Affinity Propagation Clustering of Measurements for Multiple Extended Target Tracking.
Zhang, Tao; Wu, Renbiao
2015-01-01
More measurements are generated by the target per observation interval, when the target is detected by a high resolution sensor, or there are more measurement sources on the target surface. Such a target is referred to as an extended target. The probability hypothesis density filter is considered an efficient method for tracking multiple extended targets. However, the crucial problem of how to accurately and effectively partition the measurements of multiple extended targets remains unsolved. In this paper, affinity propagation clustering is introduced into measurement partitioning for extended target tracking, and the elliptical gating technique is used to remove the clutter measurements, which makes the affinity propagation clustering capable of partitioning the measurement in a densely cluttered environment with high accuracy. The Gaussian mixture probability hypothesis density filter is implemented for multiple extended target tracking. Numerical results are presented to demonstrate the performance of the proposed algorithm, which provides improved performance, while obviously reducing the computational complexity. PMID:26370998
Affinity Propagation Clustering of Measurements for Multiple Extended Target Tracking
Zhang, Tao; Wu, Renbiao
2015-01-01
More measurements are generated by the target per observation interval, when the target is detected by a high resolution sensor, or there are more measurement sources on the target surface. Such a target is referred to as an extended target. The probability hypothesis density filter is considered an efficient method for tracking multiple extended targets. However, the crucial problem of how to accurately and effectively partition the measurements of multiple extended targets remains unsolved. In this paper, affinity propagation clustering is introduced into measurement partitioning for extended target tracking, and the elliptical gating technique is used to remove the clutter measurements, which makes the affinity propagation clustering capable of partitioning the measurement in a densely cluttered environment with high accuracy. The Gaussian mixture probability hypothesis density filter is implemented for multiple extended target tracking. Numerical results are presented to demonstrate the performance of the proposed algorithm, which provides improved performance, while obviously reducing the computational complexity. PMID:26370998
An extended affinity propagation clustering method based on different data density types.
Zhao, XiuLi; Xu, WeiXiang
2015-01-01
Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself. PMID:25685144
Scaling analysis of affinity propagation.
Furtlehner, Cyril; Sebag, Michèle; Zhang, Xiangliang
2010-06-01
We analyze and exploit some scaling properties of the affinity propagation (AP) clustering algorithm proposed by Frey and Dueck [Science 315, 972 (2007)]. Following a divide and conquer strategy we setup an exact renormalization-based approach to address the question of clustering consistency, in particular, how many cluster are present in a given data set. We first observe that the divide and conquer strategy, used on a large data set hierarchically reduces the complexity O(N2) to O(N((h+2)/(h+1))) , for a data set of size N and a depth h of the hierarchical strategy. For a data set embedded in a d -dimensional space, we show that this is obtained without notably damaging the precision except in dimension d=2 . In fact, for d larger than 2 the relative loss in precision scales such as N((2-d)/(h+1)d). Finally, under some conditions we observe that there is a value s* of the penalty coefficient, a free parameter used to fix the number of clusters, which separates a fragmentation phase (for ss*) of the underlying hidden cluster structure. At this precise point holds a self-similarity property which can be exploited by the hierarchical strategy to actually locate its position, as a result of an exact decimation procedure. From this observation, a strategy based on AP can be defined to find out how many clusters are present in a given data set. PMID:20866473
Classification of neocortical interneurons using affinity propagation
Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael
2013-01-01
In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339
Classification of neocortical interneurons using affinity propagation.
Santana, Roberto; McGarry, Laura M; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael
2013-01-01
In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339
Zhang, Jiang; Liu, Qi; Chen, Huafu; Yuan, Zhen; Huang, Jin; Deng, Lihua; Lu, Fengmei; Zhang, Junpeng; Wang, Yuqing; Wang, Mingwen; Chen, Liangyin
2015-01-01
Clustering analysis methods have been widely applied to identifying the functional brain networks of a multitask paradigm. However, the previously used clustering analysis techniques are computationally expensive and thus impractical for clinical applications. In this study a novel method, called SOM-SAPC that combines self-organizing mapping (SOM) and supervised affinity propagation clustering (SAPC), is proposed and implemented to identify the motor execution (ME) and motor imagery (MI) networks. In SOM-SAPC, SOM was first performed to process fMRI data and SAPC is further utilized for clustering the patterns of functional networks. As a result, SOM-SAPC is able to significantly reduce the computational cost for brain network analysis. Simulation and clinical tests involving ME and MI were conducted based on SOM-SAPC, and the analysis results indicated that functional brain networks were clearly identified with different response patterns and reduced computational cost. In particular, three activation clusters were clearly revealed, which include parts of the visual, ME and MI functional networks. These findings validated that SOM-SAPC is an effective and robust method to analyze the fMRI data with multitasks. PMID:26236217
Dolgounitcheva, O; Díaz-Tinoco, Manuel; Zakrzewski, V G; Richard, Ryan M; Marom, Noa; Sherrill, C David; Ortiz, J V
2016-02-01
Comparison of ab initio electron-propagator predictions of vertical ionization potentials and electron affinities of organic, acceptor molecules with benchmark calculations based on the basis set-extrapolated, coupled cluster single, double, and perturbative triple substitution method has enabled identification of self-energy approximations with mean, unsigned errors between 0.1 and 0.2 eV. Among the self-energy approximations that neglect off-diagonal elements in the canonical, Hartree-Fock orbital basis, the P3 method for electron affinities, and the P3+ method for ionization potentials provide the best combination of accuracy and computational efficiency. For approximations that consider the full self-energy matrix, the NR2 methods offer the best performance. The P3+ and NR2 methods successfully identify the correct symmetry label of the lowest cationic state in two cases, naphthalenedione and benzoquinone, where some other methods fail. PMID:26730459
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
A multiobjective evolutionary algorithm to find community structures based on affinity propagation
NASA Astrophysics Data System (ADS)
Shang, Ronghua; Luo, Shuang; Zhang, Weitong; Stolkin, Rustam; Jiao, Licheng
2016-07-01
Community detection plays an important role in reflecting and understanding the topological structure of complex networks, and can be used to help mine the potential information in networks. This paper presents a Multiobjective Evolutionary Algorithm based on Affinity Propagation (APMOEA) which improves the accuracy of community detection. Firstly, APMOEA takes the method of affinity propagation (AP) to initially divide the network. To accelerate its convergence, the multiobjective evolutionary algorithm selects nondominated solutions from the preliminary partitioning results as its initial population. Secondly, the multiobjective evolutionary algorithm finds solutions approximating the true Pareto optimal front through constantly selecting nondominated solutions from the population after crossover and mutation in iterations, which overcomes the tendency of data clustering methods to fall into local optima. Finally, APMOEA uses an elitist strategy, called "external archive", to prevent degeneration during the process of searching using the multiobjective evolutionary algorithm. According to this strategy, the preliminary partitioning results obtained by AP will be archived and participate in the final selection of Pareto-optimal solutions. Experiments on benchmark test data, including both computer-generated networks and eight real-world networks, show that the proposed algorithm achieves more accurate results and has faster convergence speed compared with seven other state-of-art algorithms.
Caso, Giuseppe; de Nardis, Luca; di Benedetto, Maria-Gabriella
2015-01-01
The weighted k-nearest neighbors (WkNN) algorithm is by far the most popular choice in the design of fingerprinting indoor positioning systems based on WiFi received signal strength (RSS). WkNN estimates the position of a target device by selecting k reference points (RPs) based on the similarity of their fingerprints with the measured RSS values. The position of the target device is then obtained as a weighted sum of the positions of the k RPs. Two-step WkNN positioning algorithms were recently proposed, in which RPs are divided into clusters using the affinity propagation clustering algorithm, and one representative for each cluster is selected. Only cluster representatives are then considered during the position estimation, leading to a significant computational complexity reduction compared to traditional, flat WkNN. Flat and two-step WkNN share the issue of properly selecting the similarity metric so as to guarantee good positioning accuracy: in two-step WkNN, in particular, the metric impacts three different steps in the position estimation, that is cluster formation, cluster selection and RP selection and weighting. So far, however, the only similarity metric considered in the literature was the one proposed in the original formulation of the affinity propagation algorithm. This paper fills this gap by comparing different metrics and, based on this comparison, proposes a novel mixed approach in which different metrics are adopted in the different steps of the position estimation procedure. The analysis is supported by an extensive experimental campaign carried out in a multi-floor 3D indoor positioning testbed. The impact of similarity metrics and their combinations on the structure and size of the resulting clusters, 3D positioning accuracy and computational complexity are investigated. Results show that the adoption of metrics different from the one proposed in the original affinity propagation algorithm and, in particular, the combination of different
Caso, Giuseppe; de Nardis, Luca; di Benedetto, Maria-Gabriella
2015-01-01
The weighted k-nearest neighbors (WkNN) algorithm is by far the most popular choice in the design of fingerprinting indoor positioning systems based on WiFi received signal strength (RSS). WkNN estimates the position of a target device by selecting k reference points (RPs) based on the similarity of their fingerprints with the measured RSS values. The position of the target device is then obtained as a weighted sum of the positions of the k RPs. Two-step WkNN positioning algorithms were recently proposed, in which RPs are divided into clusters using the affinity propagation clustering algorithm, and one representative for each cluster is selected. Only cluster representatives are then considered during the position estimation, leading to a significant computational complexity reduction compared to traditional, flat WkNN. Flat and two-step WkNN share the issue of properly selecting the similarity metric so as to guarantee good positioning accuracy: in two-step WkNN, in particular, the metric impacts three different steps in the position estimation, that is cluster formation, cluster selection and RP selection and weighting. So far, however, the only similarity metric considered in the literature was the one proposed in the original formulation of the affinity propagation algorithm. This paper fills this gap by comparing different metrics and, based on this comparison, proposes a novel mixed approach in which different metrics are adopted in the different steps of the position estimation procedure. The analysis is supported by an extensive experimental campaign carried out in a multi-floor 3D indoor positioning testbed. The impact of similarity metrics and their combinations on the structure and size of the resulting clusters, 3D positioning accuracy and computational complexity are investigated. Results show that the adoption of metrics different from the one proposed in the original affinity propagation algorithm and, in particular, the combination of different
Low affinity binding site clusters confer hox specificity and regulatory robustness.
Crocker, Justin; Abe, Namiko; Rinaldi, Lucrezia; McGregor, Alistair P; Frankel, Nicolás; Wang, Shu; Alsawadi, Ahmad; Valenti, Philippe; Plaza, Serge; Payre, François; Mann, Richard S; Stern, David L
2015-01-15
In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression. PMID:25557079
Xu, Ziyue; Bagci, Ulas; Seidel, Jurgen; Thomasson, David; Solomon, Jeff; Mollura, Daniel J
2014-01-01
Delineation and noise removal play a significant role in clinical quantification of PET images. Conventionally, these two tasks are considered independent, however, denoising can improve the performance of boundary delineation by enhancing SNR while preserving the structural continuity of local regions. On the other hand, we postulate that segmentation can help denoising process by constraining the smoothing criteria locally. Herein, we present a novel iterative approach for simultaneous PET image denoising and segmentation. The proposed algorithm uses generalized Anscombe transformation priori to non-local means based noise removal scheme and affinity propagation based delineation. For nonlocal means denoising, we propose a new regional means approach where we automatically and efficiently extract the appropriate subset of the image voxels by incorporating the class information from affinity propagation based segmentation. PET images after denoising are further utilized for refinement of the segmentation in an iterative manner. Qualitative and quantitative results demonstrate that the proposed framework successfully removes the noise from PET images while preserving the structures, and improves the segmentation accuracy. PMID:25333180
Reliability Evaluation for Clustered WSNs under Malware Propagation
Shen, Shigen; Huang, Longjun; Liu, Jianhua; Champion, Adam C.; Yu, Shui; Cao, Qiying
2016-01-01
We consider a clustered wireless sensor network (WSN) under epidemic-malware propagation conditions and solve the problem of how to evaluate its reliability so as to ensure efficient, continuous, and dependable transmission of sensed data from sensor nodes to the sink. Facing the contradiction between malware intention and continuous-time Markov chain (CTMC) randomness, we introduce a strategic game that can predict malware infection in order to model a successful infection as a CTMC state transition. Next, we devise a novel measure to compute the Mean Time to Failure (MTTF) of a sensor node, which represents the reliability of a sensor node continuously performing tasks such as sensing, transmitting, and fusing data. Since clustered WSNs can be regarded as parallel-serial-parallel systems, the reliability of a clustered WSN can be evaluated via classical reliability theory. Numerical results show the influence of parameters such as the true positive rate and the false positive rate on a sensor node’s MTTF. Furthermore, we validate the method of reliability evaluation for a clustered WSN according to the number of sensor nodes in a cluster, the number of clusters in a route, and the number of routes in the WSN. PMID:27294934
Reliability Evaluation for Clustered WSNs under Malware Propagation.
Shen, Shigen; Huang, Longjun; Liu, Jianhua; Champion, Adam C; Yu, Shui; Cao, Qiying
2016-01-01
We consider a clustered wireless sensor network (WSN) under epidemic-malware propagation conditions and solve the problem of how to evaluate its reliability so as to ensure efficient, continuous, and dependable transmission of sensed data from sensor nodes to the sink. Facing the contradiction between malware intention and continuous-time Markov chain (CTMC) randomness, we introduce a strategic game that can predict malware infection in order to model a successful infection as a CTMC state transition. Next, we devise a novel measure to compute the Mean Time to Failure (MTTF) of a sensor node, which represents the reliability of a sensor node continuously performing tasks such as sensing, transmitting, and fusing data. Since clustered WSNs can be regarded as parallel-serial-parallel systems, the reliability of a clustered WSN can be evaluated via classical reliability theory. Numerical results show the influence of parameters such as the true positive rate and the false positive rate on a sensor node's MTTF. Furthermore, we validate the method of reliability evaluation for a clustered WSN according to the number of sensor nodes in a cluster, the number of clusters in a route, and the number of routes in the WSN. PMID:27294934
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.
Cluster algebra structure on the finite dimensional representations of affine quantum group
NASA Astrophysics Data System (ADS)
Yang, Yan-Min; Ma, Hai-Tao; Lin, Bing-Sheng; Zheng, Zhu-Jun
2015-01-01
In this paper, we prove one case of conjecture given by Hernandez and Leclerc. We give a cluster algebra structure on the Grothendieck ring of a full subcategory of the finite dimensional representations of affine quantum group . As a conclusion, for every exchange relation of cluster algebra, there exists an exact sequence of the full subcategory corresponding to it. Project supported by the National Natural Science Foundation of China (Grant No. 11475178).
Liu, Jiahui; Liu, Miao; Zheng, Bo; Yao, Zhongping; Xia, Jiang
2016-01-01
High-affinity binders are desirable tools to probe the function that specific protein−protein interactions play in cell. In the process of seeking a general strategy to design high-affinity binders, we found a clue from the βPIX (p21-activated kinase interacting exchange factor)−Shank PDZ interaction in synaptic assembly: three PDZ-binding sites are clustered by a parallel coiled-coil trimer but bind to Shank PDZ protein with 1:1 stoichiometry (1 trimer/1 PDZ). Inspired by this architecture, we proposed that peptide dendrimer, mimicking the ligand clustering in βPIX, will also show enhanced binding affinity, yet with 1:1 stoichiometry. This postulation has been proven here, as we synthesized a set of monomeric, dimeric and trimeric peptides and measured their binding affinity and stoichiometry with Shank PDZ domains by isothermal titration calorimetry, native mass spectrometry and surface plasmon resonance. This affinity enhancement, best explained by proximity effect, will be useful to guide the design of high-affinity blockers for protein−protein interactions. PMID:26918521
A general method of community detection by identifying community centers with affinity propagation
NASA Astrophysics Data System (ADS)
Guo, Wei-Feng; Zhang, Shao-Wu
2016-04-01
Detection of community structures is beneficial to analyzing the structures and properties of networks. It is of theoretical interest and practical significance in modern science. So far, a large number of algorithms have been proposed to detect community structures in complex networks, but most of them are suitable for a specific network structure. In this paper, a novel method (called CDMIC) is proposed to detect the communities in un-weighted, weighted, un-directed, directed and signed networks by constructing a dissimilarity distance matrix of network and identifying community centers with maximizing modularity. For a given network, we first estimate the distance between all pairs of nodes for constructing the dissimilarity distance matrix of the network. Then, this distance matrix is input to the affinity propagation (AP) algorithm to extract a candidate center set of community. Thirdly, we rank these centers in descending order according to the sum of their availability and responsibility. Finally, we determine the community structure by selecting the center subset from the candidate center set in an incremental manner to make the modularity maximization. On three real-world networks and some synthetic networks, experimental results show that our CDMIC method has higher performance in terms of classification accuracy and normalized mutual information (NMI), and ability to tolerate the resolution limitation.
Spatiotemporal Variability and Propagation of Equatorial Noise Observed by Cluster
NASA Technical Reports Server (NTRS)
Santolik, O.; Pickett, J. S.; Gurnett, D. A.; Maksimovic, M.; Cornilleau-Wehrlin, N.
2002-01-01
We report a multipoint case study of the electromagnetic equatorial noise observed by the Cluster project. High-resolution data were measured in three close points in space located in the morning sector of the outer plasmasphere. We demonstrate a narrow latitudinal extent of the emissions with a typical width of 2 degrees, centered near the minimum-B equator. Power spectra recorded by the different satellites show a complex structure of emission lines whose relative intensities and positions vary at timescales of 1-2 min and/or at spatial scales of tens of wavelengths. These lines do not match harmonics of the local proton cyclotron frequency, as it would be expected if the waves are generated by energetic ions and observed near the source region. We bring observational evidence that the waves propagate with a significant radial component and thus can propagate from a distant generation region located at different radial distances where ion cyclotron frequencies match the observed fine structure.
Ahmed, Afaz Uddin; Islam, Mohammad Tariqul; Ismail, Mahamod; Kibria, Salehin; Arshad, Haslina
2014-01-01
An artificial neural network (ANN) and affinity propagation (AP) algorithm based user categorization technique is presented. The proposed algorithm is designed for closed access femtocell network. ANN is used for user classification process and AP algorithm is used to optimize the ANN training process. AP selects the best possible training samples for faster ANN training cycle. The users are distinguished by using the difference of received signal strength in a multielement femtocell device. A previously developed directive microstrip antenna is used to configure the femtocell device. Simulation results show that, for a particular house pattern, the categorization technique without AP algorithm takes 5 indoor users and 10 outdoor users to attain an error-free operation. While integrating AP algorithm with ANN, the system takes 60% less training samples reducing the training time up to 50%. This procedure makes the femtocell more effective for closed access operation. PMID:25133214
Weber, Thomas C
2008-11-01
It has recently been shown [Weber, T. C. et al. (2007). "Acoustic propagation through clustered bubble clouds," IEEE J. Ocean. Eng. 32, 513-523] that gas bubble clustering plays a role in determining the acoustic field characteristics of bubbly fluids. In particular, it has been shown that clustering changes the bubble-induced attenuation as well as the ping-to-ping variability in the acoustic field. The degree to which bubble clustering exists in nature, however, is unknown. This paper describes a method for quantifying bubble clustering using a high frequency (400 kHz) multibeam sonar, and reports on observations of near-surface bubble clustering during a storm (14.6 m/s wind speed) in the Gulf of Maine. The multibeam sonar data are analyzed to estimate the pair correlation function, a measure of bubble clustering. In order to account for clustering in the mean acoustic field, a modification to the effective medium wave number is made. With this modification, the multibeam sonar observations are used to predict the effect of clustering on the attenuation of the mean field for short-range propagation (1 m) at frequencies between 10 and 350 kHz. Results for this specific case show that clustering can cause the attenuation to change by 20%-80% over this frequency range. PMID:19045766
Computational study on the negative electron affinities of NO2 -.(H2O)n clusters (n=0-30).
Ejsing, Anne Marie; Brøndsted Nielsen, Steen
2007-04-21
Here we report negative electron affinities of NO(2)(-).(H2O)n clusters (n=0-30) obtained from density functional theory calculations and a simple correction to Koopmans' theorem. The method relies on the calculation of the detachment energy of the monoanion and its highest occupied molecular orbital and lowest unoccupied molecular orbital energies, and explicit calculations on the dianion itself are avoided. A good agreement with resonances in the cross section for neutral production in electron scattering experiments is found for n=0, 1, and 2. We find several isomeric structures of NO(2)(-).(H2O)2 of similar energy that elucidate the interplay between water-water and ion-water interactions. The topology is predicted to influence the electron affinity by 0.5 and 0.4 eV for NO(2)(-).(H2O) and NO(2)(-).(H2O)2, respectively. The electron affinity of larger clusters is shown to follow a (n+delta)-1/3 dependence, where delta=3 represents the number of water molecules that in volume, could replace NO(2) (-). PMID:17461632
A Hybrid Algorithm for Clustering of Time Series Data Based on Affinity Search Technique
Aghabozorgi, Saeed; Ying Wah, Teh; Herawan, Tutut; Jalab, Hamid A.; Shaygan, Mohammad Amin; Jalali, Alireza
2014-01-01
Time series clustering is an important solution to various problems in numerous fields of research, including business, medical science, and finance. However, conventional clustering algorithms are not practical for time series data because they are essentially designed for static data. This impracticality results in poor clustering accuracy in several systems. In this paper, a new hybrid clustering algorithm is proposed based on the similarity in shape of time series data. Time series data are first grouped as subclusters based on similarity in time. The subclusters are then merged using the k-Medoids algorithm based on similarity in shape. This model has two contributions: (1) it is more accurate than other conventional and hybrid approaches and (2) it determines the similarity in shape among time series data with a low complexity. To evaluate the accuracy of the proposed model, the model is tested extensively using syntactic and real-world time series datasets. PMID:24982966
Craig, Hugh; Berretta, Regina; Moscato, Pablo
2016-01-01
In this study we propose a novel, unsupervised clustering methodology for analyzing large datasets. This new, efficient methodology converts the general clustering problem into the community detection problem in graph by using the Jensen-Shannon distance, a dissimilarity measure originating in Information Theory. Moreover, we use graph theoretic concepts for the generation and analysis of proximity graphs. Our methodology is based on a newly proposed memetic algorithm (iMA-Net) for discovering clusters of data elements by maximizing the modularity function in proximity graphs of literary works. To test the effectiveness of this general methodology, we apply it to a text corpus dataset, which contains frequencies of approximately 55,114 unique words across all 168 written in the Shakespearean era (16th and 17th centuries), to analyze and detect clusters of similar plays. Experimental results and comparison with state-of-the-art clustering methods demonstrate the remarkable performance of our new method for identifying high quality clusters which reflect the commonalities in the literary style of the plays. PMID:27571416
Naeni, Leila M; Craig, Hugh; Berretta, Regina; Moscato, Pablo
2016-01-01
In this study we propose a novel, unsupervised clustering methodology for analyzing large datasets. This new, efficient methodology converts the general clustering problem into the community detection problem in graph by using the Jensen-Shannon distance, a dissimilarity measure originating in Information Theory. Moreover, we use graph theoretic concepts for the generation and analysis of proximity graphs. Our methodology is based on a newly proposed memetic algorithm (iMA-Net) for discovering clusters of data elements by maximizing the modularity function in proximity graphs of literary works. To test the effectiveness of this general methodology, we apply it to a text corpus dataset, which contains frequencies of approximately 55,114 unique words across all 168 written in the Shakespearean era (16th and 17th centuries), to analyze and detect clusters of similar plays. Experimental results and comparison with state-of-the-art clustering methods demonstrate the remarkable performance of our new method for identifying high quality clusters which reflect the commonalities in the literary style of the plays. PMID:27571416
NASA Astrophysics Data System (ADS)
Pickett, J. S.; Christopher, I. W.; Grison, B.; Grimald, S.; Santolík, O.; Décréau, P. M. E.; Lefebvre, B.; Engebretson, M. J.; Kistler, L. M.; Constantinescu, D.; Chen, L.-J.; Omura, Y.; Lakhina, G. S.; Gurnett, D. A.; Cornilleau-Wehrlin, N.; Fazakerley, A. N.; Dandouras, I.; Lucek, E.
2011-01-01
We present the results of a study of Electrostatic Solitary Waves (ESWs) in which propagation of a series of noncyclical ESWs is observed from one Cluster spacecraft to another over distances as great as tens of km and time lags as great as a few tens of ms. This propagation study was conducted for locations near the magnetopause on the magnetosheath side. Propagation was found primarily toward the earth with speeds on the order of 1500 to 2400 km/s. The sizes of the ESWs obtained from these velocities were on the order of 1 km along the magnetic field direction and several tens of km perpendicular. These results are consistent with measurements on single spacecraft in which the ESW propagation is observed with time lags of only ˜0.1 ms. Our results thus show the stability of ESWs over time periods much greater than their own characteristic pulse durations of a few 100s of microseconds. We present also the results of a study of ESW modulation at the magnetopause on the earthward side. We found that ESWs were modulated at ˜1.3 Hz, consistent with a Pc1 wave which was observed concurrently. During this time, tens of eV electron beams are present. We propose a Buneman type instability in which the E″″ component of the Pc1 waves provides a mechanism for accelerating electrons, resulting in the generation of the ESWs modulated at the Pc1 frequency.
Directions of equatorial noise propagation determined using Cluster and DEMETER spacecraft
NASA Astrophysics Data System (ADS)
Nemec, Frantisek; Hrbackova, Zuzana; Santolik, Ondrej; Pickett, Jolene S.; Parrot, Michel; Cornilleau-Wehrlin, Nicole
2013-04-01
Equatorial noise emissions are electromagnetic waves at frequencies between the proton cyclotron frequency and the lower hybrid frequency routinely observed within a few degrees of the geomagnetic equator at radial distances from about 2 to 6 Re. High resolution data reveal that the emissions are formed by a system of spectral lines, being generated by instabilities of proton distribution functions at harmonics of the proton cyclotron frequency in the source region. The waves propagate in the fast magnetosonic mode nearly perpendicularly to the ambient magnetic field, i.e. the corresponding magnetic field fluctuations are almost linearly polarized along the ambient magnetic field and the corresponding electric field fluctuations are elliptically polarized in the equatorial plane, with the major polarization axis having the same direction as wave and Poynting vectors. We conduct a systematic analysis of azimuthal propagation of equatorial noise. Combined WBD and STAFF-SA measurements performed on the Cluster spacecraft are used to determine not only the azimuthal angle of the wave vector direction, but also to estimate the corresponding beaming angle. It is found that the beaming angle is generally rather large, i.e. the detected waves come from a significant range of directions, and a traditionally used approximation of a single plane wave fails. The obtained results are complemented by a raytracing analysis in order to get a comprehensive picture of equatorial noise propagation in the inner magnetosphere. Finally, high resolution multi-component measurements performed by the low-altitude DEMETER spacecraft are used to demonstrate that equatorial noise emissions can reach altitudes as low as 660 km, and that the observed propagation properties are in agreement with the overall propagation picture.
NASA Astrophysics Data System (ADS)
Korona, Tatiana
2012-02-01
A possibility to calculate electron affinities (EAs) by a software devised for electron excitations is exploited to examine the accuracy of a partly local EA-EOM-CCSD method. In the proposed approach local approximations are applied to the ground-state coupled cluster wave function, while the EAs themselves are obtained in a full configurational space. The results of a numerical test for 14 molecules show that already with standard local settings the method reproduces the nonlocal EAs with the average error of 0.009 eV. Since the EA-EOM step of the calculation requires less computational resources than the computation of the CCSD ground state, the proposed hybrid approach can become a valuable tool for obtaining the EAs for molecules, which are too large for a canonical CCSD calculation, but still small enough for the EA-EOM step to be performed in a nonlocal way.
NASA Astrophysics Data System (ADS)
Bankura, Arindam; Klein, Michael L.; Carnevale, Vincenzo
2013-08-01
Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and Nɛ positions of the imidazole group to estimate the pKas. Anticipating our results, we will see that the estimated pKa for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.
NASA Astrophysics Data System (ADS)
Satyapal, S.; Watson, Dan M.; Pipher, J. L.; Forrest, W. J.; Greenhouse, M. A.; Smith, H. A.; Fischer, J.; Woodward, Charles E.
1997-07-01
Near-Infrared spectroscopy combined with high spatial resolution imaging have been used in this work to probe the central 500 pc of M82. Imaging observations in the 2.36 μm CO band head are added to our previously published near-infrared hydrogen recombination line imaging, near-infrared broadband imaging, and 3.29 μm dust feature imaging observations, in order to study the nature of the starburst stellar population. A starburst model is constructed and compared with the observations of the stellar clusters in the starburst complex. Our analysis implies that the typical age for the starburst clusters is 107 yr. In addition, our high spatial resolution observations indicate that there is an age dispersion within the starburst complex that is correlated with projected distance from the center of the galaxy. The inferred age dispersion is 6 × 106 yr. If the starburst in M82 is propagating outward from the center, this age dispersion corresponds to a velocity of propagation, originating in the center, of ~50 km s-1. Our quantitative analysis also reveals that a Salpeter initial mass function, extending from 0.1 to 100 M⊙, can fit the observed properties of M82 without using up more than 30% of the total dynamical mass in the starburst.
Propagation characteristics of young hot flow anomalies near the bow shock: Cluster observations
NASA Astrophysics Data System (ADS)
Xiao, T.; Zhang, H.; Shi, Q. Q.; Zong, Q.-G.; Fu, S. Y.; Tian, A. M.; Sun, W. J.; Wang, S.; Parks, G. K.; Yao, S. T.; Rème, H.; Dandouras, I.
2015-06-01
Based on Cluster observations, the propagation velocities and normal directions of hot flow anomaly (HFA) boundaries upstream the Earth's bow shock are calculated. Twenty-one young HFAs, which have clear leading and trailing boundaries, were selected, and multispacecraft timing method considering errors was employed for the investigation. According to the difference in the propagation velocity of the leading and trailing edges, we categorized these events into three groups, namely, contracting, expanding, and stable events. The contraction speed is a few tens of kilometers per second for the contracting HFAs, and the expansion speed is tens to more than hundred kilometers per second for expanding events. For the stable events, the leading and trailing edges propagate at almost the same speed within the error range. We have further investigated what causes them to contract, expand, or stay stable by carefully calculating the thermal pressure of the young HFAs which have two distinct ion populations (solar wind beam and reflected flow). It is found that the extreme value of the sum of the magnetic and thermal pressure inside the HFAs compared with that of the nearest point outside of the leading edges is higher for expanding events and lower for contracting events, and there is no significant difference for the stable events, and the total pressure (sum of thermal, magnetic, and dynamic pressure) variation has a significant effect on the evolution for most (70%) of the HFAs, which implies that the pressure plays an important role in the evolution of young HFAs.
Accelerating forward and adjoint simulations of seismic wave propagation on large GPU-clusters
NASA Astrophysics Data System (ADS)
Peter, D. B.; Rietmann, M.; Charles, J.; Messmer, P.; Komatitsch, D.; Schenk, O.; Tromp, J.
2012-12-01
In seismic tomography, waveform inversions require accurate simulations of seismic wave propagation in complex media.The current versions of our spectral-element method (SEM) packages, the local-scale code SPECFEM3D and the global-scale code SPECFEM3D_GLOBE, are widely used open-source community codes which simulate seismic wave propagation for local-, regional- and global-scale applications. These numerical simulations compute highly accurate seismic wavefields, accounting for fully 3D Earth models. However, code performance often governs whether seismic inversions become feasible or remain elusive. We report here on extending these high-order finite-element packages to further exploit graphic processing units (GPUs) and perform numerical simulations of seismic wave propagation on large GPU clusters. These enhanced packages can be readily run either on multi-core CPUs only or together with many-core GPU acceleration devices. One of the challenges in parallelizing finite element codes is the potential for race conditions during the assembly phase. We therefore investigated different methods such as mesh coloring or atomic updates on the GPU. In order to achieve strong scaling, we needed to ensure good overlap of data motion at all levels, including internode and host-accelerator transfers. These new MPI/CUDA solvers exhibit excellent scalability and achieve speedup on a node-to-node basis over the carefully tuned equivalent multi-core MPI solver. We present case studies run on a Cray XK6 GPU architecture up to 896 nodes to demonstrate the performance of both the forward and adjoint functionality of the code packages. Running simulations on such dedicated GPU clusters further reduces computation times and pushes seismic inversions into a new, higher frequency realm.
NASA Astrophysics Data System (ADS)
Lisinetskaya, Polina G.; Mitrić, Roland
2015-03-01
We demonstrate theoretically the possibility of optimal control of light propagation and exciton transfer in arrays constructed of subnanometer sized noble-metal clusters by using phase-shaped laser pulses and analyze the mechanism underlying this process. The theoretical approach for simulation of light propagation in the arrays is based on the numerical solution of the coupled time-dependent Schrödinger equation and the classical electric field propagation in an iterative self-consistent manner. The electronic eigenstates of individual clusters and the dipole couplings are obtained from ab initio TDDFT calculations. The total electric field is propagated along the array by coupling an external excitation electric field with the electric fields produced by all clusters. A genetic algorithm is used to determine optimal pulse shapes which drive the excitation in a desired direction. The described theoretical approach is applied to control the light propagation and exciton transfer dynamics into a T-shaped structure built of seven Ag8 clusters. We demonstrate that a selective switching of light localization is possible in ˜5 nm sized cluster arrays which might serve as a building block for plasmonic devices with an ultrafast operation regime.
Feller, David
2016-01-01
Benchmark quality adiabatic electron affinities for a collection of atoms and small molecules were obtained with the Feller-Peterson-Dixon composite coupled cluster theory method. Prior applications of this method demonstrated its ability to accurately predict atomization energies/heats of formation for more than 170 molecules. In the current work, the 1-particle expansion involved very large correlation consistent basis sets, ranging up to aug-cc-pV9Z (aug-cc-pV10Z for H and H2), with the goal of minimizing the residual basis set truncation error that must otherwise be approximated with extrapolation formulas. The n-particle expansion begins with coupled cluster calculations through iterative single and double excitations plus a quasiperturbative treatment of "connected" triple excitations (CCSD(T)) pushed to the complete basis set limit followed by CCSDT, CCSDTQ, or CCSDTQ5 corrections. Due to the small size of the systems examined here, it was possible in many cases to extend the n-particle expansion to the full configuration interaction wave function limit. Additional, smaller corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, and non-adiabatic effects were also included. The overall root mean square (RMS) deviation was 0.005 eV (0.12 kcal/mol). This level of agreement was comparable to what was found with molecular heats of formation. A 95% confidence level corresponds to roughly twice the RMS value or 0.01 eV. While the atomic electron affinities are known experimentally to high accuracy, the molecular values are less certain. This contributes to the difficulty of gauging the accuracy of the theoretical results. A limited number of electron affinities were determined with the explicitly correlated CCSD(T)-F12b method. After extending the VnZ-F12 orbital basis sets with additional diffuse functions, the F12b method was found to accurately reproduce the best F/F(-) value obtained with standard
NASA Astrophysics Data System (ADS)
Feller, David
2016-01-01
Benchmark quality adiabatic electron affinities for a collection of atoms and small molecules were obtained with the Feller-Peterson-Dixon composite coupled cluster theory method. Prior applications of this method demonstrated its ability to accurately predict atomization energies/heats of formation for more than 170 molecules. In the current work, the 1-particle expansion involved very large correlation consistent basis sets, ranging up to aug-cc-pV9Z (aug-cc-pV10Z for H and H2), with the goal of minimizing the residual basis set truncation error that must otherwise be approximated with extrapolation formulas. The n-particle expansion begins with coupled cluster calculations through iterative single and double excitations plus a quasiperturbative treatment of "connected" triple excitations (CCSD(T)) pushed to the complete basis set limit followed by CCSDT, CCSDTQ, or CCSDTQ5 corrections. Due to the small size of the systems examined here, it was possible in many cases to extend the n-particle expansion to the full configuration interaction wave function limit. Additional, smaller corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, and non-adiabatic effects were also included. The overall root mean square (RMS) deviation was 0.005 eV (0.12 kcal/mol). This level of agreement was comparable to what was found with molecular heats of formation. A 95% confidence level corresponds to roughly twice the RMS value or 0.01 eV. While the atomic electron affinities are known experimentally to high accuracy, the molecular values are less certain. This contributes to the difficulty of gauging the accuracy of the theoretical results. A limited number of electron affinities were determined with the explicitly correlated CCSD(T)-F12b method. After extending the VnZ-F12 orbital basis sets with additional diffuse functions, the F12b method was found to accurately reproduce the best F/F- value obtained with standard
Arefin, Ahmed Shamsul; Vimieiro, Renato; Riveros, Carlos; Craig, Hugh; Moscato, Pablo
2014-01-01
In this paper we analyse the word frequency profiles of a set of works from the Shakespearean era to uncover patterns of relationship between them, highlighting the connections within authorial canons. We used a text corpus comprising 256 plays and poems from the 16th and 17th centuries, with 17 works of uncertain authorship. Our clustering approach is based on the Jensen-Shannon divergence and a graph partitioning algorithm, and our results show that authors' characteristic styles are very powerful factors in explaining the variation of word use, frequently transcending cross-cutting factors like the differences between tragedy and comedy, early and late works, and plays and poems. Our method also provides an empirical guide to the authorship of plays and poems where this is unknown or disputed. PMID:25347727
Arefin, Ahmed Shamsul; Vimieiro, Renato; Riveros, Carlos; Craig, Hugh; Moscato, Pablo
2014-01-01
In this paper we analyse the word frequency profiles of a set of works from the Shakespearean era to uncover patterns of relationship between them, highlighting the connections within authorial canons. We used a text corpus comprising 256 plays and poems from the 16th and 17th centuries, with 17 works of uncertain authorship. Our clustering approach is based on the Jensen-Shannon divergence and a graph partitioning algorithm, and our results show that authors' characteristic styles are very powerful factors in explaining the variation of word use, frequently transcending cross-cutting factors like the differences between tragedy and comedy, early and late works, and plays and poems. Our method also provides an empirical guide to the authorship of plays and poems where this is unknown or disputed. PMID:25347727
Kotera, K.; Allard, D.; Dubois, Y.; Pierog, T.
2009-12-10
We study the survival of ultrahigh energy nuclei injected in clusters of galaxies, as well as their secondary neutrino and photon emissions, using a complete numerical propagation method and a realistic modeling of the magnetic, baryonic, and photonic backgrounds. It is found that the survival of heavy nuclei highly depends on the injection position and on the profile of the magnetic field. Taking into account the limited lifetime of the central source could also lead in some cases to the detection of a cosmic-ray afterglow, temporally decorrelated from neutrino and gamma-ray emissions. We calculate that the diffusive neutrino flux around 1 PeV coming from clusters of galaxies may have a chance to be detected by current instruments. The observation of single sources in neutrinos and in gamma rays produced by ultrahigh energy cosmic rays will be more difficult. Signals coming from lower energy cosmic rays (E approx< 1 PeV), if they exist, might however be detected by Fermi, for reasonable sets of parameters.
Radio jet propagation and wide-angle tailed radio sources in merging galaxy cluster environments
NASA Astrophysics Data System (ADS)
Loken, Chris; Roettiger, Kurt; Burns, Jack O.; Norman, Michael
1995-05-01
The intracluster medium (ICM) within merging clusters of galaxies is likely to be in a violent or turbulent dynamical state which may have a significant effect on the evolution of cluster radio sources. We present results from a recent gas + N-body simulation of a cluster merger, suggesting that mergers can result in long-lived, supersonic bulk flows, as well as shocks, within a few hundred kiloparsecs of the core of the dominant cluster. These results have motivated our new two-dimensional and three-dimensional simulations of jet propagation in such environments. The first set of simulations models the ISM/ICM transition as a contact discontinuity with a strong velocity shear. A supersonic (Mj = 6) jet crossing this discontinuity into an ICM with a transverse, supersonic wind bends continuously, becomes 'naked' on the upwind side, and forms a distended cocoon on the downwind side. In the case of a mildly supersonic jet (Mj = 3), however, a shock is driven into the ISM and ISM material is pulled along with the jet into the ICM. Instabilities excited at the ISM/ICM interface result in the jet repeatedly pinching off and reestablishing itself in a series of 'disconnection events.' The second set of simulations deals with a jet encountering a shock in the merging cluster environment. A series of relatively high-resolution two-dimensional calculations is used to confirm earlier analysis predicting that the jet will not disrupt when the jet Mach number is greater than the shock Mach number. A jet which survives the encounter with the shock will decrease in radius and disrupt shortly thereafter as a result of the growth of Kelvin-Helmholtz instabilities. We also find, in disagreement with predictions, that the jet flaring angle decreases with increasing jet density. Finally, a three-dimensional simulation of a jet crossing an oblique shock gives rise to a morphology which resembles a wide-angle tailed radio source with the jet flaring at the shock and disrupting to form
Radio jet propagation and wide-angle tailed radio sources in merging galaxy cluster environments
NASA Technical Reports Server (NTRS)
Loken, Chris; Roettiger, Kurt; Burns, Jack O.; Norman, Michael
1995-01-01
The intracluster medium (ICM) within merging clusters of galaxies is likely to be in a violent or turbulent dynamical state which may have a significant effect on the evolution of cluster radio sources. We present results from a recent gas + N-body simulation of a cluster merger, suggesting that mergers can result in long-lived, supersonic bulk flows, as well as shocks, within a few hundred kiloparsecs of the core of the dominant cluster. These results have motivated our new two-dimensional and three-dimensional simulations of jet propagation in such environments. The first set of simulations models the ISM/ICM transition as a contact discontinuity with a strong velocity shear. A supersonic (M(sub j) = 6) jet crossing this discontinuity into an ICM with a transverse, supersonic wind bends continuously, becomes 'naked' on the upwind side, and forms a distended cocoon on the downwind side. In the case of a mildly supersonic jet (M(sub j) = 3), however, a shock is driven into the ISM and ISM material is pulled along with the jet into the ICM. Instabilities excited at the ISM/ICM interface result in the jet repeatedly pinching off and reestablishing itself in a series of 'disconnection events.' The second set of simulations deals with a jet encountering a shock in the merging cluster environment. A series of relatively high-resolution two-dimensional calculations is used to confirm earlier analysis predicting that the jet will not disrupt when the jet Mach number is greater than the shock Mach number. A jet which survives the encounter with the shock will decrease in radius and disrupt shortly thereafter as a result of the growth of Kelvin-Helmholtz instabilities. We also find, in disagreement with predictions, that the jet flaring angle decreases with increasing jet density. Finally, a three-dimensional simulation of a jet crossing an oblique shock gives rise to a morphology which resembles a wide-angle tailed radio source with the jet flaring at the shock and
NASA Astrophysics Data System (ADS)
Lisinetskaya, Polina G.; Röhr, Merle I. S.; Mitrić, Roland
2016-06-01
We present a theoretical approach for the simulation of the electric field and exciton propagation in ordered arrays constructed of molecular-sized noble metal clusters bound to organic polymer templates. In order to describe the electronic coupling between individual constituents of the nanostructure we use the ab initio parameterized transition charge method which is more accurate than the usual dipole-dipole coupling. The electronic population dynamics in the nanostructure under an external laser pulse excitation is simulated by numerical integration of the time-dependent Schrödinger equation employing the fully coupled Hamiltonian. The solution of the TDSE gives rise to time-dependent partial point charges for each subunit of the nanostructure, and the spatio-temporal electric field distribution is evaluated by means of classical electrodynamics methods. The time-dependent partial charges are determined based on the stationary partial and transition charges obtained in the framework of the TDDFT. In order to treat large plasmonic nanostructures constructed of many constituents, the approximate self-consistent iterative approach presented in (Lisinetskaya and Mitrić in Phys Rev B 89:035433, 2014) is modified to include the transition-charge-based interaction. The developed methods are used to study the optical response and exciton dynamics of {Ag}3+ and porphyrin-Ag4 dimers. Subsequently, the spatio-temporal electric field distribution in a ring constructed of ten porphyrin-Ag4 subunits under the action of circularly polarized laser pulse is simulated. The presented methodology provides a theoretical basis for the investigation of coupled light-exciton propagation in nanoarchitectures built from molecular size metal nanoclusters in which quantum confinement effects are important.
NASA Astrophysics Data System (ADS)
Lisinetskaya, Polina G.; Röhr, Merle I. S.; Mitrić, Roland
2016-06-01
We present a theoretical approach for the simulation of the electric field and exciton propagation in ordered arrays constructed of molecular-sized noble metal clusters bound to organic polymer templates. In order to describe the electronic coupling between individual constituents of the nanostructure we use the ab initio parameterized transition charge method which is more accurate than the usual dipole-dipole coupling. The electronic population dynamics in the nanostructure under an external laser pulse excitation is simulated by numerical integration of the time-dependent Schrödinger equation employing the fully coupled Hamiltonian. The solution of the TDSE gives rise to time-dependent partial point charges for each subunit of the nanostructure, and the spatio-temporal electric field distribution is evaluated by means of classical electrodynamics methods. The time-dependent partial charges are determined based on the stationary partial and transition charges obtained in the framework of the TDDFT. In order to treat large plasmonic nanostructures constructed of many constituents, the approximate self-consistent iterative approach presented in (Lisinetskaya and Mitrić in Phys Rev B 89:035433, 2014) is modified to include the transition-charge-based interaction. The developed methods are used to study the optical response and exciton dynamics of Ag3+ and porphyrin-Ag4 dimers. Subsequently, the spatio-temporal electric field distribution in a ring constructed of ten porphyrin-Ag4 subunits under the action of circularly polarized laser pulse is simulated. The presented methodology provides a theoretical basis for the investigation of coupled light-exciton propagation in nanoarchitectures built from molecular size metal nanoclusters in which quantum confinement effects are important.
Pettit, Chris L; Wilson, D Keith
2007-09-01
Outdoor sound propagation predictions are compromised by uncertainty and error in the atmosphere and terrain representations, and sometimes also by simplified or incorrect physics. A model's predictive power, i.e., its accurate representation of the sound propagation, cannot be assessed without first quantifying the ensemble sound pressure variability and sensitivity to uncertainties in the model's governing parameters. This paper describes fundamental steps toward this goal for a single-frequency point source. The atmospheric surface layer is represented through Monin-Obukhov similarity theory and the acoustic ground properties with a relaxation model. Sound propagation is predicted with the parabolic equation method. Governing parameters are modeled as independent random variables across physically reasonable ranges. Latin hypercube sampling and proper orthogonal decomposition (POD) are employed in conjunction with cluster-weighted models to develop compact representations of the sound pressure random field. Full-field sensitivity of the sound pressure field is computed via the sensitivities of the POD mode coefficients to the system parameters. Ensemble statistics of the full-field sensitivities are computed to illustrate their relative importance at every down range location. The central role of sensitivity analysis in uncertainty quantification of outdoor sound propagation is discussed and pitfalls of sampling-based sensitivity analysis for outdoor sound propagation are described. PMID:17927400
Assaf, Khaleel I; Ural, Merve S; Pan, Fangfang; Georgiev, Tony; Simova, Svetlana; Rissanen, Kari; Gabel, Detlef; Nau, Werner M
2015-01-01
Dodecaborate anions of the type B12X122− and B12X11Y2− (X=H, Cl, Br, I and Y=OH, SH, NH3+, NR3+) form strong (Ka up to 106 L mol−1, for B12Br122−) inclusion complexes with γ-cyclodextrin (γ-CD). The micromolar affinities reached are the highest known for this native CD. The complexation exhibits highly negative enthalpies (up to −25 kcal mol−1) and entropies (TΔS up to −18.4 kcal mol−1, both for B12I122−), which position these guests at the bottom end of the well-known enthalpy-entropy correlation for CDs. The high driving force can be traced back to a chaotropic effect, according to which chaotropic anions have an intrinsic affinity to hydrophobic cavities in aqueous solution. In line with this argument, salting-in effects revealed dodecaborates as superchaotropic dianions. PMID:25951349
Wang, Jing; Vine, Claire E; Balasiny, Basema K; Rizk, John; Bradley, Charlene L; Tinajero-Trejo, Mariana; Poole, Robert K; Bergaust, Linda L; Bakken, Lars R; Cole, Jeffrey A
2016-06-01
The hybrid cluster protein, Hcp, contains a 4Fe-2S-2O iron-sulfur-oxygen cluster that is currently considered to be unique in biology. It protects various bacteria from nitrosative stress, but the mechanism is unknown. We demonstrate that the Escherichia coli Hcp is a high affinity nitric oxide (NO) reductase that is the major enzyme for reducing NO stoichiometrically to N2 O under physiologically relevant conditions. Deletion of hcp results in extreme sensitivity to NO during anaerobic growth and inactivation of the iron-sulfur proteins, aconitase and fumarase, by accumulated cytoplasmic NO. Site directed mutagenesis revealed an essential role in NO reduction for the conserved glutamate 492 that coordinates the hybrid cluster. The second gene of the hcp-hcr operon encodes an NADH-dependent reductase, Hcr. Tight interaction between Hcp and Hcr was demonstrated. Although Hcp and Hcr purified individually were inactive or when recombined, a co-purified preparation reduced NO in vitro with a Km for NO of 500 nM. In an hcr mutant, Hcp is reversibly inactivated by NO concentrations above 200 nM, indicating that Hcr protects Hcp from nitrosylation by its substrate, NO. PMID:26879449
High-order finite-element seismic wave propagation modeling with MPI on a large GPU cluster
Komatitsch, Dimitri; Erlebacher, Gordon; Goeddeke, Dominik; Michea, David
2010-10-01
We implement a high-order finite-element application, which performs the numerical simulation of seismic wave propagation resulting for instance from earthquakes at the scale of a continent or from active seismic acquisition experiments in the oil industry, on a large cluster of NVIDIA Tesla graphics cards using the CUDA programming environment and non-blocking message passing based on MPI. Contrary to many finite-element implementations, ours is implemented successfully in single precision, maximizing the performance of current generation GPUs. We discuss the implementation and optimization of the code and compare it to an existing very optimized implementation in C language and MPI on a classical cluster of CPU nodes. We use mesh coloring to efficiently handle summation operations over degrees of freedom on an unstructured mesh, and non-blocking MPI messages in order to overlap the communications across the network and the data transfer to and from the device via PCIe with calculations on the GPU. We perform a number of numerical tests to validate the single-precision CUDA and MPI implementation and assess its accuracy. We then analyze performance measurements and depending on how the problem is mapped to the reference CPU cluster, we obtain a speedup of 20x or 12x.
Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363.
Peters, Daniel T; Fung, Herman K H; Levdikov, Vladimir M; Irmscher, Tobias; Warrander, Fiona C; Greive, Sandra J; Kovalevskiy, Oleg; Isaacs, Harry V; Coles, Mark; Antson, Alfred A
2016-09-13
Lin28A is a post-transcriptional regulator of gene expression that interacts with and negatively regulates the biogenesis of let-7 family miRNAs. Recent data suggested that Lin28A also binds the putative tumor suppressor miR-363, a member of the 106~363 cluster of miRNAs. Affinity for this miRNA and the stoichiometry of the protein-RNA complex are unknown. Characterization of human Lin28's interaction with RNA has been complicated by difficulties in producing stable RNA-free protein. We have engineered a maltose binding protein fusion with Lin28, which binds let-7 miRNA with a Kd of 54.1 ± 4.2 nM, in agreement with previous data on a murine homologue. We show that human Lin28A binds miR-363 with a 1:1 stoichiometry and with a similar, if not higher, affinity (Kd = 16.6 ± 1.9 nM). Further analysis suggests that the interaction of the N-terminal cold shock domain of Lin28A with RNA is salt-dependent, supporting a model in which the cold shock domain allows the protein to sample RNA substrates through transient electrostatic interactions. PMID:27559824
High-order Finite-Element Seismic Wave Propagation Modeling with MPI on a large GPU Cluster
NASA Astrophysics Data System (ADS)
Göddeke, D.; Komatitsch, D.; Erlebacher, G.; Michéa, D.
2011-12-01
We develop a hybrid multi-GPU and CPU version of an algorithm to model seismic wave propagation based on the spectral-element method. We implement an open-source high-order finite-element application, called SPECFEM3D that performs the numerical simulation of seismic wave propagation resulting for instance from earthquakes at the scale of a continent or from active seismic acquisition experiments in the oil industry, on a large cluster of NVIDIA graphics cards using the CUDA programming environment and non-blocking message passing based on MPI. This allows users to handle large numerical grids and simulate a large number of time steps for each geophysical model under study. Contrary to many other numerical techniques, ours is implemented successfully in single precision, maximizing the performance of current generation GPUs. Our GPU code can handle models of the Earth containing both fluid and solid layers (which is the case for instance at the scale of the full Earth, whose outer core is fluid). We will discuss the implementation and optimization of the code and compare it to an existing very optimized implementation in C language and MPI on a classical cluster of CPU nodes. We remove dependencies between neighboring mesh elements, which cannot easily be handled in parallel, based upon a mesh coloring technique to create subsets of independent elements. Thus, we efficiently handle summation operations over degrees of freedom on an unstructured mesh. Non-blocking MPI messages allow overlap between communications across the network and the data transfer to and from the device via the PCI-Express bus with calculations on the GPU. We perform a number of numerical tests to validate the single-precision CUDA and MPI implementation and assess its accuracy. We then analyze performance measurements and depending on how the problem is mapped to the reference CPU cluster, we obtain a speedup of 20x or 12x. Thanks to the overlapping of communications and computation, we
Kuizenga, Merel H; Sia, Tiong C; Dodds, Kelsi N; Wiklendt, Lukasz; Arkwright, John W; Thomas, A; Brookes, Simon J; Spencer, Nick J; Wattchow, David A; Dinning, Phil G; Costa, Marcello
2015-01-01
Narrow muscle strips have been extensively used to study intestinal contractility. Larger specimens from laboratory animals have provided detailed understanding of mechanisms that underlie patterned intestinal motility. Despite progress in animal tissue, investigations of motor patterns in large, intact specimens of human gut ex vivo have been sparse. In this study, we tested whether neurally dependent motor patterns could be detected in isolated specimens of intact human ileum. Specimens (n = 14; 7-30 cm long) of terminal ileum were obtained with prior informed consent from patients undergoing colonic surgery for removal of carcinomas. Preparations were set up in an organ bath with an array of force transducers, a fiberoptic manometry catheter, and a video camera. Spontaneous and distension-evoked motor activity was recorded, and the effects of lidocaine, which inhibits neural activity, were studied. Myogenic contractions (ripples) occurred in all preparations (6.17 ± 0.36/min). They were of low amplitude and formed complex patterns by colliding and propagating in both directions along the specimen at anterograde velocities of 4.1 ± 0.3 mm/s and retrogradely at 4.9 ± 0.6 mm/s. In five specimens, larger amplitude clusters of contractions were seen (discrete clustered contractions), which propagated aborally at 1.05 ± 0.13 mm/s and orally at 1.07 ± 0.09 mm/s. These consisted of two to eight phasic contractions that aligned with ripples. These motor patterns were abolished by addition of lidocaine (0.3 mM). The ripples continued unchanged in the presence of this neural blocking agent. These results demonstrate that both myogenic and neurogenic motor patterns can be studied in isolated specimens of human small intestine. PMID:25394659
NASA Astrophysics Data System (ADS)
Balabanov, Nikolai B.; Peterson, Kirk A.
2006-08-01
Recently developed correlation consistent basis sets for the first row transition metal elements Sc-Zn have been utilized to determine complete basis set (CBS) scalar relativistic electron affinities, ionization potentials, and 4s23dn -2-4s1dn -1 electronic excitation energies with single reference coupled cluster methods [CCSD(T), CCSDT, and CCSDTQ] and multireference configuration interaction with three reference spaces: 3d4s, 3d4s4p, and 3d4s4p3d'. The theoretical values calculated with the highest order coupled cluster techniques at the CBS limit, including extrapolations to full configuration interaction, are well within 1kcal/mol of the corresponding experimental data. For the early transition metal elements (Sc-Mn) the internally contracted multireference averaged coupled pair functional method yielded excellent agreement with experiment; however, the atomic properties for the late transition metals (Mn-Zn) proved to be much more difficult to describe with this level of theory, even with the largest reference function of the present work.
NASA Astrophysics Data System (ADS)
Iwamoto, Hiroyuki; Tanaka, Nobuo; Hill, Simon G.
2012-10-01
This study presents the feedback control of flexural waves propagating in a rectangular panel. The objective of this paper (part 2) is to experimentally implement the feedback wave control method which was proposed in part 1 of the two series papers. Firstly, based on the collocation of sensors and actuators, clustered velocity and displacement feedback (C-VDFB) is newly proposed. Next, linking C-VDFB with the active wave control proposed in part 1, it is clarified that the active wave control system can be realized to a limited extent. Then, from a viewpoint of numerical simulations, the characteristics of the feedback gains of C-VDFB and its control performance are clarified. It is shown that C-VDFB enables the inactivation of vibration modes at the target frequencies. Furthermore, it is clarified that even at the non-target frequencies, the proposed method sufficiently reduces the structural vibration. Finally, experiments on the reflected wave absorbing control using clustered direct velocity and displacement feedback are carried out. The experimental results show good agreement with those obtained in the simulation.
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)
Constrained Clustering With Imperfect Oracles.
Zhu, Xiatian; Loy, Chen Change; Gong, Shaogang
2016-06-01
While clustering is usually an unsupervised operation, there are circumstances where we have access to prior belief that pairs of samples should (or should not) be assigned with the same cluster. Constrained clustering aims to exploit this prior belief as constraint (or weak supervision) to influence the cluster formation so as to obtain a data structure more closely resembling human perception. Two important issues remain open: 1) how to exploit sparse constraints effectively and 2) how to handle ill-conditioned/noisy constraints generated by imperfect oracles. In this paper, we present a novel pairwise similarity measure framework to address the above issues. Specifically, in contrast to existing constrained clustering approaches that blindly rely on all features for constraint propagation, our approach searches for neighborhoods driven by discriminative feature selection for more effective constraint diffusion. Crucially, we formulate a novel approach to handling the noisy constraint problem, which has been unrealistically ignored in the constrained clustering literature. Extensive comparative results show that our method is superior to the state-of-the-art constrained clustering approaches and can generally benefit existing pairwise similarity-based data clustering algorithms, such as spectral clustering and affinity propagation. PMID:25622327
Lin, Lin; Yang, Jucai
2015-06-01
The structures and energies of copper-doped small silicon clusters CuSi n (n = 4-10) and their anions were investigated systematically using CCSD(T)/aug-cc-pVTZ-DK//MP2/6-31G(2df,p), G4//MP2/6-31G(2df,p), and the B3LYP/6-311+G* basis set. The performance of the methods used for the prediction of energetic and thermodynamic properties was evaluated. Comparing experimental [Xu et al. (2012) J Chem Phys 136:104308] and theoretical calculations, it was concluded that the CCSD(T) results are very accurate and exhibit the best performance; the mean absolute deviation from experimental data was 0.043 eV. The excellent agreement of vertical detachment energy (VDE) between experimental results and CCSD(T) calculations indicates that the ground state structures of CuSi n (-) (n = 4-10) presented in this paper are reliable. For CuSi10, assigning 2.90±0.08 eV to the experimental adiabatic electron affinity (AEA) and 3.90±0.08 eV to the VDE is more reasonable than to 3.46±0.08 eV and 3.62±0.08 eV, respectively, based on the CCSD(T) calculations and the previous photoelectron spectrum of CuSi10 (-) (Xu et al., op. cit.). The AEAs of CuSi n (n = 4-10), excluding CuSi7, are in excellent agreement with experimental data, showing that the ground state structures of CuSi n (n = 4-6, 8-10) reported in this paper are reliable. CuSi10 is suggested to be the smallest endohedral ground state structure. However, adding an additional electron to CuSi10 pulls out the Cu atom from the center location, forming an exohedral ground state structure of CuSi10 (-). The charge transfer and dissociation energy of Cu from CuSi n and their anions determined to examine the nature of bonding and their relative stabilities. PMID:26003428
NASA Astrophysics Data System (ADS)
Pourfathi, M.; Kuzma, N. N.; Kara, H.; Ghosh, R. K.; Shaghaghi, H.; Kadlecek, S. J.; Rizi, R. R.
2013-10-01
Earlier Dynamic Nuclear Polarization (DNP) experiments with frozen xenon/1-propanol/trityl mixtures have demonstrated spontaneous formation of pure xenon clusters above 120 K, enabling spectrally-resolved real-time measurements of 129Xe nuclear magnetization in the clusters and in the surrounding radical-rich matrix. A spin-diffusion bottleneck was postulated to explain the peculiar time evolution of 129Xe signals in the clusters as well as the apparent discontinuity of 129Xe polarization across the cluster boundaries. A self-contained ab initio model of nuclear spin diffusion in heterogeneous systems is developed here, incorporating the intrinsic T1 relaxation towards the temperature-dependent equilibrium polarization and the spin-diffusion coefficients based on the measured NMR line widths and the known atomic densities in each compartment. This simple model provides the physical basis for the observed spin-diffusion bottleneck and is in a good quantitative agreement with the earlier measurements. A simultaneous fit of the model to the time-dependent NMR data at two different DNP frequencies provides excellent estimates of the cluster size, the intrinsic sample temperature, and 129Xe T1 constants. The model was also applied to the NMR data acquired during relaxation towards the thermal equilibrium after the microwaves were turned off, to estimate T1 relaxation time constants inside and outside the clusters. Fitting the model to the data during and after DNP provides consistent estimates of the cluster size.
A Novel Vertex Affinity for Community Detection
Yoo, Andy; Sanders, Geoffrey; Henson, Van; Vassilevski, Panayot
2015-10-05
We propose a novel vertex affinity measure in this paper. The new vertex affinity quantifies the proximity between two vertices in terms of their clustering strength and is ideal for such graph analytics applications as community detection. We also developed a framework that combines simple graph searches and resistance circuit formulas to compute the vertex affinity efficiently. We study the properties of the new affinity measure empirically in comparison to those of other popular vertex proximity metrics. Our results show that the existing metrics are ill-suited for community detection due to their lack of fundamental properties that are essential for correctly capturing inter- and intra-cluster vertex proximity.
Vega, Yolanda; Delgado, Elena; Fernández-García, Aurora; Cuevas, Maria Teresa; Thomson, Michael M.; Montero, Vanessa; Sánchez, Monica; Sánchez, Ana Maria; Pérez-Álvarez, Lucia
2015-01-01
Our objectives were to carry out an epidemiological surveillance study on transmitted drug resistance (TDR) among individuals newly diagnosed of HIV-1 infection during a nine year period in Spain and to assess the role of transmission clusters (TC) in the propagation of resistant strains. An overall of 1614 newly diagnosed individuals were included in the study from January 2004 through December 2012. Individuals come from two different Spanish regions: Galicia and the Basque Country. Resistance mutations to reverse transcriptase inhibitors (RTI) and protease inhibitors (PI) were analyzed according to mutations included in the surveillance drug-resistance mutations list updated in 2009. TC were defined as those comprising viruses from five or more individuals whose sequences clustered in maximum likelihood phylogenetic trees with a bootstrap value ≥90%. The overall prevalence of TDR to any drug was 9.9%: 4.9% to nucleoside RTIs (NRTIs), 3.6% to non-nucleoside RTIs (NNRTIs), and 2.7% to PIs. A significant decrease of TDR to NRTIs over time was observed [from 10% in 2004 to 2% in 2012 (p=0.01)]. Sixty eight (42.2%) of 161 sequences with TDR were included in 25 TC composed of 5 or more individuals. Of them, 9 clusters harbored TDR associated with high level resistance to antiretroviral drugs. T215D revertant mutation was transmitted in a large cluster comprising 25 individuals. The impact of epidemiological networks on TDR frequency may explain its persistence in newly diagnosed individuals. The knowledge of the populations involved in TC would facilitate the design of prevention programs and public health interventions. PMID:26010948
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)
Han, Wen-Ge; Sandala, Gregory M.; Giammona, Debra Ann; Bashford, Donald; Noodleman, Louis
2013-01-01
The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their Mössbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976–5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed 57Fe Mössbauer quadrupole splitting (2.41 mm s−1) and lower isomer shift (0.45 mm s−1) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol−1. Therefore our calculations support the proposal of the previous Mössbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al. PMID:21837345
Full Text Clustering and Relationship Network Analysis of Biomedical Publications
Guan, Renchu; Yang, Chen; Marchese, Maurizio; Liang, Yanchun; Shi, Xiaohu
2014-01-01
Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP) to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers. PMID:25250864
Full text clustering and relationship network analysis of biomedical publications.
Guan, Renchu; Yang, Chen; Marchese, Maurizio; Liang, Yanchun; Shi, Xiaohu
2014-01-01
Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP) to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers. PMID:25250864
Special Report: Affinity Chromatography.
ERIC Educational Resources Information Center
Parikh, Indu; Cuatrecasas, Pedro
1985-01-01
Describes the nature of affinity chromatography and its use in purifying enzymes, studying cell interactions, exploring hormone receptors, and other areas. The potential the technique may have in treating disease is also considered. (JN)
Join-Graph Propagation Algorithms
Mateescu, Robert; Kask, Kalev; Gogate, Vibhav; Dechter, Rina
2010-01-01
The paper investigates parameterized approximate message-passing schemes that are based on bounded inference and are inspired by Pearl's belief propagation algorithm (BP). We start with the bounded inference mini-clustering algorithm and then move to the iterative scheme called Iterative Join-Graph Propagation (IJGP), that combines both iteration and bounded inference. Algorithm IJGP belongs to the class of Generalized Belief Propagation algorithms, a framework that allowed connections with approximate algorithms from statistical physics and is shown empirically to surpass the performance of mini-clustering and belief propagation, as well as a number of other state-of-the-art algorithms on several classes of networks. We also provide insight into the accuracy of iterative BP and IJGP by relating these algorithms to well known classes of constraint propagation schemes. PMID:20740057
NASA Technical Reports Server (NTRS)
Embleton, Tony F. W.; Daigle, Gilles A.
1991-01-01
Reviewed here is the current state of knowledge with respect to each basic mechanism of sound propagation in the atmosphere and how each mechanism changes the spectral or temporal characteristics of the sound received at a distance from the source. Some of the basic processes affecting sound wave propagation which are present in any situation are discussed. They are geometrical spreading, molecular absorption, and turbulent scattering. In geometrical spreading, sound levels decrease with increasing distance from the source; there is no frequency dependence. In molecular absorption, sound energy is converted into heat as the sound wave propagates through the air; there is a strong dependence on frequency. In turbulent scattering, local variations in wind velocity and temperature induce fluctuations in phase and amplitude of the sound waves as they propagate through an inhomogeneous medium; there is a moderate dependence on frequency.
NASA Astrophysics Data System (ADS)
Komatitsch, Dimitri; Michéa, David; Erlebacher, Gordon; Göddeke, Dominik
2010-05-01
We first accelerate a three-dimensional finite-difference in the time domain (FDTD) wave propagation code by a factor of about 50 using Graphics Processing Unit (GPU) computing on a cheap NVIDIA graphics card with the CUDA programming language. We implement the code in CUDA in the case of the fully heterogeneous elastic wave equation. We also implement Convolution Perfectly Matched Layers (CPMLs) on the graphics card to efficiently absorb outgoing waves on the fictitious edges of the grid. We show that the code that runs on the graphics card gives the expected results by comparing our results to those obtained by running the same simulation on a classical processor core. The methodology that we present can be used for Maxwell's equations as well because their form is similar to that of the seismic wave equation written in velocity vector and stress tensor. We then implement a high-order finite-element (spectral-element) application, which performs the numerical simulation of seismic wave propagation resulting for instance from earthquakes at the scale of a continent or from active seismic acquisition experiments in the oil industry, on a cluster of NVIDIA Tesla graphics cards using the CUDA programming language and non blocking message passing based on MPI. We compare it to the implementation in C language and MPI on a classical cluster of CPU nodes. We use mesh coloring to efficiently handle summation operations over degrees of freedom on an unstructured mesh, and we exchange information between nodes using non blocking MPI messages. Using non-blocking communications allows us to overlap the communications across the network and the data transfer between the GPU card and the CPU node on which it is installed with calculations on that GPU card. We perform a number of numerical tests to validate the single-precision CUDA and MPI implementation and assess its accuracy. We then analyze performance measurements and in average we obtain a speedup of 20x to 25x.
Affinity+: Semi-Structured Brainstorming on Large Displays
Burtner, Edwin R.; May, Richard A.; Scarberry, Randall E.; LaMothe, Ryan R.; Endert, Alexander
2013-04-27
Affinity diagraming is a powerful method for encouraging and capturing lateral thinking in a group environment. The Affinity+ Concept was designed to improve the collaborative brainstorm process through the use of large display surfaces in conjunction with mobile devices like smart phones and tablets. The system works by capturing the ideas digitally and allowing users to sort and group them on a large touch screen manually. Additionally, Affinity+ incorporates theme detection, topic clustering, and other processing algorithms that help bring structured analytic techniques to the process without requiring explicit leadership roles and other overhead typically involved in these activities.
Noble, P. A.; Bidle, K. D.; Fletcher, M.
1997-01-01
The community compositions of free-living and particle-associated bacteria in the Chesapeake Bay estuary were analyzed by comparing banding patterns of stable low-molecular-weight RNA (SLMW RNA) which include 5S rRNA and tRNA molecules. By analyzing images of autoradiographs of SLMW RNAs on polyacrylamide gels, band intensities of 5S rRNA were converted to binary format for transmission to a back-propagating neural network (NN). The NN was trained to relate binary input to sample stations, collection times, positions in the water column, and sample types (e.g., particle-associated versus free-living communities). Dendrograms produced by using Euclidean distance and average and Ward's linkage methods on data of three independently trained NNs yielded the following results. (i) Community compositions of Chesapeake Bay water samples varied both seasonally and spatially. (ii) Although there was no difference in the compositions of free-living and particle-associated bacteria in the summer, these community types differed significantly in the winter. (iii) In the summer, most bay samples had a common 121-nucleotide 5S rRNA molecule. Although this band occurred in the top water of midbay samples, it did not occur in particle-associated communities of bottom-water samples. (iv) Regardless of the season, midbay samples had the greatest variety of 5S rRNA sizes. The utility of NNs for interpreting complex banding patterns in electrophoresis gels was demonstrated. PMID:16535593
Delplace, Vianney; Obermeyer, Jaclyn; Shoichet, Molly S
2016-07-26
The use of hydrogels for therapeutic delivery is a burgeoning area of investigation. These water-swollen polymer matrices are ideal platforms for localized drug delivery that can be further combined with specific ligands or nanotechnologies to advance the controlled release of small-molecule drugs and proteins. Due to the advantage of hydrophobic, electrostatic, or specific extracellular matrix interactions, affinity-based strategies can overcome burst release and challenges associated with encapsulation. Future studies will provide innovative binding tools, truly stimuli-responsive systems, and original combinations of emerging technologies to control the release of therapeutics spatially and temporally. Local drug delivery can be achieved by directly injecting a therapeutic to its site of action and is advantageous because off-target effects associated with systemic delivery can be minimized. For prolonged benefit, a vehicle that provides sustained drug release is required. Hydrogels are versatile platforms for localized drug release, owing to the large library of biocompatible building blocks from which they can be formed. Injectable hydrogel formulations that gel quickly in situ and provide sustained release of therapeutics are particularly advantageous to minimize invasiveness. The incorporation of polymers, ligands or nanoparticles that have an affinity for the therapeutic of interest improve control over the release of small-molecule drugs and proteins from hydrogels, enabling spatial and temporal control over the delivery. Such affinity-based strategies can overcome drug burst release and challenges associated with protein instability, allowing more effective therapeutic molecule delivery for a range of applications from therapeutic contact lenses to ischemic tissue regeneration. PMID:27403513
Morphometric affinities of gigantopithecus.
Gelvin, B R
1980-11-01
Multivariate analyses, supplemented by univariate statistical methods, of measurements from mandibular tooth crown dimensions and the mandible of Gigantopithecus blacki, G. bilaspurensis, Plio-Plelstocene hominids, Homo erectus, and seven Neogene ape species from the genera Proconsul, Sivapithecus, Ouranopithecus, and Dryopithecus were used to assess the morphometric affinities of Gigantopithecus. The results show that Gigantopithecus displays affinities to Ouranopithecus and to the hominids, particularly the Plio-Plelstocene hominids, rather than to the apes. Ouranopithecus demonstrated dental resemblances to G. bilaspurensis and the Plio-Pleistocene hominids but mandibular similarities to the apes. Results of analyses of tooth and mandibular shape indices, combined with multivariate distance and temporal relationships, suggest that Ouranopithecus is a more likely candidate for Gigantopithecus ancestry than is Silvapithecus indicus. Shape and allometric differences between G. bilaspurensis and the robust australopithecines weaken the argument for an ancestral-descendant relationship between these groups. The results support the hypothesis that Gigantopithecus is an extinct side branch of the Hominidae. PMID:7468790
On constructing purely affine theories with matter
NASA Astrophysics Data System (ADS)
Cervantes-Cota, Jorge L.; Liebscher, D.-E.
2016-08-01
We explore ways to obtain the very existence of a space-time metric from an action principle that does not refer to it a priori. Although there are reasons to believe that only a non-local theory can viably achieve this goal, we investigate here local theories that start with Schrödinger's purely affine theory (Schrödinger in Space-time structure. Cambridge UP, Cambridge, 1950), where he gave reasons to set the metric proportional to the Ricci curvature aposteriori. When we leave the context of unified field theory, and we couple the non-gravitational matter using some weak equivalence principle, we can show that the propagation of shock waves does not define a lightcone when the purely affine theory is local and avoids the explicit use of the Ricci tensor in realizing the weak equivalence principle. When the Ricci tensor is substituted for the metric, the equations seem to have only a very limited set of solutions. This backs the conviction that viable purely affine theories have to be non-local.
Adjoint affine fusion and tadpoles
NASA Astrophysics Data System (ADS)
Urichuk, Andrew; Walton, Mark A.
2016-06-01
We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.
NASA Technical Reports Server (NTRS)
Parmentier, E. M.; Schubert, G.
1989-01-01
A model for rift propagation which treats the rift as a crack in an elastic plate which is filled from beneath by upwelling viscous asthenosphere as it lengthens and opens. Growth of the crack is driven by either remotely applied forces or the pressure of buoyant asthenosphere in the crack and is resisted by viscous stresses associated with filling the crack. The model predicts a time for a rift to form which depends primarily on the driving stress and asthenosphere viscosity. For a driving stress on the order of 10 MPa, as expected from the topography of rifted swells, the development of rifts over times of a few Myr requires an asthenosphere viscosity of 10 to the 16th Pa s (10 to the 17th poise). This viscosity, which is several orders of magnitude less than values determined by postglacial rebound and at least one order of magnitude less than that inferred for spreading center propagation, may reflect a high temperature or large amount of partial melting in the mantle beneath a rifted swell.
Affinity chromatography: a historical perspective.
Hage, David S; Matsuda, Ryan
2015-01-01
Affinity chromatography is one of the most selective and versatile forms of liquid chromatography for the separation or analysis of chemicals in complex mixtures. This method makes use of a biologically related agent as the stationary phase, which provides an affinity column with the ability to bind selectively and reversibly to a given target in a sample. This review examines the early work in this method and various developments that have lead to the current status of this technique. The general principles of affinity chromatography are briefly described as part of this discussion. Past and recent efforts in the generation of new binding agents, supports, and immobilization methods for this method are considered. Various applications of affinity chromatography are also summarized, as well as the influence this field has played in the creation of other affinity-based separation or analysis methods. PMID:25749941
Identifying survival-associated ceRNA clusters in cholangiocarcinoma.
Wan, Ming; Zhang, Fu-Min; Li, Zheng-Long; Kang, Peng-Cheng; Jiang, Ping-Ming; Wang, Yi-Min; Wang, Zhi-Dong; Zhong, Xiang-Yu; Li, Chun-Long; Wang, Hao; Zhao, Shi-Yong; Cui, Yun-Fu
2016-09-01
Competing endogenous RNAs (ceRNAs) represent a novel layer regulations of long non-coding RNAs (lncRNAs) and genes that play important roles in cancer pathogenesis by binding microRNAs (miRNAs). However, the competition mechanism of ceRNAs in cholangiocarcinoma (CHOL) is not fully understood. In this study, we constructed a dysregulated ceRNA competitive network (CCEN) to globally characterize the competing difference between CHOL and normal tissues. Then, we integrated affinity propagation and Kaplan‑Meier (K-M) methods to identify functional clusters associated with survival. A total of 7 key ceRNA clusters were identified. Further functional annotation analyses found that Cluster23 and Cluster32 involved cell based functions, and the loss of ceRNA competitive relations in clusters may contribute to CHOL, by disturbing important biological processes, such as 'Pathway in cancer', MAPK and Neurotrophin signaling pathway. This study provides further insights into understanding the competitive mechanism of ceRNAs in CHOL. PMID:27432084
Fatigue damage prognosis using affine arithmetic
NASA Astrophysics Data System (ADS)
Gbaguidi, Audrey; Kim, Daewon
2014-02-01
Among the essential steps to be taken in structural health monitoring systems, damage prognosis would be the field that is least investigated due to the complexity of the uncertainties. This paper presents the possibility of using Affine Arithmetic for uncertainty propagation of crack damage in damage prognosis. The structures examined are thin rectangular plates made of titanium alloys with central mode I cracks and a composite plate with an internal delamination caused by mixed mode I and II fracture modes, under a harmonic uniaxial loading condition. The model-based method for crack growth rates are considered using the Paris Erdogan law model for the isotropic plates and the delamination growth law model proposed by Kardomateas for the composite plate. The parameters for both models are randomly taken and their uncertainties are considered as defined by an interval instead of a probability distribution. A Monte Carlo method is also applied to check whether Affine Arithmetic (AA) leads to tight bounds on the lifetime of the structure.
Enhancing Community Detection By Affinity-based Edge Weighting Scheme
Yoo, Andy; Sanders, Geoffrey; Henson, Van; Vassilevski, Panayot
2015-10-05
Community detection refers to an important graph analytics problem of finding a set of densely-connected subgraphs in a graph and has gained a great deal of interest recently. The performance of current community detection algorithms is limited by an inherent constraint of unweighted graphs that offer very little information on their internal community structures. In this paper, we propose a new scheme to address this issue that weights the edges in a given graph based on recently proposed vertex affinity. The vertex affinity quantifies the proximity between two vertices in terms of their clustering strength, and therefore, it is ideal for graph analytics applications such as community detection. We also demonstrate that the affinity-based edge weighting scheme can improve the performance of community detection algorithms significantly.
Overview of affinity tags for protein purification.
Kimple, Michelle E; Sondek, John
2004-09-01
Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, and for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future. PMID:18429272
Overview of affinity tags for protein purification.
Kimple, Michelle E; Brill, Allison L; Pasker, Renee L
2013-01-01
Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future. PMID:24510596
Affine Contractions on the Plane
ERIC Educational Resources Information Center
Celik, D.; Ozdemir, Y.; Ureyen, M.
2007-01-01
Contractions play a considerable role in the theory of fractals. However, it is not easy to find contractions which are not similitudes. In this study, it is shown by counter examples that an affine transformation of the plane carrying a given triangle onto another triangle may not be a contraction even if it contracts edges, heights or medians.…
Quantifying Affinity among Chinese Dialects.
ERIC Educational Resources Information Center
Cheng, Chin-Chuan
A study of the relationships between Chinese dialects based on a quantitative measure of dialect affinity is summarized. First, tone values in all the dialect localities available in the early 1970s were used to calculate the dialectal differences in terms of tone height with respect to the "yin and yang" split. In the late 1970s, calculations of…
Theoretical proton affinity and fluoride affinity of nerve agent VX.
Bera, Narayan C; Maeda, Satoshi; Morokuma, Keiji; Viggiano, Al A
2010-12-23
Proton affinity and fluoride affinity of nerve agent VX at all of its possible sites were calculated at the RI-MP2/cc-pVTZ//B3LYP/6-31G* and RI-MP2/aug-cc-pVTZ//B3LYP/6-31+G* levels, respectively. The protonation leads to various unique structures, with H(+) attached to oxygen, nitrogen, and sulfur atoms; among which the nitrogen site possesses the highest proton affinity of -ΔE ∼ 251 kcal/mol, suggesting that this is likely to be the major product. In addition some H(2), CH(4) dissociation as well as destruction channels have been found, among which the CH(4) + [Et-O-P(═O)(Me)-S-(CH(2))(2)-N(+)(iPr)═CHMe] product and the destruction product forming Et-O-P(═O)(Me)-SMe + CH(2)═N(+)(iPr)(2) are only 9 kcal/mol less stable than the most stable N-protonated product. For fluoridization, the S-P destruction channel to give Et-O-P(═O)(Me)(F) + [S-(CH(2))(2)-N-(iPr)(2)](-) is energetically the most favorable, with a fluoride affinity of -ΔE ∼ 44 kcal. Various F(-) ion-molecule complexes are also found, with the one having F(-) interacting with two hydrogen atoms in different alkyl groups to be only 9 kcal/mol higher than the above destruction product. These results suggest VX behaves quite differently from surrogate systems. PMID:21117653
Lopez-Meyer, Paulo; Schuckers, Stephanie; Makeyev, Oleksandr; Fontana, Juan M.; Sazonov, Edward
2012-01-01
The number of distinct foods consumed in a meal is of significant clinical concern in the study of obesity and other eating disorders. This paper proposes the use of information contained in chewing and swallowing sequences for meal segmentation by food types. Data collected from experiments of 17 volunteers were analyzed using two different clustering techniques. First, an unsupervised clustering technique, Affinity Propagation (AP), was used to automatically identify the number of segments within a meal. Second, performance of the unsupervised AP method was compared to a supervised learning approach based on Agglomerative Hierarchical Clustering (AHC). While the AP method was able to obtain 90% accuracy in predicting the number of food items, the AHC achieved an accuracy >95%. Experimental results suggest that the proposed models of automatic meal segmentation may be utilized as part of an integral application for objective Monitoring of Ingestive Behavior in free living conditions. PMID:23125872
Lectin affinity chromatography of glycolipids
Torres, B.V.; Smith, D.F.
1987-05-01
Since glycolipids (GLs) are either insoluble or form mixed micelles in water, lectin affinity chromatography in aqueous systems has not been applied to their separation. They have overcome this problem by using tetrahydrofuran (THF) in the mobile phase during chromatography. Affinity columns prepared with the GalNAc-specific Helix pomatia agglutinin (HPA) and equilibrated in THF specifically bind the (/sup 3/H)oligosaccharide derived from Forssman GL indicating that the immobilized HPA retained its carbohydrate-binding specificity in this solvent. Intact Forssman GL was bound by the HPA-column equilibrated in THF and was specifically eluted with 0.1 mg/ml GalNAc in THF. Purification of the Forssman GL was achieved when a crude lipid extract of sheep erythrocyte membranes was applied to the HPA-column in THF. Non-specifically bound GLs were eluted from the column using a step gradient of aqueous buffer in THF, while the addition of GalNAc was required to elute the specifically bound GLs. Using this procedure the A-active GLs were purified from a crude lipid extract of type A human erythrocytes in a single chromatographic step. The use of solvents that maintain carbohydrate-binding specificity and lipid solubility will permit the application of affinity chromatography on immobilized carbohydrate-binding proteins to intact GLs.
Affinity learning with diffusion on tensor product graph.
Yang, Xingwei; Prasad, Lakshman; Latecki, Longin Jan
2013-01-01
In many applications, we are given a finite set of data points sampled from a data manifold and represented as a graph with edge weights determined by pairwise similarities of the samples. Often the pairwise similarities (which are also called affinities) are unreliable due to noise or due to intrinsic difficulties in estimating similarity values of the samples. As observed in several recent approaches, more reliable similarities can be obtained if the original similarities are diffused in the context of other data points, where the context of each point is a set of points most similar to it. Compared to the existing methods, our approach differs in two main aspects. First, instead of diffusing the similarity information on the original graph, we propose to utilize the tensor product graph (TPG) obtained by the tensor product of the original graph with itself. Since TPG takes into account higher order information, it is not a surprise that we obtain more reliable similarities. However, it comes at the price of higher order computational complexity and storage requirement. The key contribution of the proposed approach is that the information propagation on TPG can be computed with the same computational complexity and the same amount of storage as the propagation on the original graph. We prove that a graph diffusion process on TPG is equivalent to a novel iterative algorithm on the original graph, which is guaranteed to converge. After its convergence we obtain new edge weights that can be interpreted as new, learned affinities. We stress that the affinities are learned in an unsupervised setting. We illustrate the benefits of the proposed approach for data manifolds composed of shapes, images, and image patches on two very different tasks of image retrieval and image segmentation. With learned affinities, we achieve the bull's eye retrieval score of 99.99 percent on the MPEG-7 shape dataset, which is much higher than the state-of-the-art algorithms. When the data
NASA Technical Reports Server (NTRS)
Klauder, John R.
1993-01-01
For a general Hamiltonian appropriate to a single canonical degree of freedom, a universal propagator with the property that it correctly evolves the coherent-state Hilbert space representatives for an arbitrary fiducial vector is characterized and defined. The universal propagator is explicitly constructed for the harmonic oscillator, with a result that differs from the conventional propagators for this system.
Immobilized metal ion affinity chromatography.
Yip, T T; Hutchens, T W
1992-01-01
Immobilized metal ion affinity chromatography (IMAC) (1,2) is also referred to as metal chelate chromatography, metal ion interaction chromatography, and ligand-exchange chromatography. We view this affinity separation technique as an intermediate between highly specific, high-affinity bioaffinity separation methods, and wider spectrum, low-specificity adsorption methods, such as ion exchange. The IMAC stationary phases are designed to chelate certain metal ions that have selectivity for specific groups (e.g., His residues) in peptides (e.g., 3-7) and on protein surfaces (8-13). The number of stationary phases that can be synthesized for efficient chelation of metal ions is unlimited, but the critical consideration is that there must be enough exposure of the metal ion to interact with the proteins, preferably in a biospecific manner. Several examples are presented in Fig. 1. The challenge to produce new immobilized chelating groups, including protein surface metal-binding domains (14,15) is being explored continuously. Table 1 presents a list of published procedures for the synthesis and use of stationary phases with immobilized chelating groups. This is by no means exhaustive, and is intended only to give an idea of the scope and versatility of IMAC. Fig. 1 Schematic illustration of several types of immobilized metal-chelating groups, including, iminodiacetate (IDA), tris(carboxymethyl) ethylenediamine (TED), and the metal-binding peptides (GHHPH)(n)G (where n = 1,2,3, and 5) (14,15). Table 1 Immobilized Chelating Groups and Metal Ions Used for Immobilized Metal Ion Affinity Chromatography Chelating group Suitable metal ions Reference Commercial source Immodiacetate Transitional1,2 Pharmacia LKB Pierce Sigma Boehringer Mannheim TosoHaas 2-Hydroxy-3[N-(2- pyrtdylmethyl) glycme]propyl Transitional3 Not available ?-Alky1 mtrilo triacetic acid Transitional4 Not available Carboxymethylated asparhc acid Ca(II)13 Not available Tris (carboxy- methyl) ethylene Diamme
Purification of phage display-modified bacteriophage T4 by affinity chromatography
2011-01-01
Background Affinity chromatography is one of the most efficient protein purification strategies. This technique comprises a one-step procedure with a purification level in the order of several thousand-fold, adaptable for various proteins, differentiated in their size, shape, charge, and other properties. The aim of this work was to verify the possibility of applying affinity chromatography in bacteriophage purification, with the perspective of therapeutic purposes. T4 is a large, icosahedral phage that may serve as an efficient display platform for foreign peptides or proteins. Here we propose a new method of T4 phage purification by affinity chromatography after its modification with affinity tags (GST and Histag) by in vivo phage display. As any permanent introduction of extraneous DNA into a phage genome is strongly unfavourable for medical purposes, integration of foreign motifs with the phage genome was not applied. The phage was propagated in bacteria expressing fusions of the phage protein Hoc with affinity tags from bacterial plasmids, independently from the phage expression system. Results Elution profiles of phages modified with the specific affinity motifs (compared to non-specific phages) document their binding to the affinity resins and effective elution with standard competitive agents. Non-specific binding was also observed, but was 102-105 times weaker than the specific one. GST-modified bacteriophages were also effectively released from glutathione Sepharose by proteolytic cleavage. The possibility of proteolytic release was designed at the stage of expression vector construction. Decrease in LPS content in phage preparations was dependent on the washing intensity; intensive washing resulted in preparations of 11-40 EU/ml. Conclusions Affinity tags can be successfully incorporated into the T4 phage capsid by the in vivo phage display technique and they strongly elevate bacteriophage affinity to a specific resin. Affinity chromatography can be
Indian craniometric variability and affinities.
Raghavan, Pathmanathan; Bulbeck, David; Pathmanathan, Gayathiri; Rathee, Suresh Kanta
2013-01-01
Recently published craniometric and genetic studies indicate a predominantly indigenous ancestry of Indian populations. We address this issue with a fuller coverage of Indian craniometrics than any done before. We analyse metrical variability within Indian series, Indians' sexual dimorphism, differences between northern and southern Indians, index-based differences of Indian males from other series, and Indians' multivariate affinities. The relationship between a variable's magnitude and its variability is log-linear. This relationship is strengthened by excluding cranial fractions and series with a sample size less than 30. Male crania are typically larger than female crania, but there are also shape differences. Northern Indians differ from southern Indians in various features including narrower orbits and less pronounced medial protrusion of the orbits. Indians resemble Veddas in having small crania and similar cranial shape. Indians' wider geographic affinities lie with "Caucasoid" populations to the northwest, particularly affecting northern Indians. The latter finding is confirmed from shape-based Mahalanobis-D distances calculated for the best sampled male and female series. Demonstration of a distinctive South Asian craniometric profile and the intermediate status of northern Indians between southern Indians and populations northwest of India confirm the predominantly indigenous ancestry of northern and especially southern Indians. PMID:24455409
Indian Craniometric Variability and Affinities
Raghavan, Pathmanathan; Bulbeck, David; Pathmanathan, Gayathiri; Rathee, Suresh Kanta
2013-01-01
Recently published craniometric and genetic studies indicate a predominantly indigenous ancestry of Indian populations. We address this issue with a fuller coverage of Indian craniometrics than any done before. We analyse metrical variability within Indian series, Indians' sexual dimorphism, differences between northern and southern Indians, index-based differences of Indian males from other series, and Indians' multivariate affinities. The relationship between a variable's magnitude and its variability is log-linear. This relationship is strengthened by excluding cranial fractions and series with a sample size less than 30. Male crania are typically larger than female crania, but there are also shape differences. Northern Indians differ from southern Indians in various features including narrower orbits and less pronounced medial protrusion of the orbits. Indians resemble Veddas in having small crania and similar cranial shape. Indians' wider geographic affinities lie with “Caucasoid” populations to the northwest, particularly affecting northern Indians. The latter finding is confirmed from shape-based Mahalanobis-D distances calculated for the best sampled male and female series. Demonstration of a distinctive South Asian craniometric profile and the intermediate status of northern Indians between southern Indians and populations northwest of India confirm the predominantly indigenous ancestry of northern and especially southern Indians. PMID:24455409
Muetterties, Earl L.
1980-05-01
Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.
NASA Propagation Studies Website
NASA Technical Reports Server (NTRS)
Angkasa, Krisjani S.
1996-01-01
The NASA propagation studies objective is to enable the development of new commercial satellite communication systems and services by providing timely data and models about propagation of satellite radio signals through the intervening environment and to support NASA missions. In partnership with industry and academia, the program leverages unique NASA assets (currently Advanced Communications Technology Satellite) to obtain propagation data. The findings of the study are disseminated through referred journals, NASA reference publications, workshops, electronic media, and direct interface with industry.
Affine hypersurfaces with parallel difference tensor relative to affine α-connection
NASA Astrophysics Data System (ADS)
Li, Cece
2014-12-01
Li and Zhang (2014) studied affine hypersurfaces of R n + 1 with parallel difference tensor relative to the affine α-connection ∇ (α), and characterized the generalized Cayley hypersurfaces by K n - 1 ≠ 0 and ∇ (α) K = 0 for some nonzero constant α, where the affine α-connection ∇ (α) of information geometry was introduced on affine hypersurface. In this paper, by a slightly different method we continue to study affine hypersurfaces with ∇ (α) K = 0, if α = 0 we further assume that the Pick invariant vanishes and affine metric is of constant sectional curvature. It is proved that they are either hyperquadrics or improper affine hypersphere with flat indefinite affine metric, the latter can be locally given as a graph of a polynomial of at most degree n + 1 with constant Hessian determinant. In particular, if the affine metric is definite, Lorentzian, or its negative index is 2, we complete the classification of such hypersurfaces.
The maximal affinity of ligands
Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A.
1999-01-01
We explore the question of what are the best ligands for macromolecular targets. A survey of experimental data on a large number of the strongest-binding ligands indicates that the free energy of binding increases with the number of nonhydrogen atoms with an initial slope of ≈−1.5 kcal/mol (1 cal = 4.18 J) per atom. For ligands that contain more than 15 nonhydrogen atoms, the free energy of binding increases very little with relative molecular mass. This nonlinearity is largely ascribed to nonthermodynamic factors. An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands. Interesting outliers that bind unusually strongly on a per atom basis include metal ions, covalently attached ligands, and a few well known complexes such as biotin–avidin. PMID:10468550
Protein Complex Purification by Affinity Capture.
LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P
2016-01-01
Affinity capture has become a powerful technique for consistently purifying endogenous protein complexes, facilitating biochemical and biophysical assays on otherwise inaccessible biological assemblies, and enabling broader interactomic exploration. For this procedure, cells are broken and their contents separated and extracted into a solvent, permitting access to target macromolecular complexes thus released in solution. The complexes are specifically enriched from the extract onto a solid medium coupled with an affinity reagent-usually an antibody-that recognizes the target either directly or through an appended affinity tag, allowing subsequent characterization of the complex. Here, we discuss approaches and considerations for purifying endogenous yeast protein complexes by affinity capture. PMID:27371601
Structural determinants of sigma receptor affinity
Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.
1987-12-01
The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.
Compact noncontraction semigroups of affine operators
NASA Astrophysics Data System (ADS)
Voynov, A. S.; Protasov, V. Yu
2015-07-01
We analyze compact multiplicative semigroups of affine operators acting in a finite-dimensional space. The main result states that every such semigroup is either contracting, that is, contains elements of arbitrarily small operator norm, or all its operators share a common invariant affine subspace on which this semigroup is contracting. The proof uses functional difference equations with contraction of the argument. We look at applications to self-affine partitions of convex sets, the investigation of finite affine semigroups and the proof of a criterion of primitivity for nonnegative matrix families. Bibliography: 32 titles.
Structure of Greyhound hemoglobin: origin of high oxygen affinity.
Bhatt, Veer S; Zaldívar-López, Sara; Harris, David R; Couto, C Guillermo; Wang, Peng G; Palmer, Andre F
2011-05-01
This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α₁β₁ dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb near α119 was also incorporated in the comparison between GrHb and human Hb. Finally, a structural comparison with generic dog Hb and maned wolf Hb was conducted, revealing that in contrast to GrHb these structures belong to the R state of Hb and raising the intriguing possibility of an additional allosteric factor co-purifying with GrHb that can modulate its quaternary structure. PMID:21543841
Limitations in scatter propagation
NASA Astrophysics Data System (ADS)
Lampert, E. W.
1982-04-01
A short description of the main scatter propagation mechanisms is presented; troposcatter, meteor burst communication and chaff scatter. For these propagation modes, in particular for troposcatter, the important specific limitations discussed are: link budget and resulting hardware consequences, diversity, mobility, information transfer and intermodulation and intersymbol interference, frequency range and future extension in frequency range for troposcatter, and compatibility with other services (EMC).
NASA Propagation Information Center
NASA Technical Reports Server (NTRS)
Smith, Ernest K.; Flock, Warren L.
1989-01-01
The NASA Propagation Information Center became formally operational in July 1988. It is located in the Department of Electrical and Computer Engineering of the University of Colorado at Boulder. The Center is several things: a communications medium for the propagation with the outside world, a mechanism for internal communication within the program, and an aid to management.
NASA propagation information center
NASA Technical Reports Server (NTRS)
Smith, Ernest K.; Flock, Warren L.
1990-01-01
The NASA Propagation Information Center became formally operational in July 1988. It is located in the Department of Electrical and Computer Engineering of the University of Colorado at Boulder. The center is several things: a communications medium for the propagation with the outside world, a mechanism for internal communication within the program, and an aid to management.
NASA Technical Reports Server (NTRS)
Wakana, Hiromitsu
1991-01-01
L-band propagation measurements for land-mobile, maritime, and aeronautical satellite communications have been carried out by using the Japanese Engineering Test Satellite-Five (ETS-5) which was launched in Aug. 1987. This paper presents propagation characteristics for each of the mobile satellite communication channels.
Genetic affinities of central China populations.
Zhou, H Y; Wang, H W; Tan, S N; Chen, Y; Wang, W L; Tao, H X; Yin, Z C; Zou, Y H; Ouyang, S M; Ni, B
2014-01-01
Hunan locates in the south-central part of China, to the south of the middle reaches of the Yangtze River and south of Lake Dongting. According to the historical records, the peopling of Hunan by modern human ancestors can ascend to 40 thousand years ago. Thus, to trace the ancient maternal components can offer further insight into the origin of south-central China. In this study, we investigated the mitochondrial DNA of 114 individuals from Hunan Province (including 34 Han, 40 Tujia and 40 Miao). Hypervariable regions I and II of the mtDNA control region were sequenced, and the relative diagnostic variations in coding region according to the updated worldwide phylogeny tree were selected and typed by restriction fragment length polymorphism analysis or direct sequencing. All individuals were classified into specific (sub)haplogroups. By comparison with the surrounding populations, southern China-prevalent haplogroups were detected with relative higher frequency in the Tujia and Miao ethnic populations, such as haplogroup B, with more than 20%, lacking in the Han population, which illustrated its southern origin characters. In addition, we also detected northern of East Asia prevalent haplogroups with a relative higher frequency in Tujia populations than in the Miao and Yao ethnic groups, implying a gene flow from Han populations. However, the language-clustering tendency was supported by our principal component analysis and further genetic estimation results. Han and ethnic groups in central China exhibited specific ancestors related to their closer language affinity, although there was extensively genetic admixture between Han and ethnic groups. PMID:24615027
NASA Astrophysics Data System (ADS)
Groenenboom, P. H. L.
The phenomenon of wave propagation is encountered frequently in a variety of engineering disciplines. It has been realized that for a growing number of problems the solution can only be obtained by discretization of the boundary. Advantages of the Boundary Element Method (BEM) over domain-type methods are related to the reduction of the number of space dimensions and of the modelling effort. It is demonstrated how the BEM can be applied to wave propagation phenomena by establishing the fundamental relationships. A numerical solution procedure is also suggested. In connection with a discussion of the retarded potential formulation, it is shown how the wave propagation problem can be cast into a Boundary Integral Formulation (BIF). The wave propagation problem in the BIF can be solved by time-successive evaluation of the boundary integrals. The example of pressure wave propagation following a sodium-water reaction in a Liquid Metal cooled Fast Breeder Reactor steam generator is discussed.
Structure of classical affine and classical affine fractional W-algebras
Suh, Uhi Rinn
2015-01-15
We introduce a classical BRST complex (See Definition 3.2.) and show that one can construct a classical affine W-algebra via the complex. This definition clarifies that classical affine W-algebras can be considered as quasi-classical limits of quantum affine W-algebras. We also give a definition of a classical affine fractional W-algebra as a Poisson vertex algebra. As in the classical affine case, a classical affine fractional W-algebra has two compatible λ-brackets and is isomorphic to an algebra of differential polynomials as a differential algebra. When a classical affine fractional W-algebra is associated to a minimal nilpotent, we describe explicit forms of free generators and compute λ-brackets between them. Provided some assumptions on a classical affine fractional W-algebra, we find an infinite sequence of integrable systems related to the algebra, using the generalized Drinfel’d and Sokolov reduction.
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.
Gear crack propagation investigations
NASA Technical Reports Server (NTRS)
Lewicki, David G.; Ballarini, Roberto
1996-01-01
Analytical and experimental studies were performed to investigate the effect of gear rim thickness on crack propagation life. The FRANC (FRacture ANalysis Code) computer program was used to simulate crack propagation. The FRANC program used principles of linear elastic fracture mechanics, finite element modeling, and a unique re-meshing scheme to determine crack tip stress distributions, estimate stress intensity factors, and model crack propagation. Various fatigue crack growth models were used to estimate crack propagation life based on the calculated stress intensity factors. Experimental tests were performed in a gear fatigue rig to validate predicted crack propagation results. Test gears were installed with special crack propagation gages in the tooth fillet region to measure bending fatigue crack growth. Good correlation between predicted and measured crack growth was achieved when the fatigue crack closure concept was introduced into the analysis. As the gear rim thickness decreased, the compressive cyclic stress in the gear tooth fillet region increased. This retarded crack growth and increased the number of crack propagation cycles to failure.
Methods for Improving Aptamer Binding Affinity.
Hasegawa, Hijiri; Savory, Nasa; Abe, Koichi; Ikebukuro, Kazunori
2016-01-01
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers. PMID:27043498
Affine root systems and dual numbers
NASA Astrophysics Data System (ADS)
Kostyakov, I. V.; Gromov, N. A.; Kuratov, V. V.
The root systems in Carroll spaces with degenerate metric are defined. It is shown that their Cartan matrices and reflection groups are affine. Due to the geometric consideration the root system structure of affine algebras is determined by a sufficiently simple algorithm.
Loop realizations of quantum affine algebras
Cautis, Sabin; Licata, Anthony
2012-12-15
We give a simplified description of quantum affine algebras in their loop presentation. This description is related to Drinfeld's new realization via halves of vertex operators. We also define an idempotent version of the quantum affine algebra which is suitable for categorification.
Improving image segmentation by learning region affinities
Prasad, Lakshman; Yang, Xingwei; Latecki, Longin J
2010-11-03
We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.
Gear Crack Propagation Investigation
NASA Technical Reports Server (NTRS)
1995-01-01
Reduced weight is a major design goal in aircraft power transmissions. Some gear designs incorporate thin rims to help meet this goal. Thin rims, however, may lead to bending fatigue cracks. These cracks may propagate through a gear tooth or into the gear rim. A crack that propagates through a tooth would probably not be catastrophic, and ample warning of a failure could be possible. On the other hand, a crack that propagates through the rim would be catastrophic. Such cracks could lead to disengagement of a rotor or propeller from an engine, loss of an aircraft, and fatalities. To help create and validate tools for the gear designer, the NASA Lewis Research Center performed in-house analytical and experimental studies to investigate the effect of rim thickness on gear-tooth crack propagation. Our goal was to determine whether cracks grew through gear teeth (benign failure mode) or through gear rims (catastrophic failure mode) for various rim thicknesses. In addition, we investigated the effect of rim thickness on crack propagation life. A finite-element-based computer program simulated gear-tooth crack propagation. The analysis used principles of linear elastic fracture mechanics, and quarter-point, triangular elements were used at the crack tip to represent the stress singularity. The program had an automated crack propagation option in which cracks were grown numerically via an automated remeshing scheme. Crack-tip stress-intensity factors were estimated to determine crack-propagation direction. Also, various fatigue crack growth models were used to estimate crack-propagation life. Experiments were performed in Lewis' Spur Gear Fatigue Rig to validate predicted crack propagation results. Gears with various backup ratios were tested to validate crack-path predictions. Also, test gears were installed with special crack-propagation gages in the tooth fillet region to measure bending-fatigue crack growth. From both predictions and tests, gears with backup ratios
NASA Astrophysics Data System (ADS)
Nayak, P. K.; Subramaniam, A.; Choudhury, S.; Indu, G.; Sagar, Ram
2016-08-01
We have introduced a semi-automated quantitative method to estimate the age and reddening of 1072 star clusters in the Large Magellanic Cloud (LMC) using the Optical Gravitational Lensing Experiment (OGLE) III survey data. This study brings out 308 newly parameterised clusters. In a first of its kind, the LMC clusters are classified into groups based on richness/mass as very poor, poor, moderate and rich clusters, similar to the classification scheme of open clusters in the Galaxy. A major cluster formation episode is found to happen at 125±25 Myr in the inner LMC. The bar region of the LMC appears prominently in the age range 60 - 250 Myr and is found to have a relatively higher concentration of poor and moderate clusters. The eastern and the western ends of the bar are found to form clusters initially, which later propagates to the central part. We demonstrate that there is a significant difference in the distribution of clusters as a function of mass, using a movie based on the propagation (in space and time) of cluster formation in various groups. The importance of including the low mass clusters in the cluster formation history is demonstrated. The catalog with parameters, classification, and cleaned and isochrone fitted CMDs of 1072 clusters, which are available as online material, can be further used to understand the hierarchical formation of clusters in selected regions of the LMC.
Propagation of Environmental Noise
ERIC Educational Resources Information Center
Lyon, R. H.
1973-01-01
Solutions for environmental noise pollution lie in systematic study of many basic processes such as reflection, scattering, and spreading. Noise propagation processes should be identified in different situations and assessed for their relative importance. (PS)
NASA Propagation Studies Website
NASA Technical Reports Server (NTRS)
Angkasa, Krisjani S.
1996-01-01
This paper describes an Internet website which provides information to enable the development of new commerical satellite systems and services by providing timely data and models about the propagation of satellite radio signals. In partnership with industry and academia, the program leverages NASA assets, currently the Advanced Communications Technology Satellite (ACTS), to obtain propagation data. The findings of the study are disseminated through refereed journals, NASA reference publications, workshops, electronic media, and direct interface with industry.
Database for propagation models
NASA Technical Reports Server (NTRS)
Kantak, Anil V.
1991-01-01
A propagation researcher or a systems engineer who intends to use the results of a propagation experiment is generally faced with various database tasks such as the selection of the computer software, the hardware, and the writing of the programs to pass the data through the models of interest. This task is repeated every time a new experiment is conducted or the same experiment is carried out at a different location generating different data. Thus the users of this data have to spend a considerable portion of their time learning how to implement the computer hardware and the software towards the desired end. This situation may be facilitated considerably if an easily accessible propagation database is created that has all the accepted (standardized) propagation phenomena models approved by the propagation research community. Also, the handling of data will become easier for the user. Such a database construction can only stimulate the growth of the propagation research it if is available to all the researchers, so that the results of the experiment conducted by one researcher can be examined independently by another, without different hardware and software being used. The database may be made flexible so that the researchers need not be confined only to the contents of the database. Another way in which the database may help the researchers is by the fact that they will not have to document the software and hardware tools used in their research since the propagation research community will know the database already. The following sections show a possible database construction, as well as properties of the database for the propagation research.
Energy Science and Technology Software Center (ESTSC)
2007-01-08
WPP is a massively parallel, 3D, C++, finite-difference elastodynamic wave propagation code. Typical applications for wave propagation with WPP include: evaluation of seismic event scenarios and damage from earthquakes, non-destructive evaluation of materials, underground facility detection, oil and gas exploration, predicting the electro-magnetic fields in accelerators, and acoustic noise generation. For more information, see Users Manual [1].
DNA motif elucidation using belief propagation.
Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei
2013-09-01
Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM. PMID:23814189
Wang, Yong; Keck, Zhen-yong; Saha, Anasuya; Xia, Jinming; Conrad, Fraser; Lou, Jianlong; Eckart, Michael; Marks, James D.; Foung, Steven K. H.
2011-01-01
A potent neutralizing antibody to a conserved hepatitis C virus (HCV) epitope might overcome its extreme variability, allowing immunotherapy. The human monoclonal antibody HC-1 recognizes a conformational epitope on the HCV E2 glycoprotein. Previous studies showed that HC-1 neutralizes most HCV genotypes but has modest potency. To improve neutralization, we affinity-matured HC-1 by constructing a library of yeast-displayed HC-1 single chain Fv (scFv) mutants, using for selection an E2 antigen from one of the poorly neutralized HCVpp. We developed an approach by parallel mutagenesis of the heavy chain variable (VH) and κ-chain variable (Vk) genes separately, then combining the optimized VH and Vk mutants. This resulted in the generation of HC-1-related scFv variants exhibiting improved affinities. The best scFv variant had a 92-fold improved affinity. After conversion to IgG1, some of the antibodies exhibited a 30-fold improvement in neutralization activity. Both surface plasmon resonance and solution kinetic exclusion analysis showed that the increase in affinity was largely due to a lowering of the dissociation rate constant, Koff. Neutralization against a panel of HCV pseudoparticles and infectious 2a HCV virus improved with the affinity-matured IgG1 antibodies. Interestingly, some of these antibodies neutralized a viral isolate that was not neutralized by wild-type HC-1. Moreover, propagating 2a HCVcc under the selective pressure of WT HC-1 or affinity-matured HC-1 antibodies yielded no viral escape mutants and, with the affinity-matured IgG1, needed 100-fold less antibody to achieve complete virus elimination. Taken together, these findings suggest that affinity-matured HC-1 antibodies are excellent candidates for therapeutic development. PMID:22002064
Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.
2004-05-26
We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.
Affinity Proteomics in the mountains: Alpbach 2015.
Taussig, Michael J
2016-09-25
The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167
Optimized Affinity Capture of Yeast Protein Complexes.
LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P
2016-01-01
Here, we describe an affinity isolation protocol. It uses cryomilled yeast cell powder for producing cell extracts and antibody-conjugated paramagnetic beads for affinity capture. Guidelines for determining the optimal extraction solvent composition are provided. Captured proteins are eluted in a denaturing solvent (sodium dodecyl sulfate polyacrylamide gel electrophoresis sample buffer) for gel-based proteomic analyses. Although the procedures can be modified to use other sources of cell extract and other forms of affinity media, to date we have consistently obtained the best results with the method presented. PMID:27371596
Aptamers in Affinity Separations: Stationary Separation
NASA Astrophysics Data System (ADS)
Ravelet, Corinne; Peyrin, Eric
The use of DNA or RNA aptamers as tools in analytical chemistry is a very promising field of research because of their capabilities to bind specifically the target molecules with an affinity similar to that of antibodies. Notably, they appear to be of great interest as target-specific ligands for the separation and capture of various analytes in affinity chromatography and related affinity-based methods such as magnetic bead technology. In this chapter, the recent developments of these aptamer-based separation/capture approaches are addressed.
Affinity purification of heme-tagged proteins.
Asher, Wesley B; Bren, Kara L
2014-01-01
Protein affinity purification techniques are widely used for isolating pure target proteins for biochemical and structural characterization. Herein, we describe the protocol for affinity-based purification of proteins expressed in Escherichia coli that uses the coordination of a peptide tag covalently modified with heme c, known as a heme-tag, to an L-histidine immobilized Sepharose resin. This approach provides an affinity purification tag visible to the eye, facilitating tracking of the protein. In addition, we describe methods for specifically detecting heme-tagged proteins in SDS-PAGE gels using a heme-staining procedure and for quantifying the proteins using a pyridine hemochrome assay. PMID:24943311
PRINCIPLES OF AFFINITY-BASED BIOSENSORS
Despite the amount of resources that have been invested by national and international academic, government, and commercial sectors to develop affinity-based biosensor products, little obvious success has been realized through commercialization of these devices for specific applic...
Minimal information to determine affine shape equivalence.
Wagemans, J; Van Gool, L; Lamote, C; Foster, D H
2000-04-01
Participants judged the affine equivalence of 2 simultaneously presented 4-point patterns. Performance level (d') varied between 1.5 and 2.7, depending on the information available for solving the correspondence problem (insufficient in Experiment 1a, superfluous in Experiment 1b, and minimal in Experiments 1c, 2a, 2b) and on the exposure time (unlimited in Experiments 1 and 2a and 500 ms in Experiment 2b), but it did not vary much with the complexity of the affine transformation (rotation and slant in Experiment 1 and same plus tilt in Experiment 2). Performance in Experiment 3 was lower with 3-point patterns than with 4-point patterns, whereas blocking the trials according to the affine transformation parameters had little effect. Determining affine shape equivalence with minimal-information displays is based on a fast assessment of qualitatively or quasi-invariant properties such as convexity/ concavity, parallelism, and collinearity. PMID:10811156
Protein purification using PDZ affinity chromatography.
Walkup, Ward G; Kennedy, Mary B
2015-01-01
PDZ domains function in nature as protein-binding domains within scaffold and membrane-associated proteins. They comprise approximately 90 residues and undergo specific, high-affinity interactions with complementary C-terminal peptide sequences, other PDZ domains, and/or phospholipids. We have previously shown that the specific, strong interactions of PDZ domains with their ligands make them well suited for use in affinity chromatography. This unit provides protocols for the PDZ affinity chromatography procedure that are applicable for the purification of proteins that contain PDZ domains or PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We detail the preparation of affinity resins composed of PDZ domains or PDZ domain peptide ligands coupled to solid supports. These resins can be used to purify proteins containing endogenous or genetically introduced PDZ domains or ligands, eluting the proteins with free PDZ domain peptide ligands. PMID:25829303
Visualizing antibody affinity maturation in germinal centers.
Tas, Jeroen M J; Mesin, Luka; Pasqual, Giulia; Targ, Sasha; Jacobsen, Johanne T; Mano, Yasuko M; Chen, Casie S; Weill, Jean-Claude; Reynaud, Claude-Agnès; Browne, Edward P; Meyer-Hermann, Michael; Victora, Gabriel D
2016-03-01
Antibodies somatically mutate to attain high affinity in germinal centers (GCs). There, competition between B cell clones and among somatic mutants of each clone drives an increase in average affinity across the population. The extent to which higher-affinity cells eliminating competitors restricts clonal diversity is unknown. By combining multiphoton microscopy and sequencing, we show that tens to hundreds of distinct B cell clones seed each GC and that GCs lose clonal diversity at widely disparate rates. Furthermore, efficient affinity maturation can occur in the absence of homogenizing selection, ensuring that many clones can mature in parallel within the same GC. Our findings have implications for development of vaccines in which antibodies with nonimmunodominant specificities must be elicited, as is the case for HIV-1 and influenza. PMID:26912368
Cosmic axion background propagation in galaxies
NASA Astrophysics Data System (ADS)
Day, Francesca V.
2016-02-01
Many extensions of the Standard Model include axions or axion-like particles (ALPs). Here we study ALP to photon conversion in the magnetic field of the Milky Way and starburst galaxies. By modelling the effects of the coherent and random magnetic fields, the warm ionized medium and the warm neutral medium on the conversion process, we simulate maps of the conversion probability across the sky for a range of ALP energies. In particular, we consider a diffuse cosmic ALP background (CAB) analogous to the CMB, whose existence is suggested by string models of inflation. ALP-photon conversion of a CAB in the magnetic fields of galaxy clusters has been proposed as an explanation of the cluster soft X-ray excess. We therefore study the phenomenology and expected photon signal of CAB propagation in the Milky Way. We find that, for the CAB parameters required to explain the cluster soft X-ray excess, the photon flux from ALP-photon conversion in the Milky Way would be unobservably small. The ALP-photon conversion probability in galaxy clusters is 3 orders of magnitude higher than that in the Milky Way. Furthermore, the morphology of the unresolved cosmic X-ray background is incompatible with a significant component from ALP-photon conversion. We also consider ALP-photon conversion in starburst galaxies, which host much higher magnetic fields. By considering the clumpy structure of the galactic plasma, we find that conversion probabilities comparable to those in clusters may be possible in starburst galaxies.
Elevated Temperature Crack Propagation
NASA Technical Reports Server (NTRS)
Orange, Thomas W.
1994-01-01
This paper is a summary of two NASA contracts on high temperature fatigue crack propagation in metals. The first evaluated the ability of fairly simple nonlinear fracture parameters to correlate crack propagation. Hastelloy-X specimens were tested under isothermal and thermomechanical cycling at temperatures up to 980 degrees C (1800 degrees F). The most successful correlating parameter was the crack tip opening displacement derived from the J-integral. The second evaluated the ability of several path-independent integrals to correlate crack propagation behavior. Inconel 718 specimens were tested under isothermal, thermomechanical, temperature gradient, and creep conditions at temperatures up to 650 degrees C (1200 degrees F). The integrals formulated by Blackburn and by Kishimoto correlated the data reasonably well under all test conditions.
NASA Astrophysics Data System (ADS)
Budarapu, P. R.; Javvaji, B.; Sutrakar, V. K.; Roy Mahapatra, D.; Zi, G.; Rabczuk, T.
2015-08-01
The crack initiation and growth mechanisms in an 2D graphene lattice structure are studied based on molecular dynamics simulations. Crack growth in an initial edge crack model in the arm-chair and the zig-zag lattice configurations of graphene are considered. Influence of the time steps on the post yielding behaviour of graphene is studied. Based on the results, a time step of 0.1 fs is recommended for consistent and accurate simulation of crack propagation. Effect of temperature on the crack propagation in graphene is also studied, considering adiabatic and isothermal conditions. Total energy and stress fields are analyzed. A systematic study of the bond stretching and bond reorientation phenomena is performed, which shows that the crack propagates after significant bond elongation and rotation in graphene. Variation of the crack speed with the change in crack length is estimated.
Turbofan Duct Propagation Model
NASA Technical Reports Server (NTRS)
Lan, Justin H.; Posey, Joe W. (Technical Monitor)
2001-01-01
The CDUCT code utilizes a parabolic approximation to the convected Helmholtz equation in order to efficiently model acoustic propagation in acoustically treated, complex shaped ducts. The parabolic approximation solves one-way wave propagation with a marching method which neglects backwards reflected waves. The derivation of the parabolic approximation is presented. Several code validation cases are given. An acoustic lining design process for an example aft fan duct is discussed. It is noted that the method can efficiently model realistic three-dimension effects, acoustic lining, and flow within the computational capabilities of a typical computer workstation.
Automatic crack propagation tracking
NASA Technical Reports Server (NTRS)
Shephard, M. S.; Weidner, T. J.; Yehia, N. A. B.; Burd, G. S.
1985-01-01
A finite element based approach to fully automatic crack propagation tracking is presented. The procedure presented combines fully automatic mesh generation with linear fracture mechanics techniques in a geometrically based finite element code capable of automatically tracking cracks in two-dimensional domains. The automatic mesh generator employs the modified-quadtree technique. Crack propagation increment and direction are predicted using a modified maximum dilatational strain energy density criterion employing the numerical results obtained by meshes of quadratic displacement and singular crack tip finite elements. Example problems are included to demonstrate the procedure.
Affinity engineering of maltoporin: variants with enhanced affinity for particular ligands.
Clune, A; Lee, K S; Ferenci, T
1984-05-31
Affinity-chromatographic selection on immobilized starch was used to selectively enhance the affinity of the maltodextrin-specific pore protein ( maltoporin , LamB protein, or lambda receptor protein) in the outer membrane of E. coli. Selection strategies were established for rare bacteria in large populations producing maltoporin variants with enhanced affinities for both starch and maltose, for starch but not maltose and for maltose but not starch. Three classes of lamB mutants with up to eight-fold increase in affinity for particular ligands were isolated. These mutants provide a unique range of modifications in the specificity of a transport protein. PMID:6375667
Propagation of coherent light pulses with PHASE
NASA Astrophysics Data System (ADS)
Bahrdt, J.; Flechsig, U.; Grizzoli, W.; Siewert, F.
2014-09-01
The current status of the software package PHASE for the propagation of coherent light pulses along a synchrotron radiation beamline is presented. PHASE is based on an asymptotic expansion of the Fresnel-Kirchhoff integral (stationary phase approximation) which is usually truncated at the 2nd order. The limits of this approximation as well as possible extensions to higher orders are discussed. The accuracy is benchmarked against a direct integration of the Fresnel-Kirchhoff integral. Long range slope errors of optical elements can be included by means of 8th order polynomials in the optical element coordinates w and l. Only recently, a method for the description of short range slope errors has been implemented. The accuracy of this method is evaluated and examples for realistic slope errors are given. PHASE can be run either from a built-in graphical user interface or from any script language. The latter method provides substantial flexibility. Optical elements including apertures can be combined. Complete wave packages can be propagated, as well. Fourier propagators are included in the package, thus, the user may choose between a variety of propagators. Several means to speed up the computation time were tested - among them are the parallelization in a multi core environment and the parallelization on a cluster.
Li, Jun; Li, Xi; Zhai, Hua Jin; Wang, Lai S.
2003-02-07
Photoelectron spectroscopy revealed that a 20 atom gold cluster has an extremely large energy gap, which is even greater than that of C60, and an electron affinity comparable with that of C60. This observation suggests that the Au20 cluster must be extremely stable and chemically inert. Using relativistic density functional calculations, we found that Au20 possesses a remarkable tetrahedral structure, which is a fragment of the bulk face-centered cubic lattice of gold with a small structural relaxation. Au20 is thus a true cluster molecule, while at the same time it is exactly part of the bulk, but with very different properties. The tetrahedral Au20 may possess interesting catalytic properties and may be synthesized in bulk quantity or assembled on non-interacting surfaces.
NASA Astrophysics Data System (ADS)
Urrutxua, Hodei; Sanjurjo-Rivo, Manuel; Peláez, Jesús
2016-01-01
In the year 2000 an in-house orbital propagator called DROMO (Peláez et al. in Celest Mech Dyn Astron 97:131-150, 2007. doi: 10.1007/s10569-006-9056-3) was developed by the Space Dynamics Group of the Technical University of Madrid, based in a set of redundant variables including Euler-Rodrigues parameters. An original deduction of the DROMO propagator is carried out, underlining its close relation with the ideal frame concept introduced by Hansen (Abh der Math-Phys Cl der Kon Sachs Ges der Wissensch 5:41-218, 1857). Based on the very same concept, Deprit (J Res Natl Bur Stand Sect B Math Sci 79B(1-2):1-15, 1975) proposed a formulation for orbit propagation. In this paper, similarities and differences with the theory carried out by Deprit are analyzed. Simultaneously, some improvements are introduced in the formulation, that lead to a more synthetic and better performing propagator. Also, the long-term effect of the oblateness of the primary is studied in terms of DROMO variables, and new numerical results are presented to evaluate the performance of the method.
NASA Technical Reports Server (NTRS)
Nessel, James
2013-01-01
NASA Glenn Research Center has been involved in the characterization of atmospheric effects on space communications links operating at Ka-band and above for the past 20 years. This presentation reports out on the most recent activities of propagation characterization that NASA is currently involved in.
PROPER: Optical propagation routines
NASA Astrophysics Data System (ADS)
Krist, John E.
2014-05-01
PROPER simulates the propagation of light through an optical system using Fourier transform algorithms (Fresnel, angular spectrum methods). Distributed as IDL source code, it includes routines to create complex apertures, aberrated wavefronts, and deformable mirrors. It is especially useful for the simulation of high contrast imaging telescopes (extrasolar planet imagers like TPF).
Approximate Bruechner orbitals in electron propagator calculations
Ortiz, J.V.
1999-12-01
Orbitals and ground-state correlation amplitudes from the so-called Brueckner doubles approximation of coupled-cluster theory provide a useful reference state for electron propagator calculations. An operator manifold with hold, particle, two-hole-one-particle and two-particle-one-hole components is chosen. The resulting approximation, third-order algebraic diagrammatic construction [2ph-TDA, ADC (3)] and 3+ methods. The enhanced versatility of this approximation is demonstrated through calculations on valence ionization energies, core ionization energies, electron detachment energies of anions, and on a molecule with partial biradical character, ozone.
Affinity purification of aprotinin from bovine lung.
Xin, Yu; Liu, Lanhua; Chen, Beizhan; Zhang, Ling; Tong, Yanjun
2015-05-01
An affinity protocol for the purification of aprotinin from bovine lung was developed. To simulate the structure of sucrose octasulfate, a natural specific probe for aprotinin, the affinity ligand was composed of an acidic head and a hydrophobic stick, and was then linked with Sepharose. The sorbent was then subjected to adsorption analysis with pure aprotinin. The purification process consisted of one step of affinity chromatography and another step of ultrafiltration. Then purified aprotinin was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, trypsin inhibitor activity, gel-filtration, and thin-layer chromatography analysis. As calculated, the theoretical maximum adsorption (Qmax ) of the affinity sorbent was 25,476.0 ± 184.8 kallikrein inactivator unit/g wet gel; the dissociation constant of the complex "immobilized ligand-aprotinin" (Kd ) was 4.6 ± 0.1 kallikrein inactivator unit/mL. After the affinity separation of bovine lung aprotinin, reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis and gel-filtration chromatography revealed that the protein was a single polypeptide, and the purities were ∼ 97 and 100%, respectively; the purified peptide was also confirmed with aprotinin standard by gel-filtration chromatography and thin-layer chromatography. After the whole purification process, protein, and bioactivity recoveries were 2.2 and 92.6%, respectively; and the specific activity was up to 15,907.1 ± 10.2 kallikrein inactivator unit/mg. PMID:25677462
Robust Semi-Supervised Subspace Clustering via Non-Negative Low-Rank Representation.
Fang, Xiaozhao; Xu, Yong; Li, Xuelong; Lai, Zhihui; Wong, Wai Keung
2016-08-01
Low-rank representation (LRR) has been successfully applied in exploring the subspace structures of data. However, in previous LRR-based semi-supervised subspace clustering methods, the label information is not used to guide the affinity matrix construction so that the affinity matrix cannot deliver strong discriminant information. Moreover, these methods cannot guarantee an overall optimum since the affinity matrix construction and subspace clustering are often independent steps. In this paper, we propose a robust semi-supervised subspace clustering method based on non-negative LRR (NNLRR) to address these problems. By combining the LRR framework and the Gaussian fields and harmonic functions method in a single optimization problem, the supervision information is explicitly incorporated to guide the affinity matrix construction and the affinity matrix construction and subspace clustering are accomplished in one step to guarantee the overall optimum. The affinity matrix is obtained by seeking a non-negative low-rank matrix that represents each sample as a linear combination of others. We also explicitly impose the sparse constraint on the affinity matrix such that the affinity matrix obtained by NNLRR is non-negative low-rank and sparse. We introduce an efficient linearized alternating direction method with adaptive penalty to solve the corresponding optimization problem. Extensive experimental results demonstrate that NNLRR is effective in semi-supervised subspace clustering and robust to different types of noise than other state-of-the-art methods. PMID:26259210
Bramantya, M A; Motozawa, M; Sawada, T
2010-08-18
Ultrasonic propagation velocity in a magnetic fluid (MF) and magnetorheological fluid (MRF) changes with the application of an external magnetic field. The formation of clustering structures inside the MF and MRF clearly has an influence on the ultrasonic propagation velocity. Therefore, we propose a qualitative analysis of these structures by measuring properties of ultrasonic propagation. Since MF and MRF are opaque, non-contact inspection using the ultrasonic technique can be very useful for analyzing the inner structures of MF and MRF. In this study, we measured ultrasonic propagation velocity in a hydrocarbon-based MF and MRF precisely. Based on these results, the clustering structures of these fluids are analyzed experimentally in terms of elapsed time dependence and the effect of external magnetic field strength. The results reveal hysteresis and anisotropy in the ultrasonic propagation velocity. We also discuss differences of ultrasonic propagation velocity between MF and MRF. PMID:21386478
Identity, Affinity, Reality: Making the Case for Affinity Groups in Elementary School
ERIC Educational Resources Information Center
Parsons, Julie; Ridley, Kimberly
2012-01-01
Affinity groups are places where students build connections and process "ouch" moments from their classes. Children talk about the isolation they sometimes feel. The relationships students gain through race-based affinity groups enable them to feel less alone with their emotions and help them build a stronger sense of self. At the same time,…
A Database for Propagation Models
NASA Technical Reports Server (NTRS)
Kantak, Anil V.; Rucker, James
1997-01-01
The Propagation Models Database is designed to allow the scientists and experimenters in the propagation field to process their data through many known and accepted propagation models. The database is an Excel 5.0 based software that houses user-callable propagation models of propagation phenomena. It does not contain a database of propagation data generated out of the experiments. The database not only provides a powerful software tool to process the data generated by the experiments, but is also a time- and energy-saving tool for plotting results, generating tables and producing impressive and crisp hard copy for presentation and filing.
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.
The dynamics of metric-affine gravity
Vitagliano, Vincenzo; Sotiriou, Thomas P.; Liberati, Stefano
2011-05-15
Highlights: > The role and the dynamics of the connection in metric-affine theories is explored. > The most general second order action does not lead to a dynamical connection. > Including higher order invariants excites new degrees of freedom in the connection. > f(R) actions are also discussed and shown to be a non- representative class. - Abstract: Metric-affine theories of gravity provide an interesting alternative to general relativity: in such an approach, the metric and the affine (not necessarily symmetric) connection are independent quantities. Furthermore, the action should include covariant derivatives of the matter fields, with the covariant derivative naturally defined using the independent connection. As a result, in metric-affine theories a direct coupling involving matter and connection is also present. The role and the dynamics of the connection in such theories is explored. We employ power counting in order to construct the action and search for the minimal requirements it should satisfy for the connection to be dynamical. We find that for the most general action containing lower order invariants of the curvature and the torsion the independent connection does not carry any dynamics. It actually reduces to the role of an auxiliary field and can be completely eliminated algebraically in favour of the metric and the matter field, introducing extra interactions with respect to general relativity. However, we also show that including higher order terms in the action radically changes this picture and excites new degrees of freedom in the connection, making it (or parts of it) dynamical. Constructing actions that constitute exceptions to this rule requires significant fine tuned and/or extra a priori constraints on the connection. We also consider f(R) actions as a particular example in order to show that they constitute a distinct class of metric-affine theories with special properties, and as such they cannot be used as representative toy theories to
Displacement phenomena in lectin affinity chromatography.
Cho, Wonryeon
2015-10-01
The work described here examines displacement phenomena that play a role in lectin affinity chromatography and their potential to impact reproducibility. This was achieved using Lycopersicon esculentum lectin (LEL), a lectin widely used in monitoring cancer. Four small identical LEL columns were coupled in series to form a single affinity chromatography system with the last in the series connected to an absorbance detector. The serial affinity column set (SACS) was then loaded with human plasma proteins. At the completion of loading, the column set was disassembled, the four columns were eluted individually, the captured proteins were trypsin digested, the peptides were deglycosylated with PNGase F, and the parent proteins were identified through mass spectral analyses. Significantly different sets of glycoproteins were selected by each column, some proteins appearing to be exclusively bound to the first column while others were bound further along in the series. Clearly, sample displacement chromatography (SDC) occurs. Glycoproteins were bound at different places in the column train, identifying the presence of glycoforms with different affinity on a single glycoprotein. It is not possible to see these phenomena in the single column mode of chromatography. Moreover, low abundance proteins were enriched, which facilitates detection. The great advantage of this method is that it differentiates between glycoproteins on the basis of their binding affinity. Displacement phenomena are concluded to be a significant component of the separation mechanism in heavily loaded lectin affinity chromatography columns. This further suggests that care must be exercised in sample loading of lectin columns to prevent analyte displacement with nonretained proteins. PMID:26348026
Negative Electron Affinity Mechanism for Diamond Surfaces
NASA Technical Reports Server (NTRS)
Krainsky, I. L.; Asnin, V. M.
1998-01-01
The energy distribution of the secondary electrons for chemical vacuum deposited diamond films with Negative Electron Affinity (NEA) was investigated. It was found that while for completely hydrogenated diamond surfaces the negative electron affinity peak in the energy spectrum of the secondary electrons is present for any energy of the primary electrons, for partially hydrogenated diamond surfaces there is a critical energy above which the peak is present in the spectrum. This critical energy increases sharply when hydrogen coverage of the diamond surface diminishes. This effect was explained by the change of the NEA from the true type for the completely hydrogenated surface to the effective type for the partially hydrogenated surfaces.
New unitary affine-Virasoro constructions
Halpern, M.B.; Kiritsis, E.; Obers, N.A.; Poratti, M. ); Yamron, J.P. )
1990-06-20
This paper reports on a quasi-systematic investigation of the Virasoro master equation. The space of all affine-Virasoro constructions is organized by K-conjugation into affine-Virasoro nests, and an estimate of the dimension of the space shows that most solutions await discovery. With consistent ansatze for the master equation, large classes of new unitary nests are constructed, including quadratic deformation nests with continuous conformal weights, and unitary irrational central charge nests, which may dominate unitary rational central charge on compact g.
Adsorption affinity of anions on metal oxyhydroxides
NASA Astrophysics Data System (ADS)
Pechenyuk, S. I.; Semushina, Yu. P.; Kuz'mich, L. F.
2013-03-01
The dependences of anion (phosphate, carbonate, sulfate, chromate, oxalate, tartrate, and citrate) adsorption affinity anions from geometric characteristics, acid-base properties, and complex forming ability are generalized. It is shown that adsorption depends on the nature of both the anions and the ionic medium and adsorbent. It is established that anions are generally grouped into the following series of adsorption affinity reduction: PO{4/3-}, CO{3/2-} > C2O{4/2-}, C(OH)(CH2)2(COO){3/3-}, (CHOH)2(COO){2/2-} > CrO{4/2-} ≫ SO{4/2-}.
NASA Technical Reports Server (NTRS)
Cook, R. K.
1969-01-01
The propagation of sound waves at infrasonic frequencies (oscillation periods 1.0 - 1000 seconds) in the atmosphere is being studied by a network of seven stations separated geographically by distances of the order of thousands of kilometers. The stations measure the following characteristics of infrasonic waves: (1) the amplitude and waveform of the incident sound pressure, (2) the direction of propagation of the wave, (3) the horizontal phase velocity, and (4) the distribution of sound wave energy at various frequencies of oscillation. Some infrasonic sources which were identified and studied include the aurora borealis, tornadoes, volcanos, gravity waves on the oceans, earthquakes, and atmospheric instability waves caused by winds at the tropopause. Waves of unknown origin seem to radiate from several geographical locations, including one in the Argentine.
Transionospheric Propagation Code (TIPC)
Roussel-Dupre, R.; Kelley, T.A.
1990-10-01
The Transionospheric Propagation Code is a computer program developed at Los Alamos National Lab to perform certain tasks related to the detection of vhf signals following propagation through the ionosphere. The code is written in Fortran 77, runs interactively and was designed to be as machine independent as possible. A menu format in which the user is prompted to supply appropriate parameters for a given task has been adopted for the input while the output is primarily in the form of graphics. The user has the option of selecting from five basic tasks, namely transionospheric propagation, signal filtering, signal processing, DTOA study, and DTOA uncertainty study. For the first task a specified signal is convolved against the impulse response function of the ionosphere to obtain the transionospheric signal. The user is given a choice of four analytic forms for the input pulse or of supplying a tabular form. The option of adding Gaussian-distributed white noise of spectral noise to the input signal is also provided. The deterministic ionosphere is characterized to first order in terms of a total electron content (TEC) along the propagation path. In addition, a scattering model parameterized in terms of a frequency coherence bandwidth is also available. In the second task, detection is simulated by convolving a given filter response against the transionospheric signal. The user is given a choice of a wideband filter or a narrowband Gaussian filter. It is also possible to input a filter response. The third task provides for quadrature detection, envelope detection, and three different techniques for time-tagging the arrival of the transionospheric signal at specified receivers. The latter algorithms can be used to determine a TEC and thus take out the effects of the ionosphere to first order. Task four allows the user to construct a table of delta-times-of-arrival (DTOAs) vs TECs for a specified pair of receivers.
Transionospheric Propagation Code (TIPC)
NASA Astrophysics Data System (ADS)
Roussel-Dupre, Robert; Kelley, Thomas A.
1990-10-01
The Transionospheric Propagation Code is a computer program developed at Los Alamos National Lab to perform certain tasks related to the detection of VHF signals following propagation through the ionosphere. The code is written in FORTRAN 77, runs interactively and was designed to be as machine independent as possible. A menu format in which the user is prompted to supply appropriate parameters for a given task has been adopted for the input while the output is primarily in the form of graphics. The user has the option of selecting from five basic tasks, namely transionospheric propagation, signal filtering, signal processing, delta times of arrival (DTOA) study, and DTOA uncertainty study. For the first task a specified signal is convolved against the impulse response function of the ionosphere to obtain the transionospheric signal. The user is given a choice of four analytic forms for the input pulse or of supplying a tabular form. The option of adding Gaussian-distributed white noise of spectral noise to the input signal is also provided. The deterministic ionosphere is characterized to first order in terms of a total electron content (TEC) along the propagation path. In addition, a scattering model parameterized in terms of a frequency coherence bandwidth is also available. In the second task, detection is simulated by convolving a given filter response against the transionospheric signal. The user is given a choice of a wideband filter or a narrowband Gaussian filter. It is also possible to input a filter response. The third task provides for quadrature detection, envelope detection, and three different techniques for time-tagging the arrival of the transionospheric signal at specified receivers. The latter algorithms can be used to determine a TEC and thus take out the effects of the ionosphere to first order. Task four allows the user to construct a table of DTOAs vs TECs for a specified pair of receivers.
NASA Technical Reports Server (NTRS)
Helmken, Henry; Henning, Rudolf
1994-01-01
One of the key goals of the Florida Center is to obtain a maximum of useful information on propagation behavior unique to its subtropical weather and subtropical climate. Such weather data is of particular interest when it is (or has the potential to become) useful for developing and implementing techniques to compensate for adverse weather effects. Also discussed are data observations, current challenges, CDF's, sun movement, and diversity experiments.
OPEX: (Olympus Propagation EXperiment)
NASA Technical Reports Server (NTRS)
Brussaard, Gert
1988-01-01
The Olympus-1 satellite carries four distinct payloads for experimental utilization and research in the field of satellite communications: (1) the Direct Broadcasting Service (DBS) payload; (2) the Specialized Services Payload; (3) the 20/30 GHz Advanced Communications Payload; and (4) the Propagation Payload. Experimental utilization of the first three payloads involves ground transmissions to the satellite and hence sharing of available satellite time among experimenters. This is coordinated through the Olympus Utilization Program.
NASA Technical Reports Server (NTRS)
Chakraborty, D.; Davarian, Faramaz
1992-01-01
The success or failure of the ACTS experiment will depend on how accurately the rain-fade statistics and fade dynamics can be predicted in order to derive an appropriate algorithm that will combat weather vagaries, specifically for links with small terminals, such as very small aperture terminals (VSAT's) where the power margin is a premium. The planning process and hardware development program that will comply with the recommendations of the ACTS propagation study groups are described.
Olympus propagation experiments
NASA Technical Reports Server (NTRS)
Arbesser-Rastburg, Bertram
1994-01-01
A summary of the activities of the OPEX (Olympus Propagation EXperimenters) group is given and some of the recent findings are presented. OLYMPUS, a telecommunication satellite owned by the European Space Agency, was launched on 12 June 1989. After the in-orbit tests were completed (in September 1989) the first propagation experiments started. Throughout 1990 the spacecraft functioned very well and a large number of experimenters received the beacon signals. On 29 May 1991 the spacecraft became inoperational after a major technical problem. With a series of complicated procedures OLYMPUS was recovered on 15 August 1991 - the first time in history that a civilian telecommunications satellite was brought back to service after losing power and telemetry. The propagation experiments were back on track. However, the recovery had used up so much fuel that the North-South station keeping had to be abandoned, which led to a natural increase of inclination at a rate of about 0.8 deg per year. On 10 October 1992 the second 30 GHz beacon tube failed, causing a loss of this beacon signal. The other two beacon frequencies continued to deliver a stable signal for more than two years. On 12 August 1993 the spacecraft experienced another problem with the altitude control, but this time there was not enough fuel left for a recovery maneuver and thus the mission came to an end.
Olympus propagation experiments
NASA Astrophysics Data System (ADS)
Arbesser-Rastburg, Bertram
1994-08-01
A summary of the activities of the OPEX (Olympus Propagation EXperimenters) group is given and some of the recent findings are presented. OLYMPUS, a telecommunication satellite owned by the European Space Agency, was launched on 12 June 1989. After the in-orbit tests were completed (in September 1989) the first propagation experiments started. Throughout 1990 the spacecraft functioned very well and a large number of experimenters received the beacon signals. On 29 May 1991 the spacecraft became inoperational after a major technical problem. With a series of complicated procedures OLYMPUS was recovered on 15 August 1991 - the first time in history that a civilian telecommunications satellite was brought back to service after losing power and telemetry. The propagation experiments were back on track. However, the recovery had used up so much fuel that the North-South station keeping had to be abandoned, which led to a natural increase of inclination at a rate of about 0.8 deg per year. On 10 October 1992 the second 30 GHz beacon tube failed, causing a loss of this beacon signal. The other two beacon frequencies continued to deliver a stable signal for more than two years. On 12 August 1993 the spacecraft experienced another problem with the altitude control, but this time there was not enough fuel left for a recovery maneuver and thus the mission came to an end.
NASA Technical Reports Server (NTRS)
1999-01-01
Penetrating 25,000 light-years of obscuring dust and myriad stars, NASA's Hubble Space Telescope has provided the clearest view yet of one of the largest young clusters of stars inside our Milky Way galaxy, located less than 100 light-years from the very center of the Galaxy. Having the equivalent mass greater than 10,000 stars like our sun, the monster cluster is ten times larger than typical young star clusters scattered throughout our Milky Way. It is destined to be ripped apart in just a few million years by gravitational tidal forces in the galaxy's core. But in its brief lifetime it shines more brightly than any other star cluster in the Galaxy. Quintuplet Cluster is 4 million years old. It has stars on the verge of blowing up as supernovae. It is the home of the brightest star seen in the galaxy, called the Pistol star. This image was taken in infrared light by Hubble's NICMOS camera in September 1997. The false colors correspond to infrared wavelengths. The galactic center stars are white, the red stars are enshrouded in dust or behind dust, and the blue stars are foreground stars between us and the Milky Way's center. The cluster is hidden from direct view behind black dust clouds in the constellation Sagittarius. If the cluster could be seen from earth it would appear to the naked eye as a 3rd magnitude star, 1/6th of a full moon's diameter apart.
Propagation in the ionosphere, A
NASA Astrophysics Data System (ADS)
Cannon, Paul S.
1994-09-01
The use of ionospheric models and ray tracing models as components of a propagation model are discussed. These can be used as decision aids to support human interpretation of ionospheric propagation. The physical basis for ionospheric decision aids is introduced by reference to ionospheric morphology and the basic theory of ionospheric propagation, which, along with ray tracing techniques, is then reviewed.
Huang, Renhua; Gorman, Kevin T; Vinci, Chris R; Dobrovetsky, Elena; Gräslund, Susanne; Kay, Brian K
2015-01-01
Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the "affinity maturation" step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold. PMID:26437402
Huang, Renhua; Gorman, Kevin T.; Vinci, Chris R.; Dobrovetsky, Elena; Gräslund, Susanne; Kay, Brian K.
2015-01-01
Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the “affinity maturation” step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold. PMID:26437402
NASA Astrophysics Data System (ADS)
Miller, Christopher J. Miller
2012-03-01
There are many examples of clustering in astronomy. Stars in our own galaxy are often seen as being gravitationally bound into tight globular or open clusters. The Solar System's Trojan asteroids cluster at the gravitational Langrangian in front of Jupiter’s orbit. On the largest of scales, we find gravitationally bound clusters of galaxies, the Virgo cluster (in the constellation of Virgo at a distance of ˜50 million light years) being a prime nearby example. The Virgo cluster subtends an angle of nearly 8◦ on the sky and is known to contain over a thousand member galaxies. Galaxy clusters play an important role in our understanding of theUniverse. Clusters exist at peaks in the three-dimensional large-scale matter density field. Their sky (2D) locations are easy to detect in astronomical imaging data and their mean galaxy redshifts (redshift is related to the third spatial dimension: distance) are often better (spectroscopically) and cheaper (photometrically) when compared with the entire galaxy population in large sky surveys. Photometric redshift (z) [Photometric techniques use the broad band filter magnitudes of a galaxy to estimate the redshift. Spectroscopic techniques use the galaxy spectra and emission/absorption line features to measure the redshift] determinations of galaxies within clusters are accurate to better than delta_z = 0.05 [7] and when studied as a cluster population, the central galaxies form a line in color-magnitude space (called the the E/S0 ridgeline and visible in Figure 16.3) that contains galaxies with similar stellar populations [15]. The shape of this E/S0 ridgeline enables astronomers to measure the cluster redshift to within delta_z = 0.01 [23]. The most accurate cluster redshift determinations come from spectroscopy of the member galaxies, where only a fraction of the members need to be spectroscopically observed [25,42] to get an accurate redshift to the whole system. If light traces mass in the Universe, then the locations
New organization of jet calculus for colorless-cluster computations
Crespi, B.; Jones, L.M.
1983-12-01
We write equations for a new set of leading-logarithmic parton ''propagators.'' These differ from past ''color-connecting'' propagators in that they keep explicit track of the momentum of the gluons associated with the quarks in the colorless cluster. Because of this, the new functions lead in a simple and natural way to computation of the x distribution and mass distribution of colorless clusters in jets. Hence they should prove more useful for phenomenological calculations.
High affinity of lead for fetal haemoglobin.
Ong, C N; Lee, W R
1980-01-01
In-vitro experiments using 203Pb were performed to identify lead-binding components in human haemoglobin. Sephadex A-50 ion-exchange chromatography of haemolysate showed that different types of haemoglobin had different affinities for lead. For the haemolysate from adults, lead was present in both Hb A (alpha 2 beta 2) and Hb A2 (alpha 2 delta 2), whereas, in the haemolysate from new-born infants, the haemoglobin of fetal origin, Hb F (alpha 2 gamma 2) showed a much greater affinity for 203Pb than the adult haemoglobin Hb A (alpha 2 beta 2), obtained from maternal blood. Analysis of the 203 Pb-labelled haemoglobin suggested that about 82% of 203Pb was in the globin polypeptide. Further analysis with carboxylmethyl (CM) cellulose chromatography indicated that the gamma globin of fetal origin had a higher affinity for 203Pb than the beta globin, whereas alpha globin appeared to be unimportant in lead binding. The results of the different affinities for lead of different Hb types are discussed with regard to the effect of lead upon haemoglobin synthesis. PMID:6158989
Vygotsky's and Buber's Pedagogical Perspectives: Some Affinities
ERIC Educational Resources Information Center
Bartholo, Roberto; Tunes, Elizabeth; Tacca, Maria Carmen Villela Rosa
2010-01-01
The purpose of this paper is to examine the dialogical and creative character of pedagogic work by analyzing the affinities between Martin Buber's "I-Thou relation" and Lev Semenovich Vygotsky's "Zone of Proximal Development". Backed up by empirical studies on the teacher-student relation, we understand that education can only result in students'…
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…
ERIC Educational Resources Information Center
Pottawattamie County School System, Council Bluffs, IA.
The 15 occupational clusters (transportation, fine arts and humanities, communications and media, personal service occupations, construction, hospitality and recreation, health occupations, marine science occupations, consumer and homemaking-related occupations, agribusiness and natural resources, environment, public service, business and office…
NASA Astrophysics Data System (ADS)
Wagstaff, Kiri L.
2012-03-01
On obtaining a new data set, the researcher is immediately faced with the challenge of obtaining a high-level understanding from the observations. What does a typical item look like? What are the dominant trends? How many distinct groups are included in the data set, and how is each one characterized? Which observable values are common, and which rarely occur? Which items stand out as anomalies or outliers from the rest of the data? This challenge is exacerbated by the steady growth in data set size [11] as new instruments push into new frontiers of parameter space, via improvements in temporal, spatial, and spectral resolution, or by the desire to "fuse" observations from different modalities and instruments into a larger-picture understanding of the same underlying phenomenon. Data clustering algorithms provide a variety of solutions for this task. They can generate summaries, locate outliers, compress data, identify dense or sparse regions of feature space, and build data models. It is useful to note up front that "clusters" in this context refer to groups of items within some descriptive feature space, not (necessarily) to "galaxy clusters" which are dense regions in physical space. The goal of this chapter is to survey a variety of data clustering methods, with an eye toward their applicability to astronomical data analysis. In addition to improving the individual researcher’s understanding of a given data set, clustering has led directly to scientific advances, such as the discovery of new subclasses of stars [14] and gamma-ray bursts (GRBs) [38]. All clustering algorithms seek to identify groups within a data set that reflect some observed, quantifiable structure. Clustering is traditionally an unsupervised approach to data analysis, in the sense that it operates without any direct guidance about which items should be assigned to which clusters. There has been a recent trend in the clustering literature toward supporting semisupervised or constrained
Crack propagation modeling using Peridynamic theory
NASA Astrophysics Data System (ADS)
Hafezi, M. H.; Alebrahim, R.; Kundu, T.
2016-04-01
Crack propagation and branching are modeled using nonlocal peridynamic theory. One major advantage of this nonlocal theory based analysis tool is the unifying approach towards material behavior modeling - irrespective of whether the crack is formed in the material or not. No separate damage law is needed for crack initiation and propagation. This theory overcomes the weaknesses of existing continuum mechanics based numerical tools (e.g. FEM, XFEM etc.) for identifying fracture modes and does not require any simplifying assumptions. Cracks grow autonomously and not necessarily along a prescribed path. However, in some special situations such as in case of ductile fracture, the damage evolution and failure depend on parameters characterizing the local stress state instead of peridynamic damage modeling technique developed for brittle fracture. For brittle fracture modeling the bond is simply broken when the failure criterion is satisfied. This simulation helps us to design more reliable modeling tool for crack propagation and branching in both brittle and ductile materials. Peridynamic analysis has been found to be very demanding computationally, particularly for real-world structures (e.g. vehicles, aircrafts, etc.). It also requires a very expensive visualization process. The goal of this paper is to bring awareness to researchers the impact of this cutting-edge simulation tool for a better understanding of the cracked material response. A computer code has been developed to implement the peridynamic theory based modeling tool for two-dimensional analysis. A good agreement between our predictions and previously published results is observed. Some interesting new results that have not been reported earlier by others are also obtained and presented in this paper. The final objective of this investigation is to increase the mechanics knowledge of self-similar and self-affine cracks.
Donchev, Todor I.; Petrov, Ivan G.
2011-05-31
Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.
Beste, Ariana; Vazquez-Mayagoitia, Alvaro; Ortiz, J. Vincent
2013-01-01
A direct method (D-Delta-MBPT(2)) to calculate second-order ionization potentials (IPs), electron affinities (EAs), and excitation energies is developed. The Delta-MBPT(2) method is defined as the correlated extension of the Delta-HF method. Energy differences are obtained by integrating the energy derivative with respect to occupation numbers over the appropriate parameter range. This is made possible by writing the second-order energy as a function of the occupation numbers. Relaxation effects are fully included at the SCF level. This is in contrast to linear response theory, which makes the D-Delta-MBPT(2) applicable not only to single excited but also higher excited states. We show the relationship of the D-Delta-MBPT(2) method for IPs and EAs to a second-order approximation of the effective Fock-space coupled-cluster Hamiltonian and a second-order electron propagator method. We also discuss the connection between the D-Delta-MBPT(2) method for excitation energies and the CIS-MP2 method. Finally, as a proof of principle, we apply our method to calculate ionization potentials and excitation energies of some small molecules. For IPs, the Delta-MBPT(2) results compare well to the second-order solution of the Dyson equation. For excitation energies, the deviation from EOM-CCSD increases when correlation becomes more important. When using the numerical integration technique, we encounter difficulties that prevented us from reaching the Delta-MBPT(2) values. Most importantly, relaxation beyond the Hartree Fock level is significant and needs to be included in future research.
Propagation of disturbances in degenerate quantum systems
NASA Astrophysics Data System (ADS)
Chancellor, Nicholas; Haas, Stephan
2011-07-01
Disturbances in gapless quantum many-body models are known to travel an unlimited distance throughout the system. Here, we explore this phenomenon in finite clusters with degenerate ground states. The specific model studied here is the one-dimensional J1-J2 Heisenberg Hamiltonian at and close to the Majumdar-Ghosh point. Both open and periodic boundary conditions are considered. Quenches are performed using a local magnetic field. The degenerate Majumdar-Ghosh ground state allows disturbances which carry quantum entanglement to propagate throughout the system and thus dephase the entire system within the degenerate subspace. These disturbances can also carry polarization, but not energy, as all energy is stored locally. The local evolution of the part of the system where energy is stored drives the rest of the system through long-range entanglement. We also examine approximations for the ground state of this Hamiltonian in the strong field limit and study how couplings away from the Majumdar-Ghosh point affect the propagation of disturbances. We find that even in the case of approximate degeneracy, a disturbance can be propagated throughout a finite system.
Multi-Graph Matching via Affinity Optimization with Graduated Consistency Regularization.
Yan, Junchi; Cho, Minsu; Zha, Hongyuan; Yang, Xiaokang; Chu, Stephen M
2016-06-01
This paper addresses the problem of matching common node correspondences among multiple graphs referring to an identical or related structure. This multi-graph matching problem involves two correlated components: i) the local pairwise matching affinity across pairs of graphs; ii) the global matching consistency that measures the uniqueness of the pairwise matchings by different composition orders. Previous studies typically either enforce the matching consistency constraints in the beginning of an iterative optimization, which may propagate matching error both over iterations and across graph pairs; or separate affinity optimization and consistency enforcement into two steps. This paper is motivated by the observation that matching consistency can serve as a regularizer in the affinity objective function especially when the function is biased due to noises or inappropriate modeling. We propose composition-based multi-graph matching methods to incorporate the two aspects by optimizing the affinity score, meanwhile gradually infusing the consistency. We also propose two mechanisms to elicit the common inliers against outliers. Compelling results on synthetic and real images show the competency of our algorithms. PMID:26372208
Tropospheric propagation assessment
NASA Astrophysics Data System (ADS)
Anderson, K. D.; Richter, J. H.; Hitney, H. V.
1984-02-01
It is well known that microwave propagation in a marine environment frequently exhibits unexpected behavior. The deviation from 4/3 earth propagation calculations is due to the fact that the vertical refractivity distribution of the troposphere rarely follows the standard lapse rate of -39 N/km. Instead, the troposphere is generally composed of horizontally stratified layers of differing refractivity gradients. The most striking propagation anomalies result when a layer gradient is less than -157 N/km, forming a trapping layer. In the marine environment, there are two mechanisms which produce such layers. An elevated trapping layer is created by the advection of a warm, dry air mass over a cold, moist air mass producing either a surface-based or an elevated duct which may affect frequencies as low as 100 MHz. A very persistent surface trapping layer is due to water evaporation at the air-sea interface. This surface, or evaporation duct is generally thin, on the order of 10 m in vertical extent, and is an effective trapping mechanism for frequencies greater than 3 GHz. With the introduction of the Integrated Refraction Effects Prediction System (IREPS) into the US Navy, fleet units now have the capability to evaluate accurately the performance of their EM systems when the refractive environment is known. However, these units may have to plan for operations thousands of miles away under different refractivity conditions. To assist in planning, a worldwide upper air and surface climatology has been developed for use through the IREPS programs. The IREPS concept is reviewed and a description of the tropospheric ducting data base is presented.
NASA Astrophysics Data System (ADS)
Sciacchitano, Andrea; Wieneke, Bernhard
2016-08-01
This paper discusses the propagation of the instantaneous uncertainty of PIV measurements to statistical and instantaneous quantities of interest derived from the velocity field. The expression of the uncertainty of vorticity, velocity divergence, mean value and Reynolds stresses is derived. It is shown that the uncertainty of vorticity and velocity divergence requires the knowledge of the spatial correlation between the error of the x and y particle image displacement, which depends upon the measurement spatial resolution. The uncertainty of statistical quantities is often dominated by the random uncertainty due to the finite sample size and decreases with the square root of the effective number of independent samples. Monte Carlo simulations are conducted to assess the accuracy of the uncertainty propagation formulae. Furthermore, three experimental assessments are carried out. In the first experiment, a turntable is used to simulate a rigid rotation flow field. The estimated uncertainty of the vorticity is compared with the actual vorticity error root-mean-square, with differences between the two quantities within 5–10% for different interrogation window sizes and overlap factors. A turbulent jet flow is investigated in the second experimental assessment. The reference velocity, which is used to compute the reference value of the instantaneous flow properties of interest, is obtained with an auxiliary PIV system, which features a higher dynamic range than the measurement system. Finally, the uncertainty quantification of statistical quantities is assessed via PIV measurements in a cavity flow. The comparison between estimated uncertainty and actual error demonstrates the accuracy of the proposed uncertainty propagation methodology.
A global/local affinity graph for image segmentation.
Xiaofang Wang; Yuxing Tang; Masnou, Simon; Liming Chen
2015-04-01
Construction of a reliable graph capturing perceptual grouping cues of an image is fundamental for graph-cut based image segmentation methods. In this paper, we propose a novel sparse global/local affinity graph over superpixels of an input image to capture both short- and long-range grouping cues, and thereby enabling perceptual grouping laws, including proximity, similarity, continuity, and to enter in action through a suitable graph-cut algorithm. Moreover, we also evaluate three major visual features, namely, color, texture, and shape, for their effectiveness in perceptual segmentation and propose a simple graph fusion scheme to implement some recent findings from psychophysics, which suggest combining these visual features with different emphases for perceptual grouping. In particular, an input image is first oversegmented into superpixels at different scales. We postulate a gravitation law based on empirical observations and divide superpixels adaptively into small-, medium-, and large-sized sets. Global grouping is achieved using medium-sized superpixels through a sparse representation of superpixels' features by solving a ℓ0-minimization problem, and thereby enabling continuity or propagation of local smoothness over long-range connections. Small- and large-sized superpixels are then used to achieve local smoothness through an adjacent graph in a given feature space, and thus implementing perceptual laws, for example, similarity and proximity. Finally, a bipartite graph is also introduced to enable propagation of grouping cues between superpixels of different scales. Extensive experiments are carried out on the Berkeley segmentation database in comparison with several state-of-the-art graph constructions. The results show the effectiveness of the proposed approach, which outperforms state-of-the-art graphs using four different objective criteria, namely, the probabilistic rand index, the variation of information, the global consistency error, and the
Pulse Propagation in Phaseonium
NASA Astrophysics Data System (ADS)
Rahman, Ashiqur; Eberly, J. H.
1996-05-01
Phaseonium [1] is a medium where the quantum atomic phase is held fixed for long times compared with various relaxation processes. In inhomogeneously broadened two-level phaseonium, we have found a new area theorem (similar to self-induced transparency [2]) for pulse propagation, where pulses of arbitrary area can be stable instead of 2π area. We will also report results for inhomogeneously broadened three-level phaseonium. Research partially supported by NSF grant PHY94-08733. [1] M.O. Scully, Phys. Rev. Lett. 55, 2802 (1985), also Quant. Opt. 6, 203 (1994). [2] S. L. McCall and E. L. Hahn, Phys. Rev. 183, 457 (1969).
Transport with Feynman propagators
White, R.H.
1990-11-06
Richard Feynman's formulation of quantum electrodynamics suggests a Monte Carlo algorithm for calculating wave propagation. We call this the Sum Over All Paths (SOAP) method. The method is applied to calculate diffraction by double slits of finite width and by a reflection grating. Calculations of reflection by plane and parabolic mirrors of finite aperture and from several figured surfaces are shown. An application to a one-dimensional scattering problem is discussed. A variation of SOAP can be applied to the diffusion equation. 2 refs., 8 figs.
Temporal scaling in information propagation
NASA Astrophysics Data System (ADS)
Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi
2014-06-01
For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.
Temporal scaling in information propagation.
Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi
2014-01-01
For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers. PMID:24939414
Collective thermoregulation in bee clusters.
Ocko, Samuel A; Mahadevan, L
2014-02-01
Swarming is an essential part of honeybee behaviour, wherein thousands of bees cling onto each other to form a dense cluster that may be exposed to the environment for several days. This cluster has the ability to maintain its core temperature actively without a central controller. We suggest that the swarm cluster is akin to an active porous structure whose functional requirement is to adjust to outside conditions by varying its porosity to control its core temperature. Using a continuum model that takes the form of a set of advection-diffusion equations for heat transfer in a mobile porous medium, we show that the equalization of an effective 'behavioural pressure', which propagates information about the ambient temperature through variations in density, leads to effective thermoregulation. Our model extends and generalizes previous models by focusing the question of mechanism on the form and role of the behavioural pressure, and allows us to explain the vertical asymmetry of the cluster (as a consequence of buoyancy-driven flows), the ability of the cluster to overpack at low ambient temperatures without breaking up at high ambient temperatures, and the relative insensitivity to large variations in the ambient temperature. Our theory also makes testable hypotheses for the response of the cluster to external temperature inhomogeneities and suggests strategies for biomimetic thermoregulation. PMID:24335563
Collective thermoregulation in bee clusters
Ocko, Samuel A.; Mahadevan, L.
2014-01-01
Swarming is an essential part of honeybee behaviour, wherein thousands of bees cling onto each other to form a dense cluster that may be exposed to the environment for several days. This cluster has the ability to maintain its core temperature actively without a central controller. We suggest that the swarm cluster is akin to an active porous structure whose functional requirement is to adjust to outside conditions by varying its porosity to control its core temperature. Using a continuum model that takes the form of a set of advection–diffusion equations for heat transfer in a mobile porous medium, we show that the equalization of an effective ‘behavioural pressure’, which propagates information about the ambient temperature through variations in density, leads to effective thermoregulation. Our model extends and generalizes previous models by focusing the question of mechanism on the form and role of the behavioural pressure, and allows us to explain the vertical asymmetry of the cluster (as a consequence of buoyancy-driven flows), the ability of the cluster to overpack at low ambient temperatures without breaking up at high ambient temperatures, and the relative insensitivity to large variations in the ambient temperature. Our theory also makes testable hypotheses for the response of the cluster to external temperature inhomogeneities and suggests strategies for biomimetic thermoregulation. PMID:24335563
Electrodynamic properties of fractal clusters
NASA Astrophysics Data System (ADS)
Maksimenko, V. V.; Zagaynov, V. A.; Agranovski, I. E.
2014-07-01
An influence of interference on a character of light interaction both with individual fractal cluster (FC) consisting of nanoparticles and with agglomerates of such clusters is investigated. Using methods of the multiple scattering theory, effective dielectric permeability of a micron-size FC composed of non-absorbing nanoparticles is calculated. The cluster could be characterized by a set of effective dielectric permeabilities. Their number coincides with the number of particles, where space arrangement in the cluster is correlated. If the fractal dimension is less than some critical value and frequency corresponds to the frequency of the visible spectrum, then the absolute value of effective dielectric permeability becomes very large. This results in strong renormalization (decrease) of the incident radiation wavelength inside the cluster. The renormalized photons are cycled or trapped inside the system of multi-scaled cavities inside the cluster. A lifetime of a photon localized inside an agglomerate of FCs is a macroscopic value allowing to observe the stimulated emission of the localized light. The latter opens up a possibility for creation of lasers without inverse population of energy levels. Moreover, this allows to reconsider problems of optical cloaking of macroscopic objects. One more feature of fractal structures is a possibility of unimpeded propagation of light when any resistance associated with scattering disappears.
Li, Shangyong; Wang, Linna; Yang, Juan; Bao, Jing; Liu, Junzhong; Lin, Shengxiang; Hao, Jianhua; Sun, Mi
2016-06-01
In this study, an efficient affinity purification protocol for an alkaline metalloprotease from marine bacterium was developed using immobilized metal affinity chromatography. After screening and optimization of the affinity ligands and spacer arm lengths, Cu-iminmodiacetic acid was chosen as the optimal affinity ligand, which was coupled to Sepharose 6B via a 14-atom spacer arm. The absorption analysis of this medium revealed a desorption constant Kd of 21.5 μg/mL and a theoretical maximum absorption Qmax of 24.9 mg/g. Thanks to this affinity medium, the enzyme could be purified by only one affinity purification step with a purity of approximately 95% pure when analyzed by high-performance liquid chromatography and reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis. The recovery of the protease activity reached 74.6%, which is much higher than the value obtained by traditional protocols (8.9%). These results contribute to the industrial purifications and contribute a significant reference for the purification of other metalloproteases. PMID:27058973
Shaping propagation invariant laser beams
NASA Astrophysics Data System (ADS)
Soskind, Michael; Soskind, Rose; Soskind, Yakov
2015-11-01
Propagation-invariant structured laser beams possess several unique properties and play an important role in various photonics applications. The majority of propagation invariant beams are produced in the form of laser modes emanating from stable laser cavities. Therefore, their spatial structure is limited by the intracavity mode formation. We show that several types of anamorphic optical systems (AOSs) can be effectively employed to shape laser beams into a variety of propagation invariant structured fields with different shapes and phase distributions. We present a propagation matrix approach for designing AOSs and defining mode-matching conditions required for preserving propagation invariance of the output shaped fields. The propagation matrix approach was selected, as it provides a more straightforward approach in designing AOSs for shaping propagation-invariant laser beams than the alternative technique based on the Gouy phase evolution, especially in the case of multielement AOSs. Several practical configurations of optical systems that are suitable for shaping input laser beams into a diverse variety of structured propagation invariant laser beams are also presented. The laser beam shaping approach was applied by modeling propagation characteristics of several input laser beam types, including Hermite-Gaussian, Laguerre-Gaussian, and Ince-Gaussian structured field distributions. The influence of the Ince-Gaussian beam semifocal separation parameter and the azimuthal orientation between the input laser beams and the AOSs onto the resulting shape of the propagation invariant laser beams is presented as well.
An analysis of rumor propagation based on propagation force
NASA Astrophysics Data System (ADS)
Zhao, Zhen-jun; Liu, Yong-mei; Wang, Ke-xi
2016-02-01
A propagation force is introduced into the analysis of rumor propagation to address uncertainty in the process. The propagation force is portrayed as a fuzzy variable, and a category of new parameters with fuzzy variables is defined. The classic susceptible, infected, recovered (SIR) model is modified using these parameters, a fuzzy reproductive number is introduced into the modified model, and the rationality of the fuzzy reproductive number is illuminated through calculation and comparison. Rumor control strategies are also discussed.
Smooth big bounce from affine quantization
NASA Astrophysics Data System (ADS)
Bergeron, Hervé; Dapor, Andrea; Gazeau, Jean Pierre; Małkiewicz, Przemysław
2014-04-01
We examine the possibility of dealing with gravitational singularities on a quantum level through the use of coherent state or wavelet quantization instead of canonical quantization. We consider the Robertson-Walker metric coupled to a perfect fluid. It is the simplest model of a gravitational collapse, and the results obtained here may serve as a useful starting point for more complex investigations in the future. We follow a quantization procedure based on affine coherent states or wavelets built from the unitary irreducible representation of the affine group of the real line with positive dilation. The main issue of our approach is the appearance of a quantum centrifugal potential allowing for regularization of the singularity, essential self-adjointness of the Hamiltonian, and unambiguous quantum dynamical evolution.
Improved native affinity purification of RNA.
Batey, Robert T; Kieft, Jeffrey S
2007-08-01
RNA biochemical or structural studies often require an RNA sample that is chemically pure, and most protocols for its in vitro production use denaturing polyacrylamide gel electrophoresis to achieve this. Unfortunately, many RNAs do not quantitatively refold into an active conformation after denaturation, creating significant problems for downstream characterization or use. In addition, this traditional purification method is not amenable to studies demanding high-throughput RNA production. Recently, we presented the first general method for producing almost any RNA sequence that employs an affinity tag that is removed during the purification process. Because technical difficulties prevented application of this method to many RNAs, we have developed an improved version that utilizes a different activatable ribozyme and affinity tag that are considerably more robust, rapid, and broadly applicable. PMID:17548432
Protein affinity map of chemical space.
Kauvar, L M; Villar, H O; Sportsman, J R; Higgins, D L; Schmidt, D E
1998-09-11
Affinity fingerprinting is a quantitative method for mapping chemical space based on binding preferences of compounds for a reference panel of proteins. An effective reference panel of <20 proteins can be empirically selected which shows differential interaction with nearly all compounds. By using this map to iteratively sample the chemical space, identification of active ligands from a library of 30,000 candidate compounds has been accomplished for a wide spectrum of specific protein targets. In each case, <200 compounds were directly assayed against the target. Further, analysis of the fingerprint database suggests a strategy for effective selection of affinity chromatography ligands and scaffolds for combinatorial chemistry. With such a system, the large numbers of potential therapeutic targets emerging from genome research can be categorized according to ligand binding properties, complementing sequence based classification. PMID:9792501
Affinity Chromatography in Nonionic Detergent Solutions
NASA Astrophysics Data System (ADS)
Robinson, Jack B.; Strottmann, James M.; Wick, Donald G.; Stellwagen, Earle
1980-10-01
Anionic dye affinity chromatography is commonly unproductive in the presence of nonionic detergents used to extract particulate proteins. Using lactate dehydrogenase as a model protein, Cibacron blue F3GA as a model dye, and Triton X-100 as a model detergent, we find that the dye is encapsulated in nonionic detergent micelles, rendering the dye incapable of ligation with the enzyme. However, the dye can be liberated from the micelles without altering the nonionic detergent concentration by addition of an anionic detergent, such as deoxycholate or sodium dodecyl sulfate, forming mixed anionic/nonionic micelles that displace the anionic dye. Encapsulation of the anionic detergents prevents their activity as protein denaturants. These observations have been successfully translated to the dye affinity chromatography of a detergent extract of brain particulate cyclic nucleotide phosphodiesterase.
A MEMS Dielectric Affinity Glucose Biosensor.
Huang, Xian; Li, Siqi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao
2013-06-20
Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concentrations. This sensor features simplicity in sensor design, and possesses high specificity and accuracy in glucose detection. However, lack of glucose diffusion passage, this device is unable to fulfill real-time in-vivo monitoring. As a major improvement to this device, we present in this paper a fully implantable MEMS dielectric affinity glucose biosensor that contains a perforated electrode embedded in a suspended diaphragm. This capacitive-based sensor contains no moving parts, and enables glucose diffusion and real-time monitoring. The experimental results indicate that this sensor can detect glucose solutions at physiological concentrations and possesses good reversibility and reliability. This sensor has a time constant to glucose concentration change at approximately 3 min, which is comparable to commercial systems. The sensor has potential applications in fully implantable CGM that require excellent long-term stability and reliability. PMID:24511215
Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.
Thingholm, Tine E; Larsen, Martin R
2016-01-01
Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture. PMID:26584922
CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection.
Nedumpully-Govindan, Praveen; Jemec, Domen B; Ding, Feng
2016-06-27
While molecular docking with both ligand and receptor flexibilities can help capture conformational changes upon binding, correct ranking of nativelike binding poses and accurate estimation of binding affinities remains a major challenge. In addition to the commonly used scoring approach with intermolecular interaction energies, we included the contribution of intramolecular energies changes upon binding in our flexible docking method, MedusaDock. In CSAR 2013-2014 binding prediction benchmark exercises, the new scoring function MScomplex was found to better recapitulate experimental binding affinities and correctly identify ligand-binding sequences from decoy receptors. Our further analysis with the DUD data sets indicates significant improvement of virtual screening enrichment using the new scoring function when compared to the previous intermolecular energy based scoring method. Our postanalysis also suggests a new approach to select nativelike poses in the clustering-based pose ranking approach by MedusaDock. Since the calculation of intramolecular energy changes and clustering-based pose ranking and selection are not MedusaDock specific, we expect a broad application in force-field based estimation of binding affinities and pose ranking using flexible ligand-receptor docking. PMID:26252196
NASA Technical Reports Server (NTRS)
Bringi, V. N.; Chandrasekar, V.; Mueller, Eugene A.; Turk, Joseph; Beaver, John; Helmken, Henry F.; Henning, Rudy
1993-01-01
Papers on Ka-band propagation measurements using the ACTS propagation terminal and the Colorado State University CHILL multiparameter radar and on Space Communications Technology Center Florida Propagation Program are discussed. Topics covered include: microwave radiative transfer and propagation models; NASA propagation terminal status; ACTS channel characteristics; FAU receive only terminal; FAU terminal status; and propagation testbed.
ACTS mobile propagation campaign
NASA Technical Reports Server (NTRS)
Goldhirsh, Julius; Vogel, Wolfhard J.; Torrence, Geoffrey W.
1994-01-01
Preliminary results are presented for three propagation measurement campaigns involving a mobile receiving laboratory and 20 GHz transmissions from the Advanced Communications Technology Satellite (ACTS). Four 1994 campaigns were executed during weekly periods in and around Austin, Texas in February and May, in Central Maryland during March, and in Fairbanks, Alaska and environs in June. Measurements tested the following effects at 20 GHz: (1) attenuation due to roadside trees with and without foliage, (2) multipath effects for scenarios in which line-of-sight paths were unshadowed, (3) fades due to terrain and roadside obstacles, (4) fades due to structures in urban environs, (5) single tree attenuation, and (6) effects of fading at low elevation angles (8 deg in Fairbanks, Alaska) and high elevation angles (55 deg in Austin, Texas). Results presented here cover sampled measurements in Austin, Texas for foliage and non-foliage cases and in Central Maryland for non-foliage runs.
NASA Technical Reports Server (NTRS)
Barts, R. M.; Stutzman, W. L.; Pratt, T.
1989-01-01
The Virginia Tech Satellite Communications Group has participated in the Land Mobile Satellite System (LMSS) program through JPL sponsorship since 1985. Involvement has mainly been in modeling and simulation of propagation characteristics and effects. Models developed to predict cummulative fade distributions for fading LMSS signals include LMSSMOD and the Simple Models which approximate LMSSMOD. Models to predict the mean and standard deviation of signal attenuation through roadside vegetation, namely the Average Path Model, were developed. In the area of simulation, efforts have centered around the development of a software simulator that uses data bases derived from experimental data to generate simulated data with arbitrary statistical behavior. This work has progressed to the development of an integrated analysis and simulation package, LIPS. The basic theory and results for the models and simulator have been previously documented in reports and papers. All LMSS activities are summarized and details of this year's efforts are given.
NASA Technical Reports Server (NTRS)
Chakraborty, Dayamoy; Davarian, Faramaz
1991-01-01
The purpose of the Advanced Communications Technology Satellite (ACTS) is to demonstrate the feasibility of the Ka-band (20 and 30 GHz) spectrum for satellite communications, as well as to help maintain U.S. leadership in satellite communications. ACTS incorporates such innovative schemes as time division multiple access (TDMA), microwave and baseband switching, onboard regeneration, and adaptive application of coding during rain-fade conditions. The success or failure of the ACTS experiment will depend on how accurately the rain-fade statistics and fade dynamics can be predicted in order to derive an appropriate algorithm that will combat weather vagaries, specifically for links with small terminals, such as very small aperture terminals (VSAT's) where the power margin is a premium. This article describes the planning process and hardware development program that will comply with the recommendations of the ACTS propagation study groups.
Numerical propagator through PIAA optics
NASA Astrophysics Data System (ADS)
Pueyo, Laurent; Shaklan, Stuart; Give'On, Amir; Krist, John
2009-08-01
In this communication we address two outstanding issues pertaining the modeling of PIAA coronagraphs, accurate numerical propagation of edge effects and fast propagation of mid spatial frequencies for wavefront control. In order to solve them, we first derive a quadratic approximation of the Huygens wavelets that allows us to develop an angular spectrum propagator for pupil remapping. Using this result we introduce an independent method to verify the ultimate contrast floor, due to edge propagation effects, of PIAA units currently being tested in various testbeds. We then delve into the details of a novel fast algorithm, based on the recognition that angular spectrum computations with a pre-apodised system are computationally light. When used for the propagation of mid spatial frequencies, such a fast propagator will ultimately allow us to develop robust wavefront control algorithms with DMs located before the pupil remapping mirrors.
Localization of Free Field Realizations of Affine Lie Algebras
NASA Astrophysics Data System (ADS)
Futorny, Vyacheslav; Grantcharov, Dimitar; Martins, Renato A.
2015-04-01
We use localization technique to construct new families of irreducible modules of affine Kac-Moody algebras. In particular, localization is applied to the first free field realization of the affine Lie algebra or, equivalently, to imaginary Verma modules.
Interferometric Propagation Delay
NASA Technical Reports Server (NTRS)
Goldstein, Richard
1999-01-01
Radar interferometry based on (near) exact repeat passes has lately been used by many groups of scientists, worldwide, to achieve state of the art measurements of topography, glacier and ice stream motion, earthquake displacements, oil field subsidence, lava flows, crop-induced surface decorrelation, and other effects. Variations of tropospheric and ionospheric propagation delays limit the accuracy of all such measurements. We are investigating the extent of this limitation, using data from the Shuttle radar flight, SIR-C, which is sensitive to the troposphere, and the Earth Resources Satellites, ERS-1/2, which are sensitive to both the troposphere and the ionosphere. We are presently gathering statistics of the delay variations over selected, diverse areas to determine the best accuracy possible for repeat track interferometry. The phases of an interferogram depend on both the topography of the scene and variations in propagation delay. The delay variations can be caused by movement of elements in the scene, by changes in tropospheric water vapor and by changes of the charge concentrations in the ionosphere. We plan to separate these causes by using the data from a third satellite visit (three-pass interferometry). The figure gives the geometry of the three-pass observations. The page of the figure is taken to be perpendicular to the spacecraft orbits. The three observational locations are marked on the figure, giving baselines B-12 and B-13, separated by the angle alpha. These parameters are almost constant over the whole scene. However, each pixel has an individual look angle, theta, which is related to the topography, rho is the slant range. A possible spurious time delay is shown. Additional information is contained in the original.
Propagation Terminal Design and Measurements
NASA Technical Reports Server (NTRS)
Nessel, James
2015-01-01
The NASA propagation terminal has been designed and developed by the Glenn Research Center and is presently deployed at over 5 NASA and partner ground stations worldwide collecting information on the effects of the atmosphere on Ka-band and millimeter wave communications links. This lecture provides an overview of the fundamentals and requirements of the measurement of atmospheric propagation effects and, specifically, the types of hardware and digital signal processing techniques employed by current state-of-the-art propagation terminal systems.
Propagation into an unstable state
Dee, G.
1985-06-01
We describe propagating front solutions of the equations of motion of pattern-forming systems. We make a number of conjectures concerning the properties of such fronts in connection with pattern selection in these systems. We describe a calculation which can be used to calculate the velocity and state selected by certain types of propagating fronts. We investigate the propagating front solutions of the amplitude equation which provides a valid dynamical description of many pattern-forming systems near onset.
Photoelectron spectroscopy of nitromethane anion clusters
NASA Astrophysics Data System (ADS)
Pruitt, Carrie Jo M.; Albury, Rachael M.; Goebbert, Daniel J.
2016-08-01
Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic Csbnd H⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak Csbnd H⋯O hydrogen bond.
Cascade dynamics of complex propagation
NASA Astrophysics Data System (ADS)
Centola, Damon; Eguíluz, Víctor M.; Macy, Michael W.
2007-01-01
Random links between otherwise distant nodes can greatly facilitate the propagation of disease or information, provided contagion can be transmitted by a single active node. However, we show that when the propagation requires simultaneous exposure to multiple sources of activation, called complex propagation, the effect of random links can be just the opposite; it can make the propagation more difficult to achieve. We numerically calculate critical points for a threshold model using several classes of complex networks, including an empirical social network. We also provide an estimation of the critical values in terms of vulnerable nodes.
Alieva, T; Bastiaans, M J
2000-04-01
The expression for the Wigner distribution (WD) in polar coordinates was derived, based on the decomposition of coherent and partially coherent fields on the orthogonal sets of Hermite-Gauss modes. This representation allows one to analyze easily the structure of the WD and to describe the field propagation through first-order optical systems, including the self-imaging phenomenon. PMID:10757184
Winters-Hilt, Stephen; Merat, Sam
2007-01-01
Background Support Vector Machines (SVMs) provide a powerful method for classification (supervised learning). Use of SVMs for clustering (unsupervised learning) is now being considered in a number of different ways. Results An SVM-based clustering algorithm is introduced that clusters data with no a priori knowledge of input classes. The algorithm initializes by first running a binary SVM classifier against a data set with each vector in the set randomly labelled, this is repeated until an initial convergence occurs. Once this initialization step is complete, the SVM confidence parameters for classification on each of the training instances can be accessed. The lowest confidence data (e.g., the worst of the mislabelled data) then has its' labels switched to the other class label. The SVM is then re-run on the data set (with partly re-labelled data) and is guaranteed to converge in this situation since it converged previously, and now it has fewer data points to carry with mislabelling penalties. This approach appears to limit exposure to the local minima traps that can occur with other approaches. Thus, the algorithm then improves on its weakly convergent result by SVM re-training after each re-labeling on the worst of the misclassified vectors – i.e., those feature vectors with confidence factor values beyond some threshold. The repetition of the above process improves the accuracy, here a measure of separability, until there are no misclassifications. Variations on this type of clustering approach are shown. Conclusion Non-parametric SVM-based clustering methods may allow for much improved performance over parametric approaches, particularly if they can be designed to inherit the strengths of their supervised SVM counterparts. PMID:18047717
Sarmast, Mostafa Khoshhal; Salehi, Hassan; Ramezani, Amin; Abolimoghadam, Ali Asghar; Niazi, Ali; Khosh-Khui, Morteza
2012-03-01
Randomly amplified polymorphic DNA (RAPD) was used as a tool to assess the genetic fidelity of in vitro propagated Araucaria excelsa R. Br. var. glauca with explants taken from orthotropic stem along with their related mother plants after treatment with kinetin, 2iP, BA (0.02-0.26 mg/l) and TDZ (0.001-1 mg/l) to produce axillary shoots. TDZ and kinetin induced more shoot and higher length per explant. Results showed a total of 1,676 fragments were generated with 12 RAPD primers in micropropagated plants and their donor mother plants. The number of loci ranged from 6 in OPB 12-18 in OPY 07 with a size ranging from 250 bp in OPH 19-3500 bp in OPH 11. Cluster analysis of RAPD data using UPGMA (unweighted pair group method with arithmetic average) revealed more than 92% genetic similarities between tissue cultured plants and their corresponding mother plant measured by the Jaccard's similarity coefficient. Similarity matrix and PCoA (two dimensional principal coordinate analysis) resulted in the same affinity. Primers had shown 36% polymorphism. However, careful monitoring of tissue culture derived plants might be needed to determine that rooted shoots are adventitious in origin. PMID:21667314
Hemphill, B E
1998-07-01
Discovery of a previously unknown Bronze Age civilization (Oxus Civilization) centered on the oases of Central Asia immediately raised questions concerning the origin and interregional impacts of this civilization. Fifteen craniometric variables from 12 Bronze Age samples--encompassing 544 adults from Central Asia, Iran, the Indus Valley, and Anatolia--are compared to test which, if any, of the current hypotheses offered by archaeologists are best supported by the pattern of phenetic affinities possessed by the Oxus Civilization inhabitants of the north Bactrian oasis. Craniometric differences between samples are compared with Mahalanobis generalized distance, and patterns of phenetic affinity are assessed with two types of cluster analysis (WPGMA, neighbor-joining method), multidimensional scaling, and principal coordinates analysis. Results obtained by this analysis indicate that current hypotheses for both the origin and interregional impacts of Oxus Civilization populations are incomplete. PMID:9696149
Fluctuation-controlled front propagation
NASA Astrophysics Data System (ADS)
Ridgway, Douglas Thacher
1997-09-01
the symmetry of the absorbing state, but which is unsuccessful at capturing the behavior of diffusion-limited growth. In an effort to find a simpler model system, we turned to modelling fitness increases in evolution. The work was motivated by an experiment on vesicular stomatitis virus, a short (˜9600bp) single-stranded RNA virus. A highly bottlenecked viral population increases in fitness rapidly until a certain point, after which the fitness increases at a slower rate. This is well modeled by a constant population reproducing and mutating on a smooth fitness landscape. Mean field theory of this system displays the same infinite propagation velocity blowup as mean field diffusion-limited aggregation. However, we have been able to make progress on a number of fronts. One is solving systems of moment equations, where a hierarchy of moments is truncated arbitrarily at some level. Good results for front propagation velocity are found with just two moments, corresponding to inclusion of the basic finite population clustering effect ignored by mean field theory. In addition, for small mutation rates, most of the population will be entirely on a single site or two adjacent sites, and the density of these cases can be described and solved. (Abstract shortened by UMI.)
Measuring an antibody affinity distribution molecule by molecule
Bradbury, Andrew M; Werner, James H; Temirov, Jamshid
2008-01-01
Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.
On the structure of self-affine convex bodies
Voynov, A S
2013-08-31
We study the structure of convex bodies in R{sup d} that can be represented as a union of their affine images with no common interior points. Such bodies are called self-affine. Vallet's conjecture on the structure of self-affine bodies was proved for d = 2 by Richter in 2011. In the present paper we disprove the conjecture for all d≥3 and derive a detailed description of self-affine bodies in R{sup 3}. Also we consider the relation between properties of self-affine bodies and functional equations with a contraction of an argument. Bibliography: 10 titles.
Metal-affinity separations: A new dimension in protein processing
Arnold, F.H. )
1991-02-01
Rapid growth in the preparative and high-resolution analytical applications of metal-affinity chromatography demonstrate the appeal of metal recognition as a basis for protein separations. Stable, inexpensive chelated metals effectively mimic biospecific interactions, providing selective ligands for protein binding. This article reviews recent progress in understanding the mechanisms of metal-protein recognition that underlie metal-affinity separations. Also discussed are schemes for integrating metal-affinity purifications into the expression and bioprocessing of recombinant proteins. Promising future developments include new metal-affinity processes for analytical and preparative-scale separations and a range of techniques for enhancing the selectivity of metal-affinity separations.
Analysis of Network Clustering Algorithms and Cluster Quality Metrics at Scale
Kobourov, Stephen; Gallant, Mike; Börner, Katy
2016-01-01
Overview Notions of community quality underlie the clustering of networks. While studies surrounding network clustering are increasingly common, a precise understanding of the realtionship between different cluster quality metrics is unknown. In this paper, we examine the relationship between stand-alone cluster quality metrics and information recovery metrics through a rigorous analysis of four widely-used network clustering algorithms—Louvain, Infomap, label propagation, and smart local moving. We consider the stand-alone quality metrics of modularity, conductance, and coverage, and we consider the information recovery metrics of adjusted Rand score, normalized mutual information, and a variant of normalized mutual information used in previous work. Our study includes both synthetic graphs and empirical data sets of sizes varying from 1,000 to 1,000,000 nodes. Cluster Quality Metrics We find significant differences among the results of the different cluster quality metrics. For example, clustering algorithms can return a value of 0.4 out of 1 on modularity but score 0 out of 1 on information recovery. We find conductance, though imperfect, to be the stand-alone quality metric that best indicates performance on the information recovery metrics. Additionally, our study shows that the variant of normalized mutual information used in previous work cannot be assumed to differ only slightly from traditional normalized mutual information. Network Clustering Algorithms Smart local moving is the overall best performing algorithm in our study, but discrepancies between cluster evaluation metrics prevent us from declaring it an absolutely superior algorithm. Interestingly, Louvain performed better than Infomap in nearly all the tests in our study, contradicting the results of previous work in which Infomap was superior to Louvain. We find that although label propagation performs poorly when clusters are less clearly defined, it scales efficiently and accurately to large
Avoiding degenerate coframes in an affine gauge approach to quantum gravity
Mielke, E.W.; McCrea, J.D.; Ne`eman, Y.; Hehl, F.W.
1993-04-01
This report discusses the following concepts on quantum gravity: The affine gauge approach; affine gauge transformations versus active differomorphisms; affine gauge approach to quantum gravity with topology change.
Aluminum monocation basicity and affinity scales.
Gal, Jean-François; Yáñez, Manuel; Mó, Otilia
2015-01-01
The experimental aspects of the determination of thermochemical data for the attachment of the aluminum monocation Al(+) to neutral atoms and molecules are reviewed. Literature aluminum cation affinities (enthalpy scale) and basicities (Gibbs energy scale) are tabulated and discussed. Ab initio quantum chemical calculations at the G4 level on 43 adducts provide a consistent picture of the energetics of the adducts and their structures. The Al(+)-ligand bonding is analyzed in terms of natural bond orbital and atom-in molecule analyses. A brief comparison of the Al(+) basicity scales and other gas- phase cation basicities is presented. PMID:26307732
Contractions of affine Kac-Moody algebras
NASA Astrophysics Data System (ADS)
Daboul, J.; Daboul, C.; de Montigny, M.
2008-08-01
I review our recent work on contractions of affine Kac-Moody algebras (KMA) and present new results. We study generalized contractions of KMA with respect to their twisted and untwisted KM subalgebras. As a concrete example, we discuss contraction of D(1)4 and D(3)4, based on Z3-grading. We also describe examples of 'level-dependent' contractions, which are based on Z-gradings of KMA. Our work generalizes the Inönü-Wigner contraction of P. Majumdar in several directions. We also give an algorithm for constructing Kac-Moody-like algebras hat g for any Lie algebra g.
Seismic wave propagation modeling
Jones, E.M.; Olsen, K.B.
1998-12-31
This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). A hybrid, finite-difference technique was developed for modeling nonlinear soil amplification from three-dimensional, finite-fault radiation patters for earthquakes in arbitrary earth models. The method was applied to the 17 January 1994 Northridge earthquake. Particle velocities were computed on a plane at 5-km depth, immediately above the causative fault. Time-series of the strike-perpendicular, lateral velocities then were propagated vertically in a soil column typical of the San Fernando Valley. Suitable material models were adapted from a suite used to model ground motions at the US Nevada Test Site. The effects of nonlinearity reduced relative spectral amplitudes by about 40% at frequencies above 1.5 Hz but only by 10% at lower frequencies. Runs made with source-depth amplitudes increased by a factor of two showed relative amplitudes above 1.5 Hz reduced by a total of 70% above 1.5 Hz and 20% at lower frequencies. Runs made with elastic-plastic material models showed similar behavior to runs made with Masing-Rule models.
NASA Astrophysics Data System (ADS)
Kocia, Lucas; Heller, Eric J.
2015-09-01
We offer a more formal justification for the successes of our recently communicated "directed Heller-Herman-Kluk-Kay" (DHK) time propagator by examining its performance in one-dimensional bound systems which exhibit at least quasi-periodic motion. DHK is distinguished by its single one-dimensional integral—a vast simplification over the usual 2N-dimensional integral in full Heller-Herman-Kluk-Kay (for an N-dimensional system). We find that DHK accurately captures particular coherent state autocorrelations when its single integral is chosen to lie along these states' fastest growing manifold, as long as it is not perpendicular to their action gradient. Moreover, the larger the action gradient, the better DHK will perform. We numerically examine DHK's accuracy in a one-dimensional quartic oscillator and illustrate that these conditions are frequently satisfied such that the method performs well. This lends some explanation for why DHK frequently seems to work so well and suggests that it may be applicable to systems exhibiting quite strong anharmonicity.
Modeling turbulent flame propagation
Ashurst, W.T.
1994-08-01
Laser diagnostics and flow simulation techniques axe now providing information that if available fifty years ago, would have allowed Damkoehler to show how turbulence generates flame area. In the absence of this information, many turbulent flame speed models have been created, most based on Kolmogorov concepts which ignore the turbulence vortical structure, Over the last twenty years, the vorticity structure in mixing layers and jets has been shown to determine the entrainment and mixing behavior and these effects need to be duplicated by combustion models. Turbulence simulations reveal the intense vorticity structure as filaments and simulations of passive flamelet propagation show how this vorticity Creates flame area and defines the shape of the expected chemical reaction surface. Understanding how volume expansion interacts with flow structure should improve experimental methods for determining turbulent flame speed. Since the last decade has given us such powerful new tools to create and see turbulent combustion microscopic behavior, it seems that a solution of turbulent combustion within the next decade would not be surprising in the hindsight of 2004.
Effective propagation in a perturbed periodic structure
NASA Astrophysics Data System (ADS)
Maurel, Agnès; Pagneux, Vincent
2008-08-01
In a recent paper [D. Torrent, A. Hakansson, F. Cervera, and J. Sánchez-Dehesa, Phys. Rev. Lett. 96, 204302 (2006)] inspected the effective parameters of a cluster containing an ensemble of scatterers with a periodic or a weakly disordered arrangement. A small amount of disorder is shown to have a small influence on the characteristics of the acoustic wave propagation with respect to the periodic case. In this Brief Report, we inspect further the effect of a deviation in the scatterer distribution from the periodic distribution. The quasicrystalline approximation is shown to be an efficient tool to quantify this effect. An analytical formula for the effective wave number is obtained in one-dimensional acoustic medium and is compared with the Berryman result in the low-frequency limit. Direct numerical calculations show a good agreement with the analytical predictions.
Effective propagation in a perturbed periodic structure
Maurel, Agnes; Pagneux, Vincent
2008-08-01
In a recent paper [D. Torrent, A. Hakansson, F. Cervera, and J. Sanchez-Dehesa, Phys. Rev. Lett. 96, 204302 (2006)] inspected the effective parameters of a cluster containing an ensemble of scatterers with a periodic or a weakly disordered arrangement. A small amount of disorder is shown to have a small influence on the characteristics of the acoustic wave propagation with respect to the periodic case. In this Brief Report, we inspect further the effect of a deviation in the scatterer distribution from the periodic distribution. The quasicrystalline approximation is shown to be an efficient tool to quantify this effect. An analytical formula for the effective wave number is obtained in one-dimensional acoustic medium and is compared with the Berryman result in the low-frequency limit. Direct numerical calculations show a good agreement with the analytical predictions.
Aptamer Affinity Maturation by Resampling and Microarray Selection.
Kinghorn, Andrew B; Dirkzwager, Roderick M; Liang, Shaolin; Cheung, Yee-Wai; Fraser, Lewis A; Shiu, Simon Chi-Chin; Tang, Marco S L; Tanner, Julian A
2016-07-19
Aptamers have significant potential as affinity reagents, but better approaches are critically needed to discover higher affinity nucleic acids to widen the scope for their diagnostic, therapeutic, and proteomic application. Here, we report aptamer affinity maturation, a novel aptamer enhancement technique, which combines bioinformatic resampling of aptamer sequence data and microarray selection to navigate the combinatorial chemistry binding landscape. Aptamer affinity maturation is shown to improve aptamer affinity by an order of magnitude in a single round. The novel aptamers exhibited significant adaptation, the complexity of which precludes discovery by other microarray based methods. Honing aptamer sequences using aptamer affinity maturation could help optimize a next generation of nucleic acid affinity reagents. PMID:27346322
Light propagation and large-scale inhomogeneities
Brouzakis, Nikolaos; Tetradis, Nikolaos; Tzavara, Eleftheria E-mail: ntetrad@phys.uoa.gr
2008-04-15
We consider the effect on the propagation of light of inhomogeneities with sizes of order 10 Mpc or larger. The Universe is approximated through a variation of the Swiss-cheese model. The spherical inhomogeneities are void-like, with central underdensities surrounded by compensating overdense shells. We study the propagation of light in this background, assuming that the source and the observer occupy random positions, so that each beam travels through several inhomogeneities at random angles. The distribution of luminosity distances for sources with the same redshift is asymmetric, with a peak at a value larger than the average one. The width of the distribution and the location of the maximum increase with increasing redshift and length scale of the inhomogeneities. We compute the induced dispersion and bias of cosmological parameters derived from the supernova data. They are too small to explain the perceived acceleration without dark energy, even when the length scale of the inhomogeneities is comparable to the horizon distance. Moreover, the dispersion and bias induced by gravitational lensing at the scales of galaxies or clusters of galaxies are larger by at least an order of magnitude.
High-affinity Cyclic Peptide Matriptase Inhibitors*
Quimbar, Pedro; Malik, Uru; Sommerhoff, Christian P.; Kaas, Quentin; Chan, Lai Y.; Huang, Yen-Hua; Grundhuber, Maresa; Dunse, Kerry; Craik, David J.; Anderson, Marilyn A.; Daly, Norelle L.
2013-01-01
The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase. PMID:23548907
Heparin affinity purification of extracellular vesicles
Balaj, Leonora; Atai, Nadia A.; Chen, Weilin; Mu, Dakai; Tannous, Bakhos A.; Breakefield, Xandra O.; Skog, Johan; Maguire, Casey A.
2015-01-01
Extracellular vesicles (EVs) are lipid membrane vesicles released by cells. They carry active biomolecules including DNA, RNA, and protein which can be transferred to recipient cells. Isolation and purification of EVs from culture cell media and biofluids is still a major challenge. The most widely used isolation method is ultracentrifugation (UC) which requires expensive equipment and only partially purifies EVs. Previously we have shown that heparin blocks EV uptake in cells, supporting a direct EV-heparin interaction. Here we show that EVs can be purified from cell culture media and human plasma using ultrafiltration (UF) followed by heparin-affinity beads. UF/heparin-purified EVs from cell culture displayed the EV marker Alix, contained a diverse RNA profile, had lower levels of protein contamination, and were functional at binding to and uptake into cells. RNA yield was similar for EVs isolated by UC. We were able to detect mRNAs in plasma samples with comparable levels to UC samples. In conclusion, we have discovered a simple, scalable, and effective method to purify EVs taking advantage of their heparin affinity. PMID:25988257
Affine conformal vectors in space-time
NASA Astrophysics Data System (ADS)
Coley, A. A.; Tupper, B. O. J.
1992-05-01
All space-times admitting a proper affine conformal vector (ACV) are found. By using a theorem of Hall and da Costa, it is shown that such space-times either (i) admit a covariantly constant vector (timelike, spacelike, or null) and the ACV is the sum of a proper affine vector and a conformal Killing vector or (ii) the space-time is 2+2 decomposable, in which case it is shown that no ACV can exist (unless the space-time decomposes further). Furthermore, it is proved that all space-times admitting an ACV and a null covariantly constant vector (which are necessarily generalized pp-wave space-times) must have Ricci tensor of Segré type {2,(1,1)}. It follows that, among space-times admitting proper ACV, the Einstein static universe is the only perfect fluid space-time, there are no non-null Einstein-Maxwell space-times, and only the pp-wave space-times are representative of null Einstein-Maxwell solutions. Otherwise, the space-times can represent anisotropic fluids and viscous heat-conducting fluids, but only with restricted equations of state in each case.
Exploring Fluorous Affinity by Liquid Chromatography.
Catani, Martina; Guzzinati, Roberta; Marchetti, Nicola; Pasti, Luisa; Cavazzini, Alberto
2015-07-01
Terms such as "fluorous affinity" and "fluorophilicity" have been used to describe the unique partition and sorption properties often exhibited by highly fluorinated organic compounds, that is molecules rich in sp(3) carbon-fluorine bonds. In this work, we made use of a highly fluorinated stationary phase and a series of benzene derivatives to study the effect of one single perfluorinated carbon on the chromatographic behavior and adsorption properties of molecules. For this purpose, the adsorption equilibria of α,α,α-trifluorotoluene, toluene, and other alkylbenzenes have been studied by means of nonlinear chromatography in a variety of acetonitrile/water eluents. Our results reveal that one single perfluorinated carbon is already enough to induce a drastic change in the adsorption properties of molecules on the perfluorinated stationary phase. In particular, it has been found that adsorption is monolayer if the perfluoroalkyl carbon is present but that, when this unit is missing, molecules arrange as multilayer stack structures. These findings can contribute to the understanding of molecular mechanisms of fluorous affinity. PMID:26047527
Quantification of hydrophobic interaction affinity of colloids
NASA Astrophysics Data System (ADS)
Saini, G.; Nasholm, N.; Wood, B. D.
2009-12-01
Colloids play an important role in a wide variety of disciplines, including water and wastewater treatment, subsurface transport of metals and organic contaminants, migration of fines in oil reservoirs, biocolloid (virus and bacteria) transport in subsurface, and are integral to laboratory transport studies. Although the role of hydrophobicity in adhesion and transport of colloids, particularly bacteria, is well known; there is scarcity of literature regarding hydrophobicity measurement of non-bacterial colloids and other micron-sized particles. Here we detail an experimental approach based on differential partitioning of colloids between two liquid phases (hydrocarbon and buffer) as a measure of the hydrophobic interaction affinity of colloids. This assay, known as Microbial adhesion to hydrocarbons or MATH, is frequently used in microbiology and bacteriology for quantifying the hydrophobicity of microbes. Monodispersed colloids and particles, with sizes ranging from 1 micron to 33 micron, were used for the experiments. A range of hydrophobicity values were observed for different particles. The hydrophobicity results are also verified against water contact angle measurements of these particles. This liquid-liquid partitioning assay is quick, easy-to-perform and requires minimal instrumentation. Estimation of the hydrophobic interaction affinity of colloids would lead to a better understanding of their adhesion to different surfaces and subsequent transport in porous media.
NA
2002-03-04
The purpose of this Analysis and Model Report (AMR) supporting the Site Recommendation/License Application (SR/LA) for the Yucca Mountain Project is the development of elementary analyses of the interactions of a hypothetical dike with a repository drift (i.e., tunnel) and with the drift contents at the potential Yucca Mountain repository. This effort is intended to support the analysis of disruptive events for Total System Performance Assessment (TSPA). This AMR supports the Process Model Report (PMR) on disruptive events (CRWMS M&O 2000a). This purpose is documented in the development plan (DP) ''Coordinate Modeling of Dike Propagation Near Drifts Consequences for TSPA-SR/LA'' (CRWMS M&O 2000b). Evaluation of that Development Plan and the work to be conducted to prepare Interim Change Notice (ICN) 1 of this report, which now includes the design option of ''Open'' drifts, indicated that no revision to that DP was needed. These analyses are intended to provide reasonable bounds for a number of expected effects: (1) Temperature changes to the waste package from exposure to magma; (2) The gas flow available to degrade waste containers during the intrusion; (3) Movement of the waste package as it is displaced by the gas, pyroclasts and magma from the intruding dike (the number of packages damaged); (4) Movement of the backfill (Backfill is treated here as a design option); (5) The nature of the mechanics of the dike/drift interaction. These analyses serve two objectives: to provide preliminary analyses needed to support evaluation of the consequences of an intrusive event and to provide a basis for addressing some of the concerns of the Nuclear Regulatory Commission (NRC) expressed in the Igneous Activity Issue Resolution Status Report.
Aguda, Adeleke H; Lavallee, Vincent; Cheng, Ping; Bott, Tina M; Meimetis, Labros G; Law, Simon; Nguyen, Nham T; Williams, David E; Kaleta, Jadwiga; Villanueva, Ivan; Davies, Julian; Andersen, Raymond J; Brayer, Gary D; Brömme, Dieter
2016-08-26
Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach. PMID:27498895
Laser Propagation in Uranium Hexafluoride
NASA Astrophysics Data System (ADS)
Chu, Danny
1990-01-01
Several researchers have simulated the laser pulse propagation through simple N-level systems; but, for UF _6 models, large CPU time and memory is required. In an attempt to efficiently yet accurately characterize laser pulse propagation through a UF _6 molecule, a model of UF_6 is created and analyzed by adiabatic excitation. A minimax numerical method is developed to solve the time -dependent Schrodinger equation and then applied to the study of laser excitation of UF_6 using various Gaussian pulses. The process of laser isotope separation is also discussed. The results from the laser excitation of UF_6 are used to simulate laser propagation through ^{235} UF_6.
Saphire, E.O.; Montero, M.; Menendez, A.; Houten, N.E.van; Irving, M.B.; Pantophlet, R.; Swick, M.B.; Parren, P.W.H.I.; Burton, D.R.; Scott, J.K.; Wilson, I.A.; /Scripps Res. Inst. /Simon Fraser U. /British Columbia U.
2007-07-13
The human antibody b12 recognizes a discontinuous epitope on gp120 and is one of the rare monoclonal antibodies that neutralize a broad range of primary human immunodeficiency virus type 1 (HIV-1) isolates. We previously reported the isolation of B2.1, a dimeric peptide that binds with high specificity to b12 and competes with gp120 for b12 antibody binding. Here, we show that the affinity of B2.1 was improved 60-fold over its synthetic-peptide counterpart by fusing it to the N terminus of a soluble protein. This affinity, which is within an order of magnitude of that of gp120, probably more closely reflects the affinity of the phage-borne peptide. The crystal structure of a complex between Fab of b12 and B2.1 was determined at 1.8 Angstrom resolution. The structural data allowed the differentiation of residues that form critical contacts with b12 from those required for maintenance of the antigenic structure of the peptide, and revealed that three contiguous residues mediate B2.1's critical contacts with b12. This single region of critical contact between the B2.1 peptide and the b12 paratope is unlikely to mimic the discontinuous key binding residues involved in the full b12 epitope for gp120, as previously identified by alanine scanning substitutions on the gp120 surface. These structural observations are supported by experiments that demonstrate that B2.1 is an ineffective immunogenic mimic of the b12 epitope on gp120. Indeed, an extensive series of immunizations with B2.1 in various forms failed to produce gp120 cross-reactive sera. The functional and structural data presented here, however, suggest that the mechanism by which b12 recognizes the two antigens is very different. Here, we present the first crystal structure of peptide bound to an antibody that was originally raised against a discontinuous protein epitope. Our results highlight the challenge of producing immunogens that mimic discontinuous protein epitopes, and the necessity of combining
Large odd{endash}even effect in RbC{sup {minus}}{sub {ital n}} cluster size distributions
Vandenbosch, R.; Will, D.I.
1996-04-01
RbC{sub {ital n}} cluster anions have been produced by Rb sputtering of graphite. The intensity ratio of clusters with an even number of carbon atoms to those with an odd number of carbons is much larger for RbC{sup {minus}}{sub {ital n}} clusters than for C{sup {minus}}{sub {ital n}} clusters. {ital Ab} {ital initio} quantum mechanical calculations suggest that this arises from RbC{sub {ital n}} electron affinities that are close to zero or negative for odd {ital n}, rather than from an enhanced odd{endash}even alternation in the affinities. {copyright} {ital 1996 American Institute of Physics.}
Automatic gesture analysis using constant affine velocity.
Cifuentes, Jenny; Boulanger, Pierre; Pham, Minh Tu; Moreau, Richard; Prieto, Flavio
2014-01-01
Hand human gesture recognition has been an important research topic widely studied around the world, as this field offers the ability to identify, recognize, and analyze human gestures in order to control devices or to interact with computer interfaces. In particular, in medical training, this approach is an important tool that can be used to obtain an objective evaluation of a procedure performance. In this paper, some obstetrical gestures, acquired by a forceps, were studied with the hypothesis that, as the scribbling and drawing movements, they obey the one-sixth power law, an empirical relationship which connects path curvature, torsion, and euclidean velocity. Our results show that obstetrical gestures have a constant affine velocity, which is different for each type of gesture and based on this idea this quantity is proposed as an appropriate classification feature in the hand human gesture recognition field. PMID:25570332
Effectively nonlocal metric-affine gravity
NASA Astrophysics Data System (ADS)
Golovnev, Alexey; Koivisto, Tomi; Sandstad, Marit
2016-03-01
In metric-affine theories of gravity such as the C-theories, the spacetime connection is associated to a metric that is nontrivially related to the physical metric. In this article, such theories are rewritten in terms of a single metric, and it is shown that they can be recast as effectively nonlocal gravity. With some assumptions, known ghost-free theories with nonsingular and cosmologically interesting properties may be recovered. Relations between different formulations are analyzed at both perturbative and nonperturbative levels, taking carefully into account subtleties with boundary conditions in the presence of integral operators in the action, and equivalences between theories related by nonlocal redefinitions of the fields are verified at the level of equations of motion. This suggests a possible geometrical interpretation of nonlocal gravity as an emergent property of non-Riemannian spacetime structure.
Affinities of the Swartkrans early Homo mandibles.
Curnoe, Darren
2008-01-01
The southern African early Homo assemblage continues to make important contributions to understanding the systematics, adaptations and evolutionary history of the human genus. However, the taxonomy of this sample is in a state of flux. This study examines the size and shape of the mandibular bodies of Swartkrans SK 15 and SK 45 comparing them with variation in two early Homo taxa (H. habilis sensu lato and H. sapiens erectus). The research aims to clarify their phenetic affinities and systematics through univariate statistics, inferential testing and multivariate analysis employing size (Log-transformed) and shape (Mosimann variables). Neither of them strongly resembles H. habilis sensu lato or H. sapiens erectus, rather, they probably sample a novel species of Homo not seen in East Africa. Moreover, there is considerable morphological variability within the Swartkrans sample and the possibility of more than one novel species being sampled at this site cannot be excluded. PMID:18402959
Wetting on rough self-affine surfaces
NASA Astrophysics Data System (ADS)
Palasantzas, George
1995-05-01
In this paper, we present a general investigation of the effective potential for complete wetting on self-affine rough surfaces. The roughness effect is investigated by means of the height-height correlation model in Fourier space ~(1+aξ2q2)-1-H. The parameters H and ξ are, respectively, the roughness exponent and the substrate in-plane correlation length. It is observed that the effect of H on the free interface profile is significant for ξ
A database for propagation models
NASA Technical Reports Server (NTRS)
Kantak, Anil V.; Suwitra, Krisjani S.
1992-01-01
In June 1991, a paper at the fifteenth NASA Propagation Experimenters Meeting (NAPEX 15) was presented outlining the development of a database for propagation models. The database is designed to allow the scientists and experimenters in the propagation field to process their data through any known and accepted propagation model. The architecture of the database also incorporates the possibility of changing the standard models in the database to fit the scientist's or the experimenter's needs. The database not only provides powerful software to process the data generated by the experiments, but is also a time- and energy-saving tool for plotting results, generating tables, and producing impressive and crisp hard copy for presentation and filing.
Reconstruction of nonlinear wave propagation
Fleischer, Jason W; Barsi, Christopher; Wan, Wenjie
2013-04-23
Disclosed are systems and methods for characterizing a nonlinear propagation environment by numerically propagating a measured output waveform resulting from a known input waveform. The numerical propagation reconstructs the input waveform, and in the process, the nonlinear environment is characterized. In certain embodiments, knowledge of the characterized nonlinear environment facilitates determination of an unknown input based on a measured output. Similarly, knowledge of the characterized nonlinear environment also facilitates formation of a desired output based on a configurable input. In both situations, the input thus characterized and the output thus obtained include features that would normally be lost in linear propagations. Such features can include evanescent waves and peripheral waves, such that an image thus obtained are inherently wide-angle, farfield form of microscopy.
The NASA radiowave propagation program
NASA Technical Reports Server (NTRS)
Davarian, Faramaz
1990-01-01
The objectives of the NASA radiowave Propagation Program are to enable new satellite communication applications and to enhance existing satellite communication networks. These objectives are achieved by supporting radio wave propagation studies and disseminating the study results in a timely fashion. Studies initiated by this program in the 1980s enabled the infant concept of conducting mobile communications via satellite to reach a state of relative maturity in 1990. The program also supported the satellite communications community by publishing and revising two handbooks dealing with radio wave propagation effects for frequencies below and above 10 GHz, respectively. The program has served the international community through its support of the International Telecommunications Union. It supports state of the art work at universities. Currently, the program is focusing on the Advanced Communications Technology Satellite (ACTS) and its propagation needs. An overview of the program's involvement in the ACTS project is given.
Dye affinity cryogels for plasmid DNA purification.
Çimen, Duygu; Yılmaz, Fatma; Perçin, Işık; Türkmen, Deniz; Denizli, Adil
2015-11-01
The aim of this study is to prepare megaporous dye-affinity cryogel discs for the purification of plasmid DNA (pDNA) from bacterial lysate. Poly(hydroxyethyl methacrylate) [PHEMA] cryogel discs were produced by free radical polymerization initiated by N,N,N',N'-tetramethylene diamine (TEMED) and ammonium persulfate (APS) redox pair in an ice bath. Cibacron Blue F3GA was used as an affinity ligand (loading amount: 68.9μmol/g polymer). The amount of pDNA adsorbed onto the PHEMA-Cibacron Blue F3GA cryogel discs first increased and then reached a plateau value (i.e., 32.5mg/g cryogel) at 3.0mg/mL pDNA concentration. Compared with the PHEMA cryogel (0.11mg/g cryogel), the pDNA adsorption capacity of the PHEMA-Cibacron Blue F3GA cryogel (32.4mg/g polymer) was improved significantly due to the Cibacron Blue 3GA immobilization onto the polymeric matrix. pDNA adsorption amount decreased from 11.7mg/g to 1.1mg/g with the increasing of NaCl concentration. The maximum pDNA adsorption was achieved at 4°C. The overall recovery of pDNA was calculated as 90%. The PHEMA-Cibacron Blue F3GA cryogel discs could be used five times without decreasing the pDNA adsorption capacity significantly. The results show that the PHEMA-Cibacron Blue F3GA cryogel discs promise high selectivity for pDNA. PMID:26249596
Nonlinear competition in nematicon propagation.
Laudyn, Urszula A; Kwasny, Michał; Piccardi, Armando; Karpierz, Mirosław A; Dabrowski, Roman; Chojnowska, Olga; Alberucci, Alessandro; Assanto, Gaetano
2015-11-15
We investigate the role of competing nonlinear responses in the formation and propagation of bright spatial solitons. We use nematic liquid crystals (NLCs) exhibiting both thermo-optic and reorientational nonlinearities with continuous-wave beams. In a suitably prepared dye-doped sample and dual beam collinear geometry, thermal heating in the visible affects reorientational self-focusing in the near infrared, altering light propagation and self-trapping. PMID:26565843
Li, Bing; Fouts, Ashley E; Stengel, Katharina; Luan, Peng; Dillon, Michael; Liang, Wei-Ching; Feierbach, Becket; Kelley, Robert F; Hötzel, Isidro
2014-01-01
Antibodies isolated from human donors are increasingly being developed for anti-infective therapeutics. These antibodies undergo affinity maturation in vivo, minimizing the need for engineering of therapeutic leads for affinity. However, the affinities required for some therapeutic applications may be higher than the affinities of the leads obtained, requiring further affinity maturation in vitro. To improve the neutralization potency of natural human antibody MSL-109 targeting human cytomegalovirus (CMV), we affinity matured the antibody against the gH/gL glycoprotein complex. A phage display library where most of the six complementary-determining regions (CDRs) were allowed to vary in only one amino acid residue at a time was used to scan for mutations that improve binding affinity. A T55R mutation and multiple mutations in position 53 of the heavy chain were identified that, when present individually or in combination, resulted in higher apparent affinities to gH/gL and improved CMV neutralization potency of Fab fragments expressed in bacterial cells. Three of these mutations in position 53 introduced glycosylation sites in heavy chain CDR 2 (CDR H2) that impaired binding of antibodies expressed in mammalian cells. One high affinity (KD < 10 pM) variant was identified that combined the D53N and T55R mutations while avoiding glycosylation of CDR H2. However, all the amino acid substitutions identified by phage display that improved binding affinity without introducing glycosylation sites required between two and four simultaneous nucleotide mutations to avoid glycosylation. These results indicate that the natural human antibody MSL-109 is close to a local affinity optimum. We show that affinity maturation by phage display can be used to identify and bypass barriers to in vivo affinity maturation of antibodies imposed by glycosylation and codon usage. These constraints may be relatively prevalent in human antibodies due to the codon usage and the amino acid
Prediction of Neutral Salt Elution Profiles for Affinity Chromatography
NASA Astrophysics Data System (ADS)
Robinson, Jack B.; Strottmann, James M.; Stellwagen, Earle
1981-04-01
Neutral salts exhibit very marked differences as eluants of proteins from affinity columns. We observe: (i) that the relative potencies of neutral salts as eluants are independent of the protein or the affinity ligand in the systems studied, (ii) that the absolute salt concentration necessary to elute any given protein bound to the affinity matrix is proportional to the algebraic sum of a set of elution coefficients defined herein for the separate ions present in the solution, and (iii) that the proportionality between elution potency and elution coefficient is a function of the affinity of the protein for the immobilized ligand. Given the concentration of one neutral salt required for elution of a protein of interest from an affinity column, the elution capability of any neutral salt at any temperature can be quantitatively predicted for that protein. Accordingly, application and elution protocols for affinity chromatography can be designed to optimize the yield and fold purification of proteins.
Semiclassical propagation of Wigner functions
Dittrich, T.; Gomez, E. A.; Pachon, L. A.
2010-06-07
We present a comprehensive study of semiclassical phase-space propagation in the Wigner representation, emphasizing numerical applications, in particular as an initial-value representation. Two semiclassical approximation schemes are discussed. The propagator of the Wigner function based on van Vleck's approximation replaces the Liouville propagator by a quantum spot with an oscillatory pattern reflecting the interference between pairs of classical trajectories. Employing phase-space path integration instead, caustics in the quantum spot are resolved in terms of Airy functions. We apply both to two benchmark models of nonlinear molecular potentials, the Morse oscillator and the quartic double well, to test them in standard tasks such as computing autocorrelation functions and propagating coherent states. The performance of semiclassical Wigner propagation is very good even in the presence of marked quantum effects, e.g., in coherent tunneling and in propagating Schroedinger cat states, and of classical chaos in four-dimensional phase space. We suggest options for an effective numerical implementation of our method and for integrating it in Monte-Carlo-Metropolis algorithms suitable for high-dimensional systems.
Affine Vertex Operator Algebras and Modular Linear Differential Equations
NASA Astrophysics Data System (ADS)
Arike, Yusuke; Kaneko, Masanobu; Nagatomo, Kiyokazu; Sakai, Yuichi
2016-05-01
In this paper, we list all affine vertex operator algebras of positive integral levels whose dimensions of spaces of characters are at most 5 and show that a basis of the space of characters of each affine vertex operator algebra in the list gives a fundamental system of solutions of a modular linear differential equation. Further, we determine the dimensions of the spaces of characters of affine vertex operator algebras whose numbers of inequivalent simple modules are not exceeding 20.
Lotz, Martin K.; Otsuki, Shuhei; Grogan, Shawn P.; Sah, Robert; Terkeltaub, Robert; D’Lima, Darryl
2010-01-01
The formation of new cell clusters is a histological hallmark of arthritic cartilage but the biology of clusters and their role in disease are poorly understood. This is the first comprehensive review of clinical and experimental conditions associated with cluster formation. Genes and proteins that are expressed in cluster cells, the cellular origin of the clusters, mechanisms that lead to cluster formation and the role of cluster cells in pathogenesis are discussed. PMID:20506158