with sound-pressure measurements near the TM to compute middle-ear input impedance and power reflectance at the TM. The results are generally consistent with other published data. A phenomenological model that behaved qualitatively like the data was used to quantify the relative magnitude and spatial frequencies of the modal and traveling-wave-like displacement components on the TM surface. This model suggests the modal magnitudes are generally larger than those of the putative traveling waves, and the computed wave speeds are much slower than wave speeds predicted by estimates of middle-ear delay. While the data are inconsistent with simple modal displacements of the TM, an alternate model based on the combination of modal motions in a lossy membrane can also explain these measurements without invoking traveling waves. PMID:23363110

  8. Investigation of a model vertical motion liquid damper: comparing numerical simulation and experimental evidence

    NASA Astrophysics Data System (ADS)

    Papadopoulos, Chris; Tabatabai, Habib; Buechel, Craig

    2005-05-01

    Tuned Liquid Dampers (TLD) are used to limit horizontal vibrations in structures, and offer practical alternatives to Tuned Mass Dampers (TMD). However, to our knowledge, liquid damping systems have not been developed to reduce vertical vibrations. In this work, we develop a model for a Vertical Motion Liquid Damper (VMLD), idealized as a discrete, two degree of freedom system. One degree of freedom represents the 'target' structure that is to be damped, and the other represents the approximate, one-dimensional motion of a liquid in a U-shaped tube. Internal losses due to the fluid oscillation serve to limit and control motions of the target structure. The U-shaped tube has a flexible joint such that one vertical portion and the horizontal portion of the tube remain fixed, and the remaining vertical portion of the tube is affixed to the vibrating structure, allowing the liquid to become excited. The equations of motion are derived using Lagrange's Equations, and are integrated using Runge-Kutta algorithms that are available in Matlab. An experimental model was built in the laboratory, consisting of a mass attached to the end of a cantilevered beam (corresponding to the target structure), and a U-tube made from PVC pipe. The various damping and stiffness parameters of the system were calibrated independently based on experimental data. Measured data from the experimental model show reasonable agreement with numerical simulations.

  9. Sensory vestibular contributions to constructing internal models of self-motion

    NASA Astrophysics Data System (ADS)

    Green, Andrea M.; Shaikh, Aasef G.; Angelaki, Dora E.

    2005-09-01

    The ability to navigate in the world and execute appropriate behavioral and motor responses depends critically on our capacity to construct an accurate internal representation of our current motion and orientation in space. Vestibular sensory signals are among those that may make an essential contribution to the construction of such 'internal models'. Movement in a gravitational environment represents a situation where the construction of internal models becomes particularly important because the otolith organs, like any linear accelerometer, sense inertial and gravitational accelerations equivalently. Otolith afferents thus provide inherently ambiguous motion information, as they respond identically to translation and head reorientation relative to gravity. Resolution of this ambiguity requires the nonlinear integration of linear acceleration and angular velocity cues, as predicted by the physical equations of motion. Here, we summarize evidence that during translations and tilts from upright the firing rates of brainstem and cerebellar neurons encode a combination of dynamically processed semicircular canal and otolith signals appropriate to construct an internal model representation of the computations required for inertial motion detection.

  10. Wave motion on the surface of the human tympanic membrane: holographic measurement and modeling analysis.

    PubMed

    Cheng, Jeffrey Tao; Hamade, Mohamad; Merchant, Saumil N; Rosowski, John J; Harrington, Ellery; Furlong, Cosme

    2013-02-01

    Sound-induced motions of the surface of the tympanic membrane (TM) were measured using stroboscopic holography in cadaveric human temporal bones at frequencies between 0.2 and 18 kHz. The results are consistent with the combination of standing-wave-like modal motions and traveling-wave-like motions on the TM surface. The holographic techniques also quantified sound-induced displacements of the umbo of the malleus, as well as volume velocity of the TM. These measurements were combined with sound-pressure measurements near the TM to compute middle-ear input impedance and power reflectance at the TM. The results are generally consistent with other published data. A phenomenological model that behaved qualitatively like the data was used to quantify the relative magnitude and spatial frequencies of the modal and traveling-wave-like displacement components on the TM surface. This model suggests the modal magnitudes are generally larger than those of the putative traveling waves, and the computed wave speeds are much slower than wave speeds predicted by estimates of middle-ear delay. While the data are inconsistent with simple modal displacements of the TM, an alternate model based on the combination of modal motions in a lossy membrane can also explain these measurements without invoking traveling waves. PMID:23363110

  11. A model to simulate the mastication motion at the temporomandibular joint

    NASA Astrophysics Data System (ADS)

    Villamil, Marta B.; Nedel, Luciana P.; Freitas, Carla M. D. S.; Maciel, Anderson

    2005-04-01

    The understanding of the mastication system motion is essential to maxillofacial surgeons and dentists in the procedures concerning jaw and teeth corrections. The temporomandibular joint (TMJ), despite its complexity, is one of the most frequently used joints of the human body. The incidence of a great number of injuries in this joint is influenced not only by its regular use during the mastication, but also by the strong forces applied by the muscles and the wide range of movements it is capable to perform. In this work, we propose the development of a jaw simulator capable of reproducing the complete mastication movement. Our jaw simulator is basically composed by three triangle meshes representing the 3D model of the cranium, mandible and teeth; and an anatomically-based joint model conceived to represent the TMJ motion. The polygonal meshes describing the bones and teeth are obtained from CT images and the jaw motion is simulated using the joint model guided by a 3D motion curve obtained from the composition of the standard 2D curves available in the medical literature. The scale, height and width of these original curves are modified to simulate different kind and size of food and to represent the movements" variability depending on patient morphology (teeth, bones, joints and muscles). The evaluation of preliminary results involved the comparison of a dynamic MRI of a healthy person with the respective simulation.

  12. A Simulation Model for Local Harmonic Motion Monitoring of Focused Ultrasound Surgery

    NASA Astrophysics Data System (ADS)

    Heikkilä, Janne; Curiel, Laura; Hynynen, Kullervo

    2009-04-01

    A computational model for local harmonic motion (LHM) imaging-based monitoring of high-intensity focused ultrasound surgery (FUS) is presented. LMH technique is based on a focused ultrasound radiation force excitation, which induces local mechanical vibrations at the focal region. These pulse-echo imaged vibrations are then used to estimate the mechanical properties of the sonication region. LHM has been proven to be feasible for FUS monitoring because changes in the material properties during the coagulation affect the measured displacements. The presented model includes separate models to simulate acoustic fields, sonication induced temperature elevation and mechanical vibrations, and pulse-echo imaging of the induced motions. These simulation models are based on Rayleigh integral, finite element, and spatial impulse response methods. Simulated temperature rise and vibration amplitudes have been compared with in vivo rabbit experiments with noninvasive MRI thermometry.

  13. Amoeba-like motion of an oil droplet. Chemical model of self-motile organisms

    NASA Astrophysics Data System (ADS)

    Sumino, Y.; Yoshikawa, K.

    2014-06-01

    In this paper, we demonstrate our recent attempt to construct a chemical model system of amoeboid motion. The system is intended to mimic biological motility based on the generation and collapse of an elastic aggregate; it is composed of oil, water, and surfactants. In this chemical system, the oil-water interface shows extension and retreat of spherical extrusions accompanied by the generation of aggregate on the interface. This instability of the oil-water interface can cause autonomous splitting and motion of a floating oil droplet. The current mathematical model based on the generation of a passive elastic gel is explained, as well as the discrepancy between the model and the experiments. We further describe recently observed microscopic characteristics of the aggregate formation process that might cause the interfacial instability. Finally, we discuss the disadvantage of a chemical model system compared with active colloid and in vitro biological systems, and also mention its potential advantages.

  14. A Simulation Model for Local Harmonic Motion Monitoring of Focused Ultrasound Surgery

    SciTech Connect

    Heikkilae, Janne; Curiel, Laura; Hynynen, Kullervo

    2009-04-14

    A computational model for local harmonic motion (LHM) imaging-based monitoring of high-intensity focused ultrasound surgery (FUS) is presented. LMH technique is based on a focused ultrasound radiation force excitation, which induces local mechanical vibrations at the focal region. These pulse-echo imaged vibrations are then used to estimate the mechanical properties of the sonication region. LHM has been proven to be feasible for FUS monitoring because changes in the material properties during the coagulation affect the measured displacements. The presented model includes separate models to simulate acoustic fields, sonication induced temperature elevation and mechanical vibrations, and pulse-echo imaging of the induced motions. These simulation models are based on Rayleigh integral, finite element, and spatial impulse response methods. Simulated temperature rise and vibration amplitudes have been compared with in vivo rabbit experiments with noninvasive MRI thermometry.

  15. Integration of MATLAB Simulink(Registered Trademark) Models with the Vertical Motion Simulator

    NASA Technical Reports Server (NTRS)

    Lewis, Emily K.; Vuong, Nghia D.

    2012-01-01

    This paper describes the integration of MATLAB Simulink(Registered TradeMark) models into the Vertical Motion Simulator (VMS) at NASA Ames Research Center. The VMS is a high-fidelity, large motion flight simulator that is capable of simulating a variety of aerospace vehicles. Integrating MATLAB Simulink models into the VMS needed to retain the development flexibility of the MATLAB environment and allow rapid deployment of model changes. The process developed at the VMS was used successfully in a number of recent simulation experiments. This accomplishment demonstrated that the model integrity was preserved, while working within the hard real-time run environment of the VMS architecture, and maintaining the unique flexibility of the VMS to meet diverse research requirements.

  16. On low-frequency errors of uniformly modulated filtered white-noise models for ground motions

    USGS Publications Warehouse

    Safak, Erdal; Boore, David M.

    1988-01-01

    Low-frequency errors of a commonly used non-stationary stochastic model (uniformly modulated filtered white-noise model) for earthquake ground motions are investigated. It is shown both analytically and by numerical simulation that uniformly modulated filter white-noise-type models systematically overestimate the spectral response for periods longer than the effective duration of the earthquake, because of the built-in low-frequency errors in the model. The errors, which are significant for low-magnitude short-duration earthquakes, can be eliminated by using the filtered shot-noise-type models (i. e. white noise, modulated by the envelope first, and then filtered).

  17. Long-term dynamics beyond Neptune: secular models to study the regular motions

    NASA Astrophysics Data System (ADS)

    Saillenfest, Melaine; Fouchard, Marc; Tommei, Giacomo; Valsecchi, Giovanni B.

    2016-06-01

    Two semi-analytical one-degree-of-freedom secular models are presented for the motion of small bodies beyond Neptune. A special attention is given to trajectories entirely exterior to the planetary orbits. The first one is the well-known non-resonant model of Kozai (Astron J 67:591, 1962) adapted to the transneptunian region. Contrary to previous papers, the dynamics is fully characterized with respect to the fixed parameters. A maximum perihelion excursion possible of 16.4 AU is determined. The second model handles the occurrence of a mean-motion resonance with one of the planets. In that case, the one-degree-of-freedom integrable approximation is obtained by postulating the adiabatic invariance, and is much more general and accurate than previous secular models found in the literature. It brings out in a plain way the possibility of perihelion oscillations with a very high amplitude. Such a model could thus be used in future studies to deeper explore that kind of motion. For complex resonant orbits (especially of type 1 : k), a segmented secular description is necessary since the trajectories are only "integrable by parts". The two models are applied to the Solar System but the notations are kept general so that it could be used for any quasi-circular and coplanar planetary system.

  18. Efficient spiking neural network model of pattern motion selectivity in visual cortex.

    PubMed

    Beyeler, Michael; Richert, Micah; Dutt, Nikil D; Krichmar, Jeffrey L

    2014-07-01

    Simulating large-scale models of biological motion perception is challenging, due to the required memory to store the network structure and the computational power needed to quickly solve the neuronal dynamics. A low-cost yet high-performance approach to simulating large-scale neural network models in real-time is to leverage the parallel processing capability of graphics processing units (GPUs). Based on this approach, we present a two-stage model of visual area MT that we believe to be the first large-scale spiking network to demonstrate pattern direction selectivity. In this model, component-direction-selective (CDS) cells in MT linearly combine inputs from V1 cells that have spatiotemporal receptive fields according to the motion energy model of Simoncelli and Heeger. Pattern-direction-selective (PDS) cells in MT are constructed by pooling over MT CDS cells with a wide range of preferred directions. Responses of our model neurons are comparable to electrophysiological results for grating and plaid stimuli as well as speed tuning. The behavioral response of the network in a motion discrimination task is in agreement with psychophysical data. Moreover, our implementation outperforms a previous implementation of the motion energy model by orders of magnitude in terms of computational speed and memory usage. The full network, which comprises 153,216 neurons and approximately 40 million synapses, processes 20 frames per second of a 40 × 40 input video in real-time using a single off-the-shelf GPU. To promote the use of this algorithm among neuroscientists and computer vision researchers, the source code for the simulator, the network, and analysis scripts are publicly available. PMID:24497233

  19. Fiducial marker-based correction for involuntary motion in weight-bearing C-arm CT scanning of knees. Part I. Numerical model-based optimization

    PubMed Central

    Choi, Jang-Hwan; Fahrig, Rebecca; Keil, Andreas; Besier, Thor F.; Pal, Saikat; McWalter, Emily J.; Beaupré, Gary S.; Maier, Andreas

    2013-01-01

    Purpose: Human subjects in standing positions are apt to show much more involuntary motion than in supine positions. The authors aimed to simulate a complicated realistic lower body movement using the four-dimensional (4D) digital extended cardiac-torso (XCAT) phantom. The authors also investigated fiducial marker-based motion compensation methods in two-dimensional (2D) and three-dimensional (3D) space. The level of involuntary movement-induced artifacts and image quality improvement were investigated after applying each method. Methods: An optical tracking system with eight cameras and seven retroreflective markers enabled us to track involuntary motion of the lower body of nine healthy subjects holding a squat position at 60° of flexion. The XCAT-based knee model was developed using the 4D XCAT phantom and the optical tracking data acquired at 120 Hz. The authors divided the lower body in the XCAT into six parts and applied unique affine transforms to each so that the motion (6 degrees of freedom) could be synchronized with the optical markers’ location at each time frame. The control points of the XCAT were tessellated into triangles and 248 projection images were created based on intersections of each ray and monochromatic absorption. The tracking data sets with the largest motion (Subject 2) and the smallest motion (Subject 5) among the nine data sets were used to animate the XCAT knee model. The authors defined eight skin control points well distributed around the knees as pseudo-fiducial markers which functioned as a reference in motion correction. Motion compensation was done in the following ways: (1) simple projection shifting in 2D, (2) deformable projection warping in 2D, and (3) rigid body warping in 3D. Graphics hardware accelerated filtered backprojection was implemented and combined with the three correction methods in order to speed up the simulation process. Correction fidelity was evaluated as a function of number of markers used (4–12) and

  20. Pyrazolo[1,5-c]quinazoline derivatives and their simplified analogues as adenosine receptor antagonists: synthesis, structure-affinity relationships and molecular modeling studies.

    PubMed

    Catarzi, Daniela; Colotta, Vittoria; Varano, Flavia; Poli, Daniela; Squarcialupi, Lucia; Filacchioni, Guido; Varani, Katia; Vincenzi, Fabrizio; Borea, Pier Andrea; Dal Ben, Diego; Lambertucci, Catia; Cristalli, Gloria

    2013-01-01

    A number of 5-oxo-pyrazolo[1,5-c]quinazolines (series B-1), bearing at position-2 the claimed (hetero)aryl moiety (compounds 1-8) but also a carboxylate group (9-14), were designed as hA(3) AR antagonists. This study produced some interesting compounds endowed with good hA(3) receptor affinity and high selectivity, being totally inactive at all the other AR subtypes. In contrast, the corresponding 5-ammino derivatives (series B-2) do not bind or bind with very low affinity at the hA(3) AR, the only exception being the 5-N-benzoyl compound 19 that shows a hA(3)K(i) value in the high μ-molar range. Evaluation of the synthetic intermediates led to the identification of some 5(3)-(2-aminophenyl)-3(5)-(hetero)arylpyrazoles 20-24 with modest affinity but high selectivity toward the hA(3) AR subtype. Molecular docking of the herein reported tricyclic and simplified derivatives was carried out to depict their hypothetical binding mode to our model of hA(3) receptor. PMID:23171656

  1. Reevaluation of plate motion models based on hotspot tracks in the Atlantic and Indian Oceans

    SciTech Connect

    Baksi, A.K.

    1999-01-01

    Plate motion models based on hotspot tracks in the Atlantic and Indian Oceans predict minimal movement (less than a few millimeters per year) between these hotspots and their counterparts in the Pacific Ocean for the past {approximately}100 m.yr., whereas plate circuit exercises indicate relative motions of {approximately}20 mm/yr. Hotspot-based models also suggest that the Rajmahal Traps, India, were located {approximately}1,000 km away from the Kerguelen hotspot at {approximately}115 Ma, and the Deccan Traps, India, were located a similar distance from the Reunion hotspot at {approximately}65 Ma; this is at odds with conclusions derived from paleomagnetism, plate circuits, and geochemical parameters that suggest a genetic link between flood basalt provinces in India and hotspots in the Indian Ocean. These divergent views may be explained by plume action {approximately}1,000 km from its center or errors in the hotspot motion models. The latter hypothesis is scrutinized in this article by examination of the radiometric ages for hotspot tracks in the Atlantic and Indian Oceans. The {sup 40}/{sup 39}Ar step-heating data for rocks defining the tracks of the Reunion and Kerguelen hotspots in the Indian Ocean and the Great Metero and Tristan da Cunha hotspots in the Atlantic Ocean are critically reexamined. Of {approximately}35 such ages utilized for deriving plate motion models for the past 130 m.yr., at best, only three ({approximately}32, {approximately}50, and {approximately}52 Ma) in the Indian Ocean and one ({approximately}65 Ma) for the Atlantic Ocean may be treated as crystallization ages. Conclusions based on hotspot track modeling for Late Cretaceous to Eocene time are suspect, and those for the Early to Late Cretaceous period are untenable. In the absence of precise age data for the tracks of hotspots in the Atlantic and Indian Oceans, and inconsistent age progressions noted within a single volcanic chain, plate circuit models serve as the superior technique

  2. The importance of being equivalent: Newton's two models of one-body motion

    NASA Astrophysics Data System (ADS)

    Pourciau, Bruce

    2004-05-01

    As an undergraduate at Cambridge, Newton entered into his "Waste Book" an assumption that we have named the Equivalence Assumption (The Younger): "If a body move progressively in some crooked line [about a center of motion] ..., [then this] crooked line may bee conceived to consist of an infinite number of streight lines. Or else in any point of the croked line the motion may bee conceived to be on in the tangent". In this assumption, Newton somewhat imprecisely describes two mathematical models, a "polygonal limit model" and a "tangent deflected model", for "one-body motion", that is, for the motion of a "body in orbit about a fixed center", and then claims that these two models are equivalent. In the first part of this paper, we study the Principia to determine how the elder Newton would more carefully describe the polygonal limit and tangent deflected models. From these more careful descriptions, we then create Equivalence Assumption (The Elder), a precise interpretation of Equivalence Assumption (The Younger) as it might have been restated by Newton, after say 1687. We then review certain portions of the Waste Book and the Principia to make the case that, although Newton never restates nor even alludes to the Equivalence Assumption after his youthful Waste Book entry, still the polygonal limit and tangent deflected models, as well as an unspoken belief in their equivalence, infuse Newton's work on orbital motion. In particular, we show that the persuasiveness of the argument for the Area Property in Proposition 1 of the Principia depends crucially on the validity of Equivalence Assumption (The Elder). After this case is made, we present the mathematical analysis required to establish the validity of the Equivalence Assumption (The Elder). Finally, to illustrate the fundamental nature of the resulting theorem, the Equivalence Theorem as we call it, we present three significant applications: we use the Equivalence Theorem first to clarify and resolve questions

  3. Application of data assimilation methods for analysis and integration of observed and modeled Arctic Sea ice motions

    NASA Astrophysics Data System (ADS)

    Meier, Walter Neil

    This thesis demonstrates the applicability of data assimilation methods to improve observed and modeled ice motion fields and to demonstrate the effects of assimilated motion on Arctic processes important to the global climate and of practical concern to human activities. Ice motions derived from 85 GHz and 37 GHz SSM/I imagery and estimated from two-dimensional dynamic-thermodynamic sea ice models are compared to buoy observations. Mean error, error standard deviation, and correlation with buoys are computed for the model domain. SSM/I motions generally have a lower bias, but higher error standard deviations and lower correlation with buoys than model motions. There are notable variations in the statistics depending on the region of the Arctic, season, and ice characteristics. Assimilation methods are investigated and blending and optimal interpolation strategies are implemented. Blending assimilation improves error statistics slightly, but the effect of the assimilation is reduced due to noise in the SSM/I motions and is thus not an effective method to improve ice motion estimates. However, optimal interpolation assimilation reduces motion errors by 25--30% over modeled motions and 40--45% over SSM/I motions. Optimal interpolation assimilation is beneficial in all regions, seasons and ice conditions, and is particularly effective in regimes where modeled and SSM/I errors are high. Assimilation alters annual average motion fields. Modeled ice products of ice thickness, ice divergence, Fram Strait ice volume export, transport across the Arctic and interannual basin averages are also influenced by assimilated motions. Assimilation improves estimates of pollutant transport and corrects synoptic-scale errors in the motion fields caused by incorrect forcings or errors in model physics. The portability of the optimal interpolation assimilation method is demonstrated by implementing the strategy in an ice thickness distribution (ITD) model. This research presents an

  4. Motion corrected LV quantification based on 3D modelling for improved functional assessment in cardiac MRI

    NASA Astrophysics Data System (ADS)

    Liew, Y. M.; McLaughlin, R. A.; Chan, B. T.; Aziz, Y. F. Abdul; Chee, K. H.; Ung, N. M.; Tan, L. K.; Lai, K. W.; Ng, S.; Lim, E.

    2015-04-01

    Cine MRI is a clinical reference standard for the quantitative assessment of cardiac function, but reproducibility is confounded by motion artefacts. We explore the feasibility of a motion corrected 3D left ventricle (LV) quantification method, incorporating multislice image registration into the 3D model reconstruction, to improve reproducibility of 3D LV functional quantification. Multi-breath-hold short-axis and radial long-axis images were acquired from 10 patients and 10 healthy subjects. The proposed framework reduced misalignment between slices to subpixel accuracy (2.88 to 1.21 mm), and improved interstudy reproducibility for 5 important clinical functional measures, i.e. end-diastolic volume, end-systolic volume, ejection fraction, myocardial mass and 3D-sphericity index, as reflected in a reduction in the sample size required to detect statistically significant cardiac changes: a reduction of 21-66%. Our investigation on the optimum registration parameters, including both cardiac time frames and number of long-axis (LA) slices, suggested that a single time frame is adequate for motion correction whereas integrating more LA slices can improve registration and model reconstruction accuracy for improved functional quantification especially on datasets with severe motion artefacts.

  5. Conditional spectrum computation incorporating multiple causal earthquakes and ground-motion prediction models

    USGS Publications Warehouse

    Lin, Ting; Harmsen, Stephen C.; Baker, Jack W.; Luco, Nicolas

    2013-01-01

    The conditional spectrum (CS) is a target spectrum (with conditional mean and conditional standard deviation) that links seismic hazard information with ground-motion selection for nonlinear dynamic analysis. Probabilistic seismic hazard analysis (PSHA) estimates the ground-motion hazard by incorporating the aleatory uncertainties in all earthquake scenarios and resulting ground motions, as well as the epistemic uncertainties in ground-motion prediction models (GMPMs) and seismic source models. Typical CS calculations to date are produced for a single earthquake scenario using a single GMPM, but more precise use requires consideration of at least multiple causal earthquakes and multiple GMPMs that are often considered in a PSHA computation. This paper presents the mathematics underlying these more precise CS calculations. Despite requiring more effort to compute than approximate calculations using a single causal earthquake and GMPM, the proposed approach produces an exact output that has a theoretical basis. To demonstrate the results of this approach and compare the exact and approximate calculations, several example calculations are performed for real sites in the western United States. The results also provide some insights regarding the circumstances under which approximate results are likely to closely match more exact results. To facilitate these more precise calculations for real applications, the exact CS calculations can now be performed for real sites in the United States using new deaggregation features in the U.S. Geological Survey hazard mapping tools. Details regarding this implementation are discussed in this paper.

  6. Transient pressure changes in the vertebral canal during whiplash motion--A hydrodynamic modeling approach.

    PubMed

    Yao, Hua-Dong; Svensson, Mats Y; Nilsson, Håkan

    2016-02-01

    In vehicle collisions, the occupant's torso is accelerated in a given direction while the unsupported head tends to lag behind. This mechanism results in whiplash motion to the neck. In whiplash experiments conducted for animals, pressure transients have been recorded in the spinal canal. It was hypothesized that the transients caused dorsal root ganglion dysfunction. Neck motion introduces volume changes inside the vertebral canal. The changes require an adaptation which is likely achieved by redistribution of blood volume in the internal vertebral venous plexus (IVVP). Pressure transients then arise from the rapid redistribution. The present study aimed to explore the hypothesis theoretically and analytically. Further, the objectives were to quantify the effect of the neck motion on the pressure generation and to identify the physical factors involved. We developed a hydrodynamic system of tubes that represent the IVVP and its lateral intervertebral vein connections. An analytical model was developed for an anatomical geometrical relation that the venous blood volume changes with respect to the vertebral angular displacement. This model was adopted in the hydrodynamic tube system so that the system can predict the pressure transients on the basis of the neck vertebral motion data from a whiplash experiment. The predicted pressure transients were in good agreement with the earlier experimental data. A parametric study was conducted and showed that the system can be used to assess the influences of anatomical geometrical properties and vehicle collision severity on the pressure generation. PMID:26827171

  7. Spatially-constrained probability distribution model of incoherent motion (SPIM) for abdominal diffusion-weighted MRI.

    PubMed

    Kurugol, Sila; Freiman, Moti; Afacan, Onur; Perez-Rossello, Jeannette M; Callahan, Michael J; Warfield, Simon K

    2016-08-01

    Quantitative diffusion-weighted MR imaging (DW-MRI) of the body enables characterization of the tissue microenvironment by measuring variations in the mobility of water molecules. The diffusion signal decay model parameters are increasingly used to evaluate various diseases of abdominal organs such as the liver and spleen. However, previous signal decay models (i.e., mono-exponential, bi-exponential intra-voxel incoherent motion (IVIM) and stretched exponential models) only provide insight into the average of the distribution of the signal decay rather than explicitly describe the entire range of diffusion scales. In this work, we propose a probability distribution model of incoherent motion that uses a mixture of Gamma distributions to fully characterize the multi-scale nature of diffusion within a voxel. Further, we improve the robustness of the distribution parameter estimates by integrating spatial homogeneity prior into the probability distribution model of incoherent motion (SPIM) and by using the fusion bootstrap solver (FBM) to estimate the model parameters. We evaluated the improvement in quantitative DW-MRI analysis achieved with the SPIM model in terms of accuracy, precision and reproducibility of parameter estimation in both simulated data and in 68 abdominal in-vivo DW-MRIs. Our results show that the SPIM model not only substantially reduced parameter estimation errors by up to 26%; it also significantly improved the robustness of the parameter estimates (paired Student's t-test, p < 0.0001) by reducing the coefficient of variation (CV) of estimated parameters compared to those produced by previous models. In addition, the SPIM model improves the parameter estimates reproducibility for both intra- (up to 47%) and inter-session (up to 30%) estimates compared to those generated by previous models. Thus, the SPIM model has the potential to improve accuracy, precision and robustness of quantitative abdominal DW-MRI analysis for clinical applications. PMID

  8. Simulation of single microorganism motion in fluid based on granular model

    NASA Astrophysics Data System (ADS)

    Viridi, S.; Nuraini, N.

    2016-04-01

    Microorganism model for simulating its motion is proposed in this work. It consists of granular particles which can interact to each other through linear spring mimicking microorganism muscles, which is simpler than other model. As a part of the organism organ is moving, while the other remains at its position, it will push the surrounding fluid through Stoke's force and as reaction the fluid pushes back the microorganism. Contracting force is used to change the distance between two points in the organ. Gravity influence is simply neglected in this work. All the considered forces are used to get motion parameters of organism through molecular dynamics method. It is observed that the use of contracting (push-pull) organ constructs slightly more effective model than shrink- and swell-organs as previously investigated, if weighted effectiveness formula is used as function of number of considered forces and involved particles.

  9. New models for frequency content prediction of earthquake records based on Iranian ground-motion data

    NASA Astrophysics Data System (ADS)

    Yaghmaei-Sabegh, Saman

    2015-10-01

    This paper presents the development of new and simple empirical models for frequency content prediction of ground-motion records to resolve the assumed limitations on the useable magnitude range of previous studies. Three period values are used in the analysis for describing the frequency content of earthquake ground-motions named as the average spectral period ( T avg), the mean period ( T m), and the smoothed spectral predominant period ( T 0). The proposed models could predict these scalar indicators as function of magnitude, closest site-to-source distance and local site condition. Three site classes as rock, stiff soil, and soft soil has been considered in the analysis. The results of the proposed relationships have been compared with those of other published models. It has been found that the resulting regression equations can be used to predict scalar frequency content estimators over a wide range of magnitudes including magnitudes below 5.5.

  10. Sensitivity of a mesoscale model to initial specification of relative humidity, liquid water and vertical motion

    NASA Technical Reports Server (NTRS)

    Kalb, M. W.; Perkey, D. J.

    1985-01-01

    The influence of synoptic scale initial conditions on the accuracy of mesoscale precipitation modeling is investigated. Attention is focused on the relative importance of the water vapor, cloud water, rain water, and vertical motion, with the analysis carried out using the Limited Area Mesoscale Prediction System (LAMPS). The fully moist primitive equation model has 15 levels and a terrain-following sigma coordinate system. A K-theory approach was implemented to model the planetary boundary layer. A total of 15 sensitivity simulations were run to investigate the effects of the synoptic initial conditions of the four atmospheric variables. The absence of synoptic cloud and rain water amounts in the initialization caused a 2 hr delay in the onset of precipitation. The delay was increased if synoptic-scale vertical motion was used instead of mesoscale values. Both the delays and a choice of a smoothed moisture field resulted in underestimations of the total rainfall.

  11. In-room breathing motion estimation from limited projection views using a sliding deformation model

    NASA Astrophysics Data System (ADS)

    Delmon, V.; Vandemeulebroucke, J.; Pinho, R.; Vila Oliva, M.; Sarrut, D.; Rit, S.

    2014-03-01

    Purpose: To estimate in-room breathing motion from a limited number of 2D cone-beam (CB) projection images by registering them to a phase of the 4D planning CT. Methods: Breathing motion was modelled using a piecewise continuous B-spline representation [1], allowing to preserve the sliding along the thoracic wall while limiting the degrees of freedom. The deformed target 3D image was subsequently used to generate Digitally Reconstructed Radiographs (DRR). The Normalized Correlation Coefficient (NCC) between the measured projection images and the DRR was computed in the 2D projection space. However, the partial derivatives of the NCC relative to the transform parameters were backprojected into the 3D space, avoiding the projection of the transform Jacobian matrix which is computationally intractable [2]. Results: The method was quantitatively evaluated on 16 lung cancer patients. 40 CB projection images were simulated using the end-exhale phase of the 4D planning CT and the geometric parameters of a clinical CB protocol. The end-inhale phase was deformed to match these simulated projections. The Target Registration Error (TRE) decreased from 8.8 mm to 2.0 mm while the TRE obtained from the 3D/3D registration of the reconstructed CBCT was significantly worse (2.6 mm), due to view aliasing artefacts. We also provide the motion compensated image reconstructed from a real CB acquisition showing the quality improvement brought by the in-room deformation model compared to the planning motion model. Conclusions: We have developed a 2D/3D deformable registration algorithm that enables in-room breathing motion estimation from cone-beam projection images.

  12. Toward in vivo lung's tissue incompressibility characterization for tumor motion modeling in radiation therapy

    SciTech Connect

    Shirzadi, Zahra; Sadeghi-Naini, Ali; Samani, Abbas

    2013-05-15

    Purpose: A novel technique is proposed to characterize lung tissue incompressibility variation during respiration. Estimating lung tissue incompressibility parameter variations resulting from air content variation throughout respiration is critical for computer assisted tumor motion tracking. Continuous tumor motion is a major challenge in lung cancer radiotherapy, especially with external beam radiotherapy. If not accounted for, this motion may lead to areas of radiation overdosage for normal tissue. Given the unavailability of imaging modality that can be used effectively for real-time lung tumor tracking, computer assisted approach based on tissue deformation estimation can be a good alternative. This approach involves lung biomechanical model where its fidelity depends on input tissue properties. This investigation shows that considering variable tissue incompressibility parameter is very important for predicting tumor motion accurately, hence improving the lung radiotherapy outcome. Methods: First, an in silico lung phantom study was conducted to demonstrate the importance of employing variable Poisson's ratio for tumor motion predication. After it was established that modeling this variability is critical for accurate tumor motion prediction, an optimization based technique was developed to estimate lung tissue Poisson's ratio as a function of respiration cycle time. In this technique, the Poisson's ratio and lung pressure value were varied systematically until optimal values were obtained, leading to maximum similarity between acquired and simulated 4D CT lung images. This technique was applied in an ex vivo porcine lung study where simulated images were constructed using the end exhale CT image and deformation fields obtained from the lung's FE modeling of each respiration time increment. To model the tissue, linear elastic and Marlow hyperelastic material models in conjunction with variable Poisson's ratio were used. Results: The phantom study showed that

  13. Motion Estimation for Dynamic Texture Videos Based on Locally and Globally Varying Models.

    PubMed

    Sakaino, Hidetomo

    2015-11-01

    Motion estimation, i.e., optical flow, of fluid-like and dynamic texture (DT) images/videos is an important challenge, particularly for understanding outdoor scene changes created by objects and/or natural phenomena. Most optical flow models use smoothness-based constraints using terms such as fluidity from the fluid dynamics framework, with constraints typically being incompressibility and low Reynolds numbers (Re ). Such constraints are assumed to impede the clear capture of locally abrupt image intensity and motion changes, i.e., discontinuities and/or high Re over time. This paper exploits novel physics-based optical flow models/constraints for both smooth and discontinuous changes using a wave generation theory that imposes no constraint on Re or compressibility of an image sequence. Iterated two-step optimization between local and global optimization is also used: first, an objective function with varying multiple sine/cosine bases with new local image properties, i.e., orientation and frequency, and with a novel transformed dispersion relationship equation are used. Second, the statistical property of image features is used to globally optimize model parameters. Experiments on synthetic and real DT image sequences with smooth and discontinuous motions demonstrate that the proposed locally and globally varying models outperform the previous optical flow models. PMID:26099146

  14. Modeling of an Oil-Free Carbon Dioxide Compressor Using Sanderson-Rocker Arm Motion (S-RAM) Mechanism

    NASA Astrophysics Data System (ADS)

    Yang, Bin; Kurtulus, Orkan; Groll, Eckhard A.

    2015-08-01

    A simulation model to predict the performance of a prototype CO2 compressor is presented. This prototype compressor employs the Sanderson-Rocker Arm Motion (S-RAM) mechanism, which converts the rotary motion of the shaft into a linear reciprocating motion of the cylinders. The piston stroke can be variable by changing the incline angle between the connecting rod and compressor main shaft centerline. The compressor model is mainly composed of two main sub-models simulating the kinematics of the drive mechanism and the compression process. A valve sub-model is included in the compression process model.

  15. Automated 3D Motion Tracking using Gabor Filter Bank, Robust Point Matching, and Deformable Models

    PubMed Central

    Wang, Xiaoxu; Chung, Sohae; Metaxas, Dimitris; Axel, Leon

    2013-01-01

    Tagged Magnetic Resonance Imaging (tagged MRI or tMRI) provides a means of directly and noninvasively displaying the internal motion of the myocardium. Reconstruction of the motion field is needed to quantify important clinical information, e.g., the myocardial strain, and detect regional heart functional loss. In this paper, we present a three-step method for this task. First, we use a Gabor filter bank to detect and locate tag intersections in the image frames, based on local phase analysis. Next, we use an improved version of the Robust Point Matching (RPM) method to sparsely track the motion of the myocardium, by establishing a transformation function and a one-to-one correspondence between grid tag intersections in different image frames. In particular, the RPM helps to minimize the impact on the motion tracking result of: 1) through-plane motion, and 2) relatively large deformation and/or relatively small tag spacing. In the final step, a meshless deformable model is initialized using the transformation function computed by RPM. The model refines the motion tracking and generates a dense displacement map, by deforming under the influence of image information, and is constrained by the displacement magnitude to retain its geometric structure. The 2D displacement maps in short and long axis image planes can be combined to drive a 3D deformable model, using the Moving Least Square method, constrained by the minimization of the residual error at tag intersections. The method has been tested on a numerical phantom, as well as on in vivo heart data from normal volunteers and heart disease patients. The experimental results show that the new method has a good performance on both synthetic and real data. Furthermore, the method has been used in an initial clinical study to assess the differences in myocardial strain distributions between heart disease (left ventricular hypertrophy) patients and the normal control group. The final results show that the proposed method

  16. Structure-based modeling of dye-fiber affinity with SOM-4D-QSAR paradigm: application to set of anthraquinone derivatives.

    PubMed

    Bak, Andrzej; Wyszomirski, Miroslaw; Magdziarz, Tomasz; Smolinski, Adam; Polanski, Jaroslaw

    2014-01-01

    A comparative structure-affinity study of anthraquinone dyes adsorption on cellulose fibre is presented in this paper. We used receptor-dependent 4D-QSAR methods based on grid and neural (SOM) methodology coupled with IVEPLS procedure. The applied RD 4D-QSAR approach focuses mainly on the ability of mapping dye properties to verify the concept of tinctophore in dye chemistry. Moreover, the stochastic SMV procedure to investigate the predictive ability of the method for a large population of 4D-QSAR models was employed. The obtained findings were compared with the previously published RI 3D/4D-QSAR models for the corresponding anthraquinone trainings sets. The neutral (protonated) and anionic (deprotonated) forms of anthraquinone scaffold were examined in order to deal with the uncertainty of the dye ionization state. The results are comparable to both the neutral and anionic dye sets regardless of the occupancy and charge descriptors applied, respectively. It is worth noting that the SOM-4D-QSAR behaves comparably to the cubic counterpart which is observed in each training/test subset specification (4D-QSAR-Jo vs SOM- 4D-QSARo and 4D-QSAR-Jq vs SOM-4D-QSARq). Additionally, an attempt was made to specify a common set of variables contributing significantly to dye-fiber binding affinity; it was simultaneously performed for some arbitrary chosen SMV models. The presented RD 4D-QSAR methodology together with IVE-PLS procedure provides a robust and predictive modeling technique, which facilitates detailed specification of the molecular motifs significantly contributing to the fiber-dye affinity. PMID:24499310

  17. Modelling Strong Ground Motions for Subduction Events in the Wellington Region, New Zealand

    NASA Astrophysics Data System (ADS)

    Francois-Holden, C.; Zhao, J.

    2010-12-01

    This work is a part of the “It’s Our Fault” programme, whose goal is to make Wellington, New Zealand, a more resilient city regarding earthquake hazards. We are working on defining ground motions from large plate boundary earthquakes at specified locations in the Wellington region in terms of response spectra and acceleration time histories. These motions will provide input for risk modelling for a potential major earthquake additional to those associated with the active faults of the region. Broadband waveforms are modelled applying the hybrid technique combining deterministic and stochastic approaches. We follow the proposed recipe by Irikura et al. (2004) to predict strong ground motions. We validated Irikura’s code and recipe using the strong motion dataset from the 2003 Mw 7.2 Fiordland earthquake, with both empirical and stochastic Green’s functions. The method was satisfactorily tested using an intraslab rupture and a record from a nearby aftershock as the empirical Green’s function (EGF). Although the event generated many aftershocks, it was difficult to find small events with 2 orders of magnitude smaller than the mainshock, recorded at a well distributed set of stations, with a rupture mechanism close enough to the mainshock. The alternative to using EGF is the stochastic Green’s functions (SGF) approach. We chose the Motazedian and Atkinson (2005) method for its assumption of a finite fault source model (instead of a point source). This assumption is closer to reality for Green’s functions in our case study where events have magnitudes greater than 5, and distances less than 200 km. We are now applying this method to a source scenario representing a locked interface underneath Wellington. A range of rupture scenarios will be modelled with varying hypocentre location, asperity locations, and overall rupture area. Finally, recent advances in detailed modelling of the Wellington basin geology will allow us to include site effects in our

  18. Two modes of motion of the alligator lizard cochlea: Measurements and model predictions

    NASA Astrophysics Data System (ADS)

    Aranyosi, A. J.; Freeman, Dennis M.

    2005-09-01

    Measurements of motion of an in vitro preparation of the alligator lizard basilar papilla in response to sound demonstrate elliptical trajectories. These trajectories are consistent with the presence of both a translational and rotational mode of motion. The translational mode is independent of frequency, and the rotational mode has a displacement peak near 5 kHz. These measurements can be explained by a simple mechanical system in which the basilar papilla is supported asymmetrically on the basilar membrane. In a quantitative model, the translational admittance is compliant while the rotational admittance is second order. Best-fit model parameters are consistent with estimates based on anatomy and predict that fluid flow across hair bundles is a primary source of viscous damping. The model predicts that the rotational mode contributes to the high-frequency slopes of auditory nerve fiber tuning curves, providing a physical explanation for a low-pass filter required in models of this cochlea. The combination of modes makes the sensitivity of hair bundles more uniform with radial position than that which would result from pure rotation. A mechanical analogy with the organ of Corti suggests that these two modes of motion may also be present in the mammalian cochlea.

  19. Simulation, prediction and analysis of Polar Motion with a dynamic Earth system model

    NASA Astrophysics Data System (ADS)

    Seitz, F.

    2012-04-01

    Variations of Earth rotation are associated with the redistribution and motion of mass elements in the Earth system. On seasonal to inter-annual time scales, the largest effects are due to mass redistributions within atmosphere and hydrosphere. In order to study the Earth's reaction on geophysical excitations, the dynamic Earth system model DyMEG has been developed. It is based on the balance of angular momentum in the Earth system which is physically described by the Liouville equation. This coupled system of three first-order differential equations is solved numerically in DyMEG. Simulations of polar motion and length-of-day variations are performed with DyMEG for time spans of up to 200 years using angular momentum variations from five ensemble runs of a consistently coupled atmosphere-hydrosphere model as model forcing. Besides, deformations induced by tides, loading and variations of Earth rotation are considered. In particular the contribution focuses on the simulation results of the Earth's free polar motion (Chandler oscillation). It is shown that the simulations over 200 years (1860-2059) are capable of exciting realistic variations of the Chandler oscillation. The application of an adaptive Kalman filter on DyMEG allows for the simultaneous simulation of Earth rotation and the estimation of critical model parameters, such as physical Earth parameters (e.g. Love numbers). The results of the estimated parameters will be presented and discussed with respect to values that can be found in the literature.

  20. A continuous 4D motion model from multiple respiratory cycles for use in lung radiotherapy.

    PubMed

    McClelland, Jamie R; Blackall, Jane M; Tarte, Ségolène; Chandler, Adam C; Hughes, Simon; Ahmad, Shahreen; Landau, David B; Hawkes, David J

    2006-09-01

    Respiratory motion causes errors when planning and delivering radiotherapy treatment to lung cancer patients. To reduce these errors, methods of acquiring and using four-dimensional computed tomography (4DCT) datasets have been developed. We have developed a novel method of constructing computational motion models from 4DCT. The motion models attempt to describe an average respiratory cycle, which reduces the effects of variation between different cycles. They require substantially less memory than a 4DCT dataset, are continuous in space and time, and facilitate automatic target propagation and combining of doses over the respiratory cycle. The motion models are constructed from CT data acquired in cine mode while the patient is free breathing (free breathing CT - FBCT). A "slab" of data is acquired at each couch position, with 3-4 contiguous slabs being acquired per patient. For each slab a sequence of 20 or 30 volumes was acquired over 20 seconds. A respiratory signal is simultaneously recorded in order to calculate the position in the respiratory cycle for each FBCT. Additionally, a high quality reference CT volume is acquired at breath hold. The reference volume is nonrigidly registered to each of the FBCT volumes. A motion model is then constructed for each slab by temporally fitting the nonrigid registration results. The value of each of the registration parameters is related to the position in the respiratory cycle by fitting an approximating B spline to the registration results. As an approximating function is used, and the data is acquired over several respiratory cycles, the function should model an average respiratory cycle. This can then be used to calculate the value of each degree of freedom at any desired position in the respiratory cycle. The resulting nonrigid transformation will deform the reference volume to predict the contents of the slab at the desired position in the respiratory cycle. The slab model predictions are then concatenated to

  1. Advances and challenges in deformable image registration: From image fusion to complex motion modelling.

    PubMed

    Schnabel, Julia A; Heinrich, Mattias P; Papież, Bartłomiej W; Brady, Sir J Michael

    2016-10-01

    Over the past 20 years, the field of medical image registration has significantly advanced from multi-modal image fusion to highly non-linear, deformable image registration for a wide range of medical applications and imaging modalities, involving the compensation and analysis of physiological organ motion or of tissue changes due to growth or disease patterns. While the original focus of image registration has predominantly been on correcting for rigid-body motion of brain image volumes acquired at different scanning sessions, often with different modalities, the advent of dedicated longitudinal and cross-sectional brain studies soon necessitated the development of more sophisticated methods that are able to detect and measure local structural or functional changes, or group differences. Moving outside of the brain, cine imaging and dynamic imaging required the development of deformable image registration to directly measure or compensate for local tissue motion. Since then, deformable image registration has become a general enabling technology. In this work we will present our own contributions to the state-of-the-art in deformable multi-modal fusion and complex motion modelling, and then discuss remaining challenges and provide future perspectives to the field. PMID:27364430

  2. Models of Postural Control: Shared Variance in Joint and COM Motions

    PubMed Central

    Kilby, Melissa C.; Molenaar, Peter C. M.; Newell, Karl M.

    2015-01-01

    This paper investigated the organization of the postural control system in human upright stance. To this aim the shared variance between joint and 3D total body center of mass (COM) motions was analyzed using multivariate canonical correlation analysis (CCA). The CCA was performed as a function of established models of postural control that varied in their joint degrees of freedom (DOF), namely, an inverted pendulum ankle model (2DOF), ankle-hip model (4DOF), ankle-knee-hip model (5DOF), and ankle-knee-hip-neck model (7DOF). Healthy young adults performed various postural tasks (two-leg and one-leg quiet stances, voluntary AP and ML sway) on a foam and rigid surface of support. Based on CCA model selection procedures, the amount of shared variance between joint and 3D COM motions and the cross-loading patterns we provide direct evidence of the contribution of multi-DOF postural control mechanisms to human balance. The direct model fitting of CCA showed that incrementing the DOFs in the model through to 7DOF was associated with progressively enhanced shared variance with COM motion. In the 7DOF model, the first canonical function revealed more active involvement of all joints during more challenging one leg stances and dynamic posture tasks. Furthermore, the shared variance was enhanced during the dynamic posture conditions, consistent with a reduction of dimension. This set of outcomes shows directly the degeneracy of multivariate joint regulation in postural control that is influenced by stance and surface of support conditions. PMID:25973896

  3. Models of Postural Control: Shared Variance in Joint and COM Motions.

    PubMed

    Kilby, Melissa C; Molenaar, Peter C M; Newell, Karl M

    2015-01-01

    This paper investigated the organization of the postural control system in human upright stance. To this aim the shared variance between joint and 3D total body center of mass (COM) motions was analyzed using multivariate canonical correlation analysis (CCA). The CCA was performed as a function of established models of postural control that varied in their joint degrees of freedom (DOF), namely, an inverted pendulum ankle model (2DOF), ankle-hip model (4DOF), ankle-knee-hip model (5DOF), and ankle-knee-hip-neck model (7DOF). Healthy young adults performed various postural tasks (two-leg and one-leg quiet stances, voluntary AP and ML sway) on a foam and rigid surface of support. Based on CCA model selection procedures, the amount of shared variance between joint and 3D COM motions and the cross-loading patterns we provide direct evidence of the contribution of multi-DOF postural control mechanisms to human balance. The direct model fitting of CCA showed that incrementing the DOFs in the model through to 7DOF was associated with progressively enhanced shared variance with COM motion. In the 7DOF model, the first canonical function revealed more active involvement of all joints during more challenging one leg stances and dynamic posture tasks. Furthermore, the shared variance was enhanced during the dynamic posture conditions, consistent with a reduction of dimension. This set of outcomes shows directly the degeneracy of multivariate joint regulation in postural control that is influenced by stance and surface of support conditions. PMID:25973896

  4. Molecular Motion of the Junction Points in Model Networks Prepared by Acyclic Triene Metathesis.

    PubMed

    da Silva, Lucas Caire; Bowers, Clifford R; Graf, Robert; Wagener, Kenneth B

    2016-03-01

    The junction dynamics in a selectively deuterated model polymer network containing junctions on every 21st chain carbon is studied by solid state (2) H echo NMR. Polymer networks are prepared via acyclic triene metathesis of deuteron-labeled symmetric trienes with deuteron probes precisely placed at the alpha carbon relative to the junction point. The effect of decreasing the cross-link density on the junction dynamics is studied by introduction of polybutadiene chains in-between junctions. The networks are characterized by swelling, gel content, and solid state (1) H MAS NMR. Line shape analysis of the (2) H quadrupolar echo spectra reveals that the degree of motion anisotropy and the distribution of motion correlation times depend on the cross-link density and structural heterogeneity of the polymer networks. A detailed model of the junction dynamics at different temperatures is proposed and explained in terms of the intermolecular cooperativity in densely-packed systems. PMID:26787457

  5. An improved Reynolds-equation model for gas damping of microbeam motion.

    SciTech Connect

    Gallis, Michail A.; Torczynski, John Robert

    2003-09-01

    An improved gas-damping model for the out-of-plane motion of a near-substrate microbeam is developed based on the Reynolds equation (RE). A boundary condition for the RE is developed that relates the pressure at the beam edge to the beam motion. The coefficients in this boundary condition are determined from Navier-Stokes slip-jump (NSSJ) simulations for small slip lengths (relative to the gap height) and from direct simulation Monte Carlo (DSMC) molecular gas dynamics simulations for larger slip lengths. This boundary condition significantly improves the accuracy of the RE when the microbeam width is only slightly greater than the gap height between the microbeam and the substrate. The improved RE model is applied to microbeams fabricated using the SUMMiT V process.

  6. Strong ground motions of the 2009 L'Aquila earthquake: modeling and scenario simulations

    NASA Astrophysics Data System (ADS)

    Gallovič, F.; Ameri, G.; Pacor, F.

    2012-04-01

    On April 6, 2009 a Mw 6.3 earthquake struck the L'Aquila city, one of the largest urban centers in the Abruzzo region (Central Italy), causing a large number of casualties and damage in the town and surrounding villages. The earthquake has been recorded by several digital stations of the Italian Strong-Motion Network. The collected records represent a unique dataset in Italy in terms of number and quality of records, azimuthal coverage and presence of near-fault recordings. Soon after the earthquake the damage in the epicentral area was also assessed providing macroseismic intensity estimates, in MCS scale, for 314 localities (I ≥5). Despite the moderate magnitude of the L'Aquila earthquake, the strong-motion and macroseismic data in the vicinity of the fault depict a large variability of the observed shaking and damage. In this study we present broadband (0.1 - 10 Hz) ground motion simulations of the 2009 L'Aquila earthquake to be used for engineering purposes in the region. We utilize Hybrid Integral-Composite (HIC, Gallovič and Brokešová, 2007) approach based on a k-square kinematic rupture model, combining low-frequency coherent and high-frequency incoherent source radiation and providing omega-squared source spectral decay. We first model the recorded seismograms in order to calibrate source parameters and to assess the capabilities of the broadband simulation model. To this end, position and slip amount of the two main asperities, the largest asperity time delay and the rupture velocity distribution on the fault is constrained, based on the low-frequency slip inversion result. Synthetic Green's functions are calculated in a 1D-layered crustal model including 1D soil profiles to account for site-specific response (where available). The goodness-of-fit is evaluated in time (peak values and duration) and frequency domains (elastic and inelastic response spectra) and shows a remarkable agreement between observed and simulated data at most of the stations

  7. Color-gradient lattice Boltzmann model for simulating droplet motion with contact-angle hysteresis

    NASA Astrophysics Data System (ADS)

    Ba, Yan; Liu, Haihu; Sun, Jinju; Zheng, Rongye

    2013-10-01

    Lattice Boltzmann method (LBM) is an effective tool for simulating the contact-line motion due to the nature of its microscopic dynamics. In contact-line motion, contact-angle hysteresis is an inherent phenomenon, but it is neglected in most existing color-gradient based LBMs. In this paper, a color-gradient based multiphase LBM is developed to simulate the contact-line motion, particularly with the hysteresis of contact angle involved. In this model, the perturbation operator based on the continuum surface force concept is introduced to model the interfacial tension, and the recoloring operator proposed by Latva-Kokko and Rothman is used to produce phase segregation and resolve the lattice pinning problem. At the solid surface, the color-conserving wetting boundary condition [Hollis , IMA J. Appl. Math.IJAMDM0272-496010.1093/imamat/hxr008 76, 726 (2011)] is applied to improve the accuracy of simulations and suppress spurious currents at the contact line. In particular, we present a numerical algorithm to allow for the effect of the contact-angle hysteresis, in which an iterative procedure is used to determine the dynamic contact angle. Numerical simulations are conducted to verify the developed model, including the droplet partial wetting process and droplet dynamical behavior in a simple shear flow. The obtained results are compared with theoretical solutions and experimental data, indicating that the model is able to predict the equilibrium droplet shape as well as the dynamic process of partial wetting and thus permits accurate prediction of contact-line motion with the consideration of contact-angle hysteresis.

  8. Dynamics of satellite motion and situational modeling in the INTERSHOCK project

    SciTech Connect

    Boyarskii, M.N.; Pavlov, V.P.; Prokhorenko, V.I.; Smirnov, V.N.; Zastenker, G.N.

    1986-09-01

    Several problems in the ballistic support for the INTERSHOCK experiment are discussed: selection of the optimal satellite orbit, the modeling of its crossings of the earth bow shock, and the analysis of the satellite's motion about its center of mass. Results are given from a determination of the earth bow shock after 6-month orbiting of the Prognoz-10-Interkosmos satellite (April-November, 1985).

  9. Real-time modeling of transverse emittance growth due to ground motion

    SciTech Connect

    Shiltsev, V.D.; Parkhomchuk, V.V. |

    1993-09-01

    Ground motion noise at frequencies around 1 kHz causes growth of transverse emittance of the Superconducting Super Collider (SSC) collider beams. The effect was quantitatively investigated using real-time signals from seismometers installed at the tunnel depth and on the surface. The SSC beam was modeled as an ensemble of oscillators with a spread of betatron frequencies. The effect of transverse feedback on emittance growth was investigated.

  10. 3D model-based catheter tracking for motion compensation in EP procedures

    NASA Astrophysics Data System (ADS)

    Brost, Alexander; Liao, Rui; Hornegger, Joachim; Strobel, Norbert

    2010-02-01

    Atrial fibrillation is the most common sustained heart arrhythmia and a leading cause of stroke. Its treatment by radio-frequency catheter ablation, performed using fluoroscopic image guidance, is gaining increasingly more importance. Two-dimensional fluoroscopic navigation can take advantage of overlay images derived from pre-operative 3-D data to add anatomical details otherwise not visible under X-ray. Unfortunately, respiratory motion may impair the utility of these static overlay images for catheter navigation. We developed an approach for image-based 3-D motion compensation as a solution to this problem. A bi-plane C-arm system is used to take X-ray images of a special circumferential mapping catheter from two directions. In the first step of the method, a 3-D model of the device is reconstructed. Three-dimensional respiratory motion at the site of ablation is then estimated by tracking the reconstructed catheter model in 3-D. This step involves bi-plane fluoroscopy and 2-D/3-D registration. Phantom data and clinical data were used to assess our model-based catheter tracking method. Experiments involving a moving heart phantom yielded an average 2-D tracking error of 1.4 mm and an average 3-D tracking error of 1.1 mm. Our evaluation of clinical data sets comprised 469 bi-plane fluoroscopy frames (938 monoplane fluoroscopy frames). We observed an average 2-D tracking error of 1.0 mm +/- 0.4 mm and an average 3-D tracking error of 0.8 mm +/- 0.5 mm. These results demonstrate that model-based motion-compensation based on 2-D/3-D registration is both feasible and accurate.

  11. A Motion Detection Model Inspired by the Neuronal Propagation in the Hippocampus

    NASA Astrophysics Data System (ADS)

    Liang, Haichao; Morie, Takashi

    We propose a motion detection model, which is suitable for higher speed operation than the video rate, inspired by the neuronal propagation in the hippocampus in the brain. The model detects motion of edges, which are extracted from monocular image sequences, on specified 2D maps without image matching. We introduce gating units into a CA3-CA1 model, where CA3 and CA1 are the names of hippocampal regions. We use the function of gating units to reduce mismatching for applying our model in complicated situations. We also propose a map-division method to achieve accurate detection. We have evaluated the performance of the proposed model by using artificial and real image sequences. The results show that the proposed model can run up to 1.0ms/frame if using a resolution of 64 × 60 units division of 320 × 240 pixels image. The detection rate of moving edges is achieved about 99% under a complicated situation. We have also verified that the proposed model can achieve accurate detection of approaching objects at high frame rate (> 100fps), which is better than conventional models, provided we can obtain accurate positions of image features and filter out the origins of false positive results in the post-processing.

  12. Dynamic modeling and motion simulation for a winged hybrid-driven underwater glider

    NASA Astrophysics Data System (ADS)

    Wang, Shu-Xin; Sun, Xiu-Jun; Wang, Yan-Hui; Wu, Jian-Guo; Wang, Xiao-Ming

    2011-03-01

    PETREL, a winged hybrid-driven underwater glider is a novel and practical marine survey platform which combines the features of legacy underwater glider and conventional AUV (autonomous underwater vehicle). It can be treated as a multi-rigid-body system with a floating base and a particular hydrodynamic profile. In this paper, theorems on linear and angular momentum are used to establish the dynamic equations of motion of each rigid body and the effect of translational and rotational motion of internal masses on the attitude control are taken into consideration. In addition, due to the unique external shape with fixed wings and deflectable rudders and the dual-drive operation in thrust and glide modes, the approaches of building dynamic model of conventional AUV and hydrodynamic model of submarine are introduced, and the tailored dynamic equations of the hybrid glider are formulated. Moreover, the behaviors of motion in glide and thrust operation are analyzed based on the simulation and the feasibility of the dynamic model is validated by data from lake field trials.

  13. The unified ideal model of mean motion resonance of artificial satellites due to geopotential perturbations

    NASA Astrophysics Data System (ADS)

    Zhang, MingJiang; Zhao, ChangYin; Xiong, YongQing; Sun, RongYu; Zhu, TingLei

    2013-04-01

    From Kaula's Earth gravitational potential written in classical orbital elements, the unified ideal model of mean motion resonance of artificial satellites due to geopotential perturbations is developed in this paper first, through a suitable sequence of canonical transformations constructed by implicit functions. This unified ideal orbital resonance model is valid for all the commensurabilities between the rotational angular velocity of the Earth and the angular velocities of mean orbital motion of artificial satellites with arbitrary inclination and small eccentricity, and can be also transformed into Garfinkel's general expression of ideal resonance problem. Then 1/1 resonance of the 24-hour satellite with arbitrary inclination and small eccentricity is analyzed under the effect of harmonics of J 2 and J 22 of the geopotential, based on the unified ideal model of mean motion resonance. The analytical expressions of the libration period and libration half width of the 1/1 resonance of the 24-hour satellite with arbitrary inclination and small eccentricity are presented.

  14. Some tentative models of molecular motion applied to water in small reversed micelles

    SciTech Connect

    Llor, A.; Rigny, P.

    1986-11-26

    The molecular dynamics of water in small, swollen, reversed micelles of sodium bis(2-ethyl-1-hexyl)sulfosuccinate (AOT) in cyclohexane has been investigated using proton NMR relaxation methods. When the water content drops from 15 to 3 molecules per AOT molecule, the /sup 1/H NMR relaxation time T/sub 1/ is considerably reduced. This is due in part to slower motions of water molecules and also to the increased influence of external relaxation processes, such as the dipolar interactions with the surfactant protons. By progressive substitution of the micellized water by heavy water, the dipolar water-water effects have been distinguished from other relaxation processes. Using standard models of motion, this substitution has shown the water movements to be slower than in pure water by at most a factor of 5. This somewhat unusual result is in agreement with data from concentrated ionic solutions. The external relaxation effects displayed a frequency dependence which is typically induced by slow motions. Some dynamical models have been discussed to explain them, but the main effects seem to be induced by the dipole-dipole interaction with the protons of the AOT polar heads. The complex modulation of this interaction could not be described precisely, and a simplified model was used to deduce qualitative dynamical information from the experimental data. The water-polar head movements were then found to be in the range of 5 x 10/sup -10/ s.

  15. Depth information in natural environments derived from optic flow by insect motion detection system: a model analysis

    PubMed Central

    Schwegmann, Alexander; Lindemann, Jens P.; Egelhaaf, Martin

    2014-01-01

    Knowing the depth structure of the environment is crucial for moving animals in many behavioral contexts, such as collision avoidance, targeting objects, or spatial navigation. An important source of depth information is motion parallax. This powerful cue is generated on the eyes during translatory self-motion with the retinal images of nearby objects moving faster than those of distant ones. To investigate how the visual motion pathway represents motion-based depth information we analyzed its responses to image sequences recorded in natural cluttered environments with a wide range of depth structures. The analysis was done on the basis of an experimentally validated model of the visual motion pathway of insects, with its core elements being correlation-type elementary motion detectors (EMDs). It is the key result of our analysis that the absolute EMD responses, i.e., the motion energy profile, represent the contrast-weighted nearness of environmental structures during translatory self-motion at a roughly constant velocity. In other words, the output of the EMD array highlights contours of nearby objects. This conclusion is largely independent of the scale over which EMDs are spatially pooled and was corroborated by scrutinizing the motion energy profile after eliminating the depth structure from the natural image sequences. Hence, the well-established dependence of correlation-type EMDs on both velocity and textural properties of motion stimuli appears to be advantageous for representing behaviorally relevant information about the environment in a computationally parsimonious way. PMID:25136314

  16. Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.

    PubMed

    Riley, Todd R; Lazarovici, Allan; Mann, Richard S; Bussemaker, Harmen J

    2015-01-01

    Transcription factors are crucial regulators of gene expression. Accurate quantitative definition of their intrinsic DNA binding preferences is critical to understanding their biological function. High-throughput in vitro technology has recently been used to deeply probe the DNA binding specificity of hundreds of eukaryotic transcription factors, yet algorithms for analyzing such data have not yet fully matured. Here, we present a general framework (FeatureREDUCE) for building sequence-to-affinity models based on a biophysically interpretable and extensible model of protein-DNA interaction that can account for dependencies between nucleotides within the binding interface or multiple modes of binding. When training on protein binding microarray (PBM) data, we use robust regression and modeling of technology-specific biases to infer specificity models of unprecedented accuracy and precision. We provide quantitative validation of our results by comparing to gold-standard data when available. PMID:26701911

  17. Adenine Nucleotide Translocase Is Acetylated in Vivo in Human Muscle: Modeling Predicts a Decreased ADP Affinity and Altered Control of Oxidative Phosphorylation

    PubMed Central

    2015-01-01

    Proteomics techniques have revealed that lysine acetylation is abundant in mitochondrial proteins. This study was undertaken (1) to determine the relationship between mitochondrial protein acetylation and insulin sensitivity in human skeletal muscle, identifying key acetylated proteins, and (2) to use molecular modeling techniques to understand the functional consequences of acetylation of adenine nucleotide translocase 1 (ANT1), which we found to be abundantly acetylated. Eight lean and eight obese nondiabetic subjects had euglycemic clamps and muscle biopsies for isolation of mitochondrial proteins and proteomics analysis. A number of acetylated mitochondrial proteins were identified in muscle biopsies. Overall, acetylation of mitochondrial proteins was correlated with insulin action (r = 0.60; P < 0.05). Of the acetylated proteins, ANT1, which catalyzes ADP–ATP exchange across the inner mitochondrial membrane, was acetylated at lysines 10, 23, and 92. The extent of acetylation of lysine 23 decreased following exercise, depending on insulin sensitivity. Molecular dynamics modeling and ensemble docking simulations predicted the ADP binding site of ANT1 to be a pocket of positively charged residues, including lysine 23. Calculated ADP–ANT1 binding affinities were physiologically relevant and predicted substantial reductions in affinity upon acetylation of lysine 23. Insertion of these derived binding affinities as parameters into a complete mathematical description of ANT1 kinetics predicted marked reductions in adenine nucleotide flux resulting from acetylation of lysine 23. Therefore, acetylation of ANT1 could have dramatic physiological effects on ADP–ATP exchange. Dysregulation of acetylation of mitochondrial proteins such as ANT1 therefore could be related to changes in mitochondrial function that are associated with insulin resistance. PMID:24884163

  18. Nonlinear and linear local cartesian relative motion state models for J2 pertubed elliptical orbits

    NASA Astrophysics Data System (ADS)

    Theron, A.; Kara-Zaitri, M.; Arzelier, D.; Louembet, C.

    2009-10-01

    Formulating a relative motion model between artificial satellites keeps a very actual interest in order to achieve devices adapted to autonomous rendezvous operating or formation flying control. Scanning the existing models field leads to distinguish them according to their nature -- linear or nonlinear -- the relative state variables -- local cartesian or curvilinear variables, relative orbital elements, classical or not -- the reference state variables -- inertial cartesian or spherical variables, orbital elements -- the pertubations taken into account -- drag, J2, ... -- and other assumptions as eccentricity of the reference satellite. The historical Clohessy-Wiltshire and Tschauner-Hempel models have been outclassed by improved linear models that include J2 pertubation [1, 2, 3] or drag [4] but do not take rigorously into account the perturbed dynamics of the reference local frame. As far as this fundamental point is concerned, Kechichian's nonlinear model [5] provides an interesting but complex formulation because of a non optimal derivation method. More over, it does not take full advantage of the Lagrange conditions [6] implied by orbital elements definition which allows simplifications without loss of generality. These elements are presented in this article to reach an improved relative motion nonlinear model under J2 perturbation assumption which results are validated by comparison with those produced by a nonlinear equinoctial propagator. A linear model is also proposed.

  19. Molecular modeling of the surface charging of hematite. I. The calculation of proton affinities and acidities on a surface

    NASA Astrophysics Data System (ADS)

    Wasserman, Evgeny; Rustad, James R.; Felmy, Andrew R.

    1999-03-01

    Calculation of the energy of a charged defect on a surface in supercell geometry is discussed. An important example of such a calculation is evaluation of surface proton affinities and acidities, as adding or removing a proton creates a charged unit cell. Systems with periodic boundary conditions in three spatial directions and a vacuum gap between slabs are demonstrated to be inadequate for unit cells having non-zero ionic charge and uniform neutralizing background. In such a system the calculated energy diverges linearly with the thickness of the vacuum gap. A system periodic in two directions and finite in the direction perpendicular to the surface (2-D PBC) with the neutralizing background distributed as the surface charge density is free from this problem. Furthermore, the correction for the interaction of the charged defect with its own translational images is needed to speed up the convergence to the infinite dilution limit. The expression for the asymptotic correction for the energy of interaction of a charged defect with its translational images in 2-D PBC geometry has been developed in this study. The asymptotic correction is evaluated as the interaction energy of a 2-D translationally periodic array of point charges located above and below the plate of non-uniform dielectric. This is a generalization of the method of M. Leslie and M.J. Gillan [J. Phys. C, 18 (1985) 973] for the calculation of the energy of a charged defect in bulk crystals. The usefulness of this correction was demonstrated on two test cases involving the calculation of proton affinity and acidity at the (012) surface of hematite. The proposed method is likely to be important in ab initio calculations of the energy effect of the surface protonation reactions, where computational limitations dictate a small size for the unit cell.

  20. Vesicle Motion during Sustained Exocytosis in Chromaffin Cells: Numerical Model Based on Amperometric Measurements

    PubMed Central

    Jarukanont, Daungruthai; Bonifas Arredondo, Imelda; Femat, Ricardo; Garcia, Martin E.

    2015-01-01

    Chromaffin cells release catecholamines by exocytosis, a process that includes vesicle docking, priming and fusion. Although all these steps have been intensively studied, some aspects of their mechanisms, particularly those regarding vesicle transport to the active sites situated at the membrane, are still unclear. In this work, we show that it is possible to extract information on vesicle motion in Chromaffin cells from the combination of Langevin simulations and amperometric measurements. We developed a numerical model based on Langevin simulations of vesicle motion towards the cell membrane and on the statistical analysis of vesicle arrival times. We also performed amperometric experiments in bovine-adrenal Chromaffin cells under Ba2+ stimulation to capture neurotransmitter releases during sustained exocytosis. In the sustained phase, each amperometric peak can be related to a single release from a new vesicle arriving at the active site. The amperometric signal can then be mapped into a spike-series of release events. We normalized the spike-series resulting from the current peaks using a time-rescaling transformation, thus making signals coming from different cells comparable. We discuss why the obtained spike-series may contain information about the motion of all vesicles leading to release of catecholamines. We show that the release statistics in our experiments considerably deviate from Poisson processes. Moreover, the interspike-time probability is reasonably well described by two-parameter gamma distributions. In order to interpret this result we computed the vesicles’ arrival statistics from our Langevin simulations. As expected, assuming purely diffusive vesicle motion we obtain Poisson statistics. However, if we assume that all vesicles are guided toward the membrane by an attractive harmonic potential, simulations also lead to gamma distributions of the interspike-time probability, in remarkably good agreement with experiment. We also show that

  1. Modeling of marangoni-induced droplet motion and melt convection during solidification of hypermonotectic alloys

    NASA Astrophysics Data System (ADS)

    Wu, Menghuai; Ludwig, Andreas; Ratke, Lorenz

    2003-12-01

    A two-phase volume averaging approach to model Marangoni-induced droplet motion of the minority liquid phase and the convection in the parent melt during solidification of the hypermonotectic alloys is presented. The minority liquid phase decomposed from the parent melt as droplets in the miscibility gap was treated as the second-phase L 2. The parent melt including the solidified monotectic matrix was treated as the first phase L 1. Both phases were considered as different and spatially interpenetrating continua. The conservation equations of mass, momentum, solute, and enthalpy for both phases, and an additional transport equation for the droplet density, were solved. Nucleation of the L 2 droplets, diffusion-controlled growth, interphase interactions such as Marangoni force at the L 1- L 2 interface, Stokes force, solute partitioning, and heat release of decomposition were taken into account by corresponding source and exchange terms in the conservation equations. The monotectic reaction was modeled by adding the latent heat on the L 1 phase during monotectic reaction, and applying an enlarged viscosity to the solidified monotectic matrix. A two-dimensional (2-D) square casting with hypermonotectic composition (Al-10 wt pct Bi) was simulated. This paper focused on Marangoni motion, hence gravity was not included. Results with nucleation, droplet evolution, Marangoni-induced droplet motion, solute transport, and macrosegregation formation were obtained and discussed.

  2. Visual fatigue modeling for stereoscopic video shot based on camera motion

    NASA Astrophysics Data System (ADS)

    Shi, Guozhong; Sang, Xinzhu; Yu, Xunbo; Liu, Yangdong; Liu, Jing

    2014-11-01

    As three-dimensional television (3-DTV) and 3-D movie become popular, the discomfort of visual feeling limits further applications of 3D display technology. The cause of visual discomfort from stereoscopic video conflicts between accommodation and convergence, excessive binocular parallax, fast motion of objects and so on. Here, a novel method for evaluating visual fatigue is demonstrated. Influence factors including spatial structure, motion scale and comfortable zone are analyzed. According to the human visual system (HVS), people only need to converge their eyes to the specific objects for static cameras and background. Relative motion should be considered for different camera conditions determining different factor coefficients and weights. Compared with the traditional visual fatigue prediction model, a novel visual fatigue predicting model is presented. Visual fatigue degree is predicted using multiple linear regression method combining with the subjective evaluation. Consequently, each factor can reflect the characteristics of the scene, and the total visual fatigue score can be indicated according to the proposed algorithm. Compared with conventional algorithms which ignored the status of the camera, our approach exhibits reliable performance in terms of correlation with subjective test results.

  3. Fast Computation of Ground Motion Shaking Map base on the Modified Stochastic Finite Fault Modeling

    NASA Astrophysics Data System (ADS)

    Shen, W.; Zhong, Q.; Shi, B.

    2012-12-01

    Rapidly regional MMI mapping soon after a moderate-large earthquake is crucial to loss estimation, emergency services and planning of emergency action by the government. In fact, many countries show different degrees of attention on the technology of rapid estimation of MMI , and this technology has made significant progress in earthquake-prone countries. In recent years, numerical modeling of strong ground motion has been well developed with the advances of computation technology and earthquake science. The computational simulation of strong ground motion caused by earthquake faulting has become an efficient way to estimate the regional MMI distribution soon after earthquake. In China, due to the lack of strong motion observation in network sparse or even completely missing areas, the development of strong ground motion simulation method has become an important means of quantitative estimation of strong motion intensity. In many of the simulation models, stochastic finite fault model is preferred to rapid MMI estimating for its time-effectiveness and accuracy. In finite fault model, a large fault is divided into N subfaults, and each subfault is considered as a small point source. The ground motions contributed by each subfault are calculated by the stochastic point source method which is developed by Boore, and then summed at the observation point to obtain the ground motion from the entire fault with a proper time delay. Further, Motazedian and Atkinson proposed the concept of Dynamic Corner Frequency, with the new approach, the total radiated energy from the fault and the total seismic moment are conserved independent of subfault size over a wide range of subfault sizes. In current study, the program EXSIM developed by Motazedian and Atkinson has been modified for local or regional computations of strong motion parameters such as PGA, PGV and PGD, which are essential for MMI estimating. To make the results more reasonable, we consider the impact of V30 for the

  4. Fluid particle motion and Lagrangian velocities for pulsatile flow through a femoral artery branch model

    NASA Technical Reports Server (NTRS)

    Cho, Y. I.; Crawford, D. W.; Back, L. H.; Back, M. R.

    1987-01-01

    A flow visualization study using selective dye injection and frame by frame analysis of a movie provided qualitative and quantitative data on the motion of marked fluid particles in a 60 degree artery branch model for simulation of physiological femoral artery flow. Physical flow features observed included jetting of the branch flow into the main lumen during the brief reverse flow period, flow separation along the main lumen wall during the near zero flow phase of diastole when the core flow was in the downstream direction, and inference of flow separation conditions along the wall opposite the branch later in systole at higher branch flow ratios. There were many similarities between dye particle motions in pulsatile flow and the comparative steady flow observations.

  5. Simplified unified model for estimating the motion of magnetic nanoparticles within electrohydrodynamic field.

    PubMed

    Seo, Hyeon-Seok; Lee, Sangyoup; Lee, Jong-Chul

    2014-11-01

    In previous research, we studied the electrical breakdown characteristics of a transformer oil-based magnetic fluid; mailnly, those were carried out by the experimental measurements. The first study was aimed at enhancing the dielectric breakdown voltage of transformer oil by adding magnetic nanoparticles experimentally under the official testing condition of dielectric liquids. The next study was focused on explaining the reason why the dielectric characterisitics of the fluids were changed through optically visualizing the particles motion in a microchannel using an optical microscopic measurement and numerically calculating the dielectrophoretic force induced in the fluids with considering only the properties of magnetic nanoparticles. In this study, we developed a simplified unified model for calculating further the motion of magnetic nanoparticles suspended in the presence of electrohydrodynamic field using the COMSOL multiphysics finite element simulation suite and investigated the effects of magnetic nanoparticle dielectrophoretic activity aimed at enhancing the electrical breakdown characteristics of transformer oil. PMID:25958577

  6. Model predictive driving simulator motion cueing algorithm with actuator-based constraints

    NASA Astrophysics Data System (ADS)

    Garrett, Nikhil J. I.; Best, Matthew C.

    2013-08-01

    The simulator motion cueing problem has been considered extensively in the literature; approaches based on linear filtering and optimal control have been presented and shown to perform reasonably well. More recently, model predictive control (MPC) has been considered as a variant of the optimal control approach; MPC is perhaps an obvious candidate for motion cueing due to its ability to deal with constraints, in this case the platform workspace boundary. This paper presents an MPC-based cueing algorithm that, unlike other algorithms, uses the actuator positions and velocities as the constraints. The result is a cueing algorithm that can make better use of the platform workspace whilst ensuring that its bounds are never exceeded. The algorithm is shown to perform well against the classical cueing algorithm and an algorithm previously proposed by the authors, both in simulation and in tests with human drivers.

  7. Uncertainty of earthquake losses due to model uncertainty of input ground motions in the Los Angeles area

    USGS Publications Warehouse

    Cao, T.; Petersen, M.D.

    2006-01-01

    In a recent study we used the Monte Carlo simulation method to evaluate the ground-motion uncertainty of the 2002 update of the California probabilistic seismic hazard model. The resulting ground-motion distribution is used in this article to evaluate the contribution of the hazard model to the uncertainty in earthquake loss ratio, the ratio of the expected loss to the total value of a structure. We use the Hazards U.S. (HAZUS) methodology for loss estimation because it is a widely used and publicly available risk model and intended for regional studies by public agencies and for use by governmental decision makers. We found that the loss ratio uncertainty depends not only on the ground-motion uncertainty but also on the mean ground-motion level. The ground-motion uncertainty, as measured by the coefficient of variation (COV), is amplified when converting to the loss ratio uncertainty because loss increases concavely with ground motion. By comparing the ground-motion uncertainty with the corresponding loss ratio uncertainty for the structural damage of light wood-frame buildings in Los Angeles area, we show that the COV of loss ratio is almost twice the COV of ground motion with a return period of 475 years around the San Andreas fault and other major faults in the area. The loss ratio for the 2475-year ground-motion maps is about a factor of three higher than for the 475-year maps. However, the uncertainties in ground motion and loss ratio for the longer return periods are lower than for the shorter return periods because the uncertainty parameters in the hazard logic tree are independent of the return period, but the mean ground motion increases with return period.

  8. Self Motion Perception and Motion Sickness

    NASA Technical Reports Server (NTRS)

    Fox, Robert A. (Principal Investigator)

    1991-01-01

    The studies conducted in this research project examined several aspects of motion sickness in animal models. A principle objective of these studies was to investigate the neuroanatomy that is important in motion sickness with the objectives of examining both the utility of putative models and defining neural mechanisms that are important in motion sickness.

  9. Internal models of target motion: expected dynamics overrides measured kinematics in timing manual interceptions.

    PubMed

    Zago, Myrka; Bosco, Gianfranco; Maffei, Vincenzo; Iosa, Marco; Ivanenko, Yuri P; Lacquaniti, Francesco

    2004-04-01

    Prevailing views on how we time the interception of a moving object assume that the visual inputs are informationally sufficient to estimate the time-to-contact from the object's kinematics. Here we present evidence in favor of a different view: the brain makes the best estimate about target motion based on measured kinematics and an a priori guess about the causes of motion. According to this theory, a predictive model is used to extrapolate time-to-contact from expected dynamics (kinetics). We projected a virtual target moving vertically downward on a wide screen with different randomized laws of motion. In the first series of experiments, subjects were asked to intercept this target by punching a real ball that fell hidden behind the screen and arrived in synchrony with the visual target. Subjects systematically timed their motor responses consistent with the assumption of gravity effects on an object's mass, even when the visual target did not accelerate. With training, the gravity model was not switched off but adapted to nonaccelerating targets by shifting the time of motor activation. In the second series of experiments, there was no real ball falling behind the screen. Instead the subjects were required to intercept the visual target by clicking a mousebutton. In this case, subjects timed their responses consistent with the assumption of uniform motion in the absence of forces, even when the target actually accelerated. Overall, the results are in accord with the theory that motor responses evoked by visual kinematics are modulated by a prior of the target dynamics. The prior appears surprisingly resistant to modifications based on performance errors. PMID:14627663

  10. A DFT and semiempirical model-based study of opioid receptor affinity and selectivity in a group of molecules with a morphine structural core.

    PubMed

    Bruna-Larenas, Tamara; Gómez-Jeria, Juan S

    2012-01-01

    We report the results of a search for model-based relationships between mu, delta, and kappa opioid receptor binding affinity and molecular structure for a group of molecules having in common a morphine structural core. The wave functions and local reactivity indices were obtained at the ZINDO/1 and B3LYP/6-31G(∗∗) levels of theory for comparison. New developments in the expression for the drug-receptor interaction energy expression allowed several local atomic reactivity indices to be included, such as local electronic chemical potential, local hardness, and local electrophilicity. These indices, together with a new proposal for the ordering of the independent variables, were incorporated in the statistical study. We found and discussed several statistically significant relationships for mu, delta, and kappa opioid receptor binding affinity at both levels of theory. Some of the new local reactivity indices incorporated in the theory appear in several equations for the first time in the history of model-based equations. Interaction pharmacophores were generated for mu, delta, and kappa receptors. We discuss possible differences regulating binding and selectivity in opioid receptor subtypes. This study, contrarily to the statistically backed ones, is able to provide a microscopic insight of the mechanisms involved in the binding process. PMID:25379287

  11. A DFT and Semiempirical Model-Based Study of Opioid Receptor Affinity and Selectivity in a Group of Molecules with a Morphine Structural Core

    PubMed Central

    Bruna-Larenas, Tamara; Gómez-Jeria, Juan S.

    2012-01-01

    We report the results of a search for model-based relationships between mu, delta, and kappa opioid receptor binding affinity and molecular structure for a group of molecules having in common a morphine structural core. The wave functions and local reactivity indices were obtained at the ZINDO/1 and B3LYP/6-31G∗∗ levels of theory for comparison. New developments in the expression for the drug-receptor interaction energy expression allowed several local atomic reactivity indices to be included, such as local electronic chemical potential, local hardness, and local electrophilicity. These indices, together with a new proposal for the ordering of the independent variables, were incorporated in the statistical study. We found and discussed several statistically significant relationships for mu, delta, and kappa opioid receptor binding affinity at both levels of theory. Some of the new local reactivity indices incorporated in the theory appear in several equations for the first time in the history of model-based equations. Interaction pharmacophores were generated for mu, delta, and kappa receptors. We discuss possible differences regulating binding and selectivity in opioid receptor subtypes. This study, contrarily to the statistically backed ones, is able to provide a microscopic insight of the mechanisms involved in the binding process. PMID:25379287

  12. Velocity and Density Models Incorporating the Cascadia Subduction Zone for 3D Earthquake Ground Motion Simulations

    USGS Publications Warehouse

    Stephenson, William J.

    2007-01-01

    INTRODUCTION In support of earthquake hazards and ground motion studies in the Pacific Northwest, three-dimensional P- and S-wave velocity (3D Vp and Vs) and density (3D rho) models incorporating the Cascadia subduction zone have been developed for the region encompassed from about 40.2?N to 50?N latitude, and from about -122?W to -129?W longitude. The model volume includes elevations from 0 km to 60 km (elevation is opposite of depth in model coordinates). Stephenson and Frankel (2003) presented preliminary ground motion simulations valid up to 0.1 Hz using an earlier version of these models. The version of the model volume described here includes more structural and geophysical detail, particularly in the Puget Lowland as required for scenario earthquake simulations in the development of the Seattle Urban Hazards Maps (Frankel and others, 2007). Olsen and others (in press) used the model volume discussed here to perform a Cascadia simulation up to 0.5 Hz using a Sumatra-Andaman Islands rupture history. As research from the EarthScope Program (http://www.earthscope.org) is published, a wealth of important detail can be added to these model volumes, particularly to depths of the upper-mantle. However, at the time of development for this model version, no EarthScope-specific results were incorporated. This report is intended to be a reference for colleagues and associates who have used or are planning to use this preliminary model in their research. To this end, it is intended that these models will be considered a beginning template for a community velocity model of the Cascadia region as more data and results become available.

  13. The sea urchin embryo as a model for mammalian developmental neurotoxicity: ontogenesis of the high-affinity choline transporter and its role in cholinergic trophic activity.

    PubMed Central

    Qiao, Dan; Nikitina, Lyudmila A; Buznikov, Gennady A; Lauder, Jean M; Seidler, Frederic J; Slotkin, Theodore A

    2003-01-01

    Embryonic development in the sea urchin requires trophic actions of the same neurotransmitters that participate in mammalian brain assembly. We evaluated the development of the high-affinity choline transporter, which controls acetylcholine synthesis. A variety of developmental neurotoxicants affect this transporter in mammalian brain. [3H]Hemicholinium-3 binding to the transporter was found in the cell membrane fraction at stages from the unfertilized egg to pluteus, with a binding affinity comparable with that seen in mammalian brain. Over the course of development, the concentration of transporter sites rose more than 3-fold, achieving concentrations comparable with those of cholinergically enriched mammalian brain regions. Dimethylaminoethanol (DMAE), a competitive inhibitor of choline transport, elicited dysmorphology beginning at the mid-blastula stage, with anomalies beginning progressively later as the concentration of DMAE was lowered. Pretreatment, cotreatment, or delayed treatment with acetylcholine or choline prevented the adverse effects of DMAE. Because acetylcholine was protective at a lower threshold, the DMAE-induced defects were most likely mediated by its effects on acetylcholine synthesis. Transient removal of the hyaline layer enabled a charged transport inhibitor, hemicholinium-3, to penetrate sufficiently to elicit similar anomalies, which were again prevented by acetylcholine or choline. These results indicate that the developing sea urchin possesses a high-affinity choline transporter analogous to that found in the mammalian brain, and, as in mammals, the functioning of this transporter plays a key role in the developmental, trophic activity of acetylcholine. The sea urchin model may thus be useful in high-throughput screening of suspected developmental neurotoxicants. PMID:14594623

  14. 4D motion modeling of the coronary arteries from CT images for robotic assisted minimally invasive surgery

    NASA Astrophysics Data System (ADS)

    Zhang, Dong Ping; Edwards, Eddie; Mei, Lin; Rueckert, Daniel

    2009-02-01

    In this paper, we present a novel approach for coronary artery motion modeling from cardiac Computed Tomography( CT) images. The aim of this work is to develop a 4D motion model of the coronaries for image guidance in robotic-assisted totally endoscopic coronary artery bypass (TECAB) surgery. To utilize the pre-operative cardiac images to guide the minimally invasive surgery, it is essential to have a 4D cardiac motion model to be registered with the stereo endoscopic images acquired intraoperatively using the da Vinci robotic system. In this paper, we are investigating the extraction of the coronary arteries and the modelling of their motion from a dynamic sequence of cardiac CT. We use a multi-scale vesselness filter to enhance vessels in the cardiac CT images. The centerlines of the arteries are extracted using a ridge traversal algorithm. Using this method the coronaries can be extracted in near real-time as only local information is used in vessel tracking. To compute the deformation of the coronaries due to cardiac motion, the motion is extracted from a dynamic sequence of cardiac CT. Each timeframe in this sequence is registered to the end-diastole timeframe of the sequence using a non-rigid registration algorithm based on free-form deformations. Once the images have been registered a dynamic motion model of the coronaries can be obtained by applying the computed free-form deformations to the extracted coronary arteries. To validate the accuracy of the motion model we compare the actual position of the coronaries in each time frame with the predicted position of the coronaries as estimated from the non-rigid registration. We expect that this motion model of coronaries can facilitate the planning of TECAB surgery, and through the registration with real-time endoscopic video images it can reduce the conversion rate from TECAB to conventional procedures.

  15. Calibration of strong motion models for Central America region and its use in seismic hazard assessment

    NASA Astrophysics Data System (ADS)

    Climent, A.; Benito, M. B.; Piedra, R.; Lindholm, C.; Gaspar-Escribano, J.

    2013-05-01

    We present the results of a study aimed at choosing the more suitable strong-motion models for seismic hazard analysis in the Central America (CA) Region. After a careful revision of the state of the art, different models developed for subduction and volcanic crustal zones, in tectonic environment similar to those of CA, were selected. These models were calibrated with accelerograms recorded in Costa Rica, Nicaragua and El Salvador. The peak ground acceleration PGA and Spectral Acceleration SA (T) derived from the records were compared with the ones predicted by the models in similar conditions of magnitude, distance and soil. The type of magnitude (Ms, Mb, MW), distance (Rhyp, Rrup, etc) and ground motion parameter (maximum horizontal component, geometrical mean, etc ) was taken into account in the comparison with the real data. As results of the analysis, the models which present a best fit with the local data were identified. These models have been applied for carrying out seismic hazard analysis in the region, in the frame of the RESIS II project financed by the Norwegian Foreign Department and also by the Spanish project SISMOCAES. The methodology followed is based on the direct comparison between PGA and SA 5 % damped response values extracted from actual records with the corresponding acceleration values predicted by the selected ground-motion models for similar magnitude, distance and soil conditions. Residuals between observed and predicted values for PGA, and SA (1sec) are calculated and plotted as a function of distance and magnitude, analyzing their deviation from the mean value. Besides and most important, a statistical analysis of the normalized residuals was carry out using the criteria proposed by Scherbaum et al. (2004), which consists in categorizing ground motion models based in a likelihood parameter that reflects the goodness-of-fit of the median values as well as the shape of the underlying distribution of ground motion residuals. Considering

  16. Using model order tests to determine sensory inputs in a motion study

    NASA Technical Reports Server (NTRS)

    Repperger, D. W.; Junker, A. M.

    1977-01-01

    In the study of motion effects on tracking performance, a problem of interest is the determination of what sensory inputs a human uses in controlling his tracking task. In the approach presented here a simple canonical model (FID or a proportional, integral, derivative structure) is used to model the human's input-output time series. A study of significant changes in reduction of the output error loss functional is conducted as different permutations of parameters are considered. Since this canonical model includes parameters which are related to inputs to the human (such as the error signal, its derivatives and integration), the study of model order is equivalent to the study of which sensory inputs are being used by the tracker. The parameters are obtained which have the greatest effect on reducing the loss function significantly. In this manner the identification procedure converts the problem of testing for model order into the problem of determining sensory inputs.

  17. Evaluation of a computational model to predict elbow range of motion

    PubMed Central

    Nishiwaki, Masao; Johnson, James A.; King, Graham J. W.; Athwal, George S.

    2014-01-01

    Computer models capable of predicting elbow flexion and extension range of motion (ROM) limits would be useful for assisting surgeons in improving the outcomes of surgical treatment of patients with elbow contractures. A simple and robust computer-based model was developed that predicts elbow joint ROM using bone geometries calculated from computed tomography image data. The model assumes a hinge-like flexion-extension axis, and that elbow passive ROM limits can be based on terminal bony impingement. The model was validated against experimental results with a cadaveric specimen, and was able to predict the flexion and extension limits of the intact joint to 0° and 3°, respectively. The model was also able to predict the flexion and extension limits to 1° and 2°, respectively, when simulated osteophytes were inserted into the joint. Future studies based on this approach will be used for the prediction of elbow flexion-extension ROM in patients with primary osteoarthritis to help identify motion-limiting hypertrophic osteophytes, and will eventually permit real-time computer-assisted navigated excisions. PMID:24841799

  18. Modeling Pancreatic Tumor Motion Using 4-Dimensional Computed Tomography and Surrogate Markers

    SciTech Connect

    Huguet, Florence; Yorke, Ellen D.; Davidson, Margaret; Zhang, Zhigang; Jackson, Andrew; Mageras, Gig S.; Wu, Abraham J.; Goodman, Karyn A.

    2015-03-01

    Purpose: To assess intrafractional positional variations of pancreatic tumors using 4-dimensional computed tomography (4D-CT), their impact on gross tumor volume (GTV) coverage, the reliability of biliary stent, fiducial seeds, and the real-time position management (RPM) external marker as tumor surrogates for setup of respiratory gated treatment, and to build a correlative model of tumor motion. Methods and Materials: We analyzed the respiration-correlated 4D-CT images acquired during simulation of 36 patients with either a biliary stent (n=16) or implanted fiducials (n=20) who were treated with RPM respiratory gated intensity modulated radiation therapy for locally advanced pancreatic cancer. Respiratory displacement relative to end-exhalation was measured for the GTV, the biliary stent, or fiducial seeds, and the RPM marker. The results were compared between the full respiratory cycle and the gating interval. Linear mixed model was used to assess the correlation of GTV motion with the potential surrogate markers. Results: The average ± SD GTV excursions were 0.3 ± 0.2 cm in the left-right direction, 0.6 ± 0.3 cm in the anterior-posterior direction, and 1.3 ± 0.7 cm in the superior-inferior direction. Gating around end-exhalation reduced GTV motion by 46% to 60%. D95% was at least the prescribed 56 Gy in 76% of patients. GTV displacement was associated with the RPM marker, the biliary stent, and the fiducial seeds. The correlation was better with fiducial seeds and with biliary stent. Conclusions: Respiratory gating reduced the margin necessary for radiation therapy for pancreatic tumors. GTV motion was well correlated with biliary stent or fiducial seed displacements, validating their use as surrogates for daily assessment of GTV position during treatment. A patient-specific internal target volume based on 4D-CT is recommended both for gated and not-gated treatment; otherwise, our model can be used to predict the degree of GTV motion.

  19. Three-dimensional semi-idealized model for tidal motion in tidal estuaries. An application to the Ems estuary

    NASA Astrophysics Data System (ADS)

    Kumar, Mohit; Schuttelaars, Henk M.; Roos, Pieter C.; Möller, Matthias

    2016-01-01

    In this paper, a three-dimensional semi-idealized model for tidal motion in a tidal estuary of arbitrary shape and bathymetry is presented. This model aims at bridging the gap between idealized and complex models. The vertical profiles of the velocities are obtained analytically in terms of the first-order and the second-order partial derivatives of surface elevation, which itself follows from an elliptic partial differential equation. The surface elevation is computed numerically using the finite element method and its partial derivatives are obtained using various methods. The newly developed semi-idealized model allows for a systematic investigation of the influence of geometry and bathymetry on the tidal motion which was not possible in previously developed idealized models. The new model also retains the flexibility and computational efficiency of previous idealized models, essential for sensitivity analysis. As a first step, the accuracy of the semi-idealized model is investigated. To this end, an extensive comparison is made between the model results of the semi-idealized model and two other idealized models: a width-averaged model and a three-dimensional idealized model. Finally, the semi-idealized model is used to understand the influence of local geometrical effects on the tidal motion in the Ems estuary. The model shows that local convergence and meandering effects can have a significant influence on the tidal motion. Finally, the model is applied to the Ems estuary. The model results agree well with observations and results from a complex numerical model.

  20. Special Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Parikh, Indu; Cuatrecasas, Pedro

    1985-01-01

    Describes the nature of affinity chromatography and its use in purifying enzymes, studying cell interactions, exploring hormone receptors, and other areas. The potential the technique may have in treating disease is also considered. (JN)

  1. Topographic modelling of caldera analogues using Structure from Motion - Multiview stereo-photogrammetry

    NASA Astrophysics Data System (ADS)

    Ulusoy, İnan; Aydın, Eda; Evren Çubukçu, H.

    2016-04-01

    Analogue caldera models have long been used in volcanology to investigate structural evolution of volcanoes during tumescence and collapse periods. Influence of tectonic forces on volcanic features are also in the scope of those experiments. As well as interior modelling of the caldera experiments, topographic modelling is essential for digital monitoring and quantification purposes. Topographic modelling of those sandbox models is possible using laser scanning techniques. Particle tracking using still images is another way to demonstrate and quantify the structure and movement during the experiment. The quantum leap in the digital photography and computation tools and ease of access to both, provides the use of a new modelling technique in various scales and applications in Geology. Although the roots are older, Structure from Motion - Multiview stereo-photogrammetry (SfM-MVS) is a relatively new technique for surface modelling via several high resolution photographs. We have used SfM-MVS to digitally model the elevation of the tumescence and collapse cycles in analogue caldera experiments. Several sandbox experiments have been modelled using SfM-MVS technique stage by stage during tumescence and collapse periods. It has been possible to evaluate the structural evolution of the collapse models. Additionally, using particle tracking via still images acquired during the experiments, we have modelled the superficial evolution of the caldera structure. SfM-MVS is an effective low budget method for modelling in decimetric scale down to millimetre/micrometre precision.

  2. Simulation of strong ground motion in northern Iran using the specific barrier model

    NASA Astrophysics Data System (ADS)

    Soghrat, M. R.; Khaji, N.; Zafarani, H.

    2012-02-01

    In this study, based upon the calibrated specific barrier model (SBM) against the latest available strong motion data, ground motion prediction equations for soil and rock sites in northern Iran are developed. The SBM may provide the most complete, simple and self-consistent description of the faulting process, which is applicable in both 'near-fault' and 'far-field' regions. Consequently, the SBM may provide consistent ground motion simulations over the entire necessary frequency range and for all distances of engineering interests. To determine source parameters in this study, we used 163 three-component records of 32 earthquakes with magnitude ranging from MW 4.9 to 7.4 in northern Iran. In the database, records with hypocentral distances less than 200 km are chosen and only earthquakes whose moment-magnitude estimates are available have been used. Furthermore, using the best available information, recording sites are classified into two main geologic categories: rock and soil. Because of the lack of site amplification information in the most regions of the world including Iran, we used the H/V ratio method for estimating the site amplification. Moreover, the Kappa factor that shows diminishing the high-frequency amplitude is determined. In this study, two data sets are considered for determining the source parameters (ΔσG and ΔσL) and the H/V ratio and the Kappa factor. Only S-wave part of signals is used in each analysis. Regression analysis is performed using 'random effects' method that considers both interseismic (event-to-event) and coseismic (within-event) variabilities to effectively deal with the problem of weighting observations from different earthquakes. The residuals are controlled against available northern Iranian strong ground motion data to verify that the model predictions are unbiased and that there are no significant residual trends with magnitude and distance. At first, it is assumed that no sign of self-similarity breakdown is observed

  3. The geocenter motion from decadal to geological time-scales: geophysical modelling

    NASA Astrophysics Data System (ADS)

    Greff-Lefftz, M.; Métivier, L.

    2012-04-01

    Among the coefficients of the spherical harmonics expansion of elasto-gravitational deformations, the degree-one has particular characteristics related to geodesy as well as to mechanics. It is linked to the position of the Earth centre of mass and is strongly dependent on the choice of the origin of the reference frame. We investigate here the geocenter motion, that is to say the geometric centre of the translated external surface with respect to the centre of mass, for different internal excitation sources at different time-scales. At decadal time-scale, we find that the geocenter motion induced by geostrophic pressures within the fluid core acting at both the core-mantle and inner core boundaries is at a level of 0.1 mm/yr. At secular time-scale, geocenter motions induced by post-glacial rebound have been shown to be at the level of -0.4 - 0.2 mm/yr Finally, at geological time-scale, we quantify degree-one deformations induced by internal loads within the mantle. We use a simple model in which we assume that subducted plates sink vertically through the mantle, and in which upwelling domes are stable over the last 120 Ma. We found that, although the associated geocenter secular motion is one order of magnitude smaller than the one induced by post-glacial rebound, there is a significant discrepancy of about a few hundred meters between the centre of figure and the centre of mass of the Earth. Is it possible to detect, at the present time, with geodetic measurements, such a permanent translation?

  4. SU-E-J-01: 3D Fluoroscopic Image Estimation From Patient-Specific 4DCBCT-Based Motion Models

    SciTech Connect

    Dhou, S; Hurwitz, M; Lewis, J; Mishra, P

    2014-06-01

    Purpose: 3D motion modeling derived from 4DCT images, taken days or weeks before treatment, cannot reliably represent patient anatomy on the day of treatment. We develop a method to generate motion models based on 4DCBCT acquired at the time of treatment, and apply the model to estimate 3D time-varying images (referred to as 3D fluoroscopic images). Methods: Motion models are derived through deformable registration between each 4DCBCT phase, and principal component analysis (PCA) on the resulting displacement vector fields. 3D fluoroscopic images are estimated based on cone-beam projections simulating kV treatment imaging. PCA coefficients are optimized iteratively through comparison of these cone-beam projections and projections estimated based on the motion model. Digital phantoms reproducing ten patient motion trajectories, and a physical phantom with regular and irregular motion derived from measured patient trajectories, are used to evaluate the method in terms of tumor localization, and the global voxel intensity difference compared to ground truth. Results: Experiments included: 1) assuming no anatomic or positioning changes between 4DCT and treatment time; and 2) simulating positioning and tumor baseline shifts at the time of treatment compared to 4DCT acquisition. 4DCBCT were reconstructed from the anatomy as seen at treatment time. In case 1) the tumor localization error and the intensity differences in ten patient were smaller using 4DCT-based motion model, possible due to superior image quality. In case 2) the tumor localization error and intensity differences were 2.85 and 0.15 respectively, using 4DCT-based motion models, and 1.17 and 0.10 using 4DCBCT-based models. 4DCBCT performed better due to its ability to reproduce daily anatomical changes. Conclusion: The study showed an advantage of 4DCBCT-based motion models in the context of 3D fluoroscopic images estimation. Positioning and tumor baseline shift uncertainties were mitigated by the 4DCBCT

  5. From behavioural analyses to models of collective motion in fish schools

    PubMed Central

    Lopez, Ugo; Gautrais, Jacques; Couzin, Iain D.; Theraulaz, Guy

    2012-01-01

    Fish schooling is a phenomenon of long-lasting interest in ethology and ecology, widely spread across taxa and ecological contexts, and has attracted much interest from statistical physics and theoretical biology as a case of self-organized behaviour. One topic of intense interest is the search of specific behavioural mechanisms at stake at the individual level and from which the school properties emerges. This is fundamental for understanding how selective pressure acting at the individual level promotes adaptive properties of schools and in trying to disambiguate functional properties from non-adaptive epiphenomena. Decades of studies on collective motion by means of individual-based modelling have allowed a qualitative understanding of the self-organization processes leading to collective properties at school level, and provided an insight into the behavioural mechanisms that result in coordinated motion. Here, we emphasize a set of paradigmatic modelling assumptions whose validity remains unclear, both from a behavioural point of view and in terms of quantitative agreement between model outcome and empirical data. We advocate for a specific and biologically oriented re-examination of these assumptions through experimental-based behavioural analysis and modelling. PMID:24312723

  6. Computational modeling and analysis for left ventricle motion using CT/Echo image fusion

    NASA Astrophysics Data System (ADS)

    Kim, Ji-Yeon; Kang, Nahyup; Lee, Hyoung-Euk; Kim, James D. K.

    2014-03-01

    In order to diagnose heart disease such as myocardial infarction, 2D strain through the speckle tracking echocardiography (STE) or the tagged MRI is often used. However out-of-plane strain measurement using STE or tagged MRI is inaccurate. Therefore, strain for whole organ which are analyzed by simulation of 3D cardiac model can be applied in clinical diagnosis. To simulate cardiac contraction in a cycle, cardiac physical properties should be reflected in cardiac model. The myocardial wall in left ventricle is represented as a transversely orthotropic hyperelastic material, with the fiber orientation varying sequentially from the epicardial surface, through about 0° at the midwall, to the endocardial surface. A time-varying elastance model is simulated to contract myocardial fiber, and physiological intraventricular systolic pressure curves are employed for the cardiac dynamics simulation in a cycle. And an exact description of the cardiac motion should be acquired in order that essential boundary conditions for cardiac simulation are obtained effectively. Real time cardiac motion can be acquired by using echocardiography and exact cardiac geometrical 3D model can be reconstructed using 3D CT data. In this research, image fusion technology from CT and echocardiography is employed in order to consider patient-specific left ventricle movement. Finally, longitudinal strain from speckle tracking echocardiography which is known to fit actual left ventricle deformation relatively well is used to verify these results.

  7. Predicting muscle activation patterns from motion and anatomy: modelling the skull of Sphenodon (Diapsida: Rhynchocephalia)

    PubMed Central

    Curtis, Neil; Jones, Marc E. H.; Evans, Susan E.; Shi, JunFen; O'Higgins, Paul; Fagan, Michael J.

    2010-01-01

    The relationship between skull shape and the forces generated during feeding is currently under widespread scrutiny and increasingly involves the use of computer simulations such as finite element analysis. The computer models used to represent skulls are often based on computed tomography data and thus are structurally accurate; however, correctly representing muscular loading during food reduction remains a major problem. Here, we present a novel approach for predicting the forces and activation patterns of muscles and muscle groups based on their known anatomical orientation (line of action). The work was carried out for the lizard-like reptile Sphenodon (Rhynchocephalia) using a sophisticated computer-based model and multi-body dynamics analysis. The model suggests that specific muscle groups control specific motions, and that during certain times in the bite cycle some muscles are highly active whereas others are inactive. The predictions of muscle activity closely correspond to data previously recorded from live Sphenodon using electromyography. Apparent exceptions can be explained by variations in food resistance, food size, food position and lower jaw motions. This approach shows considerable promise in advancing detailed functional models of food acquisition and reduction, and for use in other musculoskeletal systems where no experimental determination of muscle activity is possible, such as in rare, endangered or extinct species. PMID:19474084

  8. THE SIMULATION OF FINE SCALE NOCTURNAL BOUNDARY LAYER MOTIONS WITH A MESO-SCALE ATMOSPHERIC MODEL

    SciTech Connect

    Werth, D.; Kurzeja, R.; Parker, M.

    2009-04-02

    A field project over the Atmospheric Radiation Measurement-Clouds and Radiation Testbed (ARM-CART) site during a period of several nights in September, 2007 was conducted to explore the evolution of the low-level jet (LLJ). Data was collected from a tower and a sodar and analyzed for turbulent behavior. To study the full range of nocturnal boundary layer (NBL) behavior, the Regional Atmospheric Modeling System (RAMS) was used to simulate the ARM-CART NBL field experiment and validated against the data collected from the site. This model was run at high resolution, and is ideal for calculating the interactions among the various motions within the boundary layer and their influence on the surface. The model reproduces adequately the synoptic situation and the formation and dissolution cycles of the low-level jet, although it suffers from insufficient cloud production and excessive nocturnal cooling. The authors suggest that observed heat flux data may further improve the realism of the simulations both in the cloud formation and in the jet characteristics. In a higher resolution simulation, the NBL experiences motion on a range of timescales as revealed by a wavelet analysis, and these are affected by the presence of the LLJ. The model can therefore be used to provide information on activity throughout the depth of the NBL.

  9. Research on the modeling of the missile's disturbance motion and the initial control point optimization

    NASA Astrophysics Data System (ADS)

    Guo, Jie; Zhu, Dalin; Tang, Shengjing

    2012-11-01

    The initial trajectory design of the missile is an important part of the overall design, but often a tedious calculation and analysis process due to the large dimension nonlinear differential equations and the traditional statistical analysis methods. To improve the traditional design methods, a robust optimization concept and method are introduced in this paper to deal with the determination of the initial control point. First, the Gaussian Radial Basis Network is adopted to establish the approximate model of the missile's disturbance motion based on the disturbance motion and disturbance factors analysis. Then, a direct analytical relationship between the disturbance input and statistical results is deduced on the basis of Gaussian Radial Basis Network model. Subsequently, a robust optimization model is established aiming at the initial control point design problem and the niche Pareto genetic algorithm for multi-objective optimization is adopted to solve this optimization model. An integral design example is give at last and the simulation results have verified the validity of this method.

  10. Nonlinear state-space modeling of human motion using 2-D marker observations.

    PubMed

    Vartiainen, Paavo; Bragge, Timo; Arokoski, Jari P; Karjalainen, Pasi A

    2014-07-01

    A novel method for the estimation of human kinematics, based on state-space modeling, is proposed. The state consists of the positions, orientations, velocities, and accelerations of an articulated model. Estimation is performed using the unscented Kalman filter (UKF) algorithm with a fixed-interval smoother. Impulsive acceleration at floor contact of the foot is estimated by implementing a contact constraint in the UKF evolution model. The constraint inserts an acceleration impulse into the model state. The estimation method was applied to marker-based motion analysis in a motion laboratory. Validation measurements were performed with a rigid test device and with human gait. A triaxial accelerometer was used to evaluate acceleration estimates. Comparison between the proposed method and the extended Kalman smoother showed a clear difference in the quality of estimates during impulsive accelerations. The proposed approach enables estimation of human kinematics during both continuous and transient accelerations. The approach provides a novel way of estimating acceleration at foot initial contact, and thus enables more accurate evaluation of loading from the beginning of the floor contact. PMID:24760898

  11. Investigating motion and stability of particles in flows using numerical models

    NASA Astrophysics Data System (ADS)

    Khurana, Nidhi

    The phenomenon of transport of particles in a fluid is ubiquitous in nature and a detailed understanding of its mechanism continues to remain a fundamental question for physicists. In this thesis, we use numerical methods to study the dynamics and stability of particles advected in flows. First, we investigate the dynamics of a single, motile particle advected in a two-dimensional chaotic flow. The particle can be either spherical or ellipsoidal. Particle activity is modeled as a constant intrinsic swimming velocity and stochastic fluctuations in both the translational and rotational motions are also taken into account. Our results indicate that interaction of swimming with flow structures causes a reduction in long-term transport at low speeds. Swimmers can get trapped at the transport barriers of the flow. We show that elongated swimmers respond more strongly to the dynamical structures of the flow field. At low speeds, their macroscopic transport is reduced even further than in the case of spherical swimmers. However, at high speeds these elongated swimmers tend to get attracted to the stable manifolds of hyperbolic fixed points, leading to increased transport. We then investigate the collective dynamics of a system of particles. The particles may interact both with each other and with the background flow. We focus on two different cases. In the fist case, we examine the stability of aggregation models in a turbulent-like flow. We use a simple aggregation model in which a point-like particle moves with a constant intrinsic speed while its velocity vector is reoriented according to the average direction of motion of its neighbors. We generate a strongly fluctuating, spatially correlated background flow using Kinematic Simulation, and show that flocks are highly sensitive to this background flow and break into smaller clusters. Our results indicate that such environmental perturbations must be taken into account for models which aim to capture the collective

  12. AQM router design for TCP network via input constrained fuzzy control of time-delay affine Takagi-Sugeno fuzzy models

    NASA Astrophysics Data System (ADS)

    Chang, Wen-Jer; Meng, Yu-Teh; Tsai, Kuo-Hui

    2012-12-01

    In this article, Takagi-Sugeno (T-S) fuzzy control theory is proposed as a key tool to design an effective active queue management (AQM) router for the transmission control protocol (TCP) networks. The probability control of packet marking in the TCP networks is characterised by an input constrained control problem in this article. By modelling the TCP network into a time-delay affine T-S fuzzy model, an input constrained fuzzy control methodology is developed in this article to serve the AQM router design. The proposed fuzzy control approach, which is developed based on the parallel distributed compensation technique, can provide smaller probability of dropping packets than previous AQM design schemes. Lastly, a numerical simulation is provided to illustrate the usefulness and effectiveness of the proposed design approach.

  13. A Little Knowledge of Ground Motion: Explaining 3-D Physics-Based Modeling to Engineers

    NASA Astrophysics Data System (ADS)

    Porter, K.

    2014-12-01

    Users of earthquake planning scenarios require the ground-motion map to be credible enough to justify costly planning efforts, but not all ground-motion maps are right for all uses. There are two common ways to create a map of ground motion for a hypothetical earthquake. One approach is to map the median shaking estimated by empirical attenuation relationships. The other uses 3-D physics-based modeling, in which one analyzes a mathematical model of the earth's crust near the fault rupture and calculates the generation and propagation of seismic waves from source to ground surface by first principles. The two approaches produce different-looking maps. The more-familiar median maps smooth out variability and correlation. Using them in a planning scenario can lead to a systematic underestimation of damage and loss, and could leave a community underprepared for realistic shaking. The 3-D maps show variability, including some very high values that can disconcert non-scientists. So when the USGS Science Application for Risk Reduction's (SAFRR) Haywired scenario project selected 3-D maps, it was necessary to explain to scenario users—especially engineers who often use median maps—the differences, advantages, and disadvantages of the two approaches. We used authority, empirical evidence, and theory to support our choice. We prefaced our explanation with SAFRR's policy of using the best available earth science, and cited the credentials of the maps' developers and the reputation of the journal in which they published the maps. We cited recorded examples from past earthquakes of extreme ground motions that are like those in the scenario map. We explained the maps on theoretical grounds as well, explaining well established causes of variability: directivity, basin effects, and source parameters. The largest mapped motions relate to potentially unfamiliar extreme-value theory, so we used analogies to human longevity and the average age of the oldest person in samples of

  14. Ground-motion modeling of the 1906 San Francisco Earthquake, part II: Ground-motion estimates for the 1906 earthquake and scenario events

    USGS Publications Warehouse

    Aagaard, B.T.; Brocher, T.M.; Dolenc, D.; Dreger, D.; Graves, R.W.; Harmsen, S.; Hartzell, S.; Larsen, S.; McCandless, K.; Nilsson, S.; Petersson, N.A.; Rodgers, A.; Sjogreen, B.; Zoback, M.L.

    2008-01-01

    We estimate the ground motions produce by the 1906 San Francisco earthquake making use of the recently developed Song et al. (2008) source model that combines the available geodetic and seismic observations and recently constructed 3D geologic and seismic velocity models. Our estimates of the ground motions for the 1906 earthquake are consistent across five ground-motion modeling groups employing different wave propagation codes and simulation domains. The simulations successfully reproduce the main features of the Boatwright and Bundock (2005) ShakeMap, but tend to over predict the intensity of shaking by 0.1-0.5 modified Mercalli intensity (MMI) units. Velocity waveforms at sites throughout the San Francisco Bay Area exhibit characteristics consistent with rupture directivity, local geologic conditions (e.g., sedimentary basins), and the large size of the event (e.g., durations of strong shaking lasting tens of seconds). We also compute ground motions for seven hypothetical scenarios rupturing the same extent of the northern San Andreas fault, considering three additional hypocenters and an additional, random distribution of slip. Rupture directivity exerts the strongest influence on the variations in shaking, although sedimentary basins do consistently contribute to the response in some locations, such as Santa Rosa, Livermore, and San Jose. These scenarios suggest that future large earthquakes on the northern San Andreas fault may subject the current San Francisco Bay urban area to stronger shaking than a repeat of the 1906 earthquake. Ruptures propagating southward towards San Francisco appear to expose more of the urban area to a given intensity level than do ruptures propagating northward.

  15. Structure-based model profiles affinity constant of drugs with hPEPT1 for rapid virtual screening of hPEPT1's substrate.

    PubMed

    Sun, L; Meng, S

    2016-08-01

    The human proton-coupled peptide transporter (hPEPT1) with broad substrates is an important route for improving the pharmacokinetic performance of drugs. Thus, it is essential to predict the affinity constant between drug molecule and hPEPT1 for rapid virtual screening of hPEPT1's substrate during lead optimization, candidate selection and hPEPT1 prodrug design. Here, a structure-based in silico model for 114 compounds was constructed based on eight structural parameters. This model was built by the multiple linear regression method and satisfied all the prerequisites of the regression models. For the entire data set, the r(2) and adjusted r(2) values were 0.74 and 0.72, respectively. Then, this model was used to perform substrate/non-substrate classification. For 29 drugs from DrugBank database, all were correctly classified as substrates of hPEPT1. This model was also used to perform substrate/non-substrate classification for 18 drugs and their prodrugs; this QSAR model also can distinguish between the substrate and non-substrate. In conclusion, the QSAR model in this paper was validated by a large external data set, and all results indicated that the developed model was robust, stable, and can be used for rapid virtual screening of hPEPT1's substrate in the early stage of drug discovery. PMID:27586363

  16. Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI.

    PubMed

    Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

    2015-01-01

    Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. PMID:25157446

  17. Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI

    PubMed Central

    Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

    2016-01-01

    Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. PMID:25157446

  18. Heliospheric Termination Shock Motion Due to Fluctuations in the Solar Wind Upstream Conditions: Spherically Symmetric Model

    NASA Technical Reports Server (NTRS)

    Ratkiewicz, R.; Barnes, A.; Molvik, G. A.; Spreiter, J. R.; Stahara, S. S.; Cuzzi, Jeffery N. (Technical Monitor)

    1995-01-01

    Large-scale fluctuations in the solar wind plasma upstream of the heliospheric termination shock (TS) will cause inward and outward motions of the shock. Using numerical techniques, we extend an earlier strictly one-dimensional (planar) analytic gas dynamic model to spherical symmetry to investigate the features of global behavior of shock motion. Our starting point is to establish a steady numerical solution of the gasdynamic equations describing the interaction between the solar wind and the interstellar medium. We then introduce disturbances of the solar wind dynamic pressure at an inner boundary, and follow the subsequent evolution of the system, especially the motion of the termination shock. Our model solves spherically symmetric gasdynamic equations as an initial-boundary value problem. The equations in conservative form are solved using a fully implicit Total Variation Diminishing (TVD) upwind scheme with Roe-type Riemann solver. Boundary conditions are given by the solar wind parameters on an inner spherical boundary, where they are allowed to vary with time for unsteady calculations, and by a constant pressure (roughly simulating the effect of the local interstellar medium) on an outer boundary. We find that immediately after the interaction, the shock moves with speeds given by the earlier analogous analytic models. However, as the termination shock propagates it begins to slow down, seeking a new equilibrium position. In addition, the disturbance transmitted through the TS, either a shock or rarefaction wave, will encounter the heliopause boundary and be reflected back. The reflected signal will encounter the TS, causing it to oscillate. The phenomenon may be repeated for a number of reflections, resulting in a "ringing" of the outer heliosphere.

  19. Using an external surrogate for predictor model training in real-time motion management of lung tumors

    SciTech Connect

    Rottmann, Joerg; Berbeco, Ross

    2014-12-15

    Purpose: Precise prediction of respiratory motion is a prerequisite for real-time motion compensation techniques such as beam, dynamic couch, or dynamic multileaf collimator tracking. Collection of tumor motion data to train the prediction model is required for most algorithms. To avoid exposure of patients to additional dose from imaging during this procedure, the feasibility of training a linear respiratory motion prediction model with an external surrogate signal is investigated and its performance benchmarked against training the model with tumor positions directly. Methods: The authors implement a lung tumor motion prediction algorithm based on linear ridge regression that is suitable to overcome system latencies up to about 300 ms. Its performance is investigated on a data set of 91 patient breathing trajectories recorded from fiducial marker tracking during radiotherapy delivery to the lung of ten patients. The expected 3D geometric error is quantified as a function of predictor lookahead time, signal sampling frequency and history vector length. Additionally, adaptive model retraining is evaluated, i.e., repeatedly updating the prediction model after initial training. Training length for this is gradually increased with incoming (internal) data availability. To assess practical feasibility model calculation times as well as various minimum data lengths for retraining are evaluated. Relative performance of model training with external surrogate motion data versus tumor motion data is evaluated. However, an internal–external motion correlation model is not utilized, i.e., prediction is solely driven by internal motion in both cases. Results: Similar prediction performance was achieved for training the model with external surrogate data versus internal (tumor motion) data. Adaptive model retraining can substantially boost performance in the case of external surrogate training while it has little impact for training with internal motion data. A minimum

  20. Dynamic modeling and sensitivity analysis of dAFM in the transient and steady state motions.

    PubMed

    Payam, Amir Farokh

    2016-10-01

    In this paper, based on the slow time varying function theory, dynamical equations for the amplitude and phase of the dynamic atomic force microscope are derived. Then, the sensitivity of the amplitude and phase to the dissipative and conservative parts of interaction force is investigated. The most advantage of this dynamical model is the ability to simulate and analysis the dynamics behavior of amplitude and phase of the AFM tip motion not only in the steady state but also in the transient regime. Using numerical analysis the transient and steady state behavior of amplitude and phase is studied and the sensitivity of amplitude and phase to the interaction force is analyzed. PMID:27448201

  1. Modelling surface motion and spall at the Nevada Test Site. Los Alamos Source Region Project

    SciTech Connect

    App, F.N.; Brunish, W.M.

    1992-01-01

    Spallation of the ground surface accompanies all underground nuclear explosions of significant yield. This report discusses computer modelling used to investigate the physical processes that govern spallation and the amplitude and wavelength of motion at the free surface under a variety of conditions. Four events are selected: MERLIN which was conducted in desert alluvium; HEARTS which was conducted in tuff beneath the water table in Yucca Flat; TOWANDA which was conducted beneath the water table on Pahute Mesa; and HOUSTON which was conducted above the water table in very dense rock and Pahute Mesa. These span the range of test environments for Los Alamos underground nuclear tests.

  2. Hamiltonian Formulation of the 5-D Kaluza-Klein Model and Test-Particle Motion

    NASA Astrophysics Data System (ADS)

    Lacquaniti, Valentino; Montani, Giovanni

    2008-09-01

    We examine the ADM reformulation of the 5-D KK model: the dimensional reduction is provided to commute with the ADM splitting and we show how the time component of the gauge vector is given by combination of the Lagrangian multipliers for the 5-D gravitational field. We consider 5D particles motion and after dimensional reduction the definition of charge is recovered within electrodynamic coupling. A time-varying fine structure constant is recognized because an extra scalar field is present in the 4-D theory.

  3. Mathematical Modeling of Mass Transfer in Laminar Motion of a Droplet in a Liquid Medium

    NASA Astrophysics Data System (ADS)

    Elizarov, D. V.; Elizarov, V. V.; Kamaliev, T. S.; D‧yakonov, S. G.

    2016-03-01

    Consideration is given to mathematical modeling of the process of nonstationary liquid-liquid extraction in apparatuses with free motion of a dispersed phase. Solutions of nonstationary equations of transfer of momentum and mass in the boundary layer on the droplet and inside the droplet near the phase boundary are given. Equations for calculation of the coefficients of mass transfer and concentration of the extracted component are obtained. A comparison is made of the calculated data and experimental results in extracting various liquid mixtures.

  4. Emergence of Collective Motion in a Model of Interacting Brownian Particles

    NASA Astrophysics Data System (ADS)

    Dossetti, Victor; Sevilla, Francisco J.

    2015-07-01

    By studying a system of Brownian particles that interact among themselves only through a local velocity-alignment force that does not affect their speed, we show that self-propulsion is not a necessary feature for the flocking transition to take place as long as underdamped particle dynamics can be guaranteed. Moreover, the system transits from stationary phases close to thermal equilibrium, with no net flux of particles, to far-from-equilibrium ones exhibiting collective motion, phase coexistence, long-range order, and giant number fluctuations, features typically associated with ordered phases of models where self-propelled particles with overdamped dynamics are considered.

  5. Emergence of Collective Motion in a Model of Interacting Brownian Particles.

    PubMed

    Dossetti, Victor; Sevilla, Francisco J

    2015-07-31

    By studying a system of Brownian particles that interact among themselves only through a local velocity-alignment force that does not affect their speed, we show that self-propulsion is not a necessary feature for the flocking transition to take place as long as underdamped particle dynamics can be guaranteed. Moreover, the system transits from stationary phases close to thermal equilibrium, with no net flux of particles, to far-from-equilibrium ones exhibiting collective motion, phase coexistence, long-range order, and giant number fluctuations, features typically associated with ordered phases of models where self-propelled particles with overdamped dynamics are considered. PMID:26274444

  6. Biomechanical model-based displacement estimation in micro-sensor motion capture

    NASA Astrophysics Data System (ADS)

    Meng, X. L.; Zhang, Z. Q.; Sun, S. Y.; Wu, J. K.; Wong, W. C.

    2012-05-01

    In micro-sensor motion capture systems, the estimation of the body displacement in the global coordinate system remains a challenge due to lack of external references. This paper proposes a self-contained displacement estimation method based on a human biomechanical model to track the position of walking subjects in the global coordinate system without any additional supporting infrastructures. The proposed approach makes use of the biomechanics of the lower body segments and the assumption that during walking there is always at least one foot in contact with the ground. The ground contact joint is detected based on walking gait characteristics and used as the external references of the human body. The relative positions of the other joints are obtained from hierarchical transformations based on the biomechanical model. Anatomical constraints are proposed to apply to some specific joints of the lower body to further improve the accuracy of the algorithm. Performance of the proposed algorithm is compared with an optical motion capture system. The method is also demonstrated in outdoor and indoor long distance walking scenarios. The experimental results demonstrate clearly that the biomechanical model improves the displacement accuracy within the proposed framework.

  7. Storage for free: a surprising property of a simple gain-control model of motion aftereffects.

    PubMed

    van de Grind, Wim A; van der Smagt, Maarten J; Verstraten, Frans A J

    2004-01-01

    If a motion aftereffect (MAE) for given adaptation conditions has a duration T s, and the eyes are closed after adaptation during a waiting period tw=T s before testing, an unexpected MAE of a 'residual' duration TrT s is experienced. This effect is called 'storage' and it is often quantified by a storage factor sigma=TrT/T, which can reach values up to about 0.7-0.8. The phenomenon and its name have invited explanations in terms of inhibition of recovery during darkness. We present a model based on the opposite idea, that an effective test stimulus quickens recovery relative to darkness or other ineffective test stimuli. The model is worked out in mathematical detail and proves to explain 'storage' data from the literature, on the static MAE (sMAE: an MAE experienced for static test stimuli). We also present results of a psychophysical experiment with moving random pixel arrays, quantifying storage phenomena both for the sMAE and the dynamic MAE (dMAE: an MAE experienced for a random dynamic noise test stimulus). Storage factors for the dMAE are lower than for the sMAE. Our model also gives an excellent description of these new data on storage of the dMAE. The term 'storage' might therefore be a misnomer. If an effective test stimulus influences all direction tuned motion sensors indiscriminately and thus speeds up equalization of gains, one gets the storage phenomenon for free. PMID:15208013

  8. Modeling of mesoscale flux-tube interchange motions in the inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Sazykin, Stanislav; Wolf, Richard Alan; Yang, Jian; Rocco Toffoletto, Frank

    2015-04-01

    Mesoscale flux-tube interchange motions associated with bursty bulk flows and dipolarization fronts play a significant role in particle transport from the plasma sheet into the inner magnetosphere. One of the challenges is to quantify the relative role of these processes compared to large-scale particle energization as part of global-scale convection. In this paper, we will describe latest progress in attempting quantitative modeling of flux-tube interchange processes using a high-resolution version of the Rice Convection Model (RCM) that includes effects of inertial drifts. Including effects of inertial drifts is necessary to allow oscillatory motion of flux tubes in inner magnetospheric models. We generalized the formulation of the RCM by making three simplifying assumptions: (i) the communication between the equatorial plane and ionosphere occurs either instantaneously or with a given time lag, (ii) the pressure is isotropic and therefore constant along field lines, and (iii) for purposes of calculating the effect of inertia, all of a flux tube's mass is assumed to be concentrated in the equatorial plane. We will present idealized numerical simulations of a depleted flux tube propagation in the magnetosphere, and quantify particle injection signatures. Our analysis of the simulations will include ionospheric electric fields and particle precipitation signatures of the flow channels associated with propagation of depleted flux tubes, and address the sensitivity of the results to the assumptions made in the inclusion of the inertia effects.

  9. Understanding Ground Motion in Las Vegas: Insights from Data Analysis and Two-Dimensional Modeling

    SciTech Connect

    Rodgers, A; Tkalcic, H; McCallen, D

    2004-02-05

    Seismic ground motions are amplified in low velocity sedimentary basins relative to adjacent sites on high velocity hard rock. We used historical recordings of NTS nuclear explosions and earthquake recordings in Las Vegas Valley to quantify frequency-dependent basin amplification using Standard Spectral Ratios. We show that amplifications, referred to as site response, can reach a factor of 10 in the frequency band 0.4-2.0 Hz. Band-averaged site response between 0.4-2.0 Hz is strongly correlated with basin depth. However, it is also well known that site response is related to shallow shear-wave velocity structure. We simulated low frequency (f<1Hz) ground motion and site response with two-dimensional elastic finite difference simulations. We demonstrate that physically plausible models of the shallow subsurface, including low velocity sedimentary structure, can predict relative amplification as well as some of the complexity in the observed waveforms. This study demonstrates that site response can be modeled without invoking complex and computationally expensive three-dimensional structural models.

  10. SU-E-J-150: Four-Dimensional Cone-Beam CT Algorithm by Extraction of Physical and Motion Parameter of Mobile Targets Retrospective to Image Reconstruction with Motion Modeling

    SciTech Connect

    Ali, I; Ahmad, S; Alsbou, N

    2015-06-15

    Purpose: To develop 4D-cone-beam CT (CBCT) algorithm by motion modeling that extracts actual length, CT numbers level and motion amplitude of a mobile target retrospective to image reconstruction by motion modeling. Methods: The algorithm used three measurable parameters: apparent length and blurred CT number distribution of a mobile target obtained from CBCT images to determine actual length, CT-number value of the stationary target, and motion amplitude. The predictions of this algorithm were tested with mobile targets that with different well-known sizes made from tissue-equivalent gel which was inserted into a thorax phantom. The phantom moved sinusoidally in one-direction to simulate respiratory motion using eight amplitudes ranging 0–20mm. Results: Using this 4D-CBCT algorithm, three unknown parameters were extracted that include: length of the target, CT number level, speed or motion amplitude for the mobile targets retrospective to image reconstruction. The motion algorithms solved for the three unknown parameters using measurable apparent length, CT number level and gradient for a well-defined mobile target obtained from CBCT images. The motion model agreed with measured apparent lengths which were dependent on the actual target length and motion amplitude. The gradient of the CT number distribution of the mobile target is dependent on the stationary CT number level, actual target length and motion amplitude. Motion frequency and phase did not affect the elongation and CT number distribution of the mobile target and could not be determined. Conclusion: A 4D-CBCT motion algorithm was developed to extract three parameters that include actual length, CT number level and motion amplitude or speed of mobile targets directly from reconstructed CBCT images without prior knowledge of the stationary target parameters. This algorithm provides alternative to 4D-CBCT without requirement to motion tracking and sorting of the images into different breathing phases

  11. Information Sharing Between Ground Motion Models from Different Regions via Dirichlet Process Priors

    NASA Astrophysics Data System (ADS)

    Hermkes, M.; Kuehn, N.; Riggelsen, C.; Vogel, K.

    2012-04-01

    In probabilistic seismic hazard analysis (PSHA) seismic ground motion data, induced by earthquakes, are collected at different geographical regions. Instead of building ground motion models, which estimates intensity parameters, e.g. peak ground acceleration or spectral acceleration, given earthquake and site related parameters, for each region individually, it is preferable to share information across the regions to increase the overall prediction performance. One of the most important methods to share information correlation between models is Hierarchical Bayesian modeling, where parameters of the region-specific models are coupled by a common prior. As a result of learning the parameters of the model and the hyperparameters of the common prior jointly, the function estimation of a specific region is affected by its own training data and by data from the other region related through the coupled prior. Generally, the common prior is specified in a parametric form with unknown hyperparameters. A drawback of such a prior by reason of its modality is that the relationship between all ground motion models are treated equally, but it is desirable that only similar models share information to permit negative transfer. To deal with these issues we propose a nonparametric hierarchical Bayesian model where the common prior is drawn from a Dirichlet Process (DP). Such a nonparametric prior has the ability to fit the model well with respect to the data without restriction about the functional form of the prior distribution. Furthermore, the employed DP prior induces a partition of region-specific models, so that models within each cluster share the same parameterization. First of all, we present a linear regression model, for which the weights of the covariates and the model variance are drawn from a DP prior. As base distribution for the DP we have chosen a normal inverse-Gamma prior which is the natural conjugate prior to the normal likelihood of the applied regression

  12. Tumor Tracking Method Based on a Deformable 4D CT Breathing Motion Model Driven by an External Surface Surrogate

    SciTech Connect

    Fassi, Aurora; Schaerer, Joël; Fernandes, Mathieu; Riboldi, Marco; Sarrut, David; Baroni, Guido

    2014-01-01

    Purpose: To develop a tumor tracking method based on a surrogate-driven motion model, which provides noninvasive dynamic localization of extracranial targets for the compensation of respiration-induced intrafraction motion in high-precision radiation therapy. Methods and Materials: The proposed approach is based on a patient-specific breathing motion model, derived a priori from 4-dimensional planning computed tomography (CT) images. Model parameters (respiratory baseline, amplitude, and phase) are retrieved and updated at each treatment fraction according to in-room radiography acquisition and optical surface imaging. The baseline parameter is adapted to the interfraction variations obtained from the daily cone beam (CB) CT scan. The respiratory amplitude and phase are extracted from an external breathing surrogate, estimated from the displacement of the patient thoracoabdominal surface, acquired with a noninvasive surface imaging device. The developed method was tested on a database of 7 lung cancer patients, including the synchronized information on internal and external respiratory motion during a CBCT scan. Results: About 30 seconds of simultaneous acquisition of CBCT and optical surface images were analyzed for each patient. The tumor trajectories identified in CBCT projections were used as reference and compared with the target trajectories estimated from surface displacement with the a priori motion model. The resulting absolute differences between the reference and estimated tumor motion along the 2 image dimensions ranged between 0.7 and 2.4 mm; the measured phase shifts did not exceed 7% of the breathing cycle length. Conclusions: We investigated a tumor tracking method that integrates breathing motion information provided by the 4-dimensional planning CT with surface imaging at the time of treatment, representing an alternative approach to point-based external–internal correlation models. Although an in-room radiograph-based assessment of the

  13. A No-Net-Rotation Model of Present-Day Surface Motions

    NASA Astrophysics Data System (ADS)

    Kreemer, C.; Holt, W. E.

    2001-12-01

    A significant portion of the Earth's surface consists of zones of diffuse deformation. The interior regions of these diffuse zones of deformation move at distinctly different velocities from that of adjacent plates, and, because of their complexities, have been ignored in previous no-net-rotation (NNR) models (e.g., NNR-NUVEL1A). We have calculated a new NNR model from a continuous velocity field that incorporates both rigid plate motion and velocity gradients within plate boundary zones. The velocity field is obtained through a bi-cubic Bessel interpolation of almost 3000 geodetic velocities and strain rates inferred from Quaternary faults. The geodetic velocities are taken from about 50 different, mainly published, studies. For each study we have not adopted the original reference frame. Instead, we have solved for a rigid body rotation for each study that rotate the vectors of each study into a model reference frame in the process of satisfying a least-squares fit between model and observed velocities and model and observed strain rates. When compared with earlier NNR models we find significantly different angular velocities for many plates in our model. Differences between the NNR model presented here and earlier NNR models can be attributed to both the effect of including velocity gradients in diffuse plate boundary zones, as well as actual differences between geodetically derived, present-day, surface motions and geologic estimates. We find that for the Indian, Arabian, Nazca, Cocos, Philippine Sea, and the Caribbean plate the differences between our model and the NNR-NUVEL1A model are mainly due to differences between geodetic and geologic plate velocities. For the Eurasian plate the discrepancy that we find between our result and NNR-NUVEL1A model can not only be ascribed to the difference between geodetic and geologic velocities, but also to the significant effect of including plate boundary zones. The significantly different NNR rotation vectors that we

  14. Active and passive Brownian motion of charged particles in two-dimensional plasma models

    SciTech Connect

    Dunkel, Joern; Ebeling, Werner; Trigger, Sergey A.

    2004-10-01

    The dynamics of charged Coulomb grains in a plasma is numerically and analytically investigated. Analogous to recent experiments, it is assumed that the grains are trapped in an external parabolic field. Our simulations are based on a Langevin model, where the grain-plasma interaction is realized by a velocity-dependent friction coefficient and a velocity-independent diffusion coefficient. In addition to the ordinary case of positive (passive) friction between grains and plasma, we also discuss the effects of negative (active) friction. The latter case seems particularly interesting, since recent analytical calculations have shown that friction coefficients with negative parts may appear in some models of ion absorption by grains as well as in models of ion-grain scattering. Such negative friction may cause active Brownian motions of the grains. As our computer simulations show, the influence of negative friction leads to the formation of various stationary modes (rotations, oscillations), which, to some extent, can also be estimated analytically.

  15. Modelling the 3D morphology and proper motions of the planetary nebula NGC 6302

    NASA Astrophysics Data System (ADS)

    Uscanga, L.; Velázquez, P. F.; Esquivel, A.; Raga, A. C.; Boumis, P.; Cantó, J.

    2014-08-01

    We present 3D hydrodynamical simulations of an isotropic fast wind interacting with a previously ejected toroidally shaped slow wind in order to model both the observed morphology and the kinematics of the planetary nebula (PN) NGC 6302. This source, also known as the Butterfly nebula, presents one of the most complex morphologies ever observed in PNe. From our numerical simulations, we have obtained an intensity map for the Hα emission to make a comparison with the Hubble Space Telescope (HST) observations of this object. We have also carried out a proper motion (PM) study from our numerical results, in order to compare with previous observational studies. We have found that the two interacting stellar wind model reproduce well the morphology of NGC 6302, and while the PMs in the models are similar to the observations, our results suggest that an acceleration mechanism is needed to explain the Hubble-type expansion found in HST observations.

  16. The benefits of extended plate motion history in mantle circulation models

    NASA Astrophysics Data System (ADS)

    Webb, Peter; Davies, Huw; Davies, Rhodri; Hochard, Cyril; Stampfli, Gerard

    2010-05-01

    Mantle Circulation Models (MCMs) are mantle convection simulations conditioned with plate motion history. Due to difficulties in reconstructing plate motions beyond ≈ 120 Ma, MCMs often only incorporate the most recent 120 Myr of plate tectonic evolution. We find that such models are strongly influenced by initial conditions. The development of a new series of tectonic reconstructions extending back to the Triassic (230 Ma) and including careful reconstruction of the oceanic parts of the plates (modified from Stampfli and Borel, 2004, Stampfli et al. 2008 and references therein) should prove to be of huge importance to MCMs. In this study we present a comparison between the traditionally used 120 Myr and the latest 230 Myr plate motion histories. We use the three-dimensional spherical mantle convection code TERRA (Bunge et al., 2003) to simulate convection at Earth like vigour. Here we apply the plate motion history as a surface velocity boundary condition to drive the internal convection of an already well-mixed system. The forward models from a chosen starting point to present day yield information on mantle temperature (as well as pressure, velocity and material properties) throughout the volume. One of the ways to validate our results is to compare these with tomographic models. Seismic tomography provides us with a snapshot of Earth's mantle at present day. Assuming that the mantle is driven largely by thermal convection, we can assume that the seismically fast regions are associated with cooler, denser material. The most significant of these can be interpreted as remnants of subducted slabs (Hafkenscheid et al 2006, van der Meer et al. 2010). We convert the temperatures predicted by the MCM to seismic velocities using the latest techniques (e.g. Cobden et al., 2008) and compare the calculated velocities to a range of seismic tomography models (both P and S wave). This way we can examine the validity of the surface velocity boundary condition and identify

  17. Coevolutionary motion and swarming in a niche space model of ecological species interactions

    NASA Astrophysics Data System (ADS)

    Dommar, C. J.; Ryabov, A.; Blasius, B.

    2008-04-01

    Organisms are involved in coevolutionary relationships with their competitors, predators, preys and parasites. In this context, we present a simple model for the co-evolution of species in a common niche space, where the fitness of each species is defined via the network of interactions with all other species. In our model, the sign and type of the pairwise interactions (being either beneficial, harmful or neutral) is given by a pre-determined community matrix, while the interaction strength depends on the niche-overlap, i.e. the pairwise distances between species in niche space. The evolutionary process drives the species toward the places with the higher local fitness along the fitness gradient. This gives rise to a dynamic fitness landscape, since the evolutionary motion of a single species can change the landscape of the others (known as the Red Queen Principle). In the simplest case of only two-species we observe either a convergence/divergence equilibrium or a coevolutionary arms race. For a larger number of species our analysis concentrates on an antisymmetric interaction matrix, where we observe a large range of dynamic behaviour, from oscillations, quasiperiodic to chaotic dynamics. In dependence of the value of a first integral of motion we observe either quasiperiodic motion around a central region in niche space or unbounded movement, characterised by chaotic scattering of species pairs. Finally, in a linear food-chain we observe complex swarming behaviour in which the swarm moves as a whole only if the chain consists of an even number of species. Our results could be an important contribution to evolutionary niche theory.

  18. Dynamic models of interseismic deformation and stress transfer from plate motion to continental transform faults

    NASA Astrophysics Data System (ADS)

    Takeuchi, Christopher S.; Fialko, Yuri

    2012-05-01

    We present numerical models of earthquake cycles on a strike-slip fault that incorporate laboratory-derived power law rheologies with Arrhenius temperature dependence, viscous dissipation, conductive heat transfer, and far-field loading due to relative plate motion. We use these models to explore the evolution of stress, strain, and thermal regime on "geologic" timescales (˜106-107 years), as well as on timescales of the order of the earthquake recurrence (˜102 years). Strain localization in the viscoelastic medium results from thermomechanical coupling and power law dependence of strain rate on stress. For conditions corresponding to the San Andreas fault (SAF), the predicted width of the shear zone in the lower crust is ˜3-5 km; this shear zone accommodates more than 50% of the far-field plate motion. Coupled thermomechanical models predict a single-layer lithosphere in case of "dry" composition of the lower crust and upper mantle, and a "jelly sandwich" lithosphere in case of "wet" composition. Deviatoric stress in the lithosphere in our models is relatively insensitive to the water content, the far-field loading rate, and the fault strength and is of the order of 102 MPa. Thermomechanical coupling gives rise to an inverse correlation between the fault slip rate and the ductile strength of the lithosphere. We show that our models are broadly consistent with geodetic and heat flow constrains from the SAF in Northern California. Models suggest that the regionally elevated heat flow around the SAF may be at least in part due to viscous dissipation in the ductile part of the lithosphere.

  19. Ionization Energies, Electron Affinities, and Polarization Energies of Organic Molecular Crystals: Quantitative Estimations from a Polarizable Continuum Model (PCM)-Tuned Range-Separated Density Functional Approach.

    PubMed

    Sun, Haitao; Ryno, Sean; Zhong, Cheng; Ravva, Mahesh Kumar; Sun, Zhenrong; Körzdörfer, Thomas; Brédas, Jean-Luc

    2016-06-14

    We propose a new methodology for the first-principles description of the electronic properties relevant for charge transport in organic molecular crystals. This methodology, which is based on the combination of a nonempirical, optimally tuned range-separated hybrid functional with the polarizable continuum model, is applied to a series of eight representative molecular semiconductor crystals. We show that it provides ionization energies, electron affinities, and transport gaps in very good agreement with experimental values, as well as with the results of many-body perturbation theory within the GW approximation at a fraction of the computational costs. Hence, this approach represents an easily applicable and computationally efficient tool to estimate the gas-to-crystal phase shifts of the frontier-orbital quasiparticle energies in organic electronic materials. PMID:27183355

  20. Comparison of hydrological signal in polar motion excitation with those based on the FGOALS-g2 climate model

    NASA Astrophysics Data System (ADS)

    Wińska, Małgorzata; Nastula, Jolanta; Salstein, David

    2016-04-01

    Our investigations are focused on the influence of different land hydrosphere surface parameters (precipitation, evaporation, total runoff, soil moisture, accumulated snow) on polar motion excitation functions at seasonal and nonseasonal timescales. Here these different variables are obtained from the Flexible Global Ocean-Atmosphere-Land System Model, Grid point Version 2 (FGOALS-g2), which is a climate model from the fifth phase of the Coupled Model Intercomparison Project (CMIP5); with CMIP5 being composed of separate component models of the atmosphere, ocean, sea ice, and land surface. In this study Terrestrial Water Storage TWS changes were determined as: differences between the precipitation, evaporation and total surface runoff content, and as the total soil moisture content being a sum of soil moisture and snowfall flux changes. We compare the model-based data with those from estimates of the Equivalent Water Thickness determined by GRACE satellite observations from the Center for Space Research (CSR). The transfer of angular momentum from global geophysical fluids to the solid Earth is described by the equatorial components χ1 and χ2 of the polar motion excitation functions. Observationally, these so-called geodetic excitation functions of polar motion can be determined on the basis of the equations of motion by using observed x, y components of the pole. The second-degree, first-order coefficients of the Earth gravity field are proportional to variations of the equatorial component χ1, χ2 of the series of the gravimetric excitation function of polar motion. This gravimetric function can be compared with the mass term of geodetic excitation of polar motion. Our analysis comprises (1) determinations and comparisons of regional patterns of hydrological excitation functions of polar motion, and (2) comparison of the global hydrological function determined from the FGOALS-g2 and GRACE data with a hydrological signal in the geodetic excitation function of

  1. Enhanced Modeling of First-Order Plant Equations of Motion for Aeroelastic and Aeroservoelastic Applications

    NASA Technical Reports Server (NTRS)

    Pototzky, Anthony S.

    2010-01-01

    A methodology is described for generating first-order plant equations of motion for aeroelastic and aeroservoelastic applications. The description begins with the process of generating data files representing specialized mode-shapes, such as rigid-body and control surface modes, using both PATRAN and NASTRAN analysis. NASTRAN executes the 146 solution sequence using numerous Direct Matrix Abstraction Program (DMAP) calls to import the mode-shape files and to perform the aeroelastic response analysis. The aeroelastic response analysis calculates and extracts structural frequencies, generalized masses, frequency-dependent generalized aerodynamic force (GAF) coefficients, sensor deflections and load coefficients data as text-formatted data files. The data files are then re-sequenced and re-formatted using a custom written FORTRAN program. The text-formatted data files are stored and coefficients for s-plane equations are fitted to the frequency-dependent GAF coefficients using two Interactions of Structures, Aerodynamics and Controls (ISAC) programs. With tabular files from stored data created by ISAC, MATLAB generates the first-order aeroservoelastic plant equations of motion. These equations include control-surface actuator, turbulence, sensor and load modeling. Altitude varying root-locus plot and PSD plot results for a model of the F-18 aircraft are presented to demonstrate the capability.

  2. Model of J_2 perturbed satellite relative motion with time-varying differential drag

    NASA Astrophysics Data System (ADS)

    Gaias, Gabriella; Ardaens, Jean-Sébastien; Montenbruck, Oliver

    2015-12-01

    This work revisits the modeling of the relative motion between satellites flying in near-circular low-Earth-orbits. The motion is described through relative orbital elements and both Earth's oblateness and differential drag perturbations are addressed. With respect to the former formulation, the description of the J_2 effect is improved by including also the changes that this perturbation produces in both relative mean longitude and relative inclination vector during a drifting phase, when a non-vanishing relative semi-major axis is required. The second major improvement consists in a general empirical formulation to include the mean effects produced by non-conservative perturbations, such as the differential aerodynamic drag acceleration. As a result, in addition to the well-known actions on the relative semi-major axis and on the mean along-track separation, the model is able to reflect the mean variation of the relative eccentricity vector due to atmospheric density oscillations produced by day and night trans