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
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.
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.
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…
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.
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
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
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
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.
Affine group formulation of the Standard Model coupled to gravity
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.
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
Interactions between PTB RRMs induce slow motions and increase RNA binding affinity
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
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,…
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
Molecular modeling of the affinity chromatography of monoclonal antibodies.
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
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
Robust Spectral Clustering Using Statistical Sub-Graph Affinity Model
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
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.
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.
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.
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.
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.
LCD motion blur: modeling, analysis, and algorithm.
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
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'…
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.
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
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.
Phase informed model for motion and susceptibility.
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
PREDICTING ER BINDING AFFINITY FOR EDC RANKING AND PRIORITIZATION: MODEL II
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...
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
Mathematical model accurately predicts protein release from an affinity-based delivery system.
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
Locust Collective Motion and Its Modeling.
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
Locust Collective Motion and Its Modeling
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
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.
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.
Ciliary motion modeling, and dynamic multicilia interactions
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
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.
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.
Mathematical modelling of animate and intentional motion.
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
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.
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.
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.
Joint PET-MR respiratory motion models for clinical PET motion correction.
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
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).
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.
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…
Atomic Models for Motional Stark Effects Diagnostics
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.
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.
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
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
Head Motion Modeling for Human Behavior Analysis in Dyadic Interaction
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
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.
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
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.
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.
Modeling Local Interactions during the Motion of Cyanobacteria
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
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.
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.
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.
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.
A depictive neural model for the representation of motion verbs.
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
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)
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
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.
A simple model for strong ground motions and response spectra
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.
Joint model of motion and anatomy for PET image reconstruction
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.
Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.
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
Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity
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
Ground motion data for International Collider models
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.
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.
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
A true polar wander model for Neoproterozoic plate motions
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.
A deformation of quantum affine algebra in squashed Wess-Zumino-Novikov-Witten models
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.
Probabilistic approach for predicting periodic orbits in piecewise affine differential models.
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
Modelling the binding affinity of steroids to zebrafish sex hormone-binding globulin.
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
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.
Constants of motion of the four-particle Calogero model
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.
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.
Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers.
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
Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers
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
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
Neurons compute internal models of the physical laws of motion.
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
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…
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…
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.
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.
Spherical shell model description of rotational motion
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.
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…
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.
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.
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.
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…
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
Elements of an improved model of debris‐flow motion
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.
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
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.
Lagrangian speckle model and tissue-motion estimation--theory.
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
Segmentation in structure from motion: modeling and psychophysics.
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
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
Domain-wall motion in random potential and hysteresis modeling
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.}
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.
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
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.
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.
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.
Affinity comparison of different THCA synthase to CBGA using modeling computational approaches
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
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)
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
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
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.
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.
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
2d Affine XY-Spin Model/4d Gauge Theory Duality and Deconfinement
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.
Development of novel cellular model for affinity studies of histamine H(4) receptor ligands.
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
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.
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.
Meshless Modeling of Deformable Shapes and their Motion
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
On modeling animal movements using Brownian motion with measurement error.
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
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.
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.
Constraints on the affinity term for modeling long-term glass dissolution rates
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.
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
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
Elements of an improved model of debris-flow motion
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.
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)
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
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.
Energetics of ligand-receptor binding affinity on endothelial cells: An in vitro model.
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
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.
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
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
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.
Fractional-order variational optical flow model for motion estimation.
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
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.
Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation.
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
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.
Modelling the emergence of coordinated collective motion by minimizing dissatisfaction.
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
Deformable models with sparsity constraints for cardiac motion analysis.
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
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
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
Modeling the Nonlinear Motion of the Rat Central Airways.
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
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
A Pelvic Phantom for Modeling Internal Organ Motions
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.
A pelvic phantom for modeling internal organ motions.
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
Sparse deformable models with application to cardiac motion analysis.
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
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.
Model and parametric uncertainty in source-based kinematic models of earthquake ground motion
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.
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
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.
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.
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
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
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
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.
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
Towards Analytic Solutions of Step-Wise Safe Switching for Known Affine-Linear Models
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.
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
Lumped mass modeling of overburden motion during explosive blasting
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.
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
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.
Models for motion-based video indexing and retrieval.
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
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.
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.
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
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.
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.
Cytoplasm dynamics and cell motion: two-phase flow models.
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
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.
Deciphering the Crowd: Modeling and Identification of Pedestrian Group Motion
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
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.
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.
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.
Modeling closure of circular wounds through coordinated collective motion.
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
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
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
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.
Analytic model for surface ground motion with spall induced by underground nuclear tests
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.
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.…
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).
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
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.
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.
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
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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
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.
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
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
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.
Whole-Motion Model of Perception during Forward- and Backward-Facing Centrifuge Runs
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
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.
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
Motion analysis study on sensitivity of finite element model of the cervical spine to geometry.
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
Modeling Functional Motions of Biological Systems by Customized Natural Moves.
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
A general model for the perception of space and motion.
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
Scatter to volume registration for model-free respiratory motion estimation from dynamic MRIs.
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
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
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.
TU-F-17A-03: An Analytical Respiratory Perturbation Model for Lung Motion Prediction
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
Robust velocity computation from a biologically motivated model of motion perception
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.
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)
Comparison of Nonlinear Model Results Using Modified Recorded and Synthetic Ground Motions
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.
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.
Basic simple modeling of balloting motion of railgun projectiles. Technical report
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.
SU-E-J-163: A Biomechanical Lung Model for Respiratory Motion Study
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.
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.
Embodied learning of a generative neural model for biological motion perception and inference
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
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
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
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
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.
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.
A discriminative model of motion and cross ratio for view-invariant action recognition.
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
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.
Characterization of free breathing patterns with 5D lung motion model
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
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.
Autoregressive model based algorithm for correcting motion and serially correlated errors in fNIRS
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
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
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
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.
Stochastic point-source modeling of ground motions in the Cascadia region
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.
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.
Multilayer Joint Gait-Pose Manifolds for Human Gait Motion Modeling.
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
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)
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
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.
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
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.
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.
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.
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.
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
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
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
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
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.
Construction and evaluation of an integrated dynamical model of visual motion perception.
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
Construction and evaluation of an integrated dynamical model of visual motion perception
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
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.
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
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.
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.