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Sample records for dimensional directed acyclic

  1. PenPC: A Two-step Approach to Estimate the Skeletons of High Dimensional Directed Acyclic Graphs

    PubMed Central

    Ha, Min Jin; Sun, Wei; Xie, Jichun

    2015-01-01

    Summary Estimation of the skeleton of a directed acyclic graph (DAG) is of great importance for understanding the underlying DAG and causal e ects can be assessed from the skeleton when the DAG is not identifiable. We propose a novel method named PenPC to estimate the skeleton of a high-dimensional DAG by a two-step approach. We first estimate the non-zero entries of a concentration matrix using penalized regression, and then fix the difference between the concentration matrix and the skeleton by evaluating a set of conditional independence hypotheses. For high dimensional problems where the number of vertices p is in polynomial or exponential scale of sample size n, we study the asymptotic property of PenPC on two types of graphs: traditional random graphs where all the vertices have the same expected number of neighbors, and scale-free graphs where a few vertices may have a large number of neighbors. As illustrated by extensive simulations and applications on gene expression data of cancer patients, PenPC has higher sensitivity and specificity than the state-of-the-art method, the PC-stable algorithm. PMID:26406114

  2. Community detection in directed acyclic graphs

    NASA Astrophysics Data System (ADS)

    Speidel, Leo; Takaguchi, Taro; Masuda, Naoki

    2015-08-01

    Some temporal networks, most notably citation networks, are naturally represented as directed acyclic graphs (DAGs). To detect communities in DAGs, we propose a modularity for DAGs by defining an appropriate null model (i.e., randomized network) respecting the order of nodes. We implement a spectral method to approximately maximize the proposed modularity measure and test the method on citation networks and other DAGs. We find that the attained values of the modularity for DAGs are similar for partitions that we obtain by maximizing the proposed modularity (designed for DAGs), the modularity for undirected networks and that for general directed networks. In other words, if we neglect the order imposed on nodes (and the direction of links) in a given DAG and maximize the conventional modularity measure, the obtained partition is close to the optimal one in the sense of the modularity for DAGs. Contribution to the Topical Issue "Temporal Network Theory and Applications", edited by Petter Holme.

  3. Exploring the randomness of directed acyclic networks

    NASA Astrophysics Data System (ADS)

    Goñi, Joaquín; Corominas-Murtra, Bernat; Solé, Ricard V.; Rodríguez-Caso, Carlos

    2010-12-01

    The feed-forward relationship naturally observed in time-dependent processes and in a diverse number of real systems—such as some food webs and electronic and neural wiring—can be described in terms of the so-called directed acyclic graphs (DAGs). An important ingredient of the analysis of such networks is a proper comparison of their observed architecture against an ensemble of randomized graphs, thereby quantifying the randomness of the real systems with respect to suitable null models. This approximation is particularly relevant when the finite size and/or large connectivity of real systems make inadequate a comparison with the predictions obtained from the so-called configuration model. In this paper we analyze two methods of DAG randomization as defined by the desired combination of two topological invariants (directed degree sequence and component distributions) aimed to be preserved. A highly ordered DAG, called snake graph, and an Erdös-Rényi DAG were used to validate the performance of the algorithms. Finally, three real case studies, namely, the C. elegans cell lineage network, a Ph.D. student-supervisor network, and the Milgram’s citation network, were analyzed using each randomization method. Results show how the interpretation of degree-degree relations in DAGs with respect to their randomized ensembles depends on the topological invariants imposed.

  4. Reducing bias through directed acyclic graphs

    PubMed Central

    Shrier, Ian; Platt, Robert W

    2008-01-01

    Background The objective of most biomedical research is to determine an unbiased estimate of effect for an exposure on an outcome, i.e. to make causal inferences about the exposure. Recent developments in epidemiology have shown that traditional methods of identifying confounding and adjusting for confounding may be inadequate. Discussion The traditional methods of adjusting for "potential confounders" may introduce conditional associations and bias rather than minimize it. Although previous published articles have discussed the role of the causal directed acyclic graph approach (DAGs) with respect to confounding, many clinical problems require complicated DAGs and therefore investigators may continue to use traditional practices because they do not have the tools necessary to properly use the DAG approach. The purpose of this manuscript is to demonstrate a simple 6-step approach to the use of DAGs, and also to explain why the method works from a conceptual point of view. Summary Using the simple 6-step DAG approach to confounding and selection bias discussed is likely to reduce the degree of bias for the effect estimate in the chosen statistical model. PMID:18973665

  5. [Application of directed acyclic graphs in control of confounding].

    PubMed

    Xiang, R; Dai, W J; Xiong, Y; Wu, X; Yang, Y F; Wang, L; Dai, Z H; Li, J; Liu, A Z

    2016-07-01

    Observational study is a method most commonly used in the etiology study of epidemiology, but confounders, always distort the true causality between exposure and outcome when local inferencing. In order to eliminate these confounding, the determining of variables which need to be adjusted become a key issue. Directed acyclic graph(DAG)could visualize complex causality, provide a simple and intuitive way to identify the confounding, and convert it into the finding of the minimal sufficient adjustment for the control of confounding. On the one hand, directed acyclic graph can choose less variables, which increase statistical efficiency of the analysis. On the other hand, it could help avoiding variables that is not measured or with missing values. In a word, the directed acyclic graph could facilitate the reveal of the real causality effectively.

  6. Learning directed acyclic graphical structures with genetical genomics data.

    PubMed

    Gao, Bin; Cui, Yuehua

    2015-12-15

    Large amount of research efforts have been focused on estimating gene networks based on gene expression data to understand the functional basis of a living organism. Such networks are often obtained by considering pairwise correlations between genes, thus may not reflect the true connectivity between genes. By treating gene expressions as quantitative traits while considering genetic markers, genetical genomics analysis has shown its power in enhancing the understanding of gene regulations. Previous works have shown the improved performance on estimating the undirected network graphical structure by incorporating genetic markers as covariates. Knowing that gene expressions are often due to directed regulations, it is more meaningful to estimate the directed graphical network. In this article, we introduce a covariate-adjusted Gaussian graphical model to estimate the Markov equivalence class of the directed acyclic graphs (DAGs) in a genetical genomics analysis framework. We develop a two-stage estimation procedure to first estimate the regression coefficient matrix by [Formula: see text] penalization. The estimated coefficient matrix is then used to estimate the mean values in our multi-response Gaussian model to estimate the regulatory networks of gene expressions using PC-algorithm. The estimation consistency for high dimensional sparse DAGs is established. Simulations are conducted to demonstrate our theoretical results. The method is applied to a human Alzheimer's disease dataset in which differential DAGs are identified between cases and controls. R code for implementing the method can be downloaded at http://www.stt.msu.edu/∼cui. R code for implementing the method is freely available at http://www.stt.msu.edu/∼cui/software.html. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Estimation of Sparse Directed Acyclic Graphs for Multivariate Counts Data

    PubMed Central

    Han, Sung Won; Zhong, Hua

    2016-01-01

    Summary The next-generation sequencing data, called high throughput sequencing data, are recorded as count data, which is generally far from normal distribution. Under the assumption that the count data follow the Poisson log-normal distribution, this paper provides an L1-penalized likelihood framework and an efficient search algorithm to estimate the structure of sparse directed acyclic graphs (DAGs) for multivariate counts data. In searching for the solution, we use iterative optimization procedures to estimate the adjacency matrix and the variance matrix of the latent variables. The simulation result shows that our proposed method outperforms the approach which assumes multivariate normal distributions, and the log-transformation approach. It also shows that the proposed method outperforms the rank-based PC method under sparse network or hub network structures. As a real data example, we demonstrate the efficiency of the proposed method in estimating the gene regulatory networks of the ovarian cancer study. PMID:26849781

  8. Graphical presentation of confounding in directed acyclic graphs.

    PubMed

    Suttorp, Marit M; Siegerink, Bob; Jager, Kitty J; Zoccali, Carmine; Dekker, Friedo W

    2015-09-01

    Since confounding obscures the real effect of the exposure, it is important to adequately address confounding for making valid causal inferences from observational data. Directed acyclic graphs (DAGs) are visual representations of causal assumptions that are increasingly used in modern epidemiology. They can help to identify the presence of confounding for the causal question at hand. This structured approach serves as a visual aid in the scientific discussion by making underlying relations explicit. This article explains the basic concepts of DAGs and provides examples in the field of nephrology with and without presence of confounding. Ultimately, these examples will show that DAGs can be preferable to the traditional methods to identify sources of confounding, especially in complex research questions.

  9. Some acyclic analogues of nucleotides and their template-directed reactions

    NASA Technical Reports Server (NTRS)

    Tohidi, Mahrokh; Orgel, Leslie E.

    1989-01-01

    Bismonophosphoimidazolides of acyclic analogues of guanosine IV and adenosine V were synthesized. They undergo oligomerization in the presence of complementary polynucleotide templates. Details of their synthesis and their subsequent template- and nontemplate-directed reactions are described, and their possible relevance to the origin of life is discussed.

  10. A Directed Acyclic Graph-Large Margin Distribution Machine Model for Music Symbol Classification.

    PubMed

    Wen, Cuihong; Zhang, Jing; Rebelo, Ana; Cheng, Fanyong

    2016-01-01

    Optical Music Recognition (OMR) has received increasing attention in recent years. In this paper, we propose a classifier based on a new method named Directed Acyclic Graph-Large margin Distribution Machine (DAG-LDM). The DAG-LDM is an improvement of the Large margin Distribution Machine (LDM), which is a binary classifier that optimizes the margin distribution by maximizing the margin mean and minimizing the margin variance simultaneously. We modify the LDM to the DAG-LDM to solve the multi-class music symbol classification problem. Tests are conducted on more than 10000 music symbol images, obtained from handwritten and printed images of music scores. The proposed method provides superior classification capability and achieves much higher classification accuracy than the state-of-the-art algorithms such as Support Vector Machines (SVMs) and Neural Networks (NNs).

  11. A multiple testing method for hypotheses structured in a directed acyclic graph.

    PubMed

    Meijer, Rosa J; Goeman, Jelle J

    2015-01-01

    We present a novel multiple testing method for testing null hypotheses that are structured in a directed acyclic graph (DAG). The method is a top-down method that strongly controls the familywise error rate and can be seen as a generalization of Meinshausen's procedure for tree-structured hypotheses. Just as Meinshausen's procedure, our proposed method can be used to test for variable importance, only the corresponding variable clusters can be chosen more freely, because the method allows for multiple parent nodes and partially overlapping hypotheses. An important application of our method is in gene set analysis, in which one often wants to test multiple gene sets as well as individual genes for their association with a clinical outcome. By considering the genes and gene sets as nodes in a DAG, our method enables us to test both for significant gene sets as well as for significant individual genes within the same multiple testing procedure. The method will be illustrated by testing Gene Ontology terms for evidence of differential expression in a survival setting and is implemented in the R package cherry.

  12. Robust causal inference using directed acyclic graphs: the R package 'dagitty'.

    PubMed

    Textor, Johannes; van der Zander, Benito; Gilthorpe, Mark S; Liśkiewicz, Maciej; Ellison, George T H

    2017-01-15

    Directed acyclic graphs (DAGs), which offer systematic representations of causal relationships, have become an established framework for the analysis of causal inference in epidemiology, often being used to determine covariate adjustment sets for minimizing confounding bias. DAGitty is a popular web application for drawing and analysing DAGs. Here we introduce the R package 'dagitty', which provides access to all of the capabilities of the DAGitty web application within the R platform for statistical computing, and also offers several new functions. We describe how the R package 'dagitty' can be used to: evaluate whether a DAG is consistent with the dataset it is intended to represent; enumerate 'statistically equivalent' but causally different DAGs; and identify exposure-outcome adjustment sets that are valid for causally different but statistically equivalent DAGs. This functionality enables epidemiologists to detect causal misspecifications in DAGs and make robust inferences that remain valid for a range of different DAGs. The R package 'dagitty' is available through the comprehensive R archive network (CRAN) at [https://cran.r-project.org/web/packages/dagitty/]. The source code is available on github at [https://github.com/jtextor/dagitty]. The web application 'DAGitty' is free software, licensed under the GNU general public licence (GPL) version 2 and is available at [http://dagitty.net/].

  13. Invited commentary: the perils of birth weight--a lesson from directed acyclic graphs.

    PubMed

    Wilcox, Allen J

    2006-12-01

    The strong association of birth weight with infant mortality is complicated by a paradoxical finding: Small babies in high-risk populations usually have lower risk than small babies in low-risk populations. In this issue of the Journal, Hernández-Díaz et al. (Am J Epidemiol 2006;164:1115-20) address this "birth weight paradox" using directed acyclic graphs (DAGs). They conclude that the paradox is the result of bias created by adjustment for a factor (birth weight) that is affected by the exposure of interest and at the same time shares causes with the outcome (mortality). While this bias has been discussed before, the DAGs presented by Hernández-Díaz et al. provide more firmly grounded criticism. The DAGs demonstrate (as do many other examples) that seemingly reasonable adjustments can distort epidemiologic results. In this commentary, the birth weight paradox is shown to be an illustration of Simpson's Paradox. It is possible for a factor to be protective within every stratum of a variable and yet be damaging overall. Questions remain as to the causal role of birth weight.

  14. "Toward a clearer definition of confounding" revisited with directed acyclic graphs.

    PubMed

    Howards, Penelope P; Schisterman, Enrique F; Poole, Charles; Kaufman, Jay S; Weinberg, Clarice R

    2012-09-15

    In a 1993 paper (Am J Epidemiol. 1993;137(1):1-8), Weinberg considered whether a variable that is associated with the outcome and is affected by exposure but is not an intermediate variable between exposure and outcome should be considered a confounder in etiologic studies. As an example, she examined the common practice of adjusting for history of spontaneous abortion when estimating the effect of an exposure on the risk of spontaneous abortion. She showed algebraically that such an adjustment could substantially bias the results even though history of spontaneous abortion would meet some definitions of a confounder. Directed acyclic graphs (DAGs) were introduced into epidemiology several years later as a tool with which to identify confounders. The authors now revisit Weinberg's paper using DAGs to represent scenarios that arise from her original assumptions. DAG theory is consistent with Weinberg's finding that adjusting for history of spontaneous abortion introduces bias in her original scenario. In the authors' examples, treating history of spontaneous abortion as a confounder introduces bias if it is a descendant of the exposure and is associated with the outcome conditional on exposure or is a child of a collider on a relevant undirected path. Thoughtful DAG analyses require clear research questions but are easily modified for examining different causal assumptions that may affect confounder assessment.

  15. Automated interviews on clinical case reports to elicit directed acyclic graphs.

    PubMed

    Luciani, Davide; Stefanini, Federico M

    2012-05-01

    Setting up clinical reports within hospital information systems makes it possible to record a variety of clinical presentations. Directed acyclic graphs (Dags) offer a useful way of representing causal relations in clinical problem domains and are at the core of many probabilistic models described in the medical literature, like Bayesian networks. However, medical practitioners are not usually trained to elicit Dag features. Part of the difficulty lies in the application of the concept of direct causality before selecting all the causal variables of interest for a specific patient. We designed an automated interview to tutor medical doctors in the development of Dags to represent their understanding of clinical reports. Medical notions were analyzed to find patterns in medical reasoning that can be followed by algorithms supporting the elicitation of causal Dags. Clinical relevance was defined to help formulate only relevant questions by driving an expert's attention towards variables causally related to nodes already inserted in the graph. Key procedural features of the proposed interview are described by four algorithms. The automated interview comprises questions on medical notions, phrased in medical terms. The first elicitation session produces questions concerning the patient's chief complaints and the outcomes related to diseases serving as diagnostic hypotheses, their observable manifestations and risk factors. The second session focuses on questions that refine the initial causal paths by considering syndromes, dysfunctions, pathogenic anomalies, biases and effect modifiers. A case study concerning a gastro-enterological problem and one dealing with an infected patient illustrate the output produced by the algorithms, depending on the answers provided by the doctor. The proposed elicitation framework is characterized by strong consistency with medical background and by a progressive introduction of relevant medical topics. Revision and testing of the

  16. Wavelet Entropy and Directed Acyclic Graph Support Vector Machine for Detection of Patients with Unilateral Hearing Loss in MRI Scanning

    PubMed Central

    Wang, Shuihua; Yang, Ming; Du, Sidan; Yang, Jiquan; Liu, Bin; Gorriz, Juan M.; Ramírez, Javier; Yuan, Ti-Fei; Zhang, Yudong

    2016-01-01

    Highlights We develop computer-aided diagnosis system for unilateral hearing loss detection in structural magnetic resonance imaging.Wavelet entropy is introduced to extract image global features from brain images. Directed acyclic graph is employed to endow support vector machine an ability to handle multi-class problems.The developed computer-aided diagnosis system achieves an overall accuracy of 95.1% for this three-class problem of differentiating left-sided and right-sided hearing loss from healthy controls. Aim: Sensorineural hearing loss (SNHL) is correlated to many neurodegenerative disease. Now more and more computer vision based methods are using to detect it in an automatic way. Materials: We have in total 49 subjects, scanned by 3.0T MRI (Siemens Medical Solutions, Erlangen, Germany). The subjects contain 14 patients with right-sided hearing loss (RHL), 15 patients with left-sided hearing loss (LHL), and 20 healthy controls (HC). Method: We treat this as a three-class classification problem: RHL, LHL, and HC. Wavelet entropy (WE) was selected from the magnetic resonance images of each subjects, and then submitted to a directed acyclic graph support vector machine (DAG-SVM). Results: The 10 repetition results of 10-fold cross validation shows 3-level decomposition will yield an overall accuracy of 95.10% for this three-class classification problem, higher than feedforward neural network, decision tree, and naive Bayesian classifier. Conclusions: This computer-aided diagnosis system is promising. We hope this study can attract more computer vision method for detecting hearing loss. PMID:27807415

  17. Wavelet Entropy and Directed Acyclic Graph Support Vector Machine for Detection of Patients with Unilateral Hearing Loss in MRI Scanning.

    PubMed

    Wang, Shuihua; Yang, Ming; Du, Sidan; Yang, Jiquan; Liu, Bin; Gorriz, Juan M; Ramírez, Javier; Yuan, Ti-Fei; Zhang, Yudong

    2016-01-01

    Highlights We develop computer-aided diagnosis system for unilateral hearing loss detection in structural magnetic resonance imaging.Wavelet entropy is introduced to extract image global features from brain images. Directed acyclic graph is employed to endow support vector machine an ability to handle multi-class problems.The developed computer-aided diagnosis system achieves an overall accuracy of 95.1% for this three-class problem of differentiating left-sided and right-sided hearing loss from healthy controls. Aim: Sensorineural hearing loss (SNHL) is correlated to many neurodegenerative disease. Now more and more computer vision based methods are using to detect it in an automatic way. Materials: We have in total 49 subjects, scanned by 3.0T MRI (Siemens Medical Solutions, Erlangen, Germany). The subjects contain 14 patients with right-sided hearing loss (RHL), 15 patients with left-sided hearing loss (LHL), and 20 healthy controls (HC). Method: We treat this as a three-class classification problem: RHL, LHL, and HC. Wavelet entropy (WE) was selected from the magnetic resonance images of each subjects, and then submitted to a directed acyclic graph support vector machine (DAG-SVM). Results: The 10 repetition results of 10-fold cross validation shows 3-level decomposition will yield an overall accuracy of 95.10% for this three-class classification problem, higher than feedforward neural network, decision tree, and naive Bayesian classifier. Conclusions: This computer-aided diagnosis system is promising. We hope this study can attract more computer vision method for detecting hearing loss.

  18. Assessing causal relationships in genomics: From Bradford-Hill criteria to complex gene-environment interactions and directed acyclic graphs

    PubMed Central

    2011-01-01

    Observational studies of human health and disease (basic, clinical and epidemiological) are vulnerable to methodological problems -such as selection bias and confounding- that make causal inferences problematic. Gene-disease associations are no exception, as they are commonly investigated using observational designs. A rich body of knowledge exists in medicine and epidemiology on the assessment of causal relationships involving personal and environmental causes of disease; it includes seminal causal criteria developed by Austin Bradford Hill and more recently applied directed acyclic graphs (DAGs). However, such knowledge has seldom been applied to assess causal relationships in clinical genetics and genomics, even in studies aimed at making inferences relevant for human health. Conversely, incorporating genetic causal knowledge into clinical and epidemiological causal reasoning is still a largely unexplored area. As the contribution of genetics to the understanding of disease aetiology becomes more important, causal assessment of genetic and genomic evidence becomes fundamental. The method we develop in this paper provides a simple and rigorous first step towards this goal. The present paper is an example of integrative research, i.e., research that integrates knowledge, data, methods, techniques, and reasoning from multiple disciplines, approaches and levels of analysis to generate knowledge that no discipline alone may achieve. PMID:21658235

  19. Maximal acyclic agreement forests.

    PubMed

    Voorkamp, Josh

    2014-10-01

    Finding the hybridization number of a pair or set of trees, [Formula: see text], is a well-studied problem in phylogenetics and is equivalent to finding a maximum acyclic agreement forest (MAAF) for [Formula: see text]. This article defines a new type of acyclic agreement forest called a maximal acyclic agreement forest (mAAF). The property for which mAAFs are "simplest" is more general and could be considered more biologically relevant than the corresponding property for MAAFs, and the set of MAAFs for any [Formula: see text] is a subset of the set of mAAFs for [Formula: see text]. This article also presents two new algorithms; one finds a mAAF for any [Formula: see text] in polynomial time and the other is an exhaustive search that finds all mAAFs for some [Formula: see text], which is also a new approach to finding the hybridization number when applied to a pair of trees. The exhaustive search algorithm is applied to a real world data set, and the findings are compared to previous results.

  20. Evidence for halogen bond covalency in acyclic and interlocked halogen-bonding receptor anion recognition

    DOE PAGES

    Robinson, Sean W.; Mustoe, Chantal L.; White, Nicholas G.; ...

    2014-12-05

    The synthesis and anion binding properties of novel halogen-bonding (XB) bis-iodotriazole-pyridinium-containing acyclic and [2]catenane anion host systems are described. The XB acyclic receptor displays selectivity for acetate over halides with enhanced anion recognition properties compared to the analogous hydrogen-bonding (HB) acyclic receptor. A reversal in halide selectivity is observed in the XB [2]catenane, in comparison to the acyclic XB receptor, due to the interlocked host’s unique three-dimensional binding cavity, and no binding is observed for oxoanions. Notable halide anion association constant values determined for the [2]catenane in competitive organic–aqueous solvent mixtures demonstrate considerable enhancement of anion recognition as compared tomore » the HB catenane analogue. X-ray crystallographic analysis of a series of halide catenane complexes reveal strong XB interactions in the solid state. These interactions were studied using Cl and Br K-edge X-ray Absorption Spectroscopy (XAS) indicating intense pre-edge features characteristic of charge transfer from the halide to its bonding partner (σAX←X–* ← X1s), and providing a direct measure of the degree of covalency in the halogen bond(s). Lastly, the data reveal that the degree of covalency is similar to that which is observed in transition metal coordinate covalent bonds. These results are supported by DFT results, which correlate well with the experimental data.« less

  1. Evidence for halogen bond covalency in acyclic and interlocked halogen-bonding receptor anion recognition

    SciTech Connect

    Robinson, Sean W.; Mustoe, Chantal L.; White, Nicholas G.; Brown, Asha; Thompson, Amber L.; Kennepohl, Pierre; Beer, Paul D.

    2014-12-05

    The synthesis and anion binding properties of novel halogen-bonding (XB) bis-iodotriazole-pyridinium-containing acyclic and [2]catenane anion host systems are described. The XB acyclic receptor displays selectivity for acetate over halides with enhanced anion recognition properties compared to the analogous hydrogen-bonding (HB) acyclic receptor. A reversal in halide selectivity is observed in the XB [2]catenane, in comparison to the acyclic XB receptor, due to the interlocked host’s unique three-dimensional binding cavity, and no binding is observed for oxoanions. Notable halide anion association constant values determined for the [2]catenane in competitive organic–aqueous solvent mixtures demonstrate considerable enhancement of anion recognition as compared to the HB catenane analogue. X-ray crystallographic analysis of a series of halide catenane complexes reveal strong XB interactions in the solid state. These interactions were studied using Cl and Br K-edge X-ray Absorption Spectroscopy (XAS) indicating intense pre-edge features characteristic of charge transfer from the halide to its bonding partner (σAX←X–* ← X1s), and providing a direct measure of the degree of covalency in the halogen bond(s). Lastly, the data reveal that the degree of covalency is similar to that which is observed in transition metal coordinate covalent bonds. These results are supported by DFT results, which correlate well with the experimental data.

  2. The Teacher, the Physician and the Person: Exploring Causal Connections between Teaching Performance and Role Model Types Using Directed Acyclic Graphs

    PubMed Central

    Boerebach, Benjamin C. M.; Lombarts, Kiki M. J. M. H.; Scherpbier, Albert J. J.; Arah, Onyebuchi A.

    2013-01-01

    Background In fledgling areas of research, evidence supporting causal assumptions is often scarce due to the small number of empirical studies conducted. In many studies it remains unclear what impact explicit and implicit causal assumptions have on the research findings; only the primary assumptions of the researchers are often presented. This is particularly true for research on the effect of faculty’s teaching performance on their role modeling. Therefore, there is a need for robust frameworks and methods for transparent formal presentation of the underlying causal assumptions used in assessing the causal effects of teaching performance on role modeling. This study explores the effects of different (plausible) causal assumptions on research outcomes. Methods This study revisits a previously published study about the influence of faculty’s teaching performance on their role modeling (as teacher-supervisor, physician and person). We drew eight directed acyclic graphs (DAGs) to visually represent different plausible causal relationships between the variables under study. These DAGs were subsequently translated into corresponding statistical models, and regression analyses were performed to estimate the associations between teaching performance and role modeling. Results The different causal models were compatible with major differences in the magnitude of the relationship between faculty’s teaching performance and their role modeling. Odds ratios for the associations between teaching performance and the three role model types ranged from 31.1 to 73.6 for the teacher-supervisor role, from 3.7 to 15.5 for the physician role, and from 2.8 to 13.8 for the person role. Conclusions Different sets of assumptions about causal relationships in role modeling research can be visually depicted using DAGs, which are then used to guide both statistical analysis and interpretation of results. Since study conclusions can be sensitive to different causal assumptions, results

  3. The teacher, the physician and the person: exploring causal connections between teaching performance and role model types using directed acyclic graphs.

    PubMed

    Boerebach, Benjamin C M; Lombarts, Kiki M J M H; Scherpbier, Albert J J; Arah, Onyebuchi A

    2013-01-01

    In fledgling areas of research, evidence supporting causal assumptions is often scarce due to the small number of empirical studies conducted. In many studies it remains unclear what impact explicit and implicit causal assumptions have on the research findings; only the primary assumptions of the researchers are often presented. This is particularly true for research on the effect of faculty's teaching performance on their role modeling. Therefore, there is a need for robust frameworks and methods for transparent formal presentation of the underlying causal assumptions used in assessing the causal effects of teaching performance on role modeling. This study explores the effects of different (plausible) causal assumptions on research outcomes. This study revisits a previously published study about the influence of faculty's teaching performance on their role modeling (as teacher-supervisor, physician and person). We drew eight directed acyclic graphs (DAGs) to visually represent different plausible causal relationships between the variables under study. These DAGs were subsequently translated into corresponding statistical models, and regression analyses were performed to estimate the associations between teaching performance and role modeling. The different causal models were compatible with major differences in the magnitude of the relationship between faculty's teaching performance and their role modeling. Odds ratios for the associations between teaching performance and the three role model types ranged from 31.1 to 73.6 for the teacher-supervisor role, from 3.7 to 15.5 for the physician role, and from 2.8 to 13.8 for the person role. Different sets of assumptions about causal relationships in role modeling research can be visually depicted using DAGs, which are then used to guide both statistical analysis and interpretation of results. Since study conclusions can be sensitive to different causal assumptions, results should be interpreted in the light of causal

  4. Combining directed acyclic graphs and the change-in-estimate procedure as a novel approach to adjustment-variable selection in epidemiology

    PubMed Central

    2012-01-01

    Background Directed acyclic graphs (DAGs) are an effective means of presenting expert-knowledge assumptions when selecting adjustment variables in epidemiology, whereas the change-in-estimate procedure is a common statistics-based approach. As DAGs imply specific empirical relationships which can be explored by the change-in-estimate procedure, it should be possible to combine the two approaches. This paper proposes such an approach which aims to produce well-adjusted estimates for a given research question, based on plausible DAGs consistent with the data at hand, combining prior knowledge and standard regression methods. Methods Based on the relationships laid out in a DAG, researchers can predict how a collapsible estimator (e.g. risk ratio or risk difference) for an effect of interest should change when adjusted on different variable sets. Implied and observed patterns can then be compared to detect inconsistencies and so guide adjustment-variable selection. Results The proposed approach involves i. drawing up a set of plausible background-knowledge DAGs; ii. starting with one of these DAGs as a working DAG, identifying a minimal variable set, S, sufficient to control for bias on the effect of interest; iii. estimating a collapsible estimator adjusted on S, then adjusted on S plus each variable not in S in turn (“add-one pattern”) and then adjusted on the variables in S minus each of these variables in turn (“minus-one pattern”); iv. checking the observed add-one and minus-one patterns against the pattern implied by the working DAG and the other prior DAGs; v. reviewing the DAGs, if needed; and vi. presenting the initial and all final DAGs with estimates. Conclusion This approach to adjustment-variable selection combines background-knowledge and statistics-based approaches using methods already common in epidemiology and communicates assumptions and uncertainties in a standardized graphical format. It is probably best suited to areas where there is

  5. Cooperative two-dimensional directed transport

    NASA Astrophysics Data System (ADS)

    Zheng, Zhigang; Chen, Hongbin

    2010-11-01

    A mechanism for the cooperative directed transport in two-dimensional ratchet potentials is proposed. With the aid of mutual couplings among particles, coordinated unidirectional motion along the ratchet direction can be achieved by transforming the energy from the transversal rocking force (periodic or stochastic) to the work in the longitude direction. Analytical predictions on the relation between the current and other parameters for the ac-driven cases are given, which are in good agreement with numerical simulations. Stochastic driving forces can give rise to the resonant directional transport. The effect of the free length, which has been explored in experiments on the motility of bipedal molecular motors, is investigated for both the single- and double-channel cases. The mechanism and results proposed in this letter may both shed light on the collective locomotion of molecular motors and open ways on studies in two-dimensional collaborative ratchet dynamics.

  6. Gas recirculator for acyclic machines

    NASA Astrophysics Data System (ADS)

    Balsa, T. F.

    1985-05-01

    The present invention relates to acyclic machines of the type using liquid metal collectors, and more particularly to an improvement for retaining the liquid metal in such machines. Radial type acyclic motors and generators generally include a metallic disk rotor rotating on a shaft between electromagnetic stator poles excited by field coils wound concentric with the shaft. Instead of solid brush, current collectors at the rotor periphery, liquid metal collectors are sometimes used to close the electrical current loop between the shaft and the rotor, and an inert pressurized cover gas fills the gaps between the rotating components and the stationary housing. A cover has recirculator in an acyclic generator having liquid metal collectors for reducing entrainment of the liquid metal in the gas. Radial passages in the stator housing provide natural recirculating paths for the cover gas to flow radially outward along the sides of the rotor and return inwardly through the passages. Scoops or lips located inward of the liquid metal collector divert the outward gas flow into the passages to minimize contact of the gas with the liquid metal.

  7. Cardioleader use in acyclic types of sports

    NASA Technical Reports Server (NTRS)

    Bondin, V. I.

    1980-01-01

    The use of the cardioleader method in regulating training loads and tests for athletes in acyclic sports was investigated. It was found that the use of this method increases the effectiveness of the training process.

  8. Assessing causal effects of early life-course factors on early childhood caries in 5-year-old Ugandan children using directed acyclic graphs (DAGs): A prospective cohort study.

    PubMed

    Birungi, Nancy; Fadnes, Lars T; Kasangaki, Arabat; Nankabirwa, Victoria; Okullo, Isaac; Lie, Stein A; Tumwine, James K; Åstrøm, Anne N

    2017-06-20

    To estimate the effect of distal and proximal early life-course factors on early childhood caries (ECC) in 5-year-old Ugandan children, particularly focusing on the causal effect of exclusive breast feeding (EBF) on ECC using directed acyclic graphs (DAGs) for confounder selection. This study had a nested prospective cohort design, focusing on 5 years of follow-ups of caregiver-children pairs from the PROMISE-EBF trial (ClinicalTrials.gov no: NCT00397150) conducted in 2011 in Eastern Uganda. Data were from recruitment interviews, 24-week, 2-year and 5-year follow-ups of a cohort of 417 mother-children pairs. Trained research assistants performed interviews with caregivers in the local language and ECC was recorded under field conditions using the World Health Organization's (WHO) decayed missing or filled teeth (dmft) index. Early life-course factors in terms of socio-demographic characteristics, EBF and other feeding habits were assessed at the various follow-ups. The outcome (ECC; dmft>0) was assessed at the 5-year follow-up. Causal diagrams as DAGs were constructed to guide the selection of confounding and collider variables to be included in or excluded from the final multivariable analysis. Negative binomial regression analyses were performed based on two comparative DAGs representing different causal models. Model 1 based on DAG 1, showed EBF to be a protective factor against ECC, with an IRR and 95% CI of 0.62 (0.43-0.91). According to Model 2 based on DAG 2, EBF and having both parents living together had protective effects: the corresponding IRRs and 95% CI were 0.60 (0.41-0.88) and 0.48 (0.25-0.90), respectively. Both plausible models indicated that being exclusively breastfed for 24 weeks had a protective causal effect against ECC. Further research, examining the unmeasured variables included in the DAGs is necessary to strengthen the present finding and allow stronger causal claims. © 2017 The Authors. Community Dentistry and Oral Epidemiology

  9. PQQ-dependent alcohol dehydrogenase (QEDH) of Pseudomonas aeruginosa is involved in catabolism of acyclic terpenes.

    PubMed

    Chattopadhyay, Ava; Förster-Fromme, Karin; Jendrossek, Dieter

    2010-04-01

    Growth of Pseudomonas aeruginosa on acyclic terpene alcohols such as geraniol depends on the presence of the atuRABCDEFGH gene cluster and a functional acyclic terpene utilisation (Atu) pathway. The proteins encoded by the atu gene cluster are necessary but not sufficient for growth on acyclic terpenes. Comparative 2-dimensional polyacrylamide gel electrophoresis of soluble P. aeruginosa proteins revealed the presence of an additional spot (besides Atu proteins) that is specifically expressed in geraniol cells but is absent in isovalerate-grown cells. The spot was identified as PA1982 gene product a pyrroloquinoline quinone (PQQ) dependent ethanol oxidoreductase (QEDH). Inactivation of PA1982 by insertion mutagenesis resulted in inability of the mutant to utilise ethanol and in reduced growth on geraniol. Growth on ethanol was restored by transferring an intact copy of the PA1982 gene into the mutant. The PA1982 gene product was purified from recombinant Escherichia coli and revealed PQQ-dependent oxidoreductase activity with a variety of substrates including acyclic terpene derivates at comparable V(max)-values. Our results show that QEDH participates in oxidation of acyclic terpene derivates in addition to the well-known function in ethanol metabolism.

  10. Acyclic telluroiminium salts: isolation and characterization.

    PubMed

    Mutoh, Yuichiro; Murai, Toshiaki; Yamago, Shigeru

    2004-12-29

    The isolation, structure, and reactions of acyclic telluroiminium salts were disclosed. The delocalization of electrons on the tellurium atom and the partial double-bond character of C-Te bonds in the salts are discussed on the basis of X-ray molecular structure analysis, 13C and 125Te NMR spectroscopy, and molecular orbital calculation.

  11. Direct Linear Transformation Method for Three-Dimensional Cinematography

    ERIC Educational Resources Information Center

    Shapiro, Robert

    1978-01-01

    The ability of Direct Linear Transformation Method for three-dimensional cinematography to locate points in space was shown to meet the accuracy requirements associated with research on human movement. (JD)

  12. Refactoring Problem of Acyclic Extended Free-Choice Workflow Nets to Acyclic Well-Structured Workflow Nets

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Shingo

    A workflow net (WF-net for short) is a Petri net which represents a workflow. There are two important subclasses of WF-nets: extended free-choice (EFC for short) and well-structured (WS for short). It is known that most actual workflows can be modeled as EFC WF-nets; Acyclic WS is a subclass of acyclic EFC but has more analysis methods. An acyclic EFC WF-net may be transformed to an acyclic WS WF-net without changing the external behavior of the net. We name such a transformation Acyclic EFC WF-net refactoring. We give a formal definition of acyclic EFC WF-net refactoring problem. We also give a necessary condition and a sufficient condition for solving the problem. Those conditions can be checked in polynomial time. These result in the enhancement of the analysis power of acyclic EFC WF-nets.

  13. Modification of DIRECT for high-dimensional design problems

    NASA Astrophysics Data System (ADS)

    Tavassoli, Arash; Haji Hajikolaei, Kambiz; Sadeqi, Soheil; Wang, G. Gary; Kjeang, Erik

    2014-06-01

    DIviding RECTangles (DIRECT), as a well-known derivative-free global optimization method, has been found to be effective and efficient for low-dimensional problems. When facing high-dimensional black-box problems, however, DIRECT's performance deteriorates. This work proposes a series of modifications to DIRECT for high-dimensional problems (dimensionality d>10). The principal idea is to increase the convergence speed by breaking its single initialization-to-convergence approach into several more intricate steps. Specifically, starting with the entire feasible area, the search domain will shrink gradually and adaptively to the region enclosing the potential optimum. Several stopping criteria have been introduced to avoid premature convergence. A diversification subroutine has also been developed to prevent the algorithm from being trapped in local minima. The proposed approach is benchmarked using nine standard high-dimensional test functions and one black-box engineering problem. All these tests show a significant efficiency improvement over the original DIRECT for high-dimensional design problems.

  14. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution. PMID:20160980

  15. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol.

    PubMed

    Hatcher, Elizabeth; Guvench, Olgun; Mackerell, Alexander D

    2009-04-27

    Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution.

  16. Measurement and visualization of three-dimensional directivity pattern

    NASA Astrophysics Data System (ADS)

    Arndt, Georg-Erwin; Gebert, Anton; Klemenz, Harald; Ritter, Hartmut C.

    2005-09-01

    In order to optimize a new second-order multimicrophone technology for a KEMAR dummy head, a three-dimensional directivity measurement setup was developed. To minimize mechanical mass and to reduce total measurement time a C-Bow setup was used, containing 18 calibrated loudspeakers. Those small tweeters identical in construction are placed in every 10 deg of elevation in a semicircular arc of 2-m diameter. The only moving part of this setup is a full-circle rotating KEMAR. The ANSI Standard 3.35 for directional measurement is fully supported and the required 48 measuring points are completed in less than 3 min. Using this fast and simple setup, the various responses attained from different latitudes need to be weighted to calculate a three-dimensional directivity value. Utilizing an equally distributed number, for example 400 measuring points easily executable with this setup, weighting can be omitted and a three-dimensional plot with high resolution can be visualized. Additionally, two-dimensional cuts of different planes in horizontal, vertical, and sagittal direction can be displayed. Data of unaided KEMAR, as well as data from the hearing aid used during those measurements, are presented and discussed.

  17. Volumetric dimensional change of six direct core materials.

    PubMed

    Chutinan, Supattriya; Platt, Jeffrey A; Cochran, Michael A; Moore, B Keith

    2004-05-01

    This study evaluated the influence of water on the volumetric dimensional change of six direct placement core build-up materials by using Archimedes' principle. The effect on dimensional change due to the setting reaction was determined through the use of a silicone oil storage medium. The materials used were two dual-cured resin composites (CoreStore and Build-It FR), two chemically activated resin composites (CorePaste and Ti-Core), one metal-reinforced glass ionomer cement (Ketac-Silver), and one resin-modified glass ionomer (Fuji II LC Core). Using the manufacturers' instructions for each material, cylindrical specimens were prepared with dimensions of 7+/-0.1 mm in diameter and 2+/-0.1 mm in height. Each material had four groups (n = 5) based on storage conditions; silicone oil at 23 and 37 degrees C and distilled water at 23 and 37 degrees C. A 0.01 mg resolution balance was used to determine volumetric dimensional change using an Archimedean equation. Measurements were made 30 min after mixing, and at the time intervals of 1, 14, and 56 days. All materials exhibited dimensional change. Ketac-Silver had the most shrinkage in silicone oil and Fuji II LC showed the highest expansion in distilled water. The glass ionomer materials showed more change than did any of the resin composite materials. Current direct placement core materials show variation in the amount of volumetric dimensional change seen over a period of 56 days.

  18. Measurement of directivity index by three-dimensional spatial sampling

    NASA Astrophysics Data System (ADS)

    Julstrom, Stephen D.

    2005-09-01

    The traditional method for finding the directivity index (DI) of a microphone by extrapolation from its two-dimensional polar pattern may not be accurate when the microphone or its mounting surface is acoustically large. In situ hearing aid microphone DI determination requires knowledge of the full three-dimensional directional response. Microphone DI may be measured directly by comparison of the on-axis anechoic sensitivity to the sensitivity in a diffuse sound field, normalizing the comparison by reference to a perfect omnidirectional microphone. In practice, creating an accurately diffuse field is difficult, and is traditionally accomplished by averaging measurements taken at several locations in a reverberant room excited by multiple uncorrelated sound sources. Theoretically equivalent results can be obtained by three-dimensional spatial sampling in an anechoic environment, inferring the full spherical response from a finite number of directional measurements. The necessary density, positioning, and positioning accuracy of measurement directions is determined by sampling theory, tests employing mathematically defined polar patterns, and practical considerations, leading to a minimum specification of 48 measurement points arranged in five horizontal zones. Non-uniform spacing of these points necessitates employing a weighted average of the sensitivity measurements to obtain the best prediction of the actual diffuse field response.

  19. Directional detection of dark matter with two-dimensional targets

    NASA Astrophysics Data System (ADS)

    Hochberg, Yonit; Kahn, Yonatan; Lisanti, Mariangela; Tully, Christopher G.; Zurek, Kathryn M.

    2017-09-01

    We propose two-dimensional materials as targets for direct detection of dark matter. Using graphene as an example, we focus on the case where dark matter scattering deposits sufficient energy on a valence-band electron to eject it from the target. We show that the sensitivity of graphene to dark matter of MeV to GeV mass can be comparable, for similar exposure and background levels, to that of semiconductor targets such as silicon and germanium. Moreover, a two-dimensional target is an excellent directional detector, as the ejected electron retains information about the angular dependence of the incident dark matter particle. This proposal can be implemented by the PTOLEMY experiment, presenting for the first time an opportunity for directional detection of sub-GeV dark matter.

  20. Computer simulation of three-dimensional directional response measurements

    NASA Astrophysics Data System (ADS)

    Warren, Daniel M.

    2005-09-01

    Early in the development of methods for measuring the three-dimensional directional response of hearing aids, there were many questions on how to distribute sound sources over the sphere. The method had to be accurate, yet practical to implement. Decisions on the scheme for distributing sound sources, the density of sound sources, and the weighting of results from each source have impact on accuracy. A simulation of the directional response of an array of microphones in the direct and scattered acoustic field near a rigid sphere was created and used to evaluate various means of distributing sound sources.

  1. Microperiodic structures: direct writing of three-dimensional webs.

    PubMed

    Gratson, Gregory M; Xu, Mingjie; Lewis, Jennifer A

    2004-03-25

    Applications are emerging that require the creation of fine-scale structures in three dimensions--examples include scaffolds for tissue engineering, micro-fluidic devices and photonic materials that control light propagation over a range of frequencies. But writing methods such as dip-pen nanolithography and ink-jet printing are either confined to two dimensions or beset by wetting and spreading problems. Here we use concentrated polyelectrolyte inks to write three-dimensional microperiodic structures directly without using masks. Our technique enables us to write arbitrary three-dimensional patterns whose features are nearly two orders of magnitude smaller than those attained with other multilayer printing techniques.

  2. Acyclic archaebacterial ether lipids in swamp sediments

    NASA Astrophysics Data System (ADS)

    Pauly, George G.; Van Vleet, Edward S.

    1986-06-01

    Acyclic phytanyl diether glycerol and biphytanyl ether lipids have been quantified in two modern swamp sediment cores in concentrations ranging up to 360 μg/ml porewater. Methanogenic bacteria are the only known source organisms which can inhabit the swamp sediments. Variations in relative abundance between these lipids may reflect taxonomic changes in methanogen populations or the stage of growth. Maxima in methanogen lipid concentrations coincide with local maxima of 13C of organic matter, possibly the result of a pool effect on CO 2 or acetate. Methane production estimates calculated from lipid concentrations in swamp sediments range from 0.1 to 1.3 mmol cm -2 yr -1, values which are consistent with published methane fluxes.

  3. Neutral losses: a type of important variables in prediction of branching degree for acyclic alkenes from mass spectra.

    PubMed

    Zhang, Liangxiao; Fan, Wei; Cao, Dongsheng; Zeng, Maomao; Xiao, Hongbin; Liang, Yizeng

    2012-03-30

    Neutral losses are a type of important variables in mass spectral interpretation. Since it is hard to calculate or extract neutral losses from mass spectra, they are usually discarded. In this study, dissimilarity analysis was employed to extract mass spectral characteristics for predicting branching degree of acyclic alkenes. The relationships between branching degree and neutral loss were constructed under direction of experimental observation and mass spectral fragmentations. A branching degree predictor of acyclic alkenes was subsequently built based on the above relationships. After tested by the experimental data in previous studies, the predictor could correctly provide the branching degree from abundant ions of mass spectra. More importantly, this predictor was able to point out which acyclic alkenes could be predicted correctly or not.

  4. Regio- and Enantioselective Synthesis of Chiral Pyrimidine Acyclic Nucleosides via Rhodium-Catalyzed Asymmetric Allylation of Pyrimidines.

    PubMed

    Liang, Lei; Xie, Ming-Sheng; Qin, Tao; Zhu, Man; Qu, Gui-Rong; Guo, Hai-Ming

    2017-10-06

    A direct route to branched N-allylpyrimidine analogues is herein reported via the highly regio- and enantioselective asymmetric allylation of pyrimidines with racemic allylic carbonates. With [Rh(COD)Cl]2/chiral diphosphine as the catalyst, a range of chiral pyrimidine acyclic nucleosides could be obtained under neutral conditions in good yields (up to 95% yield) with high levels of regio- and enantioselectivities (15:1 to >40:1 B/L and up to 99% ee). Furthermore, chiral pyrimidine acyclic nucleoside bearing two adjacent chiral centers has been successfully synthesized by asymmetric dihydroxylation.

  5. Multiphoton laser direct writing of two-dimensional silver structures.

    PubMed

    Baldacchini, Tommaso; Pons, Anne-Cécile; Pons, Josefina; Lafratta, Christopher; Fourkas, John; Sun, Yong; Naughton, Michael

    2005-02-21

    We report a novel and efficient method for the laser direct writing of two-dimensional silver structures. Multiphoton absorption of a small fraction of the output of a Ti:sapphire oscillator is sufficient to photoreduce silver nitrate in a thin film of polyvinylpyrrolidone that has been spin-coated on a substrate. The polymer can then be washed away, leaving a pattern consisting of highly interconnected silver nanoparticles. We report the characterization of the silver patterns using scanning electron and atomic force microscopies, and demonstrate the application of this technique in the creation of diffraction gratings.

  6. Modeling direct interband tunneling. II. Lower-dimensional structures

    SciTech Connect

    Pan, Andrew; Chui, Chi On

    2014-08-07

    We investigate the applicability of the two-band Hamiltonian and the widely used Kane analytical formula to interband tunneling along unconfined directions in nanostructures. Through comparisons with k·p and tight-binding calculations and quantum transport simulations, we find that the primary correction is the change in effective band gap. For both constant fields and realistic tunnel field-effect transistors, dimensionally consistent band gap scaling of the Kane formula allows analytical and numerical device simulations to approximate non-equilibrium Green's function current characteristics without arbitrary fitting. This allows efficient first-order calibration of semiclassical models for interband tunneling in nanodevices.

  7. Rotational effect in two-dimensional cooperative directed transport

    NASA Astrophysics Data System (ADS)

    Qiao, Li-Yan; Li, Yun-yun; Zheng, Zhi-Gang

    2015-02-01

    In this review we investigate the rotation effect in the motion of coupled dimer in a two-dimensional asymmetric periodic potential. Free rotation does not generate directed transport in translational direction, while we find it plays an critical role in the motors motility when the dimer moves under the effect of asymmetry ratchet potential. In the presence of external force, we study the relation between the average current and the force numerically and theoretically. The numerical results show that only appropriate driving force could produce nonzero current and there are current transitions when the force is large enough. An analysis of stability analysis of limit cycles is applied to explain the occurrence of these transitions. Moreover, we numerically simulate the transport of this coupled dimer driven by the random fluctuations in the rotational direction. The existence of noise smooths the current transitions induced by the driving force and the resonance-like peaks which depend on the rod length emerge in small noise strength. Thanks to the noise in the rotational direction, autonomous motion emerges without the external force and large noise could make the current reversal happen. Eventually, the new mechanism to generate directed transport by the rotation is studied.

  8. N-Branched acyclic nucleoside phosphonates as monomers for the synthesis of modified oligonucleotides.

    PubMed

    Hocková, Dana; Rosenbergová, Šárka; Ménová, Petra; Páv, Ondřej; Pohl, Radek; Novák, Pavel; Rosenberg, Ivan

    2015-04-21

    Protected N-branched nucleoside phosphonates containing adenine and thymine bases were prepared as the monomers for the introduction of aza-acyclic nucleotide units into modified oligonucleotides. The phosphotriester and phosphoramidite methods were used for the incorporation of modified and natural units, respectively. The solid phase synthesis of a series of nonamers containing one central modified unit was successfully performed in both 3'→5' and 5'→3' directions. Hybridization properties of the prepared oligoribonucleotides and oligodeoxyribonucleotides were evaluated. The measurement of thermal characteristics of the complexes of modified nonamers with the complementary strand revealed a considerable destabilizing effect of the introduced units. We also examined the substrate/inhibitory properties of aza-acyclic nucleoside phosphono-diphosphate derivatives (analogues of nucleoside triphosphates) but neither inhibition of human and bacterial DNA polymerases nor polymerase-mediated incorporation of these triphosphate analogues into short DNA was observed.

  9. Direct Volume Rendering with Shading via Three-Dimensional Textures

    NASA Technical Reports Server (NTRS)

    Van Gelder, Allen; Kim, Kwansik

    1996-01-01

    A new and easy-to-implement method for direct volume rendering that uses 3D texture maps for acceleration, and incorporates directional lighting, is described. The implementation, called Voltx, produces high-quality images at nearly interactive speeds on workstations with hardware support for three-dimensional texture maps. Previously reported methods did not incorporate a light model, and did not address issues of multiple texture maps for large volumes. Our research shows that these extensions impact performance by about a factor of ten. Voltx supports orthographic, perspective, and stereo views. This paper describes the theory and implementation of this technique, and compares it to the shear-warp factorization approach. A rectilinear data set is converted into a three-dimensional texture map containing color and opacity information. Quantized normal vectors and a lookup table provide efficiency. A new tesselation of the sphere is described, which serves as the basis for normal-vector quantization. A new gradient-based shading criterion is described, in which the gradient magnitude is interpreted in the context of the field-data value and the material classification parameters, and not in isolation. In the rendering phase, the texture map is applied to a stack of parallel planes, which effectively cut the texture into many slabs. The slabs are composited to form an image.

  10. Direct Volume Rendering with Shading via Three-Dimensional Textures

    NASA Technical Reports Server (NTRS)

    VanGelder, Allen; Kim, Kwansik

    1996-01-01

    A new and easy-to-implement method for direct volume rendering that uses 3D texture maps for acceleration, and incorporates directional lighting, is described. The implementation, called Voltx, produces high-quality images at nearly interactive speeds on workstations with hardware support for three-dimensional texture maps. Previously reported methods did not incorporate a light model, and did not address issues of multiple texture maps for large volumes. Our research shows that these extensions impact performance by about a factor of ten. Voltx supports orthographic, perspective, and stereo views. This paper describes the theory and implementation of this technique, and compares it to the shear-warp factorization approach. A rectilinear data set is converted into a three-dimensional texture map containing color and opacity information. Quantized normal vectors and a lookup table provide efficiency. A new tesselation of the sphere is described, which serves as the basis for normal-vector quantization. A new gradient-based shading criterion is described, in which the gradient magnitude is interpreted in the context of the field-data value and the material classification parameters, and not in isolation. In the rendering phase, the texture map is applied to a stack of parallel planes, which effectively cut the texture into many slabs. The slabs are composited to form an image.

  11. Direct-writing organic three-dimensional nanofibrous structure

    NASA Astrophysics Data System (ADS)

    Wang, Han; Zheng, Gaofeng; Li, Wenwang; Wang, Xiang; Sun, Daoheng

    2011-02-01

    Direct-writing technology based on Near-Field Electrospinning (NFES) was used to fabricate an organic three-dimensional nanofibrous circle on the patterned silicon substrate. In NFES, straight jet without splitting and chaotic motion was utilized to direct-write orderly nanofiber. When the collector movement speed was lower than electrospinning rate, the relaxed nanofiber would be lead into the pendulum motion by the electrical field force and Coulomb repulsion force from the residual charges on the collector. When the relative air humidity is lower than 35%, individual nanofiber with larger elastic resistance would reveal a good self-assembly performance. Owing to the guidance of the electric field force at the edge of the micro-pattern, a nanofiber was deposited layer by layer to format a 3D nanofibrous circle on the top surface of the micro-pattern. The dimension scale of 3D nanofibrous circle was smaller than 30 µm. With the help of a microscope, a 3D nanofibrous circle can be deposited precisely on the strip micro-pattern with width of 4 µm. Furthermore, a 3D nanofibrous circle in different shapes can be obtained by using special micro-patterns. This organic three-dimensional nanofibrous circle has created a new aspect for the fabrication of organic micro/nanosystems.

  12. New Stable and Persistent Acyclic Diaminocarbenes.

    PubMed

    Schulz, Tim; Weismann, Daniel; Wallbaum, Lars; Guthardt, Robin; Thie, Charlotte; Leibold, Michael; Bruhn, Clemens; Siemeling, Ulrich

    2015-09-28

    The portfolio of acyclic diaminocarbenes (ADACs) has been substantially expanded, owing to the synthesis of eleven new formamidinium salts, mostly of the type [(iPr2N)CH(NRR')][PF6], for use as immediate carbene precursors. The corresponding ADACs (iPr2N)C(NRR') were sufficiently stable for isolation in the case of NRR' = 2-methylpiperidino (13), 3-methylpiperidino (14), 4-methylpiperidino (15), morpholino (17) and NiPrPh (20), but had to be trapped in situ in the case of NRR' = 2,2,6,6-tetramethylpiperidino (12) and NiPrMe (19). The tetraaryl-substituted ADACs (Ph2N)2C (22) and (Ph2N)C[N(C6F5)2] (24) also could only be generated and trapped in situ. Trapping with elemental selenium was particularly efficient, affording the corresponding selenourea derivative in all cases, whereas trapping with [{Rh(μ-Cl)(cod)}2] did not work for 12 and 24. The (77)Se NMR chemical shifts, δ((77)Se), of the selenourea compounds derived from the new ADACs lie in the range 450-760 ppm, which indicates a much higher electrophilicity and π-accepting capability of ADACs in comparison with NHCs, which typically exhibit δ((77)Se)<200 ppm. The extreme low-field shift of 758 ppm observed for 12Se can be rationalised by the results of DFT calculations, which revealed that ADAC 12 has a minimum energy conformation with the 2,2,6,6-tetramethylpiperidino unit perpendicular to the N2C plane, which suppresses the π donation of this amino group and causes an unusually low LUMO energy and high electrophilicity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Acyclic Tethers Mimicking Subunits of Polysaccharide Ligands: Selectin Antagonists

    PubMed Central

    2014-01-01

    We report on the design and synthesis of molecules having E- and P-selectins blocking activity both in vitro and in vivo. The GlcNAc component of the selectin ligand sialyl LewisX was replaced by an acyclic tether that links two saccharide units. The minimization of intramolecular dipole–dipole interactions and the gauche effect would be at the origin of the conformational bias imposed by this acyclic tether. The stereoselective synthesis of these molecules, their biochemical and biological evaluations using surface plasmon resonance spectroscopy (SPR), and in vivo assays are described. Because the structure of our analogues differs from the most potent E-selectin antagonists reported, our acyclic analogues offer new opportunities for chemical diversity. PMID:25221666

  14. The postpartum buffalo. II. Acyclicity and anestrus.

    PubMed

    El-Wishy, A B

    2007-02-01

    Prolonged postpartum acyclicity (absence of ovarian cyclic activity) and anestrum (absence of overt estrous signs) are major sources of economic loss to buffalo breeders. Studies on the epidemiology of these two problems are highly recommended to achieve successful control. Review of the available literature on controlled studies in dairy buffaloes revealed that first ovulation as detected by rectal palpation and progesterone analysis occurred between 28-71 and 24-55 days, respectively, after calving. Postpartum estrus in the same studies occurred between 44 and 87 days. Reports concerned with data compiled from breeding records of research stations, breeding farms and small holders where estrus is a subjective measure, gave much longer periods. Also data from Egypt, India and Pakistan indicate that only 34-49% of buffaloes showed estrus during the first 90 days after calving and 31-42% remained anestrus for more than 150 days. In swamp buffaloes both postpartum ovulation and estrus are more delayed than in dairy buffaloes. The role of suckling, nutrition, body condition score at calving, milk yield, parity, season of calving and other minor factors were discussed. First postpartum ovulation is frequently followed by one or more short estrous cycles (<18 days). Long anovulatory and anestrous periods due to prolonged inter-luteal phase were reported to occur after short cycles. Also long anestrous periods due to cessation of cyclic activity (true anestrus) for 3 or more weeks and prolonged luteal activity for 28 days or more were described to occur in about 25 and 8-11% of the buffaloes, respectively, after the first or second ovulation. These cycle irregularities certainly impose difficulties on estrus detection programs in postpartum buffaloes. Four main forms of anestrus i.e. true anestrus (inactive ovaries and small and medium sized anovulatory follicles), subestrus, prolonged luteal activity and ovarian cysts in addition to pregnancy are reviewed in this

  15. Synthesis of some novel hydrazono acyclic nucleoside analogues

    PubMed Central

    Khalafi-Nezhad, Ali; Behrouz, Somayeh

    2010-01-01

    Summary The syntheses of novel hydrazono acyclic nucleosides similar to miconazole scaffolds are described. In this series of acyclic nucleosides, pyrimidine as well as purine and other azole derivatives replaced the imidazole function in miconazole and the ether group was replaced with a hydrazone moiety using phenylhydrazine. To interpret the dominant formation of (E)-hydrazone derivatives rather than (Z)-isomers, PM3 semiempirical quantum mechanic calculations were carried out which indicated that the (E)-isomers had the lower heats of formation. PMID:20563270

  16. On the acyclicity of the solution sets of operator equations

    NASA Astrophysics Data System (ADS)

    Gel'man, Boris D.

    2010-12-01

    A parameter-dependent completely continuous map is considered. The acyclicity of the set of fixed points of this map is proved for some fixed value of the parameter under the assumption that for close values of the parameter the map has a unique fixed point. The results obtained are used to prove the acyclicity of the set of fixed points of a 'nonscattering' map, as well as to study the topological structure of the set of fixed points of an abstract Volterra map. Bibliography: 13 titles.

  17. Oscillatory cellular patterns in three-dimensional directional solidification

    DOE PAGES

    Tourret, D.; Debierre, J. -M.; Song, Y.; ...

    2015-09-11

    We present a phase-field study of oscillatory breathing modes observed during the solidification of three-dimensional cellular arrays in micro-gravity. Directional solidification experiments conducted onboard the International Space Station have allowed for the first time to observe spatially extended homogeneous arrays of cells and dendrites while minimizing the amount of gravity-induced convection in the liquid. In situ observations of transparent alloys have revealed the existence, over a narrow range of control parameters, of oscillations in cellular arrays with a period ranging from about 25 to 125 minutes. Cellular patterns are spatially disordered, and the oscillations of individual cells are spatiotemporally uncorrelatedmore » at long distance. However, in regions displaying short-range spatial ordering, groups of cells can synchronize into oscillatory breathing modes. Quantitative phase-field simulations show that the oscillatory behavior of cells in this regime is linked to a stability limit of the spacing in hexagonal cellular array structures. For relatively high cellular front undercooling (\\ie low growth velocity or high thermal gradient), a gap appears in the otherwise continuous range of stable array spacings. Close to this gap, a sustained oscillatory regime appears with a period that compares quantitatively well with experiment. For control parameters where this gap exist, oscillations typically occur for spacings at the edge of the gap. However, after a change of growth conditions, oscillations can also occur for nearby values of control parameters where this gap just closes and a continuous range of spacings exists. In addition, sustained oscillations at to the opening of this stable gap exhibit a slow periodic modulation of the phase-shift among cells with a slower period of several hours. While long-range coherence of breathing modes can be achieved in simulations for a perfect spatial arrangement of cells as initial condition, global

  18. Oscillatory cellular patterns in three-dimensional directional solidification

    SciTech Connect

    Tourret, D.; Debierre, J. -M.; Song, Y.; Mota, F. L.; Bergeon, N.; Guerin, R.; Trivedi, R.; Billia, B.; Karma, A.

    2015-09-11

    We present a phase-field study of oscillatory breathing modes observed during the solidification of three-dimensional cellular arrays in micro-gravity. Directional solidification experiments conducted onboard the International Space Station have allowed for the first time to observe spatially extended homogeneous arrays of cells and dendrites while minimizing the amount of gravity-induced convection in the liquid. In situ observations of transparent alloys have revealed the existence, over a narrow range of control parameters, of oscillations in cellular arrays with a period ranging from about 25 to 125 minutes. Cellular patterns are spatially disordered, and the oscillations of individual cells are spatiotemporally uncorrelated at long distance. However, in regions displaying short-range spatial ordering, groups of cells can synchronize into oscillatory breathing modes. Quantitative phase-field simulations show that the oscillatory behavior of cells in this regime is linked to a stability limit of the spacing in hexagonal cellular array structures. For relatively high cellular front undercooling (\\ie low growth velocity or high thermal gradient), a gap appears in the otherwise continuous range of stable array spacings. Close to this gap, a sustained oscillatory regime appears with a period that compares quantitatively well with experiment. For control parameters where this gap exist, oscillations typically occur for spacings at the edge of the gap. However, after a change of growth conditions, oscillations can also occur for nearby values of control parameters where this gap just closes and a continuous range of spacings exists. In addition, sustained oscillations at to the opening of this stable gap exhibit a slow periodic modulation of the phase-shift among cells with a slower period of several hours. While long-range coherence of breathing modes can be achieved in simulations for a perfect spatial arrangement of cells as initial condition, global disorder is

  19. Oscillatory cellular patterns in three-dimensional directional solidification

    NASA Astrophysics Data System (ADS)

    Tourret, D.; Debierre, J.-M.; Song, Y.; Mota, F. L.; Bergeon, N.; Guérin, R.; Trivedi, R.; Billia, B.; Karma, A.

    2015-10-01

    We present a phase-field study of oscillatory breathing modes observed during the solidification of three-dimensional cellular arrays in microgravity. Directional solidification experiments conducted onboard the International Space Station have allowed us to observe spatially extended homogeneous arrays of cells and dendrites while minimizing the amount of gravity-induced convection in the liquid. In situ observations of transparent alloys have revealed the existence, over a narrow range of control parameters, of oscillations in cellular arrays with a period ranging from about 25 to 125 min. Cellular patterns are spatially disordered, and the oscillations of individual cells are spatiotemporally uncorrelated at long distance. However, in regions displaying short-range spatial ordering, groups of cells can synchronize into oscillatory breathing modes. Quantitative phase-field simulations show that the oscillatory behavior of cells in this regime is linked to a stability limit of the spacing in hexagonal cellular array structures. For relatively high cellular front undercooling (i.e., low growth velocity or high thermal gradient), a gap appears in the otherwise continuous range of stable array spacings. Close to this gap, a sustained oscillatory regime appears with a period that compares quantitatively well with experiment. For control parameters where this gap exists, oscillations typically occur for spacings at the edge of the gap. However, after a change of growth conditions, oscillations can also occur for nearby values of control parameters where this gap just closes and a continuous range of spacings exists. In addition, sustained oscillations at to the opening of this stable gap exhibit a slow periodic modulation of the phase-shift among cells with a slower period of several hours. While long-range coherence of breathing modes can be achieved in simulations for a perfect spatial arrangement of cells as initial condition, global disorder is observed in both

  20. Direct three-dimensional coherently scattered x-ray microtomography

    SciTech Connect

    Cui Congwu; Jorgensen, Steven M.; Eaker, Diane R.; Ritman, Erik L.

    2010-12-15

    Purpose: It has been shown that coherently scattered x rays can be used to discriminate and identify specific components in a mixture of low atomic weight materials. The authors demonstrated a new method of doing coherently scattered x-ray tomography with a thin sheet of x ray. Methods: A collimated x-ray fan-beam, a parallel polycapillary collimator, and a phantom consisting of several biocompatible materials of low attenuation-based contrast were used to investigate the feasibility of the method. Because of the particular experimental setup, only the phantom translation perpendicular to the x-ray beam is needed and, thus, there is no need of Radon-type tomographic reconstruction, except for the correction of the attenuation to the primary and scattered x rays, which was performed by using a conventional attenuation-based tomographic image data set. The coherent scatter image contrast changes with momentum transfer among component materials in the specimen were investigated with multiple x-ray sources with narrow bandwidth spectra generated with anode and filter combinations of Cu/Ni (8 keV), Mo/Zr (18 keV), and Ag/Pd (22 keV) and at multiple scatter angles by orienting the detector and polycapillary collimator at different angles to the illuminating x ray. Results: The contrast among different materials changes with the x-ray source energy and the angle at which the image was measured. The coherent scatter profiles obtained from the coherent scatter images are consistent with the published results. Conclusions: This method can be used to directly generate the three-dimensional coherent scatter images of small animal, biopsies, or other small objects with low atomic weight biological or similar synthetic materials with low attenuation contrast. With equipment optimized, submillimeter spatial resolution may be achieved.

  1. Direct Human Cartilage Repair Using Three-Dimensional Bioprinting Technology

    PubMed Central

    Cui, Xiaofeng; Breitenkamp, Kurt; Finn, M.G.; Lotz, Martin

    2012-01-01

    Current cartilage tissue engineering strategies cannot as yet fabricate new tissue that is indistinguishable from native cartilage with respect to zonal organization, extracellular matrix composition, and mechanical properties. Integration of implants with surrounding native tissues is crucial for long-term stability and enhanced functionality. In this study, we developed a bioprinting system with simultaneous photopolymerization capable for three-dimensional (3D) cartilage tissue engineering. Poly(ethylene glycol) dimethacrylate (PEGDMA) with human chondrocytes were printed to repair defects in osteochondral plugs (3D biopaper) in layer-by-layer assembly. Compressive modulus of printed PEGDMA was 395.73±80.40 kPa, which was close to the range of the properties of native human articular cartilage. Printed human chondrocytes maintained the initially deposited positions due to simultaneous photopolymerization of surrounded biomaterial scaffold, which is ideal in precise cell distribution for anatomic cartilage engineering. Viability of printed human chondrocytes increased 26% in simultaneous polymerization than polymerized after printing. Printed cartilage implant attached firmly with surrounding tissue and greater proteoglycan deposition was observed at the interface of implant and native cartilage in Safranin-O staining. This is consistent with the enhanced interface failure strength during the culture assessed by push-out testing. Printed cartilage in 3D biopaper had elevated glycosaminoglycan (GAG) content comparing to that without biopaper when normalized to DNA. These observations were consistent with gene expression results. This study indicates the importance of direct cartilage repair and promising anatomic cartilage engineering using 3D bioprinting technology. PMID:22394017

  2. Directed assembly of three-dimensional microvascular networks

    NASA Astrophysics Data System (ADS)

    Therriault, Daniel

    Three-dimensional (3-D) microvascular networks with pervasive, interconnected channels less than 300 mum in diameter may find widespread application in microfluidic devices, biotechnology, sensors, and autonomic healing materials. Although microchannel arrays are readily constructed in two-dimensions by photolithographic or soft lithographic techniques, their construction in three-dimensions remains a challenging problem. The development of a microfabrication method to build 3-D microvascular networks based on direct-write assembly is described is this thesis. The method is based on the robotic deposition of a fugitive organic ink to form a free-standing scaffold structure. Secondary infiltration of a structural resin followed by setting of the matrix and removal of the scaffold yields an embedded pervasive network of smooth cylindrical channels (˜10--500 mum) with defined connectivity. Rheological and other material properties studies of fugitive organic ink were performed in order to identify the critical characteristics required for successful deposition of 3-D scaffolds by direct-write assembly. Guided by the results of these studies, several new ink formulations were screened for improved deposition performance. The most successful of these inks (40wt% microcrystalline wax, 60wt% petroleum jelly) showed excellent deposition and had an equilibrium modulus at room temperature (G 'eq ˜ 7.70 kPa 1 Hz) nearly two orders of magnitude higher than the original ink. The optimized ink was used to successfully build thick (i.e., ˜100 layers) scaffold structures at room temperature with negligible time-dependent deformation post-deposition. Secondary infiltration of the resin was accomplished at room temperature while maintaining the scaffold architecture. The optimized ink was also successfully extruded through small micronozzles (1 mum). The construction of 3-D microvascular networks enables microfluidic devices with unparallel geometric complexity. In one example, a

  3. Sensitivity and bias in the discrimination of two-dimensional and three-dimensional motion direction.

    PubMed

    Cooper, Emily A; van Ginkel, Marcus; Rokers, Bas

    2016-08-01

    Sensory systems are faced with an essentially infinite number of possible environmental events but have limited processing resources. Posed with this challenge, it makes sense to allocate these resources to prioritize the discrimination of events with the most behavioral relevance. Here, we asked if such relevance is reflected in the processing and perception of motion. We compared human performance on a rapid motion direction discrimination task, including monocular and binocular viewing. In particular, we determined sensitivity and bias for a binocular motion-in-depth (three-dimensional; 3D) stimulus and for its constituent monocular (two-dimensional; 2D) signals over a broad range of speeds. Consistent with prior work, we found that binocular 3D sensitivity was lower than monocular sensitivity for all speeds. Although overall sensitivity was worse for 3D discrimination, we found that the transformation from 2D to 3D motion processing also incorporated a pattern of potentially advantageous biases. One such bias is reflected by a criterion shift that occurs at the level of 3D motion processing and results in an increased hit rate for motion toward the head. We also observed an increase in sensitivity for 3D motion trajectories presented on crossed rather than uncrossed disparity pedestals, privileging motion trajectories closer to the observer. We used these measurements to determine the range of real-world trajectories for which rapid 3D motion discrimination is most useful. These results suggest that the neural mechanisms that underlie motion perception privilege behaviorally relevant motion and provide insights into the nature of human motion sensitivity in the real world.

  4. New acyclic diterpenic acids from yacon (Smallanthus sonchifolius) leaves.

    PubMed

    Mercado, María I; Coll Aráoz, María V; Grau, Alfredo; Catalán, César A N

    2010-11-01

    Two new acyclic diterpenoids, smaditerpenic acid E (1a) and F (2a), along with nineteen melampolide-type sesquiterpene lactones, six of them not previously reported in yacon, were isolated from the methylene chloride leaf rinse extract. Their structures were elucidated from 1D and 2D NMR experiments and gas chromatography coupled to mass spectrometry.

  5. Acyclic glycosidopyrroles analogues of ganciclovir: synthesis and biological activity.

    PubMed

    Diana, P; Barraja, P; Almerico, A M; Dattolo, G; Mingoia, F; Loi, A G; Congeddu, E; Musiu, C; Putzolu, M; La Colla, P

    1997-05-01

    Acyclic glycosidopyrroles of type 3 were synthetized in good overall yields, according to the Scheme. When evaluated for antiviral activity against DNA and RNA viruses, only compound in which R1 = R2 = Ph, R3 = NH2 was found to inhibit the HIV-1 replication at concentrations that were not cytotoxic for MT-4 cells.

  6. Performance and Reliability Analysis Using Directed Acyclic Graphs.

    DTIC Science & Technology

    1985-04-04

    34 ,,’. " .. .. " * " ... - .. . . . . . . - . . . , •.• ".. * 7- R- 7- A BC DEF G H Figure 1. Examples of Series-Parallel Graphs G1 G2 A B A C D B C Figure 2. Graphs which are not Series...Oct 1984), 309-312. 120] Neuts, M.F., Matriz -Geometric Solutions in Stochastic Models, The Johns Hopkins University Press, Baltimore, Md., 1981. [21...that go through BC and DC. The probability that the system does not recover is the probability of traversing the path through DF. 5. CONCLUSION AND

  7. Indirect to direct gap transition in low-dimensional nanostructures of Silicon and Germanium

    NASA Astrophysics Data System (ADS)

    Wu, Xue-ke; Huang, Wei-qi; Huang, Zhong-mei; Tang, Yan-lin

    2017-06-01

    The electronic band structures of Si and Ge low-dimensional nanostructure such as nanofilms and nanowires have been calculated using first principles based on density functional theory (DFT) with the generalized gradient approximation (GGA). The calculation results show that a direct band gap can be obtained from Si orientation [100] or in Ge orientation [111] confined low dimensional nanostructure. However, an indirect band gap is still kept in the Si orientation [111] or in the Ge orientation [110] confined low dimensional nanostructure. The calculation results are interesting and the transition mechanism from indirect to direct band gap in low dimensional nanostructures is given in the physical structures model.

  8. Anion-directed assembly: Framework conversion in dimensionality and photoluminescence

    NASA Astrophysics Data System (ADS)

    Gong, Yun; Liu, Tianfu; Tang, Wang; Wu, Fengjing; Gao, Wenliang; Hu, Changwen

    2007-04-01

    Six novel Ni(II)-fluconazole complexes formulated as (C 13H 11N 6OF 2) 2Ni 2(NO 3) 2 ( 1), (C 13H 12N 6OF 2) 2Ni(NO 3) 2·H 2O ( 2), (C 13H 12N 6OF 2)Ni(SO 4)(DMF) 2(H 2O) ( 3), (C 13H 12N 6OF 2) 2Ni(H 2O) 2(SO 4)·4H 2O ( 4), (C 13H 12N 6OF 2) 2NiCl 2·2(CH 3OH) ( 5), (C 13H 12N 6OF 2) 4Ni 2 (MoO 4) 2·6H 2O ( 6) have been hydrothermally or solvothermally synthesized under similar conditions except different anions and solvents. They are structurally characterized by elemental analysis, IR, TG and single crystal X-ray diffraction. Complex 1 is a molecular binuclear nickel cluster. Complex 2 exhibits a one-dimensional (1D) chain linked by double-stranded fluconazole-bridge. Complex 3 shows a novel 1D chain linked by double-stranded fluconazole-bridge and double-stranded SO 42--bridge. Complex 4 shows a three-dimensional (3D) architecture and SO 42- anions occupy the cavity. Complex 5 exhibits a two-dimensional (2D) structure constructed by alternating left- and right-handed helices. Complex 6 exhibits a 3D architecture, in which the 2D layers are pillared by {MoO 4} tetrahedra. Complex 2 can be irreversibly converted to complex 1 in the presence of DMF ( N, N'-dimethyllformamide). Complexes 1, 3 and 6 show antiferromagnetic interactions between the nickel (II) ions The photoluminescence properties of the six complexes indicated that the introduction of different anions can enhance or weaken the intra-ligand transitions of fluconazole.

  9. Highly directional thermal emission from two-dimensional silicon structures.

    PubMed

    Ribaudo, Troy; Peters, David W; Ellis, A Robert; Davids, Paul S; Shaner, Eric A

    2013-03-25

    We simulate, fabricate, and characterize near perfectly absorbing two-dimensional grating structures in the thermal infrared using heavily doped silicon (HdSi) that supports long wave infrared surface plasmon polaritons (LWIR SPP's). The devices were designed and optimized using both finite difference time domain (FDTD) and rigorous coupled wave analysis (RCWA) simulation techniques to satisfy stringent requirements for thermal management applications requiring high thermal radiation absorption over a narrow angular range and low visible radiation absorption over a broad angular range. After optimization and fabrication, characterization was performed using reflection spectroscopy and normal incidence emissivity measurements. Excellent agreement between simulation and experiment was obtained.

  10. Direct force wall shear measurements in pressure-driven three-dimensional turbulent boundary layers

    NASA Technical Reports Server (NTRS)

    Mcallister, J. E.; Tennant, M. H.; Pierce, F. J.

    1982-01-01

    Unique, simultaneous direct measurements of the magnitude and direction of the local wall shear stress in a pressure-driven three-dimensional turbulent boundary layer are presented. The flow is also described with an oil streak wall flow pattern, a map of the wall shear stress-wall pressure gradient orientations, a comparison of the wall shear stress directions relative to the directions of the nearest wall velocity as measured with a typical, small boundary layer directionally sensitive claw probe, as well as limiting wall streamline directions from the oil streak patterns, and a comparison of the freestream streamlines and the wall flow streamlines. A review of corrections for direct force sensing shear meters for two-dimensional flows is presented with a brief discussion of their applicability to three-dimensional devices.

  11. Direct force wall shear measurements in pressure-driven three-dimensional turbulent boundary layers

    NASA Astrophysics Data System (ADS)

    McAllister, J. E.; Tennant, M. H.; Pierce, F. J.

    1982-06-01

    Unique, simultaneous direct measurements of the magnitude and direction of the local wall shear stress in a pressure-driven three-dimensional turbulent boundary layer are presented. The flow is also described with an oil streak wall flow pattern, a map of the wall shear stress-wall pressure gradient orientations, a comparison of the wall shear stress directions relative to the directions of the nearest wall velocity as measured with a typical, small boundary layer directionally sensitive claw probe, as well as limiting wall streamline directions from the oil streak patterns, and a comparison of the freestream streamlines and the wall flow streamlines. A review of corrections for direct force sensing shear meters for two-dimensional flows is presented with a brief discussion of their applicability to three-dimensional devices.

  12. Three-dimensional track reconstruction for directional Dark Matter detection

    SciTech Connect

    Billard, J.; Mayet, F.; Santos, D. E-mail: mayet@lpsc.in2p3.fr

    2012-04-01

    Directional detection of Dark Matter is a promising search strategy. However, to perform such detection, a given set of parameters has to be retrieved from the recoiling tracks: direction, sense and position in the detector volume. In order to optimize the track reconstruction and to fully exploit the data of forthcoming directional detectors, we present a likelihood method dedicated to 3D track reconstruction. This new analysis method is applied to the MIMAC detector. It requires a full simulation of track measurements in order to compare real tracks to simulated ones. We conclude that a good spatial resolution can be achieved, i.e. sub-mm in the anode plane and cm along the drift axis. This opens the possibility to perform a fiducialization of directional detectors. The angular resolution is shown to range between 20° to 80°, depending on the recoil energy, which is however enough to achieve a high significance discovery of Dark Matter. On the contrary, we show that sense recognition capability of directional detectors depends strongly on the recoil energy and the drift distance, with small efficiency values (50%–70%). We suggest not to consider this information either for exclusion or discovery of Dark Matter for recoils below 100 keV and then to focus on axial directional data.

  13. Direct three-dimensional ordering of quasi-one-dimensional quantum dimer system near critical fields

    NASA Astrophysics Data System (ADS)

    Matsushita, Taku; Hori, Nobuyoshi; Takata, Seiya; Wada, Nobuo; Amaya, Naoki; Hosokoshi, Yuko

    2017-01-01

    Dimensionalities of X X Z spin orderings or degenerate hard-core bosons in a quasi-one-dimensional (1D) dimer system are examined by the ac susceptibility and specific heat of antiferromagnetic bond-alternating chains in pentafluorophenyl nitronyl nitroxide (F5PNN ). At intermediate fields in the gapless region, the 1D short-range order (SRO) corresponding to the Tomonaga-Luttinger liquid and three-dimensional (3D) long-range order (LRO BEC) at lower temperatures are separately observed, as expected from the small interchain interaction. In contrast, a definite region around the critical field was established where 3D LRO occurs without the development of 1D SRO at higher temperatures.

  14. Three dimensional direct numerical simulation of complex jet flows

    NASA Astrophysics Data System (ADS)

    Shin, Seungwon; Kahouadji, Lyes; Juric, Damir; Chergui, Jalel; Craster, Richard; Matar, Omar

    2016-11-01

    We present three-dimensional simulations of two types of very challenging jet flow configurations. The first consists of a liquid jet surrounded by a faster coaxial air flow and the second consists of a global rotational motion. These computations require a high spatial resolution and are performed with a newly developed high performance parallel code, called BLUE, for the simulation of two-phase, multi-physics and multi-scale incompressible flows, tested on up to 131072 threads with excellent scalability performance. The method for the treatment of the fluid interfaces uses a hybrid Front Tracking/Level Set technique that defines the interface both by a discontinuous density field as well as by a local triangular Lagrangian mesh. Coriolis forces are taken into account and solved via an exact time-integration method that ensures numerical accuracy and stability. EPSRC UK Programme Grant EP/K003976/1.

  15. Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites

    PubMed Central

    Bruno, Mark; Koschmieder, Julian; Wuest, Florian; Schaub, Patrick; Fehling-Kaschek, Mirjam; Timmer, Jens; Beyer, Peter; Al-Babili, Salim

    2016-01-01

    The Arabidopsis carotenoid cleavage dioxygenase 4 (AtCCD4) is a negative regulator of the carotenoid content of seeds and has recently been suggested as a candidate for the generation of retrograde signals that are thought to derive from the cleavage of poly-cis-configured carotene desaturation intermediates. In this work, we investigated the activity of AtCCD4 in vitro and used dynamic modeling to determine its substrate preference. Our results document strict regional specificity for cleavage at the C9–C10 double bond in carotenoids and apocarotenoids, with preference for carotenoid substrates and an obstructing effect on hydroxyl functions, and demonstrate the specificity for all-trans-configured carotenes and xanthophylls. AtCCD4 cleaved substrates with at least one ionone ring and did not convert acyclic carotene desaturation intermediates, independent of their isomeric states. These results do not support a direct involvement of AtCCD4 in generating the supposed regulatory metabolites. In contrast, the strigolactone biosynthetic enzyme AtCCD7 converted 9-cis-configured acyclic carotenes, such as 9-cis-ζ-carotene, 9'-cis-neurosporene, and 9-cis-lycopene, yielding 9-cis-configured products and indicating that AtCCD7, rather than AtCCD4, is the candidate for forming acyclic retrograde signals. PMID:27811075

  16. Parallel direct numerical simulation of three-dimensional spray formation

    NASA Astrophysics Data System (ADS)

    Chergui, Jalel; Juric, Damir; Shin, Seungwon; Kahouadji, Lyes; Matar, Omar

    2015-11-01

    We present numerical results for the breakup mechanism of a liquid jet surrounded by a fast coaxial flow of air with density ratio (water/air) ~ 1000 and kinematic viscosity ratio ~ 60. We use code BLUE, a three-dimensional, two-phase, high performance, parallel numerical code based on a hybrid Front-Tracking/Level Set algorithm for Lagrangian tracking of arbitrarily deformable phase interfaces and a precise treatment of surface tension forces. The parallelization of the code is based on the technique of domain decomposition where the velocity field is solved by a parallel GMRes method for the viscous terms and the pressure by a parallel multigrid/GMRes method. Communication is handled by MPI message passing procedures. The interface method is also parallelized and defines the interface both by a discontinuous density field as well as by a triangular Lagrangian mesh and allows the interface to undergo large deformations including the rupture and/or coalescence of interfaces. EPSRC Programme Grant, MEMPHIS, EP/K0039761/1.

  17. NMR studies of abasic sites in DNA duplexes: Deoxyadenosine stacks into the helix opposite acyclic lesions

    SciTech Connect

    Kalnik, M.W.; Chang, Chienneng; Johnson, F.; Grollman, A.P.; Patel, D.J. )

    1989-04-18

    Proton and phosphorus NMR studies are reported for two complementary nonanucleotide duplexes containing acyclic abasic sites. The first duplex, d(C-A-T-G-A-G-T-A-C){center dot}d(G-T-A-C-P-C-A-T-G), contains an acyclic propanyl moiety, P, located opposite a deoxyadenosine at the center of the helix (designated AP{sub P} 9-mer duplex). The second duplex, d(C-A-T-G-A-G-T-A-C-){center dot}d(G-T-A-C-E-C-A-T-G), contains a similarly located acyclic ethanyl moiety, E (designated AP{sub E} 9-mer duplex). The ethanyl moiety is one carbon shorter than the natural carbon-phosphodiester backbone of a single nucleotide unit of DNA. The majority of the exchangeable and nonexchangeable base and sugar protons in both the AP{sub P} 9-mer and AP{sub E} 9-mer duplexes, including those at the abasic site, have been assigned by recording and analyzing two-dimensional phase-sensitive NOESY data sets in H{sub 2}O and D{sub 2}O solution between -5 and 5{degree}C. These spectroscopic observations establish that A5 inserts into the helix opposite the abasic site (P14 and El14) and stacks between the flanking G4{center dot}C15 and G6{center dot}C13 Watson-Crick base pairs in both the AP{sub P} 9-mer and AP{sub E} 9-mer duplexes. Proton NMR parameters for the Ap{sub P} 9-mer and AP{sub E}9-mer duplexes are similar to those reported previously. These proton NMR experiments demonstrate that the structures at abasic sites are very similar whether the five-membered ring is open or closed or whether the phosphodiester backbone is shortened by one carbon atom. Phosphorus spectra of the AP{sub P} 9-mer and AP{sub E} 9-mer duplexes (5{degree}C) indicate that the backbone conformation is similarly perturbed at three phosphodiester backbone torsion angles.

  18. Direct measurement of a 27-dimensional orbital-angular-momentum state vector.

    PubMed

    Malik, Mehul; Mirhosseini, Mohammad; Lavery, Martin P J; Leach, Jonathan; Padgett, Miles J; Boyd, Robert W

    2014-01-01

    The measurement of a quantum state poses a unique challenge for experimentalists. Recently, the technique of 'direct measurement' was proposed for characterizing a quantum state in situ through sequential weak and strong measurements. While this method has been used for measuring polarization states, its real potential lies in the measurement of states with a large dimensionality. Here we show the practical direct measurement of a high-dimensional state vector in the discrete basis of orbital angular momentum. Through weak measurements of orbital angular momentum and strong measurements of angular position, we measure the complex probability amplitudes of a pure state with a dimensionality, d=27. Further, we use our method to directly observe the relationship between rotations of a state vector and the relative phase between its orbital-angular-momentum components. Our technique has important applications in high-dimensional classical and quantum information systems and can be extended to characterize other types of large quantum states.

  19. The dimensional nature of eating pathology: Evidence from a direct comparison of categorical, dimensional, and hybrid models.

    PubMed

    Luo, Xiaochen; Donnellan, M Brent; Burt, S Alexandra; Klump, Kelly L

    2016-07-01

    Eating disorders are conceptualized as categorical rather than dimensional in the current major diagnostic system (Diagnostic and Statistical Manual of Mental Disorders; 5th ed.; American Psychiatric Association, 2013) and in many previous studies. However, previous research has not critically evaluated this assumption or tested hybrid models (e.g., modeling latent variables with both dimensional and categorical features). Accordingly, the current study directly compared categorical, dimensional, and hybrid models for eating pathology in a large, population-based sample. Participants included 3,032 female and male twins (ages 9-30 years) from the Michigan State University Twin Registry. The Minnesota Eating Behaviors Survey was used to assess disordered eating symptoms including body dissatisfaction, weight preoccupation, binge eating, and compensatory behaviors. Results showed that dimensional models best fit the data in the overall sample as well as across subgroups divided by sex and pubertal status (e.g., prepubertal vs. postpubertal). It is interesting to note that the results favored more categorical models when using a case-control subset of our sample with participants who either endorsed substantial eating pathology or no/little eating pathology. Overall, findings provide support for a dimensional conceptualization of eating pathology and underscore the importance of using community samples to capture the full range of severity of eating pathology when investigating questions about taxonomy. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  20. Direct-Write Printing on Three-Dimensional Geometries for Miniaturized Detector and Electronic Assemblies

    NASA Technical Reports Server (NTRS)

    Paquette, Beth; Samuels, Margaret; Chen, Peng

    2017-01-01

    Direct-write printing techniques will enable new detector assemblies that were not previously possible with traditional assembly processes. Detector concepts were manufactured using this technology to validate repeatability. Additional detector applications and printed wires on a 3-dimensional magnetometer bobbin will be designed for print. This effort focuses on evaluating performance for direct-write manufacturing techniques on 3-dimensional surfaces. Direct-write manufacturing has the potential to reduce mass and volume for fabrication and assembly of advanced detector concepts by reducing trace widths down to 10 microns, printing on complex geometries, allowing new electronic concept production, and reduced production times of complex those electronics.

  1. Bi-directional two-dimensional/three-dimensional convertible integral imaging using scattering polarizer

    NASA Astrophysics Data System (ADS)

    Yeom, Jiwoon; Hong, Jisoo; Park, Soon-gi; Min, Sung-Wook; Lee, Byoungho

    2012-10-01

    A bi-directional 2D/3D convertible integral imaging system is proposed. Two optical modules composed of a scattering polarizer and a linear polarizer are adopted, and 2D or 3D mode operation is easily changed by converting polarization states of the projected images. In the 2D mode, the incident light is scattered at the scattering polarizer and the scattered light facing the lens-array is blocked, a 2D image is observable only at the same side as the projector. In the 3D mode, the incident light with the transmission polarization is directly projected onto a lens-array, and the 3D images are integrated. Our proposed system is able to display the 3D images as well as the 2D images for the observers who are placed in front and rear side of the system.

  2. Catabolism of citronellol and related acyclic terpenoids in pseudomonads.

    PubMed

    Förster-Fromme, Karin; Jendrossek, Dieter

    2010-07-01

    Terpenes are a huge group of natural compounds characterised by their predominantly pleasant smell. They are built up by isoprene units in cyclic or acyclic form and can be functionalised by carbonyl, hydroxyl or carboxyl groups and by presence of additional carbon-carbon double bonds (terpenoids). Currently, much more than 10,000 terpenoid compounds are known, and many thereof are present in different iso- and stereoforms. Terpenoids are secondary metabolites and can have important biological functions in living organisms. In many cases, the biological functions of terpenoids are not known at all. Nevertheless, terpenoids are used in large quantities as perfumes and aroma compounds for food additives. Terpenoids can be also precursors and building blocks for synthesis of complex chiral compounds in chemical and pharmaceutical industry. Unfortunately, only few terpenoids are available in large quantities at reasonable costs. Therefore, characterisation of suited biocatalysts specific for terpenoid compounds and development of biotransformation processes of abundant terpenoids to commercially interesting derivates becomes more and more important. This minireview summarises knowledge on catabolic pathways and biotransformations of acyclic monoterpenes that have received only little attention. Terpenoids with 20 or more carbon atoms are not a subject of this study.

  3. The a-cycle problem for transverse Ising ring

    NASA Astrophysics Data System (ADS)

    Dong, Jian-Jun; Li, Peng; Chen, Qi-Hui

    2016-11-01

    Traditionally, the transverse Ising model is mapped to the fermionic c-cycle problem, which neglects the boundary effect due to thermodynamic limit. If persisting on a perfect periodic boundary condition, we can get a so-called a-cycle problem that has not been treated seriously so far (Lieb et al 1961 Ann. Phys. 16 407). In this work, we show a little surprising but exact result in this respect. We find the odevity of the number of lattice sites, N, in the a-cycle problem plays an unexpected role even in the thermodynamic limit, N\\to ∞ , due to the boundary constraint. We pay special attention to the system with N(\\in Odd)\\to ∞ , which is in contrast to the one with N(\\in Even)\\to ∞ , because the former suffers a ring frustration. As a new effect, we find the ring frustration induces a low-energy gapless spectrum above the ground state. By proving a theorem for a new type of Toeplitz determinant, we demonstrate that the ground state in the gapless region exhibits a peculiar longitudinal spin-spin correlation. The entangled nature of the ground state is also disclosed by the evaluation of its entanglement entropy. At low temperature, new behavior of specific heat is predicted. We also propose an experimental protocol for observing the new phenomenon due to the ring frustration.

  4. Reliable determination of amidicity in acyclic amides and lactams.

    PubMed

    Glover, Stephen A; Rosser, Adam A

    2012-07-06

    Two independent computational methods have been used for determination of amide resonance stabilization and amidicities relative to N,N-dimethylacetamide for a wide range of acyclic and cyclic amides. The first method utilizes carbonyl substitution nitrogen atom replacement (COSNAR). The second, new approach involves determination of the difference in amide resonance between N,N-dimethylacetamide and the target amide using an isodesmic trans-amidation process and is calibrated relative to 1-aza-2-adamantanone with zero amidicity and N,N-dimethylacetamide with 100% amidicity. Results indicate excellent coherence between the methods, which must be regarded as more reliable than a recently reported approach to amidicities based upon enthalpies of hydrogenation. Data for acyclic planar and twisted amides are predictable on the basis of the degrees of pyramidalization at nitrogen and twisting about the C-N bonds. Monocyclic lactams are predicted to have amidicities at least as high as N,N-dimethylacetamide, and the β-lactam system is planar with greater amide resonance than that of N,N-dimethylacetamide. Bicyclic penam/em and cepham/em scaffolds lose some amidicity in line with the degree of strain-induced pyramidalization at the bridgehead nitrogen and twist about the amide bond, but the most puckered penem system still retains substantial amidicity equivalent to 73% that of N,N-dimethylacetamide.

  5. The effect of gaze direction on three-dimensional face recognition in infants.

    PubMed

    Yamashita, Wakayo; Kanazawa, So; Yamaguchi, Masami K

    2012-09-01

    Eye gaze is an important tool for social contact. In this study, we investigated whether direct gaze facilitates the recognition of three-dimensional face images in infants. We presented artificially produced face images in rotation to 6-8 month-old infants. The eye gaze of the face images was either direct or averted. Sixty-one sequential images of each face were created by rotating the vertical axis of the face from frontal view to ± 30°. The recognition performances of the infants were then compared between faces with direct gaze and faces with averted gaze. Infants showed evidence that they were able to discriminate the novel from familiarized face by 8 months of age and only when gaze is direct. These results suggest that gaze direction may affect three-dimensional face recognition in infants.

  6. Large-sized light field three-dimensional display using multi-projectors and directional diffuser

    NASA Astrophysics Data System (ADS)

    Peng, Yi-fan; Li, Hai-feng; Zhong, Qing; Xia, Xin-xing; Liu, Xu

    2013-01-01

    A scalable system to achieve large-sized light field three-dimensional display using multi-projectors and directional diffuser is presented. The system mainly employs an array of mini-projectors projecting images onto a special cylindrical directional diffuser screen. The principle of light field reconstruction, configuration of multi-projectors style, and characteristics of directional diffuser are explicitly analyzed, respectively. A prototype of a piece of equipment in mini-cinema class is proposed, with 100 mini-projectors and a special cylindrical directional diffuser performing different diffuse angles in horizontal and vertical directions. Bright and large-sized three-dimensional images displayed by the system can be observed at different horizontal viewing positions around the cylindrical display area with stereo parallax and motion parallax.

  7. Vinculin regulates directionality and cell polarity in two- and three-dimensional matrix and three-dimensional microtrack migration

    PubMed Central

    Rahman, Aniqua; Carey, Shawn P.; Kraning-Rush, Casey M.; Goldblatt, Zachary E.; Bordeleau, Francois; Lampi, Marsha C.; Lin, Deanna Y.; García, Andrés J.; Reinhart-King, Cynthia A.

    2016-01-01

    During metastasis, cells can use proteolytic activity to form tube-like “microtracks” within the extracellular matrix (ECM). Using these microtracks, cells can migrate unimpeded through the stroma. To investigate the molecular mechanisms of microtrack migration, we developed an in vitro three-dimensional (3D) micromolded collagen platform. When in microtracks, cells tend to migrate unidirectionally. Because focal adhesions are the primary mechanism by which cells interact with the ECM, we examined the roles of several focal adhesion molecules in driving unidirectional motion. Vinculin knockdown results in the repeated reversal of migration direction compared with control cells. Tracking the position of the Golgi centroid relative to the position of the nucleus centroid reveals that vinculin knockdown disrupts cell polarity in microtracks. Vinculin also directs migration on two-dimensional (2D) substrates and in 3D uniform collagen matrices, as indicated by reduced speed, shorter net displacement, and decreased directionality in vinculin-deficient cells. In addition, vinculin is necessary for focal adhesion kinase (FAK) activation in three dimensions, as vinculin knockdown results in reduced FAK activation in both 3D uniform collagen matrices and microtracks but not on 2D substrates, and, accordingly, FAK inhibition halts cell migration in 3D microtracks. Together these data indicate that vinculin plays a key role in polarization during migration. PMID:26960796

  8. The effect of gaze direction on three-dimensional face recognition in infant brain activity.

    PubMed

    Yamashita, Wakayo; Kanazawa, So; Yamaguchi, Masami K; Kakigi, Ryusuke

    2012-09-12

    In three-dimensional face recognition studies, it is well known that viewing rotating faces enhance face recognition. For infants, our previous study indicated that 8-month-old infants showed recognition of three-dimensional rotating faces with a direct gaze, and they did not learn with an averted gaze. This suggests that gaze direction may affect three-dimensional face recognition in infants. In this experiment, we used near-infrared spectroscopy to measure infants' hemodynamic responses to averted gaze and direct gaze. We hypothesized that infants would show different neural activity for averted and direct gazes. The responses were compared with the baseline activation during the presentation of non-face objects. We found that the concentration of oxyhemoglobin increased in the temporal cortex on both sides only during the presentation of averted gaze compared with that of the baseline period. This is the first study to show that infants' brain activity in three-dimensional face processing is different between averted gaze and direct gaze.

  9. Estimating changes in lighting direction in binocularly viewed three-dimensional scenes

    PubMed Central

    Gerhard, Holly E.; Maloney, Laurence T.

    2010-01-01

    We examine human ability to detect changes in scene lighting. Thirteen observers viewed three-dimensional rendered scenes stereoscopically. Each scene consisted of a randomly generated three-dimensional “Gaussian bump” surface rendered under a combination of collimated and diffuse light sources. During each trial, the collimated source underwent a small, quick change of position in one of four directions. The observer's task was to classify the direction of the lighting change. All observers were above chance in performing the task. We developed a model that combined two sources of information, a shape map and a shading map, to predict lighting change direction. We used this model to predict patterns of errors both across observers and across scenes differing in shape. We found that errors in estimating lighting direction were primarily the result of errors in representing surface shape. We characterized the surface features that affected performance in the classification task. PMID:21106676

  10. Estimating changes in lighting direction in binocularly viewed three-dimensional scenes.

    PubMed

    Gerhard, Holly E; Maloney, Laurence T

    2010-11-24

    We examine human ability to detect changes in scene lighting. Thirteen observers viewed three-dimensional rendered scenes stereoscopically. Each scene consisted of a randomly generated three-dimensional "Gaussian bump" surface rendered under a combination of collimated and diffuse light sources. During each trial, the collimated source underwent a small, quick change of position in one of four directions. The observer's task was to classify the direction of the lighting change. All observers were above chance in performing the task. We developed a model that combined two sources of information, a shape map and a shading map, to predict lighting change direction. We used this model to predict patterns of errors both across observers and across scenes differing in shape. We found that errors in estimating lighting direction were primarily the result of errors in representing surface shape. We characterized the surface features that affected performance in the classification task.

  11. Implementation of alternating direction explicit methods for higher dimensional Black-Scholes equations

    NASA Astrophysics Data System (ADS)

    Bučková, Z.; Pólvora, P.; Ehrhardt, M.; Günther, M.

    2016-10-01

    In this work we propose Alternating Direction Explicit (ADE) schemes for the two and three dimensional linear Black-Scholes pricing model. Our implemented methodology can be easily extended to higher dimensions. The main advantage of ADE schemes is that they are explicit and exhibit good stability properties. Results concerning the experimental order of convergence are included.

  12. Three-dimensional atomic force microscopy: interaction force vector by direct observation of tip trajectory.

    PubMed

    Sigdel, Krishna P; Grayer, Justin S; King, Gavin M

    2013-11-13

    The prospect of a robust three-dimensional atomic force microscope (AFM) holds significant promise in nanoscience. Yet, in conventional AFM, the tip-sample interaction force vector is not directly accessible. We scatter a focused laser directly off an AFM tip apex to rapidly and precisely measure the tapping tip trajectory in three-dimensional space. This data also yields three-dimensional cantilever spring constants, effective masses, and hence, the tip-sample interaction force components via Newton's second law. Significant lateral forces representing 49 and 13% of the normal force (Fz = 152 ± 17 pN) were observed in common tapping mode conditions as a silicon tip intermittently contacted a glass substrate in aqueous solution; as a consequence, the direction of the force vector tilted considerably more than expected. When addressing the surface of a lipid bilayer, the behavior of the force components differed significantly from that observed on glass. This is attributed to the lateral mobility of the lipid membrane coupled with its elastic properties. Direct access to interaction components Fx, Fy, and Fz provides a more complete view of tip dynamics that underlie force microscope operation and can form the foundation of a three-dimensional AFM in a plurality of conditions.

  13. Stable direct adaptive control of linear infinite-dimensional systems using a command generator tracker approach

    NASA Technical Reports Server (NTRS)

    Balas, Mark; Kaufman, Howard; Wen, John

    1984-01-01

    The topics are presented in view graph form and include the following: an adaptive model following control; adaptive control of a distributed parameter system (DPS) with a finite-dimensional controller; a direct adaptive controller; a closed-loop adaptively controlled DPS; Lyapunov stability; the asymptotic stability of the closed loop; and model control of a simply supported beam.

  14. Directional change of fluid particles in two-dimensional turbulence and of football players

    NASA Astrophysics Data System (ADS)

    Kadoch, Benjamin; Bos, Wouter J. T.; Schneider, Kai

    2017-06-01

    Multiscale directional statistics are investigated in two-dimensional incompressible turbulence. It is shown that the short-time behavior of the mean angle of directional change of fluid particles is linearly dependent on the time lag and that no inertial range behavior is observed in the directional change associated with the enstrophy-cascade range. In simulations of the inverse-cascade range, the directional change shows a power law behavior at inertial range time scales. By comparing the directional change in space-periodic and wall-bounded flow, it is shown that the probability density function of the directional change at long times carries the signature of the confinement. The geometrical origin of this effect is validated by Monte Carlo simulations. The same effect is also observed in the directional statistics computed from the trajectories of football players (soccer players in American English).

  15. Delay estimation in a two-node acyclic network

    PubMed Central

    2009-01-01

    Linear measures such as cross-correlation have been used successfully to determine time delays from the given processes. Such an analysis often precedes identifying possible causal relationships between the observed processes. The present study investigates the impact of a positively correlated driver whose correlation function decreases monotonically with lag on the delay estimation in a two-node acyclic network with one and two-delays. It is shown that cross-correlation analysis of the given processes can result in spurious identification of multiple delays between the driver and the dependent processes. Subsequently, delay estimation of increment process as opposed to the original process under certain implicit constraints is explored. Short-range and long-range correlated driver processes along with those of their coarse-grained counterparts are considered. PMID:19214240

  16. Directional interlayer spin-valley transfer in two-dimensional heterostructures

    SciTech Connect

    Schaibley, John R.; Rivera, Pasqual; Yu, Hongyi; Seyler, Kyle L.; Yan, Jiaqiang; Mandrus, David G.; Taniguchi, Takashi; Watanabe, Kenji; Yao, Wang; Xu, Xiaodong

    2016-12-14

    Van der Waals heterostructures formed by two different monolayer semiconductors have emerged as a promising platform for new optoelectronic and spin/valleytronic applications. In addition to its atomically thin nature, a two-dimensional semiconductor heterostructure is distinct from its three-dimensional counterparts due to the unique coupled spin-valley physics of its constituent monolayers. In this paper, we report the direct observation that an optically generated spin-valley polarization in one monolayer can be transferred between layers of a two-dimensional MoSe2–WSe2 heterostructure. Using non-degenerate optical circular dichroism spectroscopy, we show that charge transfer between two monolayers conserves spin-valley polarization and is only weakly dependent on the twist angle between layers. Finally, our work points to a new spin-valley pumping scheme in nanoscale devices, provides a fundamental understanding of spin-valley transfer across the two-dimensional interface, and shows the potential use of two-dimensional semiconductors as a spin-valley generator in two-dimensional spin/valleytronic devices for storing and processing information.

  17. Directional interlayer spin-valley transfer in two-dimensional heterostructures

    DOE PAGES

    Schaibley, John R.; Rivera, Pasqual; Yu, Hongyi; ...

    2016-12-14

    Van der Waals heterostructures formed by two different monolayer semiconductors have emerged as a promising platform for new optoelectronic and spin/valleytronic applications. In addition to its atomically thin nature, a two-dimensional semiconductor heterostructure is distinct from its three-dimensional counterparts due to the unique coupled spin-valley physics of its constituent monolayers. In this paper, we report the direct observation that an optically generated spin-valley polarization in one monolayer can be transferred between layers of a two-dimensional MoSe2–WSe2 heterostructure. Using non-degenerate optical circular dichroism spectroscopy, we show that charge transfer between two monolayers conserves spin-valley polarization and is only weakly dependent onmore » the twist angle between layers. Finally, our work points to a new spin-valley pumping scheme in nanoscale devices, provides a fundamental understanding of spin-valley transfer across the two-dimensional interface, and shows the potential use of two-dimensional semiconductors as a spin-valley generator in two-dimensional spin/valleytronic devices for storing and processing information.« less

  18. Directional interlayer spin-valley transfer in two-dimensional heterostructures

    PubMed Central

    Schaibley, John R.; Rivera, Pasqual; Yu, Hongyi; Seyler, Kyle L.; Yan, Jiaqiang; Mandrus, David G.; Taniguchi, Takashi; Watanabe, Kenji; Yao, Wang; Xu, Xiaodong

    2016-01-01

    Van der Waals heterostructures formed by two different monolayer semiconductors have emerged as a promising platform for new optoelectronic and spin/valleytronic applications. In addition to its atomically thin nature, a two-dimensional semiconductor heterostructure is distinct from its three-dimensional counterparts due to the unique coupled spin-valley physics of its constituent monolayers. Here, we report the direct observation that an optically generated spin-valley polarization in one monolayer can be transferred between layers of a two-dimensional MoSe2–WSe2 heterostructure. Using non-degenerate optical circular dichroism spectroscopy, we show that charge transfer between two monolayers conserves spin-valley polarization and is only weakly dependent on the twist angle between layers. Our work points to a new spin-valley pumping scheme in nanoscale devices, provides a fundamental understanding of spin-valley transfer across the two-dimensional interface, and shows the potential use of two-dimensional semiconductors as a spin-valley generator in two-dimensional spin/valleytronic devices for storing and processing information. PMID:27966524

  19. Directional interlayer spin-valley transfer in two-dimensional heterostructures.

    PubMed

    Schaibley, John R; Rivera, Pasqual; Yu, Hongyi; Seyler, Kyle L; Yan, Jiaqiang; Mandrus, David G; Taniguchi, Takashi; Watanabe, Kenji; Yao, Wang; Xu, Xiaodong

    2016-12-14

    Van der Waals heterostructures formed by two different monolayer semiconductors have emerged as a promising platform for new optoelectronic and spin/valleytronic applications. In addition to its atomically thin nature, a two-dimensional semiconductor heterostructure is distinct from its three-dimensional counterparts due to the unique coupled spin-valley physics of its constituent monolayers. Here, we report the direct observation that an optically generated spin-valley polarization in one monolayer can be transferred between layers of a two-dimensional MoSe2-WSe2 heterostructure. Using non-degenerate optical circular dichroism spectroscopy, we show that charge transfer between two monolayers conserves spin-valley polarization and is only weakly dependent on the twist angle between layers. Our work points to a new spin-valley pumping scheme in nanoscale devices, provides a fundamental understanding of spin-valley transfer across the two-dimensional interface, and shows the potential use of two-dimensional semiconductors as a spin-valley generator in two-dimensional spin/valleytronic devices for storing and processing information.

  20. Iridium-Catalyzed Diastereoselective and Enantioselective Allylic Substitutions with Acyclic α-Alkoxy Ketones

    DOE PAGES

    Jiang, Xingyu; Chen, Wenyong; Hartwig, John F.

    2016-04-01

    The asymmetric alkylation of acyclic ketones is a longstanding challenge in organic synthesis. Here, are the diastereoselective and enantioselective allylic substitutions with acyclic α-alkoxy ketones catalyzed by a metallacyclic iridium complex to form products with contiguous stereogenic centers derived from the nucleophile and electrophile. These reactions occur between allyl methyl carbonates and unstabilized copper(I) enolates generated in situ from acyclic α-alkoxy ketones. The resulting products can be readily converted into enantioenriched tertiary alcohols and tetrahydrofuran derivatives without erosion of enantiomeric purity.

  1. Amplification and directional emission of surface acoustic waves by a two-dimensional electron gas

    SciTech Connect

    Shao, Lei; Pipe, Kevin P.

    2015-01-12

    Amplification of surface acoustic waves (SAWs) by electron drift in a two-dimensional electron gas (2DEG) is analyzed analytically and confirmed experimentally. Calculations suggest that peak power gain per SAW radian occurs at a more practical carrier density for a 2DEG than for a bulk material. It is also shown that SAW emission with tunable directionality can be achieved by modulating a 2DEG's carrier density (to effect SAW generation) in the presence of an applied DC field that amplifies SAWs propagating in a particular direction while attenuating those propagating in the opposite direction.

  2. Stochastic ratcheting of two-dimensional colloids: Directed current and dynamical transitions

    NASA Astrophysics Data System (ADS)

    Chakraborty, Dipanjan; Chaudhuri, Debasish

    2015-05-01

    We present results of molecular dynamics simulations for two-dimensional repulsively interacting colloids driven by a one-dimensional asymmetric and commensurate ratchet potential, switching on and off stochastically. This drives a time-averaged directed current of colloids, exhibiting resonance with change in ratcheting frequency, where the resonance frequency itself depends nonmonotonically on density. Using scaling arguments, we obtain analytic results that show good agreement with numerical simulations. With increasing ratcheting frequency, we find nonequilibrium reentrant transitions between solid and modulated liquid phases.

  3. Direct numerical simulation of steady state, three dimensional, laminar flow around a wall mounted cube

    NASA Astrophysics Data System (ADS)

    Liakos, Anastasios; Malamataris, Nikolaos A.

    2014-05-01

    The topology and evolution of flow around a surface mounted cubical object in three dimensional channel flow is examined for low to moderate Reynolds numbers. Direct numerical simulations were performed via a home made parallel finite element code. The computational domain has been designed according to actual laboratory experiment conditions. Analysis of the results is performed using the three dimensional theory of separation. Our findings indicate that a tornado-like vortex by the side of the cube is present for all Reynolds numbers for which flow was simulated. A horseshoe vortex upstream from the cube was formed at Reynolds number approximately 1266. Pressure distributions are shown along with three dimensional images of the tornado-like vortex and the horseshoe vortex at selected Reynolds numbers. Finally, and in accordance to previous work, our results indicate that the upper limit for the Reynolds number for which steady state results are physically realizable is roughly 2000.

  4. Palladium-catalyzed allylic amination: a powerful tool for the enantioselective synthesis of acyclic nucleoside phosphonates.

    PubMed

    Azzouz, Mariam; Soriano, Sébastien; Escudero-Casao, Margarita; Matheu, M Isabel; Castillón, Sergio; Díaz, Yolanda

    2017-08-30

    Acyclic nucleoside phosphonates have been prepared in a straightforward manner and in high yields by an enantioselective palladium-catalyzed allylic substitution involving nucleic bases as nucleophiles followed by cross-metathesis reaction with diethyl allylphosphonate.

  5. From acyclic to cyclic α-amino vinylphosphonates by using ring-closing metathesis.

    PubMed

    Adler, Pauline; Fadel, Antoine; Prunet, Joëlle; Rabasso, Nicolas

    2017-01-04

    Acyclic α-amino vinylphosphonates were alkylated through the Mitsunobu reaction then diolefinic compounds hence formed were subjected to RCM. Studies on the scope and limitations of RCM with these sterically hindered α-amino vinylphosphonates are detailed.

  6. Enantioselective Pd-catalyzed allylation of acyclic α-fluorinated ketones.

    PubMed

    Wang, Wengui; Shen, Haiming; Wan, Xiao-Long; Chen, Qing-Yun; Guo, Yong

    2014-07-03

    Significant synthetic challenges remain for the asymmetric synthesis of tertiary α-fluoro ketones, which are potentially useful molecules for the development of drugs, agrochemicals, and functional materials. Herein, we describe the development of a method for the catalytic enantioselective synthesis of tertiary α-fluoro ketones via the Tsuji-Trost reaction of racemic acyclic α-fluorinated ketones. Enantioenriched acyclic α-cabonyl tertiary fluorides can be produced with the aid of a palladium/phosphinooxazoline catalyst.

  7. Direct calculation of thermal emission for three-dimensionally periodic photonic crystal slabs.

    PubMed

    Chan, David L C; Soljacić, Marin; Joannopoulos, J D

    2006-09-01

    We perform direct thermal emission calculations for three-dimensionally periodic photonic crystal slabs using stochastic electrodynamics following the Langevin approach, implemented via a finite-difference time-domain algorithm. We demonstrate that emissivity and absorptivity are equal, by showing that such photonic crystal systems emit as much radiation as they absorb, for every frequency, up to statistical fluctuations. We also study the effect of surface termination on absorption and emission spectra from these systems.

  8. Direct calculation of thermal emission for three-dimensionally periodic photonic crystal slabs

    NASA Astrophysics Data System (ADS)

    Chan, David L. C.; Soljačić, Marin; Joannopoulos, J. D.

    2006-09-01

    We perform direct thermal emission calculations for three-dimensionally periodic photonic crystal slabs using stochastic electrodynamics following the Langevin approach, implemented via a finite-difference time-domain algorithm. We demonstrate that emissivity and absorptivity are equal, by showing that such photonic crystal systems emit as much radiation as they absorb, for every frequency, up to statistical fluctuations. We also study the effect of surface termination on absorption and emission spectra from these systems.

  9. Three Dimensional Assembly in Directed Self-assembly of Block Copolymers

    SciTech Connect

    Segal-Peretz, Tamar; Zhou, Chun; Ren, Jiaxing; Dazai, Takahiro; Ocola, Leonidas E.; Divan, Ralu N. S.; Nealey, Paul F.

    2016-09-02

    The three-dimensional assembly of poly (styrene-b-methyl methacrylate) (PS-b-PMMA) in chemoepitaxy and graphoepitaxy directed self-assembly (DSA) was investigated using scanning transmission electron microscopy (STEM) tomography. The tomographic characterization revealed hidden morphologies and defects at the BCP- chemical pattern interface in lamellar DSA, and probed the formation of cylinders at the bottom of cylindrical DSA for contact hole shrink. Lastly, future work will include control over 3D assembly in sub-10 nm processes.

  10. A combined direct/inverse three-dimensional transonic wing design method for vector computers

    NASA Technical Reports Server (NTRS)

    Weed, R. A.; Carlson, L. A.; Anderson, W. K.

    1984-01-01

    A three-dimensional transonic-wing design algorithm for vector computers is developed, and the results of sample computations are presented graphically. The method incorporates the direct/inverse scheme of Carlson (1975), a Cartesian grid system with boundary conditions applied at a mean plane, and a potential-flow solver based on the conservative form of the full potential equation and using the ZEBRA II vectorizable solution algorithm of South et al. (1980). The accuracy and consistency of the method with regard to direct and inverse analysis and trailing-edge closure are verified in the test computations.

  11. A combined direct/inverse three-dimensional transonic wing design method for vector computers

    NASA Technical Reports Server (NTRS)

    Weed, R. A.; Carlson, L. A.; Anderson, W. K.

    1984-01-01

    A three-dimensional transonic-wing design algorithm for vector computers is developed, and the results of sample computations are presented graphically. The method incorporates the direct/inverse scheme of Carlson (1975), a Cartesian grid system with boundary conditions applied at a mean plane, and a potential-flow solver based on the conservative form of the full potential equation and using the ZEBRA II vectorizable solution algorithm of South et al. (1980). The accuracy and consistency of the method with regard to direct and inverse analysis and trailing-edge closure are verified in the test computations.

  12. Directed and undirected multiurn models in a one-dimensional ring

    NASA Astrophysics Data System (ADS)

    Nagler, Jan

    2005-11-01

    The flea model by Ehrenfest describes the jumps of a fixed number of fleas between two dogs. In each time step a randomly selected flea jumps on the other dog. We study directed and undirected multiurn models in a one-dimensional ring. The introduced models represent generalizations of three recently proposed multiurn models which themselves are generalizations of Ehrenfest’s model. The models are solved analytically. For the directed case we find oscillations of the average number of balls or fleas in a certain urn before the system reaches its equilibrium state. The discussed models may serve as basic models of dynamics of granular media in connected periodic compartment systems.

  13. Structural Interactions within Lithium Salt Solvates. Acyclic Carbonates and Esters

    SciTech Connect

    Afroz, Taliman; Seo, D. M.; Han, Sang D.; Boyle, Paul D.; Henderson, Wesley A.

    2015-03-06

    Solvate crystal structures serve as useful models for the molecular-level interactions within the diverse solvates present in liquid electrolytes. Although acyclic carbonate solvents are widely used for Li-ion battery electrolytes, only three solvate crystal structures with lithium salts are known for these and related solvents. The present work, therefore, reports six lithium salt solvate structures with dimethyl and diethyl carbonate: (DMC)2:LiPF6, (DMC)1:LiCF3SO3, (DMC)1/4:LiBF4, (DEC)2:LiClO4, (DEC)1:LiClO4 and (DEC)1:LiCF3SO3 and four with the structurally related methyl and ethyl acetate: (MA)2:LiClO4, (MA)1:LiBF4, (EA)1:LiClO4 and (EA)1:LiBF4.

  14. Three-dimensional broadband and high-directivity lens antenna made of metamaterials

    NASA Astrophysics Data System (ADS)

    Chen, Xi; Feng Ma, Hui; Ying Zou, Xia; Xiang Jiang, Wei; Jun Cui, Tie

    2011-08-01

    We present the theoretical modeling and prototype demonstration of a three-dimensional broadband, low-loss, dual-polarization, and high-directivity lens antenna using gradient index (GRIN) metamaterials, which is composed of multi-layer microstrip square-ring arrays. The elements of metamaterials, closed square-ring units of variable sizes, are distributed on the planar substrate to satisfy the radial gradient index function and the axial impedance matching layer configuration of the lens. The gradient-index metamaterials are designed to transform the spherical wave-front into the planar wave-front and to minimize the reflection loss. A prototype lens antenna, which consists of a metal conical horn and the gradient-index lens, are simulated, constructed, and measured. The resemblance of simulation and measurement results shows that the prototype lens antenna maintains low return loss and high directivity on the whole X-band (from 8 GHz to 12 GHz). Compared to the traditional horn antenna, the metamaterial GRIN lens antenna has much superior performance—for instance, the gain increases by 6 dBi at 12 GHz. These results demonstrate the feasibility of such a light weight slab metamaterial lens for broadband and high-directivity antenna applications, such as in radar and communication systems. We have used the lens antennas in the measurements of a three-dimensional invisibility cloak due to the high directivity.

  15. Mapping Dimensionality and Directionality of Electronic Behavior in CeCoIn5: the Normal State

    NASA Astrophysics Data System (ADS)

    Gyenis, Andras; Feldman, Benjamin E.; Randeria, Mallika T.; Peterson, Gabriel A.; Aynajian, Pegor; Bauer, Eric D.; Yazdani, Ali

    Materials made from alternating layers of different constituents can exhibit dramatic variability in their electronic properties depending on which layer is probed. This is evident in the heavy fermion compound CeCoIn5, where scanning tunneling microscopy (STM) has revealed preferential coupling to either light or heavy electron states depending on the surface termination. Here we report STM measurements of CeCoIn5 cleaved perpendicular to its basal plane that clearly shows the quasi-two-dimensional nature of the electronic behavior on a single (100) surface. We observe atomic scale modulation of tunneling into the light and heavy electron bands in the c-axis direction, with no variation visible along the basal planes in the b-axis direction. In addition, conductance maps reveal preferential scattering along the two-dimensional basal planes. Our measurements highlight the reduced effective dimensionality of electronic states in CeCoIn5, and underscore the potential insight that can be gained by imaging layered materials perpendicular to their c-axis.

  16. Direct TEM observations of growth mechanisms of two-dimensional MoS2 flakes

    NASA Astrophysics Data System (ADS)

    Fei, Linfeng; Lei, Shuijin; Zhang, Wei-Bing; Lu, Wei; Lin, Ziyuan; Lam, Chi Hang; Chai, Yang; Wang, Yu

    2016-07-01

    A microscopic understanding of the growth mechanism of two-dimensional materials is of particular importance for controllable synthesis of functional nanostructures. Because of the lack of direct and insightful observations, how to control the orientation and the size of two-dimensional material grains is still under debate. Here we discern distinct formation stages for MoS2 flakes from the thermolysis of ammonium thiomolybdates using in situ transmission electron microscopy. In the initial stage (400 °C), vertically aligned MoS2 structures grow in a layer-by-layer mode. With the increasing temperature of up to 780 °C, the orientation of MoS2 structures becomes horizontal. When the growth temperature reaches 850 °C, the crystalline size of MoS2 increases by merging adjacent flakes. Our study shows direct observations of MoS2 growth as the temperature evolves, and sheds light on the controllable orientation and grain size of two-dimensional materials.

  17. Direct TEM observations of growth mechanisms of two-dimensional MoS2 flakes

    PubMed Central

    Fei, Linfeng; Lei, Shuijin; Zhang, Wei-Bing; Lu, Wei; Lin, Ziyuan; Lam, Chi Hang; Chai, Yang; Wang, Yu

    2016-01-01

    A microscopic understanding of the growth mechanism of two-dimensional materials is of particular importance for controllable synthesis of functional nanostructures. Because of the lack of direct and insightful observations, how to control the orientation and the size of two-dimensional material grains is still under debate. Here we discern distinct formation stages for MoS2 flakes from the thermolysis of ammonium thiomolybdates using in situ transmission electron microscopy. In the initial stage (400 °C), vertically aligned MoS2 structures grow in a layer-by-layer mode. With the increasing temperature of up to 780 °C, the orientation of MoS2 structures becomes horizontal. When the growth temperature reaches 850 °C, the crystalline size of MoS2 increases by merging adjacent flakes. Our study shows direct observations of MoS2 growth as the temperature evolves, and sheds light on the controllable orientation and grain size of two-dimensional materials. PMID:27412892

  18. Three-dimensional viscous-flow computations using a directionally hybrid implicit-explicit procedure

    NASA Technical Reports Server (NTRS)

    Rizk, Y. M.; Chaussee, D. S.

    1983-01-01

    A new, directionally dependent, hybrid numerical algorithm for solving the unsteady, three-dimensional Navier-Stokes equations has been developed and used to compute the viscous supersonic flow over complex configurations, which may generate local regions of embedded subsonic or streamwise separated flows or both. The new hybrid implicit-explicit algorithm is derived from the more general implicit Beam-Warming algorithm and is particularly suitable for viscous computations in which the grid spacing in the direction outward from the body is considerably smaller than the spacing in the other two directions. Numerical results obtained from both the hybrid and implicit schemes are presented and compared on the basis of numerical stability, convergence history, and computer and core memory requirements.

  19. Dipolar colloids in apolar media: direct microscopy of two-dimensional suspensions

    PubMed Central

    Janai, Erez; Cohen, Avner P.; Butenko, Alexander V.; Schofield, Andrew B.; Schultz, Moty; Sloutskin, Eli

    2016-01-01

    Spherical colloids, in an absence of external fields, are commonly assumed to interact solely through rotationally-invariant potentials, u(r). While the presence of permanent dipoles in aqueous suspensions has been previously suggested by some experiments, the rotational degrees of freedom of spherical colloids are typically neglected. We prove, by direct experiments, the presence of permanent dipoles in commonly used spherical poly(methyl methacrylate) (PMMA) colloids, suspended in an apolar organic medium. We study, by a combination of direct confocal microscopy, computer simulations, and theory, the structure and other thermodynamical properties of organic suspensions of colloidal spheres, confined to a two-dimensional (2D) monolayer. Our studies reveal the effects of the dipolar interactions on the structure and the osmotic pressure of these fluids. These observations have far-reaching consequences for the fundamental colloidal science, opening new directions in self-assembly of complex colloidal clusters. PMID:27346611

  20. Dipolar colloids in apolar media: direct microscopy of two-dimensional suspensions

    NASA Astrophysics Data System (ADS)

    Janai, Erez; Cohen, Avner P.; Butenko, Alexander V.; Schofield, Andrew B.; Schultz, Moty; Sloutskin, Eli

    2016-06-01

    Spherical colloids, in an absence of external fields, are commonly assumed to interact solely through rotationally-invariant potentials, u(r). While the presence of permanent dipoles in aqueous suspensions has been previously suggested by some experiments, the rotational degrees of freedom of spherical colloids are typically neglected. We prove, by direct experiments, the presence of permanent dipoles in commonly used spherical poly(methyl methacrylate) (PMMA) colloids, suspended in an apolar organic medium. We study, by a combination of direct confocal microscopy, computer simulations, and theory, the structure and other thermodynamical properties of organic suspensions of colloidal spheres, confined to a two-dimensional (2D) monolayer. Our studies reveal the effects of the dipolar interactions on the structure and the osmotic pressure of these fluids. These observations have far-reaching consequences for the fundamental colloidal science, opening new directions in self-assembly of complex colloidal clusters.

  1. Dipolar colloids in apolar media: direct microscopy of two-dimensional suspensions.

    PubMed

    Janai, Erez; Cohen, Avner P; Butenko, Alexander V; Schofield, Andrew B; Schultz, Moty; Sloutskin, Eli

    2016-06-27

    Spherical colloids, in an absence of external fields, are commonly assumed to interact solely through rotationally-invariant potentials, u(r). While the presence of permanent dipoles in aqueous suspensions has been previously suggested by some experiments, the rotational degrees of freedom of spherical colloids are typically neglected. We prove, by direct experiments, the presence of permanent dipoles in commonly used spherical poly(methyl methacrylate) (PMMA) colloids, suspended in an apolar organic medium. We study, by a combination of direct confocal microscopy, computer simulations, and theory, the structure and other thermodynamical properties of organic suspensions of colloidal spheres, confined to a two-dimensional (2D) monolayer. Our studies reveal the effects of the dipolar interactions on the structure and the osmotic pressure of these fluids. These observations have far-reaching consequences for the fundamental colloidal science, opening new directions in self-assembly of complex colloidal clusters.

  2. Dimensional and material characteristics of direct deposited tool steel by CO II laser

    NASA Astrophysics Data System (ADS)

    Choi, J.

    2006-01-01

    Laser aided direct metalimaterial deposition (DMD) process builds metallic parts layer-by-layer directly from the CAD representation. In general, the process uses powdered metaUmaterials fed into a melt pool, creating fully dense parts. Success of this technology in the die and tool industry depends on the parts quality to be achieved. To obtain designed geometric dimensions and material properties, delicate control of the parameters such as laser power, spot diameter, traverse speed and powder mass flow rate is critical. In this paper, the dimensional and material characteristics of directed deposited H13 tool steel by CO II laser are investigated for the DMD process with a feedback height control system. The relationships between DMD process variables and the product characteristics are analyzed using statistical techniques. The performance of the DMD process is examined with the material characteristics of hardness, porosity, microstructure, and composition.

  3. Two-dimensional directional proton emission in dissociative ionization of H(2).

    PubMed

    Gong, Xiaochun; He, Peilun; Song, Qiying; Ji, Qinying; Pan, Haifeng; Ding, Jingxin; He, Feng; Zeng, Heping; Wu, Jian

    2014-11-14

    An intense phase-controlled orthogonally polarized two-color ultrashort laser pulse is used to singly ionize and dissociate H_{2} into a neutral hydrogen atom and a proton. Emission-direction and kinetic-energy dependent asymmetric dissociation of H_{2} is observed as a function of the relative phase of the orthogonally polarized two-color pulse. Significant asymmetric proton emission is measured in the direction between two polarization axes. Our numerical simulations of the time-dependent Schrödinger equation reproduce many of the observed features. The asymmetry is attributed to the coherent superposition of two-dimensional nuclear wave packets with opposite parities, which have the same energies and overlap in the same emission directions.

  4. Viewing-angle-enhanced integral three-dimensional imaging along all directions without mechanical movement.

    PubMed

    Jung, Sungyong; Park, Jae-Hyeung; Choi, Heejin; Lee, Byoungho

    2003-06-16

    Integral three-dimensional (3D) imaging provides full-motion parallax, unlike other conventional stereoscopy-based techniques. To maximize this advantage, a 3D system with a wide view along all directions is required. We propose and demonstrate a new integral imaging (InIm) method to enhance the viewing angle along both horizontal and vertical directions. Elemental lens switching is performed by a combination of spatial and time multiplexing by use of double display devices and orthogonal polarizations. Experimental results show that the viewing angle of the system is enhanced along all directions without any mechanical movement or any cross talk between afterimages. We believe that the proposed method has the potential to facilitate practical use of the wideviewing InIm system.

  5. Visualization of Bloch surface waves and directional propagation effects on one-dimensional photonic crystal substrate.

    PubMed

    Hung, Yu-Ju; Lin, I-Sheng

    2016-07-11

    This paper reports a novel approach to the direct observation of Bloch surface waves, wherein a layer of fluorescent material is deposited directly on the surface of a semi-infinite periodic layered cell. A set of surface nano-gratings is used to couple pumping light to Bloch surface waves, while the sample is rotated until the pumping light meets the quasi-phase matching conditions. This study investigated the directional propagation of waves on stripe and circular one-dimensional grating structures by analyzing the dispersion relationship of the first two eigen modes. Our results demonstrate the efficacy of the proposed scheme in visualizing Bloch surface waves, which could be extended to a variety of other devices.

  6. LOPA-based direct laser writing of multi-dimensional and multi-functional photonic submicrostructures

    NASA Astrophysics Data System (ADS)

    Mao, Fei; Tong, Quang Cong; Nguyen, Dam Thuy Trang; Huong, Au Thi; Odessey, Rachel; Saudrais, Florent; Lai, Ngoc Diep

    2017-02-01

    We have recently developed a simple fabrication technique, called low one-photon absorption (LOPA) direct laser writing (DLW), to realize multi-dimensional and multi-functional polymer-based photonic submicrostructures. This technique employs a continuous-wave laser at 532 nm-wavelength with only few milliwatts and a simple optical setup, allowing to decrease the cost of the fabrication system by a factor of ten as compared to a commercial DLW system. In this report, we present various photonic structures, such as 2D and 3D micro- resonators, photonic and magnetic submicrostructures, and nonlinear optical structures fabricated by this LOPA- based DLW method. We also discuss about potential applications of those fabricated multi-dimensional and multi-functional photonic submicrostructures in opto-electronics, bio, as well as in opto-mechanics.

  7. Terahertz vibrations of crystalline acyclic and cyclic diglycine: benchmarks for London force correction models.

    PubMed

    Juliano, Thomas R; Korter, Timothy M

    2013-10-10

    Terahertz spectroscopy provides direct information concerning weak intermolecular forces in crystalline molecular solids and therefore acts as an excellent method for calibrating and evaluating computational models for noncovalent interactions. In this study, the low-frequency vibrations of two dipeptides were compared, acyclic diglycine and cyclic diglycine, as benchmark systems for gauging the performance of semiempirical London force correction approaches. The diglycine samples were investigated using pulsed terahertz spectroscopy from 10 to 100 cm(-1) and then analyzed using solid-state density functional theory (DFT) augmented with existing London force corrections, as well as a new parametrization (DFT-DX) based on known experimental values. The two diglycine molecules provide a useful test for the applied models given their similarities, but more importantly the differences in the intermolecular forces displayed by each. It was found that all of the considered London force correction models were able to generate diglycine crystal structures of similar accuracy, but considerable variation occurred in their abilities to predict terahertz frequency vibrations. The DFT-DX parametrization was particularly successful in this investigation and shows promise for the improved analysis of low-frequency spectra.

  8. Acyclic diterpene glycosides, capsianosides VIII, IX, X, XIII, XV and XVI from the fruits of Paprika Capsicum annuum L. var. grossum BAILEY and Jalapeño Capsicum annuum L. var. annuum.

    PubMed

    Lee, Jong-Hyun; Kiyota, Naoko; Ikeda, Tsuyoshi; Nohara, Toshihiro

    2006-10-01

    Paprika and Jalapeño are used as vegetables and spices. We have obtained six new acyclic diterpene glycosides, called capsianosides XIII (2), XV (3), IX (4), XVI (5), X (6) and VIII (7) together with known capsianoside II (1) from the fruits of the Paprika and Jalapeño. The structures of these compounds have been elucidated by the (1)H- and (13)C-NMR spectra and two-dimensional NMR methods.

  9. Three-dimensional hypersonic rarefied flow calculations using direct simulation Monte Carlo method

    NASA Technical Reports Server (NTRS)

    Celenligil, M. Cevdet; Moss, James N.

    1993-01-01

    A summary of three-dimensional simulations on the hypersonic rarefied flows in an effort to understand the highly nonequilibrium flows about space vehicles entering the Earth's atmosphere for a realistic estimation of the aerothermal loads is presented. Calculations are performed using the direct simulation Monte Carlo method with a five-species reacting gas model, which accounts for rotational and vibrational internal energies. Results are obtained for the external flows about various bodies in the transitional flow regime. For the cases considered, convective heating, flowfield structure and overall aerodynamic coefficients are presented and comparisons are made with the available experimental data. The agreement between the calculated and measured results are very good.

  10. Rapid prototyping of three-dimensional microfluidic mixers in glass by femtosecond laser direct writing.

    PubMed

    Liao, Yang; Song, Jiangxin; Li, En; Luo, Yong; Shen, Yinglong; Chen, Danping; Cheng, Ya; Xu, Zhizhan; Sugioka, Koji; Midorikawa, Katsumi

    2012-02-21

    The creation of complex three-dimensional (3D) microfluidic systems has attracted significant attention from both scientific and applied research communities. However, it is still a formidable challenge to build 3D microfluidic structures with arbitrary configurations using conventional planar lithographic fabrication methods. Here, we demonstrate rapid fabrication of high-aspect-ratio microfluidic channels with various 3D configurations in glass substrates by femtosecond laser direct writing. Based on this approach, we demonstrate a 3D passive microfluidic mixer and characterize its functionalities. This technology will enable rapid construction of complex 3D microfluidic devices for a wide array of lab-on-a-chip applications.

  11. Three-dimensional direct cell patterning in collagen hydrogels with near-infrared femtosecond laser

    NASA Astrophysics Data System (ADS)

    Hribar, Kolin C.; Meggs, Kyle; Liu, Justin; Zhu, Wei; Qu, Xin; Chen, Shaochen

    2015-11-01

    We report a methodology for three-dimensional (3D) cell patterning in a hydrogel in situ. Gold nanorods within a cell-encapsulating collagen hydrogel absorb a focused near-infrared femtosecond laser beam, locally denaturing the collagen and forming channels, into which cells migrate, proliferate, and align in 3D. Importantly, pattern resolution is tunable based on writing speed and laser power, and high cell viability (>90%) is achieved using higher writing speeds and lower laser intensities. Overall, this patterning technique presents a flexible direct-write method that is applicable in tissue engineering systems where 3D alignment is critical (such as vascular, neural, cardiac, and muscle tissue).

  12. Three-Dimensional Waveguide Interconnection in Planar Lightwave Circuits by Direct Writing with Femtosecond Laser

    NASA Astrophysics Data System (ADS)

    Nasu, Yusuke; Kohtoku, Masaki; Hibino, Yoshinori; Inoue, Yasuyuki

    2005-11-01

    The three-dimensional (3D) interconnection of waveguides in planar lightwave circuits (PLCs) is demonstrated. A femtosecond laser successfully interconnects the waveguides of PLCs with low loss by writing 3D waveguides in the PLCs. A directly written waveguide with a length of about 2000 μm crossed over another waveguide without any interaction. The excess losses at 1550 nm were 2.7 and 2.8 dB for the transverse electric (TE) and transverse magnetic (TM) modes, respectively.

  13. Direct writing of three-dimensional woodpile BaTiO3 structures

    NASA Astrophysics Data System (ADS)

    Li, Jijiao; Li, Bo; Wu, Hongya; Zhou, Ji

    2014-05-01

    Barium titanate (BaTiO3) woodpile structures with designed, three-dimensional (3D) geometry have been fabricated by direct-writing assembly techniques. Concentrated BaTiO3 inks with suitable rheological properties were prepared to enable the fabrication of the complex 3D structures. It was demonstrated that BaTiO3 inks with a total solids volume fraction of 0.41 are shear thinning and have a high storage modulus 1 × 105Pa with a yield stress of 300 Pa. Additionally, the woodpile lattice structures exhibited an excellent self-supporting feature.

  14. Generation of two-dimensional dust vortex flows in a direct current discharge plasma

    SciTech Connect

    Uchida, Giichiro; Iizuka, Satoru; Kamimura, Tetsuo; Sato, Noriyoshi

    2009-05-15

    The two-dimensional dust vortex flows are observed in a direct current discharge plasma near the edge of a metal plate which is situated in the dust-particle levitation region. Applying negative dc potential to the metal plate, dust particles are strongly accelerated toward the metal plate edge, and two symmetric dust vortex flows are generated on both sides of the metal plate. Numerical calculation including the effect of the ion drag force well demonstrates the dust vortex formation as in the experiment. A mechanism of the dust vortex generation could be explained by effect of an asymmetry of ion drag force near the metal plate.

  15. Three-dimensional direct cell patterning in collagen hydrogels with near-infrared femtosecond laser

    PubMed Central

    Hribar, Kolin C.; Meggs, Kyle; Liu, Justin; Zhu, Wei; Qu, Xin; Chen, Shaochen

    2015-01-01

    We report a methodology for three-dimensional (3D) cell patterning in a hydrogel in situ. Gold nanorods within a cell-encapsulating collagen hydrogel absorb a focused near-infrared femtosecond laser beam, locally denaturing the collagen and forming channels, into which cells migrate, proliferate, and align in 3D. Importantly, pattern resolution is tunable based on writing speed and laser power, and high cell viability (>90%) is achieved using higher writing speeds and lower laser intensities. Overall, this patterning technique presents a flexible direct-write method that is applicable in tissue engineering systems where 3D alignment is critical (such as vascular, neural, cardiac, and muscle tissue). PMID:26603915

  16. A direct procedure for interpolation on a structured curvilinear two-dimensional grid

    NASA Technical Reports Server (NTRS)

    Zingg, David W.; Yarrow, Maurice

    1989-01-01

    A direct procedure is presented for locally bicubic interpolation on a structured, curvilinear, two-dimensional grid. The physical (Cartesian) space is transformed to a computational space in which the grid is uniform and rectangular by a generalized curvilinear coordinate transformation. Required partial derivative information is obtained by finite differences in the computational space. The partial derivatives in physical space are determined by repeated application of the chain rule for partial differentiation. A bilinear transformation is used to analytically transform the individual quadrilateral cells in physical space into unit squares. The interpolation is performed within each unit square using a piecewise bicubic spline.

  17. Full three-dimensional direction-dependent x-ray scattering tomography

    NASA Astrophysics Data System (ADS)

    Zhu, Zheyuan; Pang, Shuo

    2017-03-01

    Small-angle X-ray scattering (SAXS) detects the angular-dependent, coherently scattered X-ray photons, which provide improved contrast among different types of tissues or materials in medical diagnosis and material characterizations. By combining SAXS with computed tomography (CT), coherent scattering computed tomography (CSCT) enables the detection of spatially-resolved, material-specific scattering profile inside an extended object. However, conventional CSCT lacks the ability to distinguish direction-dependent coherent scattering signal, because of its assumptions that the materials are amorphous with isotropic scattering profiles. To overcome this issue, we propose a new CSCT imaging strategy, which can resolve the three-dimensional scattering profile for each object pixel, by incorporating detector movement into each CSCT projection measurement. The full reconstruction of the three-dimensional momentum transfer profile of a two-dimensional object has been successfully demonstrated. Our setup only requires a table-top Xray source and a panel detector. The presented method demonstrates the potential to achieve low-cost, high-specificity X-ray tissue imaging and material characterization.

  18. Direct numerical simulation of steady state, three dimensional, laminar flow around a wall mounted cube

    NASA Astrophysics Data System (ADS)

    Liakos, Anastasios; Malamataris, Nikolaos

    2014-11-01

    The topology and evolution of flow around a surface mounted cubical object in three dimensional channel flow is examined for low to moderate Reynolds numbers. Direct numerical simulations were performed via a home made parallel finite element code. The computational domain has been designed according to actual laboratory experimental conditions. Analysis of the results is performed using the three dimensional theory of separation. Our findings indicate that a tornado-like vortex by the side of the cube is present for all Reynolds numbers for which flow was simulated. A horse-shoe vortex upstream from the cube was formed at Reynolds number approximately 1266. Pressure distributions are shown along with three dimensional images of the tornado-like vortex and the horseshoe vortex at selected Reynolds numbers. Finally, and in accordance to previous work, our results indicate that the upper limit for the Reynolds number for which steady state results are physically realizable is roughly 2000. Financial support of author NM from the Office of Naval Research Global (ONRG-VSP, N62909-13-1-V016) is acknowledged.

  19. The Dimensional Nature of Externalizing Behaviors in Adolescence: Evidence from a Direct Comparison of Categorical, Dimensional, and Hybrid Models

    ERIC Educational Resources Information Center

    Walton, Kate E.; Ormel, Johan; Krueger, Robert F.

    2011-01-01

    Researchers have recognized the importance of developing an accurate classification system for externalizing disorders, though much of this work has been framed by a priori preferences for categorical vs. dimensional constructs. Newer statistical technologies now allow categorical and dimensional models of psychopathology to be compared…

  20. The Dimensional Nature of Externalizing Behaviors in Adolescence: Evidence from a Direct Comparison of Categorical, Dimensional, and Hybrid Models

    ERIC Educational Resources Information Center

    Walton, Kate E.; Ormel, Johan; Krueger, Robert F.

    2011-01-01

    Researchers have recognized the importance of developing an accurate classification system for externalizing disorders, though much of this work has been framed by a priori preferences for categorical vs. dimensional constructs. Newer statistical technologies now allow categorical and dimensional models of psychopathology to be compared…

  1. Directional disorder of ciliary metachronal waves using two-dimensional correlation map.

    PubMed

    Yi, Won-Jin; Park, Kwang-Suk; Lee, Chul-Hee; Rhee, Chae-Seo; Nam, Sang-Won

    2002-03-01

    The interrelationship of cilia and the order of wave directions are important factors that determine the effectiveness of cilia to transport materials in mucociliary systems of the respiratory tract. The interrelationship of cilia and the directional disorder of ciliary metachronal wave were analyzed using digital microscopic images. The degree of synchronization between ciliary beats was determined by the correlation factor between two different spots. To find out the uniphase directions of beating cilia, principal axes of inertia were applied to the two-dimensional correlation map calculated from sequential ciliary images. The standard deviation of determined wave directions in a region of interest (ROI) was defined as a measure of metachronal wave disorder. The pooled mean of metachronal wave disorder was 23.4 +/- 8.79 degrees in ROIs of 8 microm x 8 microm and 25.4 +/- 6.46 degrees in 32 microm x 24 microm from the sphenoid sinus mucosa of five normal subjects. Our result shows that there is a considerable variation in metachronal wave directions of cilia beating on the epithelium.

  2. Three-dimensional multiscale modeling of dendritic spacing selection during Al-Si directional solidification

    DOE PAGES

    Tourret, Damien; Clarke, Amy J.; Imhoff, Seth D.; ...

    2015-05-27

    We present a three-dimensional extension of the multiscale dendritic needle network (DNN) model. This approach enables quantitative simulations of the unsteady dynamics of complex hierarchical networks in spatially extended dendritic arrays. We apply the model to directional solidification of Al-9.8 wt.%Si alloy and directly compare the model predictions with measurements from experiments with in situ x-ray imaging. The focus is on the dynamical selection of primary spacings over a range of growth velocities, and the influence of sample geometry on the selection of spacings. Simulation results show good agreement with experiments. The computationally efficient DNN model opens new avenues formore » investigating the dynamics of large dendritic arrays at scales relevant to solidification experiments and processes.« less

  3. Three-dimensional patterning and morphological control of porous nanomaterials by gray-scale direct imprinting

    PubMed Central

    Ryckman, Judson D.; Jiao, Yang; Weiss, Sharon M.

    2013-01-01

    We present a method for direct three-dimensional (3D) patterning of porous nanomaterials through the application of a premastered and reusable gray-scale stamp. Four classes of 3D nanostructures are demonstrated for the first time in porous media: gradient profiles, digital patterns, curves and lens shapes, and sharp features including v-grooves, nano-pits, and ‘cookie-cutter’ particles. Further, we demonstrate this technique enables morphological tuning and direct tailoring of nanomaterial properties, including porosity, average pore size, dielectric constant, and plasmonic response. This work opens a rapid and low-cost route for fabricating novel nanostructures and devices utilizing porous nanomaterials, with promising applications spanning diffractive and plasmonic sensing, holography, micro- and transformation optics, and drug delivery and imaging. PMID:23518798

  4. Multi-Dimensional Effective Field Theory Analysis for Direct Detection of Dark Matter

    NASA Astrophysics Data System (ADS)

    Rogers, Hannah; SuperCDMS Collaboration

    2016-03-01

    Experiments like the Cryogenic Dark Matter Search (CDMS) attempt to find dark matter (non-luminous matter that makes up approximately 80% of the matter in the universe) through direct detection of interactions between dark matter and a target material. The Effective Field Theory (EFT) approach increases the number of considered interactions between dark matter and the normal, target matter from two (spin independent and spin dependent interactions) to eleven operators with four possible interference terms. These additional operators allow for a more complete analysis of complimentary direct dark matter searches; however, the higher dimensional likelihoods necessary to span an increase in operators requires a clever computational tool such as MultiNest. I present here analyses of published and projected data from CDMS (Si and Ge targets) and LUX (liquid Xe target) assuming operator parameter spaces ranging from 3 - 5 dimensions and folding in information on energy-dependent backgrounds when possible.

  5. Three-dimensional multiscale modeling of dendritic spacing selection during Al-Si directional solidification

    SciTech Connect

    Tourret, Damien; Clarke, Amy J.; Imhoff, Seth D.; Gibbs, Paul J.; Gibbs, John W.; Karma, Alain

    2015-05-27

    We present a three-dimensional extension of the multiscale dendritic needle network (DNN) model. This approach enables quantitative simulations of the unsteady dynamics of complex hierarchical networks in spatially extended dendritic arrays. We apply the model to directional solidification of Al-9.8 wt.%Si alloy and directly compare the model predictions with measurements from experiments with in situ x-ray imaging. The focus is on the dynamical selection of primary spacings over a range of growth velocities, and the influence of sample geometry on the selection of spacings. Simulation results show good agreement with experiments. The computationally efficient DNN model opens new avenues for investigating the dynamics of large dendritic arrays at scales relevant to solidification experiments and processes.

  6. Vorticity statistics in the direct cascade of two-dimensional turbulence.

    PubMed

    Falkovich, Gregory; Lebedev, Vladimir

    2011-04-01

    For the direct cascade of steady two-dimensional (2D) Navier-Stokes turbulence, we derive analytically the probability of strong vorticity fluctuations. When ϖ is the vorticity coarse-grained over a scale R, the probability density function (PDF), P(ϖ), has a universal asymptotic behavior lnP~-ϖ/ϖ(rms) at ϖ≫ϖ(rms)=[Hln(L/R)](1/3), where H is the enstrophy flux and L is the pumping length. Therefore, the PDF has exponential tails and is self-similar, that is, it can be presented as a function of a single argument, ϖ/ϖ(rms), in distinction from other known direct cascades.

  7. Two-Dimensional Direct Numerical Simulations of Jet Spray under High Pressure

    SciTech Connect

    Nakamura, Mariko

    2008-09-01

    Two-dimensional direct numerical simulations are applied to a planar jet spray flow in order to investigate the effects of pressure on droplet behavior. For the gaseous phase, Eulerian mass, momentum, energy, and species conservation equations are solved. For the disperse phase, the fuel droplets are tracked individually in a Lagrangian manner. Concerning the vaporization of droplets, a nonequilibrium Langmuir-Knudsen evaporation model is adopted. The results show that the droplet mean diameter increases as the distance from the nozzle increases; however, because evaporation does not progress rapidly at normal temperature, the change in the droplet mean diameter with the increase in the distance from the nozzle is small for each pressure condition. The droplet mean velocity decreases as the droplets move downstream for each pressure condition, and the gradient of the droplet mean velocity toward the axial direction differs with each pressure condition.

  8. Solution of the exact equations for three-dimensional atmospheric entry using directly matched asymptotic expansions

    NASA Technical Reports Server (NTRS)

    Busemann, A.; Vinh, N. X.; Culp, R. D.

    1976-01-01

    The problem of determining the trajectories, partially or wholly contained in the atmosphere of a spherical, nonrotating planet, is considered. The exact equations of motion for three-dimensional, aerodynamically affected flight are derived. Modified Chapman variables are introduced and the equations are transformed into a set suitable for analytic integration using asymptotic expansions. The trajectory is solved in two regions: the outer region, where the force may be considered a gravitational field with aerodynamic perturbations, and the inner region, where the force is predominantly aerodynamic, with gravity as a perturbation. The two solutions are matched directly. A composite solution, valid everywhere, is constructed by additive composition. This approach of directly matched asymptotic expansions applied to the exact equations of motion couched in terms of modified Chapman variables yields an analytical solution which should prove to be a powerful tool for aerodynamic orbit calculations.

  9. Two-dimensional SiP: an unexplored direct band-gap semiconductor

    NASA Astrophysics Data System (ADS)

    Zhang, Shengli; Guo, Shiying; Huang, Yaxin; Zhu, Zhen; Cai, Bo; Xie, Meiqiu; Zhou, Wenhan; Zeng, Haibo

    2017-03-01

    Inspired by successful synthesis of layered SiP single crystals in experiments, we explore their structures, electronic properties, and stability using first-principles calculations. The interlayer interaction in layered SiP crystal is weak, thus mechanical exfoliation is viable. We find that SiP undergoes a transition from an indirect band gap to a direct band gap of 2.59 eV when thinned from bulk to a monolayer. Our calculations also show that SiP monolayers are both dynamically and thermodynamically stable even at elevated temperatures. Monolayer SiP, with simultaneously high stability and a large direct band gap, is a promising candidate for two-dimensional blue light emitting diodes.

  10. On-chip three-dimensional high-Q microcavities fabricated by femtosecond laser direct writing.

    PubMed

    Lin, Jintian; Yu, Shangjie; Ma, Yaoguang; Fang, Wei; He, Fei; Qiao, Lingling; Tong, Limin; Cheng, Ya; Xu, Zhizhan

    2012-04-23

    We report on the fabrication of three-dimensional (3D) high-Q whispering gallery microcavities on a fused silica chip by femtosecond laser microfabriction, enabled by the 3D nature of femtosecond laser direct writing. The processing mainly consists of formation of freestanding microdisks by femtosecond laser direct writing and subsequent wet chemical etching. CO(2) laser annealing is followed to smooth the microcavity surface. Microcavities with arbitrary tilting angle, lateral and vertical positioning are demonstrated, and the quality (Q)-factor of a typical microcavity is measured to be up to 1.07 × 10(6), which is currently limited by the low spatial resolution of the motion stage used during the laser patterning and can be improved with motion stages of higher resolutions.

  11. Controlling Directionality and Dimensionality of Radiation by Perturbing Separable Bound States in the Continuum

    PubMed Central

    Rivera, Nicholas; Hsu, Chia Wei; Zhen, Bo; Buljan, Hrvoje; Joannopoulos, John D.; Soljačić, Marin

    2016-01-01

    A bound state in the continuum (BIC) is an unusual localized state that is embedded in a continuum of extended states. Here, we present the general condition for BICs to arise from wave equation separability. Then we show that by exploiting perturbations of certain symmetry such BICs can be turned into resonances that radiate with a tailorable directionality and dimensionality. Using this general framework, we construct new examples of separable BICs and resonances that can exist in optical potentials for ultracold atoms, photonic systems, and systems described by tight binding. Such resonances with easily reconfigurable radiation allow for applications such as the storage and release of waves at a controllable rate and direction, as well systems that switch between different dimensions of confinement. PMID:27641540

  12. Direct Three-Dimensional Image Reconstruction and Electronic System of a Spherical High-Resolution PET

    NASA Astrophysics Data System (ADS)

    Wu, Xuekui Ed.

    In the past decade tremendous efforts have been made to improve the performance of Positron Emission Tomography (PET). To increase photon capture efficiency and thus the intrinsic sensitivity, oblique or cross-plane coincidences are now detected and recorded with, for example, a spherical PET (S-PET) design. This requires direct three-dimensional volume image reconstruction and a high-performance electronic system. There are two types of algorithms for achieving direct three-dimensional volume image reconstruction, namely, parallel beam reconstruction and cone beam reconstruction. The advantages of the cone beam reconstruction algorithm are that it reduces the amount of data rebinning necessary and it improves spatial resolution by virtue of its geometrical structure. In this study, we propose a new analytical three-dimensional cone beam reconstruction algorithm for truncated spherical detection geometry. The basic idea of the proposed algorithm is the formation of a spatially invariant 3D blurred backprojected volumetric image by the use of the weighted backprojection of cone beam projection data and subsequent 3D filtering using an acceptance angle dependent rho filter. This approach is extended to other truncated 3D PET geometries such as truncated cylindrical geometry and Fresnel aperture-SPET (F-SPET) geometry. The proposed algorithm is derived analytically and is computationally efficient. Performance of the algorithm is evaluated by the reconstruction of 3D volumetric images from simulated data from arbitrarily truncated spherical detector geometries. In this study, we also review parallel and cone beam 3D algorithms proposed by others. As part of the high-resolution and high-sensitivity spherical F-SPET project, a partial one modular layer prototype system has been completed. The electronic designs, efficient detector calibration schemes and final resolution performance is reported in this study.

  13. Directly measuring of thermal pulse transfer in one-dimensional highly aligned carbon nanotubes

    PubMed Central

    Zhang, Guang; Liu, Changhong; Fan, Shoushan

    2013-01-01

    Using a simple and precise instrument system, we directly measured the thermo-physical properties of one-dimensional highly aligned carbon nanotubes (CNTs). A kind of CNT-based macroscopic materials named super aligned carbon nanotube (SACNT) buckypapers was measured in our experiment. We defined a new one-dimensional parameter, the “thermal transfer speed” to characterize the thermal damping mechanisms in the SACNT buckypapers. Our results indicated that the SACNT buckypapers with different densities have obviously different thermal transfer speeds. Furthermore, we found that the thermal transfer speed of high-density SACNT buckypapers may have an obvious damping factor along the CNTs aligned direction. The anisotropic thermal diffusivities of SACNT buckypapers could be calculated by the thermal transfer speeds. The thermal diffusivities obviously increase as the buckypaper-density increases. For parallel SACNT buckypapers, the thermal diffusivity could be as high as 562.2 ± 55.4 mm2/s. The thermal conductivities of these SACNT buckypapers were also calculated by the equation k = Cpαρ. PMID:23989589

  14. Bandgaps and directional properties of two-dimensional square beam-like zigzag lattices

    SciTech Connect

    Wang, Yan-Feng; Wang, Yue-Sheng; Zhang, Chuanzeng

    2014-12-15

    In this paper we propose four kinds of two-dimensional square beam-like zigzag lattice structures and study their bandgaps and directional propagation of elastic waves. The band structures are calculated by using the finite element method. Both the in-plane and out-of-plane waves are investigated simultaneously via the three-dimensional Euler beam elements. The mechanism of the bandgap generation is analyzed by studying the vibration modes at the bandgap edges. The effects of the geometry parameters of the xy- and z-zigzag lattices on the bandgaps are investigated and discussed. Multiple complete bandgaps are found owing to the separation of the degeneracy by introducing bending arms. The bandgaps are sensitive to the geometry parameters of the periodic systems. The deformed displacement fields of the harmonic responses of a finite lattice structure subjected to harmonic loads at different positions are illustrated to show the directional wave propagation. An extension of the proposed concept to the hexagonal lattices is also presented. The research work in this paper is relevant to the practical design of cellular structures with enhanced vibro-acoustics performance.

  15. Direct Imaging of a Two-Dimensional Silica Glass on Graphene

    NASA Astrophysics Data System (ADS)

    Huang, P. Y.; Kurasch, S.; Srivastava, A.; Skakalova, V.; Kotakoski, J.; Krasheninnikov, A. V.; Hovden, R. M.; Mao, Q.; Meyer, J. C.; Smet, J.; Muller, D. A.; Kaiser, U.

    2012-02-01

    Large-area graphene substrates [1] are a promising lab bench for synthesizing and characterizing novel low-dimensional materials such as two-dimensional (2D) glasses. Unlike 2D crystals such as graphene, 2D glasses are almost entirely unexplored--yet they have enormous applicability for understanding amorphous structures, which are difficult to probe in 3D. We report direct observations of the structure of an amorphous 2D silica supported on graphene. To our knowledge, these results represent the first discovery of an extended 2D glass. The 2D glass enables aberration-corrected scanning transmission electron microscopy and spectroscopy, producing the first atomically-resolved experimental images of a glass. The images strikingly resemble Zachariasen's seminal 1932 cartoons of a 2D continuous random network glass [2] and allow direct structural analyses not possible in 3D glassy materials. DFT calculations indicate that van der Waals interactions with graphene energetically favor the 2D structure over bulk SiO2, suggesting that graphene can be instrumental in stabilizing new 2D materials. [1] J. C. Meyer et al., Nature 454, 319--322 (2008). [2] W. H. Zachariasen, J. Am. Chem. Soc. 54, 3841--3851 (1932).

  16. Discontinuous Transition from Direct to Inverse Cascade in Three-Dimensional Turbulence.

    PubMed

    Sahoo, Ganapati; Alexakis, Alexandros; Biferale, Luca

    2017-04-21

    Inviscid invariants of flow equations are crucial in determining the direction of the turbulent energy cascade. In this work we investigate a variant of the three-dimensional Navier-Stokes equations that shares exactly the same ideal invariants (energy and helicity) and the same symmetries (under rotations, reflections, and scale transforms) as the original equations. It is demonstrated that the examined system displays a change in the direction of the energy cascade when varying the value of a free parameter which controls the relative weights of the triadic interactions between different helical Fourier modes. The transition from a forward to inverse cascade is shown to occur at a critical point in a discontinuous manner with diverging fluctuations close to criticality. Our work thus supports the observation that purely isotropic and three-dimensional flow configurations can support inverse energy transfer when interactions are altered and that inside all turbulent flows there is a competition among forward and backward transfer mechanisms which might lead to multiple energy-containing turbulent states.

  17. Omnidirectional multiview three-dimensional display based on direction-selective light-emitting diode array

    NASA Astrophysics Data System (ADS)

    Yan, Caijie; Liu, Xu; Liu, Di; Xie, Jing; Xia, Xin Xing; Li, Haifeng

    2011-03-01

    A volumetric display system based on a rotating light-emitting diode (LED) array panel can realize a three-dimensional (3-D) display truthfully in the space, but the drawback is missing the occlusion of a 3-D image. We propose an omnidirectional 3-D display with correct occlusion based on a direction-selective LED array panel, which is realized by setting a direction-convergent diaphragm array in front of the LED array. Every diaphragm restricts a light-emitting characteristic of every LED. By using direction-convergent diaphragm array, the observer around the display system can only see one image displayed by the LED array at the corresponding position. With the high-speed rotation of the LED panel, a series of views of a 3-D scene are displayed every angle patch in one circle. We set up an acquisition system to record 180 views of the 3-D scene with a rotating camera along a circle, and then the 180 images are displayed sequentially on the rotating direction-selective LED array to get a 360 deg 3-D display. This 3-D display technology has two main advantages: easy to get viewer-position-dependent correct occlusion and simplify the 3-D data preprocessing process which is helpful to real-time 3-D display.

  18. Direct Writing of Three-Dimensional Macroporous Photonic Crystals on Pressure-Responsive Shape Memory Polymers.

    PubMed

    Fang, Yin; Ni, Yongliang; Leo, Sin-Yen; Wang, Bingchen; Basile, Vito; Taylor, Curtis; Jiang, Peng

    2015-10-28

    Here we report a single-step direct writing technology for making three-dimensional (3D) macroporous photonic crystal patterns on a new type of pressure-responsive shape memory polymer (SMP). This approach integrates two disparate fields that do not typically intersect: the well-established templating nanofabrication and shape memory materials. Periodic arrays of polymer macropores templated from self-assembled colloidal crystals are squeezed into disordered arrays in an unusual shape memory "cold" programming process. The recovery of the original macroporous photonic crystal lattices can be triggered by direct writing at ambient conditions using both macroscopic and nanoscopic tools, like a pencil or a nanoindenter. Interestingly, this shape memory disorder-order transition is reversible and the photonic crystal patterns can be erased and regenerated hundreds of times, promising the making of reconfigurable/rewritable nanooptical devices. Quantitative insights into the shape memory recovery of collapsed macropores induced by the lateral shear stresses in direct writing are gained through fundamental investigations on important process parameters, including the tip material, the critical pressure and writing speed for triggering the recovery of the deformed macropores, and the minimal feature size that can be directly written on the SMP membranes. Besides straightforward applications in photonic crystal devices, these smart mechanochromic SMPs that are sensitive to various mechanical stresses could render important technological applications ranging from chromogenic stress and impact sensors to rewritable high-density optical data storage media.

  19. Some biochemical properties of an acyclic oligonucleotide analogue. A plausible ancestor of the DNA?

    NASA Astrophysics Data System (ADS)

    Merle, Liliane; Spach, Gérard; Merle, Yves; Sági, János; Szemzö, Attila

    1993-04-01

    As acyclic oligonucleotides have been suggested as a primitive model of DNA or RNA in prebiotic times, we compared some biochemical properties of these analogues to that of natural ones. Firstly, an acyclic analogue of deoxyribonucleoside triphosphates was tested as a potential substrate of enzymes intervening in nucleic acids synthesis. GlyTTP, a dTTP analogue with a missing 2'-methylene group is notaccepted as a substrate by either DNA polymerase or deoxynucleotidyl terminal transferase (TdT). Secondly, themodified dodecathymidylate (GlyT)12, the racemic acyclic sugar analogue of (dT)12, proved to be anefficient primer for DNA polymerase and TdT, though the associative properties of (GlyT)12 are very weak as shown by UV spectroscopy in phosphate buffer without magnesium chloride. But (GlyT)12 has the advantage to be 500-times more stable against hydrolysis by snake venom phosphodiesterase than the corresponding oligothymidylate.

  20. Acyclic cucurbit[n]uril molecular containers enhance the solubility and bioactivity of poorly soluble pharmaceuticals

    NASA Astrophysics Data System (ADS)

    Ma, Da; Hettiarachchi, Gaya; Nguyen, Duc; Zhang, Ben; Wittenberg, James B.; Zavalij, Peter Y.; Briken, Volker; Isaacs, Lyle

    2012-06-01

    The solubility characteristics of 40-70% of new drug candidates are so poor that they cannot be formulated on their own, so new methods for increasing drug solubility are highly prized. Here, we describe a new class of general-purpose solubilizing agents—acyclic cucurbituril-type containers—which increase the solubility of ten insoluble drugs by a factor of between 23 and 2,750 by forming container-drug complexes. The containers exhibit low in vitro toxicity in human liver, kidney and monocyte cell lines, and outbred Swiss Webster mice tolerate high doses of the container without sickness or weight loss. Paclitaxel solubilized by the acyclic cucurbituril-type containers kills cervical and ovarian cancer cells more efficiently than paclitaxel alone. The acyclic cucurbituril-type containers preferentially bind cationic and aromatic drugs, but also solubilize neutral drugs such as paclitaxel, and represent an attractive extension of cyclodextrin-based technology for drug solubilization and delivery.

  1. Acyclic monoterpenes in tree essential oils as a shrinking agent for waste-expanded polystyrene.

    PubMed

    Shimotori, Yasutaka; Hattori, Kazuyuki; Aoyama, Masakazu; Miyakoshi, Tetsuo

    2011-01-01

    We examined the dissolution of polystyrene (PS) into acyclic monoterpenes present in tree essential oils, to develop an environmentally friendly shrinking agent for waste-expanded polystyrene (EPS). The dissolving powers of geranyl acetate, geranylacetone, and geranyl formate [221.8-241.2 g PS (100 g solvent)(-1)] compared favorably with that of (R)-limonene [181.7 g PS (100 g solvent)(-1)]. Their favorable dissolving powers for PS can be explained by their flexible linear structures, which may be more accessible to the inside of bulk PS compared with cyclic monoterpenes. These acyclic monoterpenes and PS were recovered almost quantitatively by simple steam distillation of the PS solution.

  2. Synthesis of antisense oligonucleotides containing acyclic alkynyl nucleoside analogs and their biophysical and biological properties.

    PubMed

    Ogata, Aya; Maeda, Yusuke; Ueno, Yoshihito

    2017-04-01

    The synthesis of oligonucleotide (ON) analogs, which can be used as antisense molecules, has recently gained much attention. Here, we report the synthesis and properties of an ON analog containing acyclic thymidine and cytidine analogs with a 4-pentyl-1,2-diol instead of the d-ribofuranose moiety. The incorporation of these analogs into the ON improved its nuclease resistance to 3'-exonucleases. Furthermore, it was found that the incorporation of the acyclic thymidine analog into a DNA/RNA duplex accelerates the RNA cleavage of a DNA/RNA duplex by Escherichia coli RNase H.

  3. Synthesis and antiviral activities of hexadecyloxypropyl prodrugs of acyclic nucleoside phosphonates containing guanine or hypoxanthine and a (S)-HPMP or PEE acyclic moiety.

    PubMed

    Tichý, Tomáš; Andrei, Graciela; Snoeck, Robert; Balzarini, Jan; Dračínský, Martin; Krečmerová, Marcela

    2012-09-01

    Hexadecyloxypropyl esters of acyclic nucleoside phosphonates containing guanine (G) or hypoxanthine (Hx) and a (S)-[3-hydroxy-2-(phosphonomethoxy)propyl] [(S)-HPMP] or 2-(2-phosphonoethoxy)ethyl (PEE) acyclic moiety have been prepared. The activity of the prodrugs was evaluated in vitro against different virus families. Whereas ester derivatives of PEEHx and (S)-HPMPHx were antivirally inactive, monoesters of PEEG, and mono- and diesters of (S)-HPMPG showed pronounced antiviral activity against vaccinia virus and/or herpesviruses. Monoesters of (S)-HPMPG emerged as the most potent and selective derivatives against these DNA viruses. None of the compounds were inhibitory against RNA viruses and retroviruses. Crown Copyright © 2012. Published by Elsevier Masson SAS. All rights reserved.

  4. Direct-write Bioprinting Three-Dimensional Biohybrid Systems for Future Regenerative Therapies

    PubMed Central

    Chang, Carlos C.; Boland, Eugene D.; Williams, Stuart K.; Hoying, James B.

    2013-01-01

    Regenerative medicine seeks to repair or replace dysfunctional tissues with engineered biological or biohybrid systems. Current clinical regenerative models utilize simple uniform tissue constructs formed with cells cultured onto biocompatible scaffolds. Future regenerative therapies will require the fabrication of complex three-dimensional constructs containing multiple cell types and extracellular matrices. We believe bioprinting technologies will provide a key role in the design and construction of future engineered tissues for cell-based and regenerative therapies. This review describes the current state-of-the-art bioprinting technologies, focusing on direct-write bioprinting. We describe a number of process and device considerations for successful bioprinting of composite biohybrid constructs. In addition, we have provided baseline direct-write printing parameters for a hydrogel system (Pluronic F127) often used in cardiovascular applications. Direct-write dispensed lines (gels with viscosities ranging from 30 mPa*s to greater than 600×106 mPa*s) were measured following mechanical and pneumatic printing via three commercially available needle sizes (20ga, 25ga, and 30ga). Example patterns containing microvascular cells and isolated microvessel fragments were also bioprinted into composite 3D structures. Cells and vessel fragments remained viable and maintained in vitro behavior after incorporation into biohybrid structures. Direct-write bioprinting of biologicals provides a unique method to design and fabricate complex, multi-component 3D structures for experimental use. We hope our design insights and baseline parameter descriptions of direct-write bioprinting will provide a useful foundation for colleagues to incorporate this 3D fabrication method into future regenerative therapies. PMID:21504055

  5. Thin catheter bending in the direction perpendicular to ultrasound propagation using two-dimensional array transducer

    NASA Astrophysics Data System (ADS)

    Suzuki, Toshiya; Mochizuki, Takashi; Ushimizu, Hidetaka; Miyazawa, Shinya; Tsurui, Nobuhiro; Masuda, Kohji

    2017-07-01

    Although we have already experimented on the bending of a thin catheter with acoustic radiation force using a single transducer, it is necessary to develop a method of bending a catheter in an arbitrary direction because the installation position of ultrasound transducers on a body surface is limited for application to various shapes of in vivo blood vessels. Therefore, we examined the bending of a thin catheter in the direction perpendicular to ultrasound propagation using a two-dimensional array transducer (1 MHz), which realizes not only the temporospatial design but also the dynamic variation of acoustic fields. Forming two focal points with opposite phases, where the amplitudes of the two points instantaneously have the positive and negative relationship, we confirmed the bending of a thin catheter in the direction perpendicular to ultrasound propagation. We used a thin catheter (diameter, 200 µm length, 50 mm) to obtain the maximum displacement of 220 µm, where the displacement was proportional to the square of the maximum sound pressure and the duty ratio. From these results, the acoustic energy densities observed in front of and behind the catheter are dominant for the bending of the thin catheter independent of ultrasound propagation. We also found that the distance between two focal points may improve the bending performance without requiring a precise position setting.

  6. Three dimensional graphene transistor for ultra-sensitive pH sensing directly in biological media.

    PubMed

    Ameri, Shideh Kabiri; Singh, Pramod K; Sonkusale, Sameer R

    2016-08-31

    In this work, pH sensing directly in biological media using three dimensional liquid gated graphene transistors is presented. The sensor is made of suspended network of graphene coated all around with thin layer of hafnium oxide (HfO2), showing high sensitivity and sensing beyond the Debye-screening limit. The performance of the pH sensor is validated by measuring the pH of isotonic buffered, Dulbecco's phosphate buffered saline (DPBS) solution, and of blood serum derived from Sprague-Dawley rat. The pH sensor shows high sensitivity of 71 ± 7 mV/pH even in high ionic strength media with molarities as high as 289 ± 1 mM. High sensitivity of this device is owing to suspension of three dimensional graphene in electrolyte which provides all around liquid gating of graphene, leading to higher electrostatic coupling efficiency of electrolyte to the channel and higher gating control of transistor channel by ions in the electrolyte. Coating graphene with hafnium oxide film (HfO2) provides binding sites for hydrogen ions, which results in higher sensitivity and sensing beyond the Debye-screening limit. The 3D graphene transistor offers the possibility of real-time pH measurement in biological media without the need for desaltation or sample preparation.

  7. Direct evidence for three-dimensional off-axis trapping with single Laguerre-Gaussian beam

    PubMed Central

    Otsu, T.; Ando, T.; Takiguchi, Y.; Ohtake, Y.; Toyoda, H.; Itoh, H.

    2014-01-01

    Optical tweezers are often applied to control the dynamics of objects by scanning light. However, there is a limitation that objects fail to track the scan when the drag exceeds the trapping force. In contrast, Laguerre-Gaussian (LG) beams can directly control the torque on objects and provide a typical model for nonequilibrium systems such as Brownian motion under external fields. Although stable “mid-water” trapping is essential for removing extrinsic hydrodynamic effects in such studies, three-dimensional trapping by LG beams has not yet been clearly established. Here we report the three-dimensional off-axis trapping of dielectric spheres using high-quality LG beams generated by a special holographic method. The trapping position was estimated as ~ half the wavelength behind the beam waist. These results establish the scientific groundwork of LG trapping and the technical basis of calibrating optical torque to provide powerful tools for studying energy-conversion mechanisms and the nonequilibrium nature of biological molecules under torque. PMID:24694781

  8. Direct evidence for three-dimensional off-axis trapping with single Laguerre-Gaussian beam

    NASA Astrophysics Data System (ADS)

    Otsu, T.; Ando, T.; Takiguchi, Y.; Ohtake, Y.; Toyoda, H.; Itoh, H.

    2014-04-01

    Optical tweezers are often applied to control the dynamics of objects by scanning light. However, there is a limitation that objects fail to track the scan when the drag exceeds the trapping force. In contrast, Laguerre-Gaussian (LG) beams can directly control the torque on objects and provide a typical model for nonequilibrium systems such as Brownian motion under external fields. Although stable ``mid-water'' trapping is essential for removing extrinsic hydrodynamic effects in such studies, three-dimensional trapping by LG beams has not yet been clearly established. Here we report the three-dimensional off-axis trapping of dielectric spheres using high-quality LG beams generated by a special holographic method. The trapping position was estimated as ~ half the wavelength behind the beam waist. These results establish the scientific groundwork of LG trapping and the technical basis of calibrating optical torque to provide powerful tools for studying energy-conversion mechanisms and the nonequilibrium nature of biological molecules under torque.

  9. Direct imaging of a two-dimensional silica glass on graphene.

    PubMed

    Huang, Pinshane Y; Kurasch, Simon; Srivastava, Anchal; Skakalova, Viera; Kotakoski, Jani; Krasheninnikov, Arkady V; Hovden, Robert; Mao, Qingyun; Meyer, Jannik C; Smet, Jurgen; Muller, David A; Kaiser, Ute

    2012-02-08

    Large-area graphene substrates provide a promising lab bench for synthesizing, manipulating, and characterizing low-dimensional materials, opening the door to high-resolution analyses of novel structures, such as two-dimensional (2D) glasses, that cannot be exfoliated and may not occur naturally. Here, we report the accidental discovery of a 2D silica glass supported on graphene. The 2D nature of this material enables the first atomic resolution transmission electron microscopy of a glass, producing images that strikingly resemble Zachariasen's original 1932 cartoon models of 2D continuous random network glasses. Atomic-resolution electron spectroscopy identifies the glass as SiO(2) formed from a bilayer of (SiO(4))(2-) tetrahedra and without detectable covalent bonding to the graphene. From these images, we directly obtain ring statistics and pair distribution functions that span short-, medium-, and long-range order. Ab initio calculations indicate that van der Waals interactions with graphene energetically stabilizes the 2D structure with respect to bulk SiO(2). These results demonstrate a new class of 2D glasses that can be applied in layered graphene devices and studied at the atomic scale.

  10. Preparation of reactive three-dimensional microstructures via direct laser writing and thiol-ene chemistry.

    PubMed

    Quick, Alexander S; Fischer, Joachim; Richter, Benjamin; Pauloehrl, Thomas; Trouillet, Vanessa; Wegener, Martin; Barner-Kowollik, Christopher

    2013-02-25

    Three-dimensional microstructures are fabricated employing the direct laser writing process and radical thiol-ene polymerization. The resin system consists of a two-photon photoinitiator and multifunctional thiols and olefins. Woodpile photonic crystals with 22 layers and a rod distance of 2 μm are fabricated. The structures are characterized via scanning electron microscopy and focused ion beam milling. The thiol-ene polymerization during fabrication is verified via infrared spectroscopy. The structures are grafted in a subsequent thiol-Michael addition reaction with different functional maleimides. The success of the grafting reaction is evaluated via laser scanning microscopy and X-ray photoelectron spectroscopy. The grafting density is calculated to be close to 200 molecules μm(-2) .

  11. Three-dimensional Dendritic Needle Network model with application to Al-Cu directional solidification experiments

    DOE PAGES

    Tourret, D.; Karma, A.; Clarke, A. J.; ...

    2015-06-11

    We present a three-dimensional (3D) extension of a previously proposed multi-scale Dendritic Needle Network (DNN) approach for the growth of complex dendritic microstructures. Using a new formulation of the DNN dynamics equations for dendritic paraboloid-branches of a given thickness, one can directly extend the DNN approach to 3D modeling. We validate this new formulation against known scaling laws and analytical solutions that describe the early transient and steady-state growth regimes, respectively. Finally, we compare the predictions of the model to in situ X-ray imaging of Al-Cu alloy solidification experiments. The comparison shows a very good quantitative agreement between 3D simulationsmore » and thin sample experiments. It also highlights the importance of full 3D modeling to accurately predict the primary dendrite arm spacing that is significantly over-estimated by 2D simulations.« less

  12. Direct exfoliation and dispersion of two-dimensional materials in pure water via temperature control

    PubMed Central

    Kim, Jinseon; Kwon, Sanghyuk; Cho, Dae-Hyun; Kang, Byunggil; Kwon, Hyukjoon; Kim, Youngchan; Park, Sung O.; Jung, Gwan Yeong; Shin, Eunhye; Kim, Wan-Gu; Lee, Hyungdong; Ryu, Gyeong Hee; Choi, Minseok; Kim, Tae Hyeong; Oh, Junghoon; Park, Sungjin; Kwak, Sang Kyu; Yoon, Suk Wang; Byun, Doyoung; Lee, Zonghoon; Lee, Changgu

    2015-01-01

    The high-volume synthesis of two-dimensional (2D) materials in the form of platelets is desirable for various applications. While water is considered an ideal dispersion medium, due to its abundance and low cost, the hydrophobicity of platelet surfaces has prohibited its widespread use. Here we exfoliate 2D materials directly in pure water without using any chemicals or surfactants. In order to exfoliate and disperse the materials in water, we elevate the temperature of the sonication bath, and introduce energy via the dissipation of sonic waves. Storage stability greater than one month is achieved through the maintenance of high temperatures, and through atomic and molecular level simulations, we further discover that good solubility in water is maintained due to the presence of platelet surface charges as a result of edge functionalization or intrinsic polarity. Finally, we demonstrate inkjet printing on hard and flexible substrates as a potential application of water-dispersed 2D materials. PMID:26369895

  13. Extracting quantitative three-dimensional unsteady flow direction from tuft flow visualizations

    NASA Astrophysics Data System (ADS)

    Omata, Noriyasu; Shirayama, Susumu

    2017-10-01

    We focus on the qualitative but widely used method of tuft flow visualization, and propose a method for quantifying it using information technology. By applying stereo image processing and computer vision, the three-dimensional (3D) flow direction in a real environment can be obtained quantitatively. In addition, we show that the flow can be divided temporally by performing appropriate machine learning on the data. Acquisition of flow information in real environments is important for design development, but it is generally considered difficult to apply simulations or quantitative experiments to such environments. Hence, qualitative methods including the tuft method are still in use today. Although attempts have been made previously to quantify such methods, it has not been possible to acquire 3D information. Furthermore, even if quantitative data could be acquired, analysis was often performed empirically or qualitatively. In contrast, we show that our method can acquire 3D information and analyze the measured data quantitatively.

  14. Piezoelectric two-dimensional nanosheets/anionic layer heterojunction for efficient direct current power generation

    PubMed Central

    Kim, Kwon-Ho; Kumar, Brijesh; Lee, Keun Young; Park, Hyun-Kyu; Lee, Ju-Hyuck; Lee, Hyun Hwi; Jun, Hoin; Lee, Dongyun; Kim, Sang-Woo

    2013-01-01

    Direct current (DC) piezoelectric power generator is promising for the miniaturization of a power package and self-powering of nanorobots and body-implanted devices. Hence, we report the first use of two-dimensional (2D) zinc oxide (ZnO) nanostructure and an anionic nanoclay layer to generate piezoelectric DC output power. The device, made from 2D nanosheets and an anionic nanoclay layer heterojunction, has potential to be the smallest size power package, and could be used to charge wireless nano/micro scale systems without the use of rectifier circuits to convert alternating current into DC to store the generated power. The combined effect of buckling behaviour of the ZnO nanosheets, a self-formed anionic nanoclay layer, and coupled semiconducting and piezoelectric properties of ZnO nanosheets contributes to efficient DC power generation. The networked ZnO nanosheets proved to be structurally stable under huge external mechanical loads. PMID:23774788

  15. Piezoelectric two-dimensional nanosheets/anionic layer heterojunction for efficient direct current power generation.

    PubMed

    Kim, Kwon-Ho; Kumar, Brijesh; Lee, Keun Young; Park, Hyun-Kyu; Lee, Ju-Hyuck; Lee, Hyun Hwi; Jun, Hoin; Lee, Dongyun; Kim, Sang-Woo

    2013-01-01

    Direct current (DC) piezoelectric power generator is promising for the miniaturization of a power package and self-powering of nanorobots and body-implanted devices. Hence, we report the first use of two-dimensional (2D) zinc oxide (ZnO) nanostructure and an anionic nanoclay layer to generate piezoelectric DC output power. The device, made from 2D nanosheets and an anionic nanoclay layer heterojunction, has potential to be the smallest size power package, and could be used to charge wireless nano/micro scale systems without the use of rectifier circuits to convert alternating current into DC to store the generated power. The combined effect of buckling behaviour of the ZnO nanosheets, a self-formed anionic nanoclay layer, and coupled semiconducting and piezoelectric properties of ZnO nanosheets contributes to efficient DC power generation. The networked ZnO nanosheets proved to be structurally stable under huge external mechanical loads.

  16. Piezoelectric two-dimensional nanosheets/anionic layer heterojunction for efficient direct current power generation

    NASA Astrophysics Data System (ADS)

    Kim, Kwon-Ho; Kumar, Brijesh; Lee, Keun Young; Park, Hyun-Kyu; Lee, Ju-Hyuck; Lee, Hyun Hwi; Jun, Hoin; Lee, Dongyun; Kim, Sang-Woo

    2013-06-01

    Direct current (DC) piezoelectric power generator is promising for the miniaturization of a power package and self-powering of nanorobots and body-implanted devices. Hence, we report the first use of two-dimensional (2D) zinc oxide (ZnO) nanostructure and an anionic nanoclay layer to generate piezoelectric DC output power. The device, made from 2D nanosheets and an anionic nanoclay layer heterojunction, has potential to be the smallest size power package, and could be used to charge wireless nano/micro scale systems without the use of rectifier circuits to convert alternating current into DC to store the generated power. The combined effect of buckling behaviour of the ZnO nanosheets, a self-formed anionic nanoclay layer, and coupled semiconducting and piezoelectric properties of ZnO nanosheets contributes to efficient DC power generation. The networked ZnO nanosheets proved to be structurally stable under huge external mechanical loads.

  17. Three-dimensional Dendritic Needle Network model with application to Al-Cu directional solidification experiments

    SciTech Connect

    Tourret, D.; Karma, A.; Clarke, A. J.; Gibbs, P. J.; Imhoff, S. D.

    2015-06-11

    We present a three-dimensional (3D) extension of a previously proposed multi-scale Dendritic Needle Network (DNN) approach for the growth of complex dendritic microstructures. Using a new formulation of the DNN dynamics equations for dendritic paraboloid-branches of a given thickness, one can directly extend the DNN approach to 3D modeling. We validate this new formulation against known scaling laws and analytical solutions that describe the early transient and steady-state growth regimes, respectively. Finally, we compare the predictions of the model to in situ X-ray imaging of Al-Cu alloy solidification experiments. The comparison shows a very good quantitative agreement between 3D simulations and thin sample experiments. It also highlights the importance of full 3D modeling to accurately predict the primary dendrite arm spacing that is significantly over-estimated by 2D simulations.

  18. Three-dimensional anode engineering for the direct methanol fuel cell

    NASA Astrophysics Data System (ADS)

    Bauer, A.; Oloman, C. W.; Gyenge, E. L.

    Catalyzed graphite felt three-dimensional anodes were investigated in direct methanol fuel cells (DMFCs) operated with sulfuric acid supporting electrolyte. With a conventional serpentine channel flow field the preferred anode thickness was 100 μm, while a novel flow-by anode showed the best performance with a thickness of 200-300 μm. The effects of altering the methanol concentration, anolyte flow rate and operating temperature on the fuel cell superficial power density were studied by full (2 3 + 1) factorial experiments on a cell with anode area of 5 cm 2 and excess oxidant O 2 at 200 kPa(abs). For operation in the flow-by mode with 2 M methanol at 2 cm 3 min -1 and 353 K the peak power density was 2380 W m -2 with a PtRuMo anode catalyst, while a PtRu catalyst yielded 2240 W m -2 under the same conditions.

  19. Fabrication of three-dimensional electrical connections by means of directed actin self-organization.

    PubMed

    Galland, Rémi; Leduc, Patrick; Guérin, Christophe; Peyrade, David; Blanchoin, Laurent; Théry, Manuel

    2013-05-01

    A promising approach to improve the performance of microelectronic devices is to build three-dimensional (3D) chips made of stacked circuits. However, a major hurdle lies in the fabrication of dense arrays of electrical interconnections between these layers, where accessibility is limited. Here we show that the directed growth and self-organization of actin filaments can offer a solution to this problem. We defined the shape and orientation of 3D actin networks through both micropatterning of actin nucleation factors and biochemical control of actin filament polymerization. Networks growing from two opposing layers were able to interpenetrate and form mechanically stable connections, which were then coated with gold using a selective metallization process. The electrical conductivity, robustness and modularity of the metallized self-organized connections make this approach potentially attractive for 3D chip manufacturing.

  20. Preparing two-dimensional nano-catalytic combustion patterns using direct inkjet printing

    NASA Astrophysics Data System (ADS)

    Luo, Xi; Zeng, Zhigang; Wang, Xiaohong; Xiao, Jinhua; Gan, Zhongxue; Wu, Hao; Hu, Zhiyu

    2014-12-01

    Two-dimensional catalytic combustion patterns, which can be used as heat source in micro-nano scale MEMS devices such as gas sensor and micro-generator, are fabricated by inkjet printing (IJP). The performances of the catalytic patterns are evaluated by both traditional catalytic activity measurement and infrared thermography (IR) camera. Results show that ultra-low (0.014 mg cm-2) loading and high utilizing (34,710 mW mg-1) of Pt catalysts can be achieved by inkjet printing method. Spontaneous combustion is also observed for the printed Pt/Al2O3 powder membrane at rather low initiation temperature and small scale. The IR camera analysis indicates the uniform temperature distribution and rapid temperature response of the micro-patterned catalyst surface. With the advantages of the inkjet printing, this new direct-write method would, in principle, open up possibilities of these special catalyst patterns serving as micro energy sources for MEMS applications.

  1. Direct simulation of three-dimensional flow about the AFE vehicle at high altitudes

    NASA Technical Reports Server (NTRS)

    Celenligil, M. Cevdet; Moss, James N.; Bird, Graeme A.

    1988-01-01

    Three-dimensional hypersonic rarefied flow about the Aeroassist Flight Experiment (AFE) vehicle was studied using the direct simulation Monte Carlo (DSMC) technique. Results are presented for the transitional flow regime encountered between 120 and 200 km altitudes with a reentry velocity of 9.92 km/s. In the simulations, a five-species reacting real-gas model that accounts for internal energies (rotational and vibrational) is used. The results indicate that the transitional effects are significant even at an altitude of 200 km and influence the overall vehicle aerodynamics. For the cases considered, the aerodynamic coefficients, surface pressures, convective heating, and flow field structure variations with rarefaction effects are presented.

  2. Whistlers and plasmaspheric hiss: Wave directions and three-dimensional propagation

    SciTech Connect

    Draganov, A.B.; Inan, U.S.; Sonwalkar, V.S.; Bell, T.F.

    1993-07-01

    Wave data from the DE 1 satellite showing simultaneously nonducted whistlers and hiss are analyzed to determine wave propagation directions. At L = 3.8 and a geographic latitude of {lambda}{sub g} = 12{degrees}S, the average wave normal directions of discrete whistlers are measured to be {approximately}51{degrees} for f = 4.5 kHz and {approximately}60{degrees} for f = 3.5 kHz, forming a small (<20{degrees}) angle with the magnetic meridional plane. Hiss wave normal angles are determined as {approximately}70{degrees} and {approximately}77{degrees} for f = 3.5 kHz and f = 2.5 kHz, respectively, with the wave vector being almost perpendicular to the meridional plane. While the measured wave normal angles of whistlers and hiss are consistent with generation of hiss by magnetospheric whistlers, existence of a significant azimuthal component indicates that further assessment of this connection must be based on three-dimensional ray tracing. A new approximate analytical formulation of three-dimensional propagation of whistler waves is developed and used to model the drift of magnetospherically reflected whistlers in azimuth. The results show that depending on initial parameters, the time of arrival of whistler rays at a fixed observation point can differ by 10-20 s, with signals from different magnetospherically reflected whistlers overlapping to evolve into a hiss like signal. The total azimuthal drift of whistler rays is found to not exceed {approximately}30{degrees}, so that plasmaspheric hiss may be produced by nonducted whistlers at longitudes correlated with the location of thunderstorm activity. 22 refs., 11 figs.

  3. Common 3-dimensional coordinate system for assessment of directional changes.

    PubMed

    Ruellas, Antonio Carlos de Oliveira; Tonello, Cristiano; Gomes, Liliane Rosas; Yatabe, Marilia Sayako; Macron, Lucie; Lopinto, Julia; Goncalves, Joao Roberto; Garib Carreira, Daniela Gamba; Alonso, Nivaldo; Souki, Bernardo Quiroga; Coqueiro, Raildo da Silva; Cevidanes, Lucia Helena Soares

    2016-05-01

    The aims of this study were to evaluate how head orientation interferes with the amounts of directional change in 3-dimensional (3D) space and to propose a method to obtain a common coordinate system using 3D surface models. Three-dimensional volumetric label maps were built for pretreatment (T1) and posttreatment (T2) from cone-beam computed tomography images of 30 growing subjects. Seven landmarks were labeled in all T1 and T2 volumetric label maps. Registrations of T1 and T2 images relative to the cranial base were performed, and 3D surface models were generated. All T1 surface models were moved by orienting the Frankfort horizontal, midsagittal, and transporionic planes to match the axial, sagittal, and coronal planes, respectively, at a common coordinate system in the Slicer software (open-source, version 4.3.1; http://www.slicer.org). The matrix generated for each T1 model was applied to each corresponding registered T2 surface model, obtaining a common head orientation. The 3D differences between the T1 and registered T2 models, and the amounts of directional change in each plane of the 3D space, were quantified for before and after head orientation. Two assessments were performed: (1) at 1 time point (mandibular width and length), and (2) for longitudinal changes (maxillary and mandibular differences). The differences between measurements before and after head orientation were quantified. Statistical analysis was performed by evaluating the means and standard deviations with paired t tests (mandibular width and length) and Wilcoxon tests (longitudinal changes). For 16 subjects, 2 observers working independently performed the head orientations twice with a 1-week interval between them. Intraclass correlation coefficients and the Bland-Altman method tested intraobserver and interobserver agreements of the x, y, and z coordinates for 7 landmarks. The 3D differences were not affected by the head orientation. The amounts of directional change in each plane of 3

  4. Direct Simulation of Evolution and Control of Three-Dimensional Instabilities in Attachment-Line Boundary Layers

    NASA Technical Reports Server (NTRS)

    Joslin, Ronald D.

    1995-01-01

    The spatial evolution of three-dimensional disturbances in an attachment-line boundary layer is computed by direct numerical simulation of the unsteady, incompressible Navier-Stokes equations. Disturbances are introduced into the boundary layer by harmonic sources that involve unsteady suction and blowing through the wall. Various harmonic- source generators are implemented on or near the attachment line, and the disturbance evolutions are compared. Previous two-dimensional simulation results and nonparallel theory are compared with the present results. The three-dimensional simulation results for disturbances with quasi-two-dimensional features indicate growth rates of only a few percent larger than pure two-dimensional results; however, the results are close enough to enable the use of the more computationally efficient, two-dimensional approach. However, true three-dimensional disturbances are more likely in practice and are more stable than two-dimensional disturbances. Disturbances generated off (but near) the attachment line spread both away from and toward the attachment line as they evolve. The evolution pattern is comparable to wave packets in at-plate boundary-layer flows. Suction stabilizes the quasi-two-dimensional attachment-line instabilities, and blowing destabilizes these instabilities; these results qualitatively agree with the theory. Furthermore, suction stabilizes the disturbances that develop off the attachment line. Clearly, disturbances that are generated near the attachment line can supply energy to attachment-line instabilities, but suction can be used to stabilize these instabilities.

  5. Direct Simulation of Evolution and Control of Three-Dimensional Instabilities in Attachment-Line Boundary Layers

    NASA Technical Reports Server (NTRS)

    Joslin, Ronald D.

    1995-01-01

    The spatial evolution of three-dimensional disturbances in an attachment-line boundary layer is computed by direct numerical simulation of the unsteady, incompressible Navier-Stokes equations. Disturbances are introduced into the boundary layer by harmonic sources that involve unsteady suction and blowing through the wall. Various harmonic- source generators are implemented on or near the attachment line, and the disturbance evolutions are compared. Previous two-dimensional simulation results and nonparallel theory are compared with the present results. The three-dimensional simulation results for disturbances with quasi-two-dimensional features indicate growth rates of only a few percent larger than pure two-dimensional results; however, the results are close enough to enable the use of the more computationally efficient, two-dimensional approach. However, true three-dimensional disturbances are more likely in practice and are more stable than two-dimensional disturbances. Disturbances generated off (but near) the attachment line spread both away from and toward the attachment line as they evolve. The evolution pattern is comparable to wave packets in at-plate boundary-layer flows. Suction stabilizes the quasi-two-dimensional attachment-line instabilities, and blowing destabilizes these instabilities; these results qualitatively agree with the theory. Furthermore, suction stabilizes the disturbances that develop off the attachment line. Clearly, disturbances that are generated near the attachment line can supply energy to attachment-line instabilities, but suction can be used to stabilize these instabilities.

  6. The role of language in multi-dimensional categorization: evidence from transcranial direct current stimulation and exposure to verbal labels.

    PubMed

    Perry, Lynn K; Lupyan, Gary

    2014-08-01

    Human concepts differ in their dimensionality. Some, like green-things, require representing one dimension while abstracting over many others. Others, like bird, have higher dimensionality due to numerous category-relevant properties (feathers, two-legs). Converging evidence points to the importance of verbal labels for forming low-dimensional categories. We examined the role of verbal labels in categorization by (1) using transcranial direct current stimulation over Wernicke's area (2) providing explicit verbal labels during a category learning task. We trained participants on a novel perceptual categorization task in which categories could be distinguished by either a uni- or bi-dimensional criterion. Cathodal stimulation over Wernicke's area reduced reliance on single-dimensional solutions, while presenting informationally redundant novel labels reduced reliance on the dimension that is normally incidental in the real world. These results provide further evidence that implicit and explicit verbal labels support the process of human categorization.

  7. Direct Ink Writing of Three-Dimensional (K, Na)NbO₃-Based Piezoelectric Ceramics.

    PubMed

    Li, Yayun; Li, Longtu; Li, Bo

    2015-04-14

    A kind of piezoelectric ink was prepared with Li, Ta, Sb co-doped (K, Na)NbO₃ (KNN) powders. Piezoelectric scaffolds with diameters at micrometer scale were constructed from this ink by using direct ink writing method. According to the micro-morphology and density test, the samples sintered at 1100 °C for 2 h have formed ceramics completely with a high relative density of 98%. X-ray diffraction (XRD) test shows that the main phase of sintered samples is orthogonal (Na0.52K0.4425Li0.0375)(Nb0.87Sb0.07Ta0.06)O₃. The piezoelectric constant d33 of 280 pC/N, dielectric constant ε of 1775, remanent polarization Pr of 18.8 μC/cm² and coercive field Ec of 8.5 kV/cm prove that the sintered samples exhibit good electrical properties. The direct ink writing method allows one to design and rapidly fabricate piezoelectric structures in complex three-dimensional (3D) shapes without the need for any dies or lithographic masks, which will simplify the process of material preparation and offer new ideas for the design and application of piezoelectric devices.

  8. Degradation-mediated cellular traction directs stem cell fate in covalently crosslinked three-dimensional hydrogels

    NASA Astrophysics Data System (ADS)

    Khetan, Sudhir; Guvendiren, Murat; Legant, Wesley R.; Cohen, Daniel M.; Chen, Christopher S.; Burdick, Jason A.

    2013-05-01

    Although cell-matrix adhesive interactions are known to regulate stem cell differentiation, the underlying mechanisms, in particular for direct three-dimensional encapsulation within hydrogels, are poorly understood. Here, we demonstrate that in covalently crosslinked hyaluronic acid (HA) hydrogels, the differentiation of human mesenchymal stem cells (hMSCs) is directed by the generation of degradation-mediated cellular traction, independently of cell morphology or matrix mechanics. hMSCs within HA hydrogels of equivalent elastic moduli that permit (restrict) cell-mediated degradation exhibited high (low) degrees of cell spreading and high (low) tractions, and favoured osteogenesis (adipogenesis). Moreover, switching the permissive hydrogel to a restrictive state through delayed secondary crosslinking reduced further hydrogel degradation, suppressed traction, and caused a switch from osteogenesis to adipogenesis in the absence of changes to the extended cellular morphology. Furthermore, inhibiting tension-mediated signalling in the permissive environment mirrored the effects of delayed secondary crosslinking, whereas upregulating tension induced osteogenesis even in the restrictive environment.

  9. Three-dimensional direct measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections

    PubMed Central

    Bensley, Jonathan Guy; De Matteo, Robert; Harding, Richard; Black, Mary Jane

    2016-01-01

    Quantitative assessment of myocardial development and disease requires accurate measurement of cardiomyocyte volume, nuclearity (nuclei per cell), and ploidy (genome copies per cell). Current methods require enzymatically isolating cells, which excludes the use of archived tissue, or serial sectioning. We describe a method of analysis that permits the direct simultaneous measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections. To demonstrate the utility of our technique, heart tissue was obtained from four species (rat, mouse, rabbit, sheep) at up to three life stages: prenatal, weaning and adulthood. Thick (40 μm) paraffin sections were stained with Wheat Germ Agglutinin-Alexa Fluor 488 to visualise cell membranes, and DAPI (4′,6-diamidino-2-phenylindole) to visualise nuclei and measure ploidy. Previous methods have been restricted to thin sections (2–10 μm) and offer an incomplete picture of cardiomyocytes. Using confocal microscopy and three-dimensional image analysis software (Imaris Version 8.2, Bitplane AG, Switzerland), cardiomyocyte volume, nuclearity, and ploidy were measured. This method of staining and analysis of cardiomyocytes enables accurate morphometric measurements in thick histological sections, thus unlocking the potential of archived tissue. Our novel time-efficient method permits the entire cardiomyocyte to be visualised directly in 3D, eliminating the need for precise alignment of serial sections. PMID:27048757

  10. Three-dimensional direct measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections

    NASA Astrophysics Data System (ADS)

    Bensley, Jonathan Guy; de Matteo, Robert; Harding, Richard; Black, Mary Jane

    2016-04-01

    Quantitative assessment of myocardial development and disease requires accurate measurement of cardiomyocyte volume, nuclearity (nuclei per cell), and ploidy (genome copies per cell). Current methods require enzymatically isolating cells, which excludes the use of archived tissue, or serial sectioning. We describe a method of analysis that permits the direct simultaneous measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections. To demonstrate the utility of our technique, heart tissue was obtained from four species (rat, mouse, rabbit, sheep) at up to three life stages: prenatal, weaning and adulthood. Thick (40 μm) paraffin sections were stained with Wheat Germ Agglutinin-Alexa Fluor 488 to visualise cell membranes, and DAPI (4‧,6-diamidino-2-phenylindole) to visualise nuclei and measure ploidy. Previous methods have been restricted to thin sections (2–10 μm) and offer an incomplete picture of cardiomyocytes. Using confocal microscopy and three-dimensional image analysis software (Imaris Version 8.2, Bitplane AG, Switzerland), cardiomyocyte volume, nuclearity, and ploidy were measured. This method of staining and analysis of cardiomyocytes enables accurate morphometric measurements in thick histological sections, thus unlocking the potential of archived tissue. Our novel time-efficient method permits the entire cardiomyocyte to be visualised directly in 3D, eliminating the need for precise alignment of serial sections.

  11. Direct Ink Writing of Three-Dimensional (K, Na)NbO3-Based Piezoelectric Ceramics

    PubMed Central

    Li, Yayun; Li, Longtu; Li, Bo

    2015-01-01

    A kind of piezoelectric ink was prepared with Li, Ta, Sb co-doped (K, Na)NbO3 (KNN) powders. Piezoelectric scaffolds with diameters at micrometer scale were constructed from this ink by using direct ink writing method. According to the micro-morphology and density test, the samples sintered at 1100 °C for 2 h have formed ceramics completely with a high relative density of 98%. X-ray diffraction (XRD) test shows that the main phase of sintered samples is orthogonal (Na0.52K0.4425Li0.0375)(Nb0.87Sb0.07Ta0.06)O3. The piezoelectric constant d33 of 280 pC/N, dielectric constant ε of 1775, remanent polarization Pr of 18.8 μC/cm2 and coercive field Ec of 8.5 kV/cm prove that the sintered samples exhibit good electrical properties. The direct ink writing method allows one to design and rapidly fabricate piezoelectric structures in complex three-dimensional (3D) shapes without the need for any dies or lithographic masks, which will simplify the process of material preparation and offer new ideas for the design and application of piezoelectric devices. PMID:28788028

  12. Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase.

    PubMed

    Guthold, M; Zhu, X; Rivetti, C; Yang, G; Thomson, N H; Kasas, S; Hansma, H G; Smith, B; Hansma, P K; Bustamante, C

    1999-10-01

    The dynamics of nonspecific and specific Escherichia coli RNA polymerase (RNAP)-DNA complexes have been directly observed using scanning force microscopy operating in buffer. To this end, imaging conditions had to be found in which DNA molecules were adsorbed onto mica strongly enough to be imaged, but loosely enough to be able to diffuse on the surface. In sequential images of nonspecific complexes, RNAP was seen to slide along DNA, performing a one-dimensional random walk. Heparin, a substance known to disrupt nonspecific RNAP-DNA interactions, prevented sliding. These observations suggest that diffusion of RNAP along DNA constitutes a mechanism for accelerated promoter location. Sequential images of single, transcribing RNAP molecules were also investigated. Upon addition of 5 microM nucleoside triphosphates to stalled elongation complexes in the liquid chamber, RNAP molecules were seen to processively thread their template at rates of 1.5 nucleotide/s in a direction consistent with the promoter orientation. Transcription assays, performed with radiolabeled, mica-bound transcription complexes, confirmed this rate, which was about three times smaller than the rate of complexes in solution. This assay also showed that the pattern of pause sites and the termination site were affected by the surface. By using the Einstein-Sutherland friction-diffusion relation the loading force experienced by RNAP due to DNA-surface friction is estimated and discussed.

  13. Cell-directed integration into three-dimensional lipid-silica nanostructured matrices.

    PubMed

    Harper, Jason C; Khripin, Constantine Y; Khirpin, Constantine Y; Carnes, Eric C; Ashley, Carlee E; Lopez, DeAnna M; Savage, Travis; Jones, Howland D T; Davis, Ryan W; Nunez, Dominique E; Brinker, Lina M; Kaehr, Bryan; Brozik, Susan M; Brinker, C Jeffrey

    2010-10-26

    We report a unique approach in which living cells direct their integration into 3D solid-state nanostructures. Yeast cells deposited on a weakly condensed lipid/silica thin film mesophase actively reconstruct the surface to create a fully 3D bio/nano interface, composed of localized lipid bilayers enveloped by a lipid/silica mesophase, through a self-catalyzed silica condensation process. Remarkably, this integration process selects exclusively for living cells over the corresponding apoptotic cells (those undergoing programmed cell death), via the development of a pH gradient, which catalyzes silica deposition and the formation of a coherent interface between the cell and surrounding silica matrix. Added long-chain lipids or auxiliary nanocomponents are localized within the pH gradient, allowing the development of complex active and accessible bio/nano interfaces not achievable by other synthetic methods. Overall, this approach provides the first demonstration of active cell-directed integration into a nominally solid-state three-dimensional architecture. It promises a new means to integrate "bio" with "nano" into platforms useful to study and manipulate cellular behavior at the individual cell level and to interface living organisms with electronics, photonics, and fluidics.

  14. One-dimensional hybrid-direct kinetic simulation of the discharge plasma in a Hall thruster

    SciTech Connect

    Hara, Kentaro; Boyd, Iain D.; Kolobov, Vladimir I.

    2012-11-15

    In order to model the non-equilibrium plasma within the discharge region of a Hall thruster, the velocity distribution functions (VDFs) must be obtained accurately. A direct kinetic (DK) simulation method that directly solves the plasma Boltzmann equation can achieve better resolution of VDFs in comparison to particle simulations, such as the particle-in-cell (PIC) method that inherently include statistical noise. In this paper, a one-dimensional hybrid-DK simulation, which uses a DK simulation for heavy species and a fluid model for electrons, is developed and compared to a hybrid-PIC simulation. Time-averaged results obtained from the hybrid-DK simulation are in good agreement with hybrid-PIC results and experimental data. It is shown from a comparison of using a kinetic simulation and solving the continuity equation that modeling of the neutral atoms plays an important role for simulations of the Hall thruster discharge plasma. In addition, low and high frequency plasma oscillations are observed. Although the kinetic nature of electrons is not resolved due to the use of a fluid model, the hybrid-DK model provides spatially and temporally well-resolved plasma properties and an improved resolution of VDFs for heavy species with less statistical noise in comparison to the hybrid-PIC method.

  15. Acyclic and star colorings of joins of graphs and an algorithm for cographs.

    SciTech Connect

    Lyons, A.; Mathematics and Computer Science; Univ. of Chicago

    2009-01-01

    An acyclic coloring of a graph is a proper vertex coloring such that the subgraph induced by the union of any two color classes is a disjoint collection of trees. The more restricted notion of star coloring requires that the union of any two color classes induces a disjoint collection of stars. The acyclic and star chromatic numbers of a graph G are defined analogously to the chromatic number {chi}(G) and are denoted by {chi}{sub a}(G) and {chi}{sub s}(G), respectively. In this paper, we consider acyclic and star colorings of graphs that are decomposable with respect to the join operation, which builds a new graph from a collection of two or more disjoint graphs by adding all possible edges between them. In particular, we present a recursive formula for the acyclic chromatic number of joins of graphs and show that a similar formula holds for the star chromatic number. We also demonstrate the algorithmic implications of our results for the cographs, which have the unique property that they are recursively decomposable with respect to the join and disjoint union operations.

  16. Acyclic water pentamer induces novel supramolecular ribbed sheet: Cooperativity and competitiveness of weak and covalent forces?

    NASA Astrophysics Data System (ADS)

    Jana, Atish Dipankar; Saha, Rajat; Mostafa, Golam

    2010-03-01

    The 1D chain complex [{Cu(II)(bpp)(malonate)(H 2O)}(H 2O) 4] n ( 1) (bpp = 1,3-bis(4-pyridyl)propane) self-assembles to form a 2D ribbed sheet stabilized by an acyclic pentameric water cluster, which in turn, influences the conformation of the bpp ligand.

  17. Acyclic sulfides, garlicnins L-1-L-4, E, and F, from Allium sativum.

    PubMed

    Nohara, Toshihiro; Fujiwara, Yukio; Ikeda, Tsuyoshi; Yamaguchi, Koki; Manabe, Hideyuki; Murakami, Kotaro; Ono, Masateru; Nakano, Daisuke; Kinjo, Junei

    2014-01-01

    Six novel acyclic sulfides, named garlicnins L-1-L-4 (1-4), E (5), and F (6), were isolated from the acetone extracts, with the ability to suppress M2 macrophage activation, of the bulbs of garlic (Allium sativum L.), and their chemical structures were characterized.

  18. Design and Synthesis of Fluorescent Acyclic Nucleoside Phosphonates as Potent Inhibitors of Bacterial Adenylate Cyclases.

    PubMed

    Břehová, Petra; Šmídková, Markéta; Skácel, Jan; Dračínský, Martin; Mertlíková-Kaiserová, Helena; Velasquez, Monica P Soto; Watts, Val J; Janeba, Zlatko

    2016-11-21

    Bordetella pertussis adenylate cyclase toxin (ACT) and Bacillus anthracis edema factor (EF) are key virulence factors with adenylate cyclase (AC) activity that substantially contribute to the pathogenesis of whooping cough and anthrax, respectively. There is an urgent need to develop potent and selective inhibitors of bacterial ACs with prospects for the development of potential antibacterial therapeutics and to study their molecular interactions with the target enzymes. Novel fluorescent 5-chloroanthraniloyl-substituted acyclic nucleoside phosphonates (Cl-ANT-ANPs) were designed and synthesized in the form of their diphosphates (Cl-ANT-ANPpp) as competitive ACT and EF inhibitors with sub-micromolar potency (IC50 values: 11-622 nm). Fluorescence experiments indicated that Cl-ANT-ANPpp analogues bind to the ACT active site, and docking studies suggested that the Cl-ANT group interacts with Phe306 and Leu60. Interestingly, the increase in direct fluorescence with Cl-ANT-ANPpp having an ester linker was strictly calmodulin (CaM)-dependent, whereas Cl-ANT-ANPpp analogues with an amide linker, upon binding to ACT, increased the fluorescence even in the absence of CaM. Such a dependence of binding on structural modification could be exploited in the future design of potent inhibitors of bacterial ACs. Furthermore, one Cl-ANT-ANP in the form of a bisamidate prodrug was able to inhibit B. pertussis ACT activity in macrophage cells with IC50 =12 μm. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Alteration in substrate specificity of horse liver alcohol dehydrogenase by an acyclic nicotinamide analog of NAD(+).

    PubMed

    Malver, Olaf; Sebastian, Mina J; Oppenheimer, Norman J

    2014-11-01

    A new, acyclic NAD-analog, acycloNAD(+) has been synthesized where the nicotinamide ribosyl moiety has been replaced by the nicotinamide (2-hydroxyethoxy)methyl moiety. The chemical properties of this analog are comparable to those of β-NAD(+) with a redox potential of -324mV and a 341nm λmax for the reduced form. Both yeast alcohol dehydrogenase (YADH) and horse liver alcohol dehydrogenase (HLADH) catalyze the reduction of acycloNAD(+) by primary alcohols. With HLADH 1-butanol has the highest Vmax at 49% that of β-NAD(+). The primary deuterium kinetic isotope effect is greater than 3 indicating a significant contribution to the rate limiting step from cleavage of the carbon-hydrogen bond. The stereochemistry of the hydride transfer in the oxidation of stereospecifically deuterium labeled n-butanol is identical to that for the reaction with β-NAD(+). In contrast to the activity toward primary alcohols there is no detectable reduction of acycloNAD(+) by secondary alcohols with HLADH although these alcohols serve as competitive inhibitors. The net effect is that acycloNAD(+) has converted horse liver ADH from a broad spectrum alcohol dehydrogenase, capable of utilizing either primary or secondary alcohols, into an exclusively primary alcohol dehydrogenase. This is the first example of an NAD analog that alters the substrate specificity of a dehydrogenase and, like site-directed mutagenesis of proteins, establishes that modifications of the coenzyme distance from the active site can be used to alter enzyme function and substrate specificity. These and other results, including the activity with α-NADH, clearly demonstrate the promiscuity of the binding interactions between dehydrogenases and the riboside phosphate of the nicotinamide moiety, thus greatly expanding the possibilities for the design of analogs and inhibitors of specific dehydrogenases. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Dimensional Reduction of a Layered Metal Chalcogenide into a 1D Near-IR Direct Band Gap Semiconductor

    SciTech Connect

    Liu, Yi-Hsin; Porter, Spencer H.; Goldberger, Joshua E.

    2012-07-24

    Reducing the dimensionality of inorganic lattices allows for the creation of new materials that have unique optoelectronic properties. We demonstrate that a layered metal chalcogenide lattice, TiS{sub 2}, can form a dimensionally reduced crystalline one-dimensional hybrid organic/inorganic TiS{sub 2}(ethylenediamine) framework when synthesized from molecular precursors in solution. This solid has strong absorption above 1.70 eV and pronounced emission in the near-IR regime. The energy dependence of the absorption, the near-IR photoluminescence, and electronic band structure calculations confirm that TiS{sub 2}(ethylenediamine) has a direct band gap.

  1. Programmable peptide-directed two dimensional arrays of various nanoparticles on graphene sheets

    NASA Astrophysics Data System (ADS)

    Choi, Bong Gill; Yang, Min Ho; Park, Tae Jung; Huh, Yun Suk; Lee, Sang Yup; Hong, Won Hi; Park, Hoseok

    2011-08-01

    In this research, we report an innovative, chemical strategy for the in situ synthesis and direct two-dimensional (2D) arraying of various nanoparticles (NPs) on graphenes using both programmed-peptides as directing agents and graphenes as pre-formed 2D templates. The peptides were designed for manipulating the enthalpic (coupled interactions) constraint of the global system. Along with the functionalization of graphene for the stable dispersion, peptides directed the growth and array of NPs in a controllable manner. In particular, the sequences of peptides were encoded by the combination of glutamic acid (E), glycine (G), and phenylalanine (F) amino acids as follows: (E-G-F)3-G, with E for the interaction with NPs and F and G for the interaction with graphenes. For the entropic (restricted geometry) constraint, graphene was used as a 2D scaffold to tune the size, density, and position of NPs, while maintaining the intrinsic properties for electrochemical applications. The excellent quality of the resultant hybrids was demonstrated by their high electrocatalytic activity in the electrooxidation of methanol. This synergistic combination of peptides and graphenes allowed for a uniform 2D array and spontaneous organization of various NPs (i.e., Pt, Au, Pd, and Ru), which would greatly expand the utility and versatility of this approach for the synthesis and array of the advanced nanomaterials.In this research, we report an innovative, chemical strategy for the in situ synthesis and direct two-dimensional (2D) arraying of various nanoparticles (NPs) on graphenes using both programmed-peptides as directing agents and graphenes as pre-formed 2D templates. The peptides were designed for manipulating the enthalpic (coupled interactions) constraint of the global system. Along with the functionalization of graphene for the stable dispersion, peptides directed the growth and array of NPs in a controllable manner. In particular, the sequences of peptides were encoded by the

  2. Study on follicular characteristics, hormonal and biochemical profile in norgestomet+PMSG treated acyclic buffaloes

    PubMed Central

    Jerome, A.; Srivastava, S. K.; Sharma, R. K.

    2016-01-01

    This research was conducted to study the follicular dynamics, hormonal, biochemical profile and fertility response in acyclic and norgestomet+PMSG treated acyclic buffaloes in summer. The study animals were divided into two groups: group I [control (n=8): no treatment] and II [treatment group (n=15)]. In group II, seven animals were used for follicular biochemical and hormonal profile and eight animals for fertility studies following Crestar® (Intervet, France) treatment (day 0: Crestar® insertion; day 8: 500 IU PMSG; day 9: Crestar® removal; day 11 AI). Follicular fluid stradiol (E2) and progesterone (P4) in acyclic and pre-ovulatory follicle in study groups was significantly (P<0.01) higher than peripheral level. Peripheral E2 concentration, during pre-ovulatory period in group II was higher (P<0.05) than group I. Significant correlation between serum and follicular E2 was deduced (r=0.888; P<0.01) as significant difference in serum cholesterol content was shown between groups. Lower follicular total protein (P<0.05) in acyclic animals and higher follicular glucose (P<0.05) in treated group were concluded. Significant correlation (r=-0.770; P<0.05) was observed between follicular cholesterol and triglycerides. Follicular characteristics, post PMSG administration, differed significantly (0.83 ± 0.20 vs 1.32 ± 0.12; P<0.01) in all buffaloes exhibiting estrus, out of which four conceived. In conclusion, follicular hormonal and biochemical profile exhibits alteration in protein and glucose level between summer acyclic and treated buffaloes. However, peripheral E2 along with fertility response showed significant difference (P<0.01) between the study groups with significant correlation in E2, cholesterol and triglycerides between peripheral and follicular compartment. PMID:28224008

  3. Evidence that hyperprolactinaemia is associated with ovarian acyclicity in female zoo African elephants.

    PubMed

    Dow, T L; Brown, J L

    2012-01-01

    African elephants of reproductive age in zoos are experiencing high rates of ovarian cycle problems (>40%) and low reproductive success. Previously, our laboratory found that 1/3 of acyclic females exhibit hyperprolactinaemia, a likely cause of ovarian dysfunction. This follow-up study re-examined hyperprolactinaemia in African elephants and found the problem has increased significantly to 71% of acyclic females. Circulating serum progestagens and prolactin were analysed in 31 normal cycling, 13 irregular cycling and 31 acyclic elephants for 12 months. In acyclic females, overall mean prolactin concentrations differed from cycling females (P < 0.05), with concentrations being either higher (n = 22; 54.90 ± 13.31 ngmL(-1)) or lower (n = 9; 6.47 ± 1.73 ngmL(-1)) than normal. No temporal patterns of prolactin secretion were evident in elephants that lacked progestagen cycles. In cycling females, prolactin was secreted in a cyclical manner, with higher concentrations observed during nonluteal (34.38 ± 1.77 and 32.75 ± 2.61 ngmL(-1)) than luteal (10.51 ± 0.30 and 9.67 ± 0.42 ngmL(-1)) phases for normal and irregular females, respectively. Of most concern was that over two-thirds of acyclic females now are hyperprolactinemic, a dramatic increase over that observed 7 years earlier. Furthermore, females of reproductive age constituted 45% of elephants with hyperprolactinaemia. Until the cause of this problem is identified and a treatment is developed, reproductive rates will remain suboptimal and the population nonsustaining.

  4. Two-dimensional boron-nitrogen-carbon monolayers with tunable direct band gaps

    NASA Astrophysics Data System (ADS)

    Zhang, Miao; Gao, Guoying; Kutana, Alex; Wang, Yanchao; Zou, Xiaolong; Tse, John S.; Yakobson, Boris I.; Li, Hongdong; Liu, Hanyu; Ma, Yanming

    2015-07-01

    The search for new candidate semiconductors with direct band gaps of ~1.4 eV has attracted significant attention, especially among the two-dimensional (2D) materials, which have become potential candidates for next-generation optoelectronics. Herein, we systematically studied 2D Bx/2Nx/2C1-x (0 < x < 1) compounds in particular focus on the four stoichiometric Bx/2Nx/2C1-x (x = 2/3, 1/2, 2/5 and 1/3) using a recently developed global optimization method (CALYPSO) in conjunction with density functional theory. Furthermore, we examine more stoichiometries by the cluster expansion technique based on a hexagonal lattice. The results reveal that all monolayer Bx/2Nx/2C1-x stoichiometries adopt a planar honeycomb character and are dynamically stable. Remarkably, electronic structural calculations show that most of Bx/2Nx/2C1-x phases possess direct band gaps within the optical range, thereby they can potentially be used in high-efficiency conversion of solar energy to electric power, as well as in p-n junction photovoltaic modules. The present results also show that the band gaps of Bx/2Nx/2C1-x can be widely tuned within the optical range by changing the concentration of carbon, thus allowing the fast development of band gap engineered materials in optoelectronics. These new findings may enable new approaches to the design of microelectronic devices.The search for new candidate semiconductors with direct band gaps of ~1.4 eV has attracted significant attention, especially among the two-dimensional (2D) materials, which have become potential candidates for next-generation optoelectronics. Herein, we systematically studied 2D Bx/2Nx/2C1-x (0 < x < 1) compounds in particular focus on the four stoichiometric Bx/2Nx/2C1-x (x = 2/3, 1/2, 2/5 and 1/3) using a recently developed global optimization method (CALYPSO) in conjunction with density functional theory. Furthermore, we examine more stoichiometries by the cluster expansion technique based on a hexagonal lattice. The

  5. Model tags: direct three-dimensional tracking of heart wall motion from tagged magnetic resonance images.

    PubMed

    Young, A A

    1999-12-01

    Although magnetic resonance tissue tagging is a useful tool for the non-invasive measurement of three-dimensional (3-D) heart wall motion, the clinical utility of current analysis techniques is limited by the prohibitively long time required for image analysis. A method was therefore developed for the reconstruction of 3-D heart wall motion directly from tagged magnetic resonance images, without prior identification of ventricular boundaries or tag stripe locations. The method utilized a finite-element model to describe the shape and motion of the heart. Initially, the model geometry was determined at the time of tag creation by fitting a small number of guide points which were placed interactively on the images. Model tags were then created within the model as material surfaces which defined the location of the magnetic tags. An objective function was derived to measure the degree of match between the model tags and the image stripes. The objective was minimized by allowing the model to deform directly under the influence of the images, utilizing an efficient method for calculating image-derived motion constraints. The model deformation could also be manipulated interactively by guide points. Experiments were performed using clinical images of a normal volunteer, as well as simulated images in which the true motion was specified. The root-mean-squared errors between the known and calculated displacement and strain for the simulated images were similar to those obtained using previous stripe-tracking and model-fitting methods. A significant improvement in analysis time was obtained for the normal volunteer and further improvements may allow the method to be applied in a 'real-time' clinical environment.

  6. Protein-directed assembly of arbitrary three-dimensional nanoporous silica architectures.

    PubMed

    Khripin, Constantine Y; Pristinski, Denis; Dunphy, Darren R; Brinker, C Jeffrey; Kaehr, Bryan

    2011-02-22

    Through precise control of nanoscale building blocks, such as proteins and polyamines, silica condensing microorganisms are able to create intricate mineral structures displaying hierarchical features from nano- to millimeter-length scales. The creation of artificial structures of similar characteristics is facilitated through biomimetic approaches, for instance, by first creating a bioscaffold comprised of silica condensing moieties which, in turn, govern silica deposition into three-dimensional (3D) structures. In this work, we demonstrate a protein-directed approach to template silica into true arbitrary 3D architectures by employing cross-linked protein hydrogels to controllably direct silica condensation. Protein hydrogels are fabricated using multiphoton lithography, which enables user-defined control over template features in three dimensions. Silica deposition, under acidic conditions, proceeds throughout protein hydrogel templates via flocculation of silica nanoparticles by protein molecules, as indicated by dynamic light scattering (DLS) and time-dependent measurements of elastic modulus. Following silica deposition, the protein template can be removed using mild thermal processing yielding high surface area (625 m(2)/g) porous silica replicas that do not undergo significant volume change compared to the starting template. We demonstrate the capabilities of this approach to create bioinspired silica microstructures displaying hierarchical features over broad length scales and the infiltration/functionalization capabilities of the nanoporous silica matrix by laser printing a 3D gold image within a 3D silica matrix. This work provides a foundation to potentially understand and mimic biogenic silica condensation under the constraints of user-defined biotemplates and further should enable a wide range of complex inorganic architectures to be explored using silica transformational chemistries, for instance silica to silicon, as demonstrated herein.

  7. Two-dimensional boron-nitrogen-carbon monolayers with tunable direct band gaps.

    PubMed

    Zhang, Miao; Gao, Guoying; Kutana, Alex; Wang, Yanchao; Zou, Xiaolong; Tse, John S; Yakobson, Boris I; Li, Hongdong; Liu, Hanyu; Ma, Yanming

    2015-07-28

    The search for new candidate semiconductors with direct band gaps of ∼1.4 eV has attracted significant attention, especially among the two-dimensional (2D) materials, which have become potential candidates for next-generation optoelectronics. Herein, we systematically studied 2D B(x)/2N(x/2)C(1-x) (0 < x < 1) compounds in particular focus on the four stoichiometric B(x)/2N(x/2)C(1-x) (x = 2/3, 1/2, 2/5 and 1/3) using a recently developed global optimization method (CALYPSO) in conjunction with density functional theory. Furthermore, we examine more stoichiometries by the cluster expansion technique based on a hexagonal lattice. The results reveal that all monolayer B(x)/2N(x/2)C(1-x) stoichiometries adopt a planar honeycomb character and are dynamically stable. Remarkably, electronic structural calculations show that most of B(x)/2N(x/2)C(1-x) phases possess direct band gaps within the optical range, thereby they can potentially be used in high-efficiency conversion of solar energy to electric power, as well as in p-n junction photovoltaic modules. The present results also show that the band gaps of B(x)/2N(x/2)C(1-x) can be widely tuned within the optical range by changing the concentration of carbon, thus allowing the fast development of band gap engineered materials in optoelectronics. These new findings may enable new approaches to the design of microelectronic devices.

  8. Experimental observation of oscillatory cellular patterns in three-dimensional directional solidification

    NASA Astrophysics Data System (ADS)

    Pereda, J.; Mota, F. L.; Chen, L.; Billia, B.; Tourret, D.; Song, Y.; Debierre, J.-M.; Guérin, R.; Karma, A.; Trivedi, R.; Bergeon, N.

    2017-01-01

    We present a detailed analysis of oscillatory modes during three-dimensional cellular growth in a diffusive transport regime. We ground our analysis primarily on in situ observations of directional solidification experiments of a transparent succinonitrile 0.24 wt % camphor alloy performed in microgravity conditions onboard the International Space Station. This study completes our previous reports [Bergeon et al., Phys. Rev. Lett. 110, 226102 (2013), 10.1103/PhysRevLett.110.226102; Tourret et al., Phys. Rev. E 92, 042401 (2015), 10.1103/PhysRevE.92.042401] from an experimental perspective, and results are supported by additional phase-field simulations. We analyze the influence of growth parameters, crystal orientation, and sample history on promoting oscillations, and on their spatiotemporal characteristics. Cellular patterns display a remarkably uniform oscillation period throughout the entire array, despite a high array disorder and a wide distribution of primary spacing. Oscillation inhibition may be associated to crystalline disorientation, which stems from polygonization and is manifested as pattern drifting. We determine a drifting velocity threshold above which oscillations are inhibited, thereby demonstrating that inhibition is due to cell drifting and not directly to disorientation, and also explaining the suppression of oscillations when the pulling velocity history favors drifting. Furthermore, we show that the array disorder prevents long-range coherence of oscillations, but not short-range coherence in localized ordered regions. For regions of a few cells exhibiting hexagonal (square) ordering, three (two) subarrays oscillate with a phase shift of approximately ±120∘ (180∘), with square ordering occurring preferentially near subgrain boundaries.

  9. Two Dimensional Simulations of Plastic-Shell, Direct-Drive Implosions on OMEGA

    SciTech Connect

    Radha, P B; Goncharov, V N; Collins, T B; Delettrez, J A; Elbaz, Y; Glebov, V Y; Keck, R L; Keller, D E; Knauer, J P; Marozas, J A; Marshall, F J; McKenty, P W; Meyerhofer, D D; Regan, S P; Sangster, T C; Shvarts, D; Skupsky, S; Srebro, Y; Town, R J; Stoeckl, C

    2004-09-27

    Multidimensional hydrodynamic properties of high-adiabat direct-drive plastic-shell implosions on the OMEGA laser system [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)] are investigated using the multidimensional hydrodynamic code, DRACO. Multimode simulations including the effects of nonuniform illumination and target roughness indicate that shell stability during the acceleration phase plays a critical role in determining target performance. For thick shells that remain integral during the acceleration phase, target yields are significantly reduced by the combination of the long-wavelength ({ell} < 10) modes due to surface roughness and beam imbalance and the intermediate modes (20 {le} {ell} {le} 50) due to single-beam nonuniformities. The neutron-production rate for these thick shells truncates relative to one-dimensional (1-D) predictions. The yield degradation in the thin shells is mainly due to shell breakup at short wavelengths ({lambda} {approx} {Delta}, where {Delta} is the in-flight shell thickness). The neutron-rate curves for the thinner shells have significantly lower amplitudes and a fall-off that is less steep than 1-D rates. DRACO simulation results are consistent with experimental observations.

  10. Two-dimensional simulations of plastic-shell, direct-drive implosions on OMEGA

    SciTech Connect

    Radha, P.B.; Goncharov, V.N.; Collins, T.J.B.; Delettrez, J.A.; Elbaz, Y.; Glebov, V.Yu.; Keck, R.L.; Keller, D.E.; Knauer, J.P.; Marozas, J.A.; Marshall, F.J.; McKenty, P.W.; Meyerhofer, D.D.; Regan, S.P.; Sangster, T.C.; Shvarts, D.; Skupsky, S.; Srebro, Y.; Town, R.P.J.; Stoeckl, C.

    2005-03-01

    Multidimensional hydrodynamic properties of high-adiabat direct-drive plastic-shell implosions on the OMEGA laser system [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)] are investigated using the multidimensional hydrodynamic code, DRACO [D. Keller et al., Bull. Am. Phys. Soc. 44, 37 (1999)]. Multimode simulations including the effects of nonuniform illumination and target roughness indicate that shell stability during the acceleration phase plays a critical role in determining target performance. For thick shells that remain integral during the acceleration phase, target yields are significantly reduced by the combination of the long-wavelength (l<10) modes due to surface roughness and beam imbalance and the intermediate modes (20{<=}l{<=}50) due to single-beam nonuniformities. The neutron-production rate for these thick shells truncates relative to one-dimensional (1D) predictions. The yield degradation in the thin shells is mainly due to shell breakup at short wavelengths ({lambda}{approx}{delta}, where {delta} is the in-flight shell thickness). The neutron-rate curves for the thinner shells have significantly lower amplitudes and a fall-off that is less steep than 1D rates. DRACO simulation results are consistent with experimental observations.

  11. One dimensional acoustic direct nonlinear inversion using the Volterra inverse scattering series

    NASA Astrophysics Data System (ADS)

    Yao, Jie; Lesage, Anne-Cécile; Bodmann, Bernhard G.; Hussain, Fazle; Kouri, Donald J.

    2014-06-01

    Direct inversion of acoustic scattering problems is nonlinear. One way to treat the inverse scattering problem is based on the reversion of the Born-Neumann series solution of the Lippmann-Schwinger equation. An important issue for this approach is the radius of convergence of the Born-Neumann series for the forward problem. However, this issue can be tackled by employing a renormalization technique to transform the Lippmann-Schwinger equation from a Fredholm to a Volterra integral form. The Born series of a Volterra integral equation converges absolutely and uniformly in the entire complex plane. We present a further study of this new mathematical framework. A Volterra inverse scattering series (VISS) using both reflection and transmission data is derived and tested for several acoustic velocity models. For large velocity contrast, series summation techniques (e.g., Cesàro summation, Euler transform, etc) are employed to improve the rate of convergence of VISS. It is shown that the VISS method with summation techniques can provide a relatively good estimation of the velocity profile. The method is fully data-driven in the respect that no prior information of the model is required. Besides, no internal multiple removal is needed. This one dimensional VISS approach is useful for inverse scattering and serves as an important step for studying more complicated and realistic inversions.

  12. Direct numerical simulation of a turbulent pipe with systematically varied three-dimensional roughness

    NASA Astrophysics Data System (ADS)

    Chan, Leon; MacDonald, Michael; Chung, Daniel; Hutchins, Nicholas; Ooi, Andrew

    2014-11-01

    Direct Numerical Simulations (DNS) are conducted at low to medium Reynolds numbers for a turbulent pipe flow with roughness. The roughness, which is comprised of three-dimensional sinusoidal elements, causes a downward shift in the mean velocity profile known as the Hama roughness function ΔU+ . In engineering applications, ΔU+ (which is related to the coefficient of drag Cf) is an important parameter as it is used to quantify the increase in drag and the decrease in efficiency. To have a better understanding of roughness and how it affects the flow, a range of numerical studies were conducted where the roughness height h+, wavelength λ+ and Reynolds number of the flow are varied. For the range of cases simulated, it is found that the roughness average height ka+ (which is proportional to h+) is strongly correlated to the roughness function ΔU+ whereas λ+ has a weaker influence on the flow. Results from simulations of more complicated surfaces comprised of two superimposed modes of different wavelength are also presented. Analysis of the turbulence statistics convincingly supports Townsend's outer-layer hypothesis for all of the cases simulated.

  13. Direct three-dimensional imaging of structure in a strongly-coupled dusty plasma

    NASA Astrophysics Data System (ADS)

    Quinn, R. A.; Goree, J.; Pieper, J. B.

    1996-11-01

    Using direct imaging of 9 μ m plastic spheres suspended in low-power Krypton discharges, we have constructed three-dimensional images showing the crystalline structure of a strongly-coupled dusty plasma. The spheres, which are highly charged and levitated by the electrode sheath, form a strongly-coupled system. A horizontal laser sheet illuminates a slice through the suspension, and a video camera views at 90^circ . Using a vertical stack of digitized images of particles in equally-spaced horizontal planes, we reconstructed the 3-D structure. We found bcc (body-centered cubic) and simple hexagonal structures coexisting in the same suspension. This coexistence is attributed to a bistability owing to an attractive potential region downstream of a charged grain in the presence of flowing ions. The probability of the system arranging in itself in the bcc or simple hexagonal phases is found to depend on the rf power that is used to sustain the discharge, and this in turn affects the particle charge and Debye length.(J. B. Pieper, J. Goree, R. A. Quinn, submitted to Phys. Rev. E) Work supported by NSF and NASA

  14. Three-Dimensional Study of Yield Degradation for Direct-Drive Inertial Confinement Fusion

    NASA Astrophysics Data System (ADS)

    Woo, K. M.; Betti, R.; Yan, R.; Aluie, H.; Bose, A.; Zhao, D. X.; Gopalaswamy, V.

    2016-10-01

    The mechanism of yield degradation in the deceleration phase for direct-drive inertial confinement fusion was studied using a recently developed three-dimensional radiation-hydrodynamics code DEC3D. Under the approximation of adiabatic hot spot, an expression that measures the degradation of neutron rate was obtained in terms of the ratio of perturbed to the clean hot-spot volume. The characteristics of perturbed hot-spot volume is identified as a key parameter to understand the departure from spherical symmetry. The role of 3-D effects on compressibility, which affects the hot-spot volume, was examined including the 3-D vorticity dynamics in the spherical converging geometry and the jet flow in P-1 perturbations. In particular, the hot spot was found to be less compressible in the nonlinear phase of the Rayleigh-Taylor instability, resulting in a poor hydrodynamic efficiency to convert the shell kinetic energy into hot-spot pressure. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DENA0001944.

  15. Direct Numerical Simulation of Particle Behaviour in a Gas-Solid Three Dimensional Plane Jet

    SciTech Connect

    Qazi, N. A.; Tang, J. C. K.; Hawkes, E. R.; Yeoh, G. H.; Grout, Ray W.; Sitaraman, Hariswaran; Talei, M.; Taylor, R. A.; Bolla, M.; Wang, H.

    2014-12-08

    In this paper, direct numerical simulations (DNS) of a three-dimensional (3D), non-reacting, temporally evolving planar jet laden with mono-dispersed solid particles in the two-way coupling (TWC) regime are performed. Three different particles Stokes numbers (St = 0.1, 1, 10) have been considered. This has been achieved by varying the particle diameter while keeping the particle mass loading (fm = 1) and the jet Reynolds number (Rejet = 2000) unchanged. The objective is to study the effect of the particle Stokes number TWC regime on the temporal development of the planar jet. Two-way coupled momentum and heat transfer has been studied by investigating mean relative velocity and temperature. Results indicate that the relative parameters are more pronounced on the edges of the jet and decrease in time in general. At the center of the jet however, the mean value first increases and then decreases again. Additionally, lighter particles spread farther than heavier particles from the center of the jet. Furthermore, the heavier particles delay the development of the jet due to TWC effects.

  16. Direct observation of melting in a two-dimensional driven granular system

    PubMed Central

    Sun, Xiaoyan; Li, Yang; Ma, Yuqiang; Zhang, Zexin

    2016-01-01

    Melting is considered to be one of the most fundamental problems in physical science. Generally, dimensionality plays an important role in melting. In three-dimension, it’s well known that a crystal melts directly into a liquid via a first-order transition. In two-dimension (2D), however, the melting process has been widely debated whether it is a first-order transition or a two-step transition with an intermediate hexatic phase. Experimentally 2D melting has been intensively studied in equilibrium systems such as molecular and colloidal crystals, but rarely been explored in non-equilibrium system such as granular materials. In this paper, we experimentally studied the 2D melting in a driven granular model system at single particle level using video recording and particle tracking techniques. Measurements of orientational/translational correlation functions show evidences that the melting is a two-step transition. A novel concept of orientational/translational susceptibilities enable us to clearly resolve the intermediate hexatic phase. Our results are in excellent agreement with the two-step melting scenario predicted by KTHNY theory, and demonstrate that the KTHNY melting scenario can be extended to non-equilibrium systems. PMID:27052190

  17. Two-dimensional simulation of a direct-current microhollow cathode discharge

    NASA Astrophysics Data System (ADS)

    Kothnur, Prashanth S.; Raja, Laxminarayan L.

    2005-02-01

    Microhollow cathode discharges (MHCD's) are miniature direct-current discharges that operate at elevated pressures (several tens to hundreds of Torr) with electrode dimensions in the 10-100-μm range. MHCD's have been proposed for a number of applications based on their unique characteristics such as presence of intense excimer radiation and significant gas heating within the submillimeter discharge volume. A two-dimensional, self-consistent fluid model of a helium MHCD in the high-pressure (several hundreds of Torr), high-current (˜1mA) operating regime is presented in this study. Results indicate that the MHCD operates in an abnormal glow discharge mode with charged and excited metastable species with densities of ˜1020m-3, electron temperatures of approximately tens of eV, and gas temperatures of hundreds of Kelvin above room temperature. Significant discharge activity exists outside of the hollow region. The discharge volume and intensity increases with increasing current and becomes more confined with increasing pressures. Most predictions presented in this paper are in qualitative and quantitative agreement with experimental data for MHCD's under similar conditions.

  18. Direct fabrication of high-resolution three-dimensional polymeric scaffolds using electrohydrodynamic hot jet plotting

    NASA Astrophysics Data System (ADS)

    Wei, Chuang; Dong, Jingyan

    2013-02-01

    This paper presents the direct three-dimensional (3D) fabrication of polymer scaffolds with sub-10 µm structures using electrohydrodynamic jet (EHD-jet) plotting of melted thermoplastic polymers. Traditional extrusion-based fabrication approaches of 3D periodic porous structures are very limited in their resolution, due to the excessive pressure requirement for extruding highly viscous thermoplastic polymers. EHD-jet printing has become a high-resolution alternative to other forms of nozzle deposition-based fabrication approaches by generating micro-scale liquid droplets or a fine jet through the application of a large electrical voltage between the nozzle and the substrate. In this study, we successfully apply EHD-jet plotting technology with melted biodegradable polymer (polycaprolactone, or PCL) for the fabrication of 2D patterns and 3D periodic porous scaffold structures in potential tissue engineering applications. Process conditions (e.g. electrical voltage, pressure, plotting speed) have been thoroughly investigated to achieve reliable jet printing of fine filaments. We have demonstrated for the first time that the EHD-jet plotting process is capable of the fabrication of 3D periodic structures with sub-10 µm resolution, which has great potential in advanced biomedical applications, such as cell alignment and guidance.

  19. A facile method for integrating direct-write devices into three-dimensional printed parts

    NASA Astrophysics Data System (ADS)

    Chang, Yung-Hang; Wang, Kan; Wu, Changsheng; Chen, Yiwen; Zhang, Chuck; Wang, Ben

    2015-06-01

    Integrating direct-write (DW) devices into three-dimensional (3D) printed parts is key to continuing innovation in engineering applications such as smart material systems and structural health monitoring. However, this integration is challenging because: (1) most 3D printing techniques leave rough or porous surfaces if they are untreated; (2) the thermal sintering process required for most conductive inks could degrade the polymeric materials of 3D printed parts; and (3) the extensive pause needed for the DW process during layer-by-layer fabrication may cause weaker interlayer bonding and create structural weak points. These challenges are rather common during the insertion of conductive patterns inside 3D printed structures. As an avoidance tactic, we developed a simple ‘print-stick-peel’ method to transfer the DW device from the polytetrafluoroethylene or perfluoroalkoxy alkanes film onto any layer of a 3D printed object. This transfer can be achieved using the self-adhesion of 3D printing materials or applying additional adhesive. We demonstrated this method by transferring Aerosol Jet® printed strain sensors into parts fabricated by PolyJet™ printing. This report provides an investigation and discussion on the sensitivity, reliability, and influence embedding the sensor has on mechanical properties.

  20. Direct three-dimensional ultrasound-to-video registration using photoacoustic markers

    NASA Astrophysics Data System (ADS)

    Cheng, Alexis; Kang, Jin U.; Taylor, Russell H.; Boctor, Emad M.

    2013-06-01

    Modern surgical procedures often have a fusion of video and other imaging modalities to provide the surgeon with information support. This requires interventional guidance equipment and surgical navigation systems to register different tools and devices together, such as stereoscopic endoscopes and ultrasound (US) transducers. In this work, the focus is specifically on the registration between these two devices. Electromagnetic and optical trackers are typically used to acquire this registration, but they have various drawbacks typically leading to target registration errors (TRE) of approximately 3 mm. We introduce photoacoustic markers for direct three-dimensional (3-D) US-to-video registration. The feasibility of this method was demonstrated on synthetic and ex vivo porcine liver, kidney, and fat phantoms with an air-coupled laser and a motorized 3-D US probe. The resulting TRE for each experiment ranged from 380 to 850 μm with standard deviations ranging from 150 to 450 μm. We also discuss a roadmap to bring this system into the surgical setting and possible challenges along the way.

  1. Direct test of defect-mediated laser-induced melting theory for two-dimensional solids.

    PubMed

    Chaudhuri, Debasish; Sengupta, Surajit

    2006-01-01

    We investigate by direct numerical solution of appropriate renormalization flow equations the validity of a recent dislocation unbinding theory for laser-induced freezing and melting in two dimensions. The bare elastic moduli and dislocation fugacities are obtained for three different two-dimensional systems namely, the hard disk, inverse 12th power, and Derjaguin-Landau-Verwey-Overbeek potentials. A restricted Monte Carlo simulation sampling only configurations without dislocations is used to obtain these quantities. These are then used as inputs to the flow equations. Numerical solution of the flow equations then yields the phase diagrams. We conclude that (a) the flow equations need to be correct at least up to third order in defect fugacity to reproduce meaningful results, (b) there is excellent quantitative agreement between our results and earlier conventional Monte Carlo simulations for the hard disk system, and (c) while the qualitative form of the phase diagram is reproduced for systems with soft potentials there is some quantitative discrepancy which we explain.

  2. Direct three-dimensional ultrasound-to-video registration using photoacoustic markers.

    PubMed

    Cheng, Alexis; Kang, Jin U; Taylor, Russell H; Boctor, Emad M

    2013-06-01

    Modern surgical procedures often have a fusion of video and other imaging modalities to provide the surgeon with information support. This requires interventional guidance equipment and surgical navigation systems to register different tools and devices together, such as stereoscopic endoscopes and ultrasound (US) transducers. In this work, the focus is specifically on the registration between these two devices. Electromagnetic and optical trackers are typically used to acquire this registration, but they have various drawbacks typically leading to target registration errors (TRE) of approximately 3 mm. We introduce photoacoustic markers for direct three-dimensional (3-D) US-to-video registration. The feasibility of this method was demonstrated on synthetic and ex vivo porcine liver, kidney, and fat phantoms with an air-coupled laser and a motorized 3-D US probe. The resulting TRE for each experiment ranged from 380 to 850 μm with standard deviations ranging from 150 to 450 μm. We also discuss a roadmap to bring this system into the surgical setting and possible challenges along the way.

  3. Two-dimensional vanadium-doped ZnO nanosheet-based flexible direct current nanogenerator.

    PubMed

    Gupta, Manoj Kumar; Lee, Ju-Hyuck; Lee, Keun Young; Kim, Sang-Woo

    2013-10-22

    Here, we report the synthesis of lead-free single-crystalline two-dimensional (2D) vanadium(V)-doped ZnO nanosheets (NSs) and their application for high-performance flexible direct current (DC) power piezoelectric nanogenerators (NGs). The vertically aligned ZnO nanorods (NRs) converted to NS networks by V doping. Piezoresponse force microscopy studies reveal that vertical V-doped ZnO NS exhibit typical ferroelectricity with clear phase loops, butterfly, and well-defined hysteresis loops with a piezoelectric charge coefficient of up to 4 pm/V, even in 2D nanostructures. From pristine ZnO NR-based NGs, alternating current (AC)-type output current was observed, while from V-doped ZnO NS-based NGs, a DC-type output current density of up to 1.0 μAcm(-2) was surprisingly obtained under the same vertical compressive force. The growth mechanism, ferroelectric behavior, charge inverted phenomena, and high piezoelectric output performance observed from the V-doped ZnO NS are discussed in terms of the formation of an ionic layer of [V(OH)4(-)], permanent electric dipole, and the doping-induced resistive behavior of ZnO NS.

  4. Direct Observation of Three-dimensional Electroconvective Vortices on a Charge Selective Surface

    NASA Astrophysics Data System (ADS)

    Kwak, Rhokyun; Han, Jongyoon; Lee, Taikjin; Kwak, Ho-Young

    2015-11-01

    We present a visualization of three-dimensional electroconvective vortices (EC) by ion concentration polarization (ICP) on a cation selective membrane. The vortices are initiated between two transparent Nafion membranes under no-shear/shear conditions with various applied voltages and flow velocities. Fluorescent imaging and spatial Fourier transform allow us to capture vortex structures. In this 3-D system, EC shows three distinguished structures: i) polygonal shapes with no-shear and ii) transverse and/or iii) longitudinal vortex rolls with shear flow, which is reminiscent of 3-D Rayleigh-Benard instability. Under shear flow, as flow velocity (Reynolds number: Re) increases or voltage (electric Rayleigh number: Ra) decreases, pure longitudinal vortices are presented; in the inverse case, transverse vortices are also formed. It is noteworthy that if we confine EC in quasi 2-D system with high Ra (>10,000), we obtain pure transverse vortices; high Ra induces chaotic EC in this 3-D system, instead of 2-D stable transverse vortices. To the best of our knowledge, this is the first direct observation of 3-D EC, which will occur in realistic electrochemical devices, e.g. electrodialysis.

  5. A multi-dimensional finite volume cell-centered direct ALE solver for hydrodynamics

    NASA Astrophysics Data System (ADS)

    Clair, G.; Ghidaglia, J.-M.; Perlat, J.-P.

    2016-12-01

    In this paper we describe a second order multi-dimensional scheme, belonging to the class of direct Arbitrary Lagrangian-Eulerian (ALE) methods, for the solution of non-linear hyperbolic systems of conservation law. The scheme is constructed upon a cell-centered explicit Lagrangian solver completed with an edge-based upwinded formulation of the numerical fluxes, computed from the MUSCL-Hancock method, to obtain a full ALE formulation. Numerical fluxes depend on nodal grid velocities which are either set or computed to avoid most of the mesh problems typically encountered in purely Lagrangian simulations. In order to assess the robustness of the scheme, most results proposed in this paper have been obtained by computing the grid velocities as a fraction of the Lagrangian nodal velocities, the ratio being set before running the test case. The last part of the paper describes preliminary results about the triple point test case run in the ALE framework by computing the grid velocities with the fully adaptive Large Eddy Limitation (L.E.L.) method proposed in [1]. Such a method automatically computes the grid velocities at each node defining the mesh from the local characteristics of the flow. We eventually discuss the advantages and the drawback of the coupling.

  6. Stable Direct Adaptive Control of Linear Infinite-dimensional Systems Using a Command Generator Tracker Approach

    NASA Technical Reports Server (NTRS)

    Balas, M. J.; Kaufman, H.; Wen, J.

    1985-01-01

    A command generator tracker approach to model following contol of linear distributed parameter systems (DPS) whose dynamics are described on infinite dimensional Hilbert spaces is presented. This method generates finite dimensional controllers capable of exponentially stable tracking of the reference trajectories when certain ideal trajectories are known to exist for the open loop DPS; we present conditions for the existence of these ideal trajectories. An adaptive version of this type of controller is also presented and shown to achieve (in some cases, asymptotically) stable finite dimensional control of the infinite dimensional DPS.

  7. Direction Controlled Coulomb Drag in Coupled One-Dimensional Quantum Wires

    NASA Astrophysics Data System (ADS)

    Yamamoto, Michihisa

    2007-03-01

    In a one-dimensional electron gas (1DEG) with sufficiently low density at low temperature, Coulomb interaction becomes so dominant that Wigner crystallization can occur. Wigner crystal (WC) is generally characterized by collective motion of electrons and strong incompressibility. Therefore, in the presence of an external electrostatic potential, electrons forming a WC do not contribute to microscopic screening and only respond rigidly, whereas those of a Fermi liquid (FL) freely move to screen the external potential and produce a correlation hole. In this work we show that the difference between WC and FL allows us to control the direction of Coulomb drag in coupled pairs of 1DEG wires, each having two 2DEG leads. We prepare parallel coupled pairs of quantum wires in a 2DEG defined by Schottky gates to study the current drag between the two wires. The distance between the two wires and the electron density in each wire are all tunable with gate voltages. We inject a constant current into one of the wires (drive wire) and measure the induced drag current (or voltage drop for Idrag = 0) in the other wire (drag wire). Electrons in the drive wire usually drag electrons in the drag wire in the same direction because momentum is conserved in Coulombic scattering between the wires. However, when the electron density in the drive wire is sufficiently low that the drive wire has charge inhomogeneity and the electrons in the drag wire are strongly correlated, i.e. at low density, high perpendicular magnetic field and low temperature, the direction of the drag current can be reversed. The sign reversal occurs only when the drive wire is adjacent to the boundary between the drag wire and its lead, and can be controlled by changing the geometry of the coupled wires. These behaviors can be modeled by electron pump from WC in the drag wire to its 2DEG lead, driven by particle-like electrons in the drive wire. The drive wire electrons induce a positive screening charge only in the

  8. Three-dimensional culture of dental pulp stem cells in direct contact to tricalcium silicate cements.

    PubMed

    Widbiller, M; Lindner, S R; Buchalla, W; Eidt, A; Hiller, K-A; Schmalz, G; Galler, K M

    2016-03-01

    Calcium silicate cements are biocompatible dental materials applicable in contact with vital tissue. The novel tricalcium silicate cement Biodentine™ offers properties superior to commonly used mineral trioxide aggregate (MTA). Objective of this study was to evaluate its cytocompatibility and ability to induce differentiation and mineralization in three-dimensional cultures of dental pulp stem cells after direct contact with the material. Test materials included a new tricalcium silicate (Biodentine™, Septodont, Saint-Maur-des-Fossés, France), MTA (ProRoot® MTA, DENSPLY Tulsa Dental Specialities, Johnson City, TN, USA), glass ionomer (Ketac™ Molar Aplicap™, 3M ESPE, Seefeld, Germany), human dentin disks and polystyrene. Magnetic activated cell sorting for to the surface antigen STRO-1 was performed to gain a fraction enriched with mesenchymal stem cells. Samples were allowed to set and dental pulp stem cells in collagen carriers were placed on top. Scanning electron microscopy of tricalcium silicate cement surfaces with and without cells was conducted. Cell viability was measured for 14 days by MTT assay. Alkaline phosphatase activity was evaluated (days 3, 7, and 14) and expression of mineralization-associated genes (COL1A1, ALP, DSPP, and RUNX2) was quantified by real-time quantitative PCR. Nonparametric statistical analysis for cell viability and alkaline phosphatase data was performed to compare different materials as well as time points (Mann-Whitney U test, α = 0.05). Cell viability was highest on tricalcium silicate cement, followed by MTA. Viability on glass ionomer cement and dentin disks was significantly lower. Alkaline phosphatase activity was lower in cells on new tricalcium silicate cement compared to MTA, whereas expression patterns of marker genes were alike. Increased cell viability and similar levels of mineralization-associated gene expression in three-dimensional cell cultures on the novel tricalcium silicate cement and mineral

  9. Phase retrieval of singular scalar light fields using a two-dimensional directional wavelet transform and a spatial carrier.

    PubMed

    Federico, Alejandro; Kaufmann, Guillermo H

    2008-10-01

    We evaluate a method based on the two-dimensional directional wavelet transform and the introduction of a spatial carrier to retrieve optical phase distributions in singular scalar light fields. The performance of the proposed phase-retrieval method is compared with an approach based on Fourier transform. The advantages and limitations of the proposed method are discussed.

  10. Direct calculation of wall interferences and wall adaptation for two-dimensional flow in wind tunnels with closed walls

    NASA Technical Reports Server (NTRS)

    Amecke, Juergen

    1986-01-01

    A method for the direct calculation of the wall induced interference velocity in two dimensional flow based on Cauchy's integral formula was derived. This one-step method allows the calculation of the residual corrections and the required wall adaptation for interference-free flow starting from the wall pressure distribution without any model representation. Demonstrated applications are given.

  11. Rear actomyosin contractility-driven directional cell migration in three-dimensional matrices: a mechano-chemical coupling mechanism

    PubMed Central

    Chi, Qingjia; Yin, Tieying; Gregersen, Hans; Deng, Xiaoyan; Fan, Yubo; Zhao, Jingbo; Liao, Donghua; Wang, Guixue

    2014-01-01

    Cell migration is of vital importance in many biological processes, including organismal development, immune response and development of vascular diseases. For instance, migration of vascular smooth muscle cells from the media to intima is an essential part of the development of atherosclerosis and restenosis after stent deployment. While it is well characterized that cells use actin polymerization at the leading edge to propel themselves to move on two-dimensional substrates, the migration modes of cells in three-dimensional matrices relevant to in vivo environments remain unclear. Intracellular tension, which is created by myosin II activity, fulfils a vital role in regulating cell migration. We note that there is compelling evidence from theoretical and experimental work that myosin II accumulates at the cell rear, either isoform-dependent or -independent, leading to three-dimensional migration modes driven by posterior myosin II tension. The scenario is not limited to amoeboid migration, and it is also seen in mesenchymal migration in which a two-dimensional-like migration mode based on front protrusions is often expected, suggesting that there may exist universal underlying mechanisms. In this review, we aim to shed some light on how anisotropic myosin II localization induces cell motility in three-dimensional environments from a biomechanical view. We demonstrate an interesting mechanism where an interplay between mechanical myosin II recruitment and biochemical myosin II activation triggers directional migration in three-dimensional matrices. In the case of amoeboid three-dimensional migration, myosin II first accumulates at the cell rear to induce a slight polarization displayed as a uropod-like structure under the action of a tension-dependent mechanism. Subsequent biochemical signalling pathways initiate actomyosin contractility, producing traction forces on the adhesion system or creating prominent motile forces through blebbing activity, to drive cells

  12. Highly π electron-rich macro-aromatics: bis(p-aminophenyl)-carbo-benzenes and their DBA acyclic references.

    PubMed

    Rives, Arnaud; Baglai, Iaroslav; Malytskyi, Volodymyr; Maraval, Valérie; Saffon-Merceron, Nathalie; Voitenko, Zoia; Chauvin, Remi

    2012-09-11

    A series of stable quadrupolar bis(p-aminophenyl)-carbo-benzenes, featuring both donor-donor-donor π-frustration and central macro-aromaticity, is described and compared to the acyclic dibutatrienylacetylene (DBA) reference series.

  13. Numerical study of the directed polymer in a 1 + 3 dimensional random medium

    NASA Astrophysics Data System (ADS)

    Monthus, C.; Garel, T.

    2006-09-01

    The directed polymer in a 1+3 dimensional random medium is known to present a disorder-induced phase transition. For a polymer of length L, the high temperature phase is characterized by a diffusive behavior for the end-point displacement R2 ˜L and by free-energy fluctuations of order ΔF(L) ˜O(1). The low-temperature phase is characterized by an anomalous wandering exponent R2/L ˜Lω and by free-energy fluctuations of order ΔF(L) ˜Lω where ω˜0.18. In this paper, we first study the scaling behavior of various properties to localize the critical temperature Tc. Our results concerning R2/L and ΔF(L) point towards 0.76 < Tc ≤T2=0.79, so our conclusion is that Tc is equal or very close to the upper bound T2 derived by Derrida and coworkers (T2 corresponds to the temperature above which the ratio bar{Z_L^2}/(bar{Z_L})^2 remains finite as L ↦ ∞). We then present histograms for the free-energy, energy and entropy over disorder samples. For T ≫Tc, the free-energy distribution is found to be Gaussian. For T ≪Tc, the free-energy distribution coincides with the ground state energy distribution, in agreement with the zero-temperature fixed point picture. Moreover the entropy fluctuations are of order ΔS ˜L1/2 and follow a Gaussian distribution, in agreement with the droplet predictions, where the free-energy term ΔF ˜Lω is a near cancellation of energy and entropy contributions of order L1/2.

  14. Three-Dimensional Viscous Alternating Direction Implicit Algorithm and Strategies for Shape Optimization

    NASA Technical Reports Server (NTRS)

    Pandya, Mohagna J.; Baysal, Oktay

    1997-01-01

    A gradient-based shape optimization based on quasi-analytical sensitivities has been extended for practical three-dimensional aerodynamic applications. The flow analysis has been rendered by a fully implicit, finite-volume formulation of the Euler and Thin-Layer Navier-Stokes (TLNS) equations. Initially, the viscous laminar flow analysis for a wing has been compared with an independent computational fluid dynamics (CFD) code which has been extensively validated. The new procedure has been demonstrated in the design of a cranked arrow wing at Mach 2.4 with coarse- and fine-grid based computations performed with Euler and TLNS equations. The influence of the initial constraints on the geometry and aerodynamics of the optimized shape has been explored. Various final shapes generated for an identical initial problem formulation but with different optimization path options (coarse or fine grid, Euler or TLNS), have been aerodynamically evaluated via a common fine-grid TLNS-based analysis. The initial constraint conditions show significant bearing on the optimization results. Also, the results demonstrate that to produce an aerodynamically efficient design, it is imperative to include the viscous physics in the optimization procedure with the proper resolution. Based upon the present results, to better utilize the scarce computational resources, it is recommended that, a number of viscous coarse grid cases using either a preconditioned bi-conjugate gradient (PbCG) or an alternating-direction-implicit (ADI) method, should initially be employed to improve the optimization problem definition, the design space and initial shape. Optimized shapes should subsequently be analyzed using a high fidelity (viscous with fine-grid resolution) flow analysis to evaluate their true performance potential. Finally, a viscous fine-grid-based shape optimization should be conducted, using an ADI method, to accurately obtain the final optimized shape.

  15. Alterations in follicular fluid estradiol, progesterone and insulin concentrations during ovarian acyclicity in water buffalo (Bubalus bubalis).

    PubMed

    Khan, F A; Das, G K; Pande, Megha; Sarkar, M; Mahapatra, R K; Shankar, Uma

    2012-01-01

    Ovarian acyclicity is one of the most important causes of infertility in water buffalo. Recent studies have indicated alterations in the composition of follicular fluid during the condition. The aim of this study was to determine the changes in follicular fluid concentrations of estradiol, progesterone and insulin during ovarian acyclicity in water buffalo. Ovaries were collected from 50 acyclic and 95 cyclic (control) buffaloes and follicular fluid was aspirated from small (5.0-6.9 mm), medium (7.0-9.9 mm) and large (≥10.0 mm) sized follicles. Estradiol concentration was lower (P<0.0001) in acyclic (1.4 ± 0.09 ng/ml) than in cyclic (3.3 ± 0.18 ng/ml) buffaloes. Regardless of the ovarian cyclic status, there was an increase (P<0.01) in estradiol concentration with the increase in follicle size; the mean concentrations were 2.4 ± 0.16 ng/ml, 2.8 ± 0.29 ng/ml and 3.5 ± 0.41 ng/ml in small, medium and large follicles, respectively. A higher (P<0.001) progesterone concentration was recorded in acyclic (24.3 ± 2.61 ng/ml) compared to the cyclic (7.6 ± 0.79 ng/ml) group. Furthermore, acyclic buffaloes had a lower (P<0.05) concentration of insulin in the follicular fluid than that of cyclic buffaloes (15.2 ± 1.55 μIU/ml versus 25.9 ± 2.78 μIU/ml, respectively). In conclusion, acyclic buffaloes have lower concentrations of estradiol and insulin concurrent with higher concentrations of progesterone in the follicular fluid. These hormonal changes in the follicular microenvironment are possibly a manifestation of the disturbances in the normal follicular development leading to anovulation and anestrus in acyclic buffaloes.

  16. Screening of a minimal enriched P450 BM3 mutant library for hydroxylation of cyclic and acyclic alkanes.

    PubMed

    Weber, Evelyne; Seifert, Alexander; Antonovici, Mihaela; Geinitz, Christopher; Pleiss, Jürgen; Urlacher, Vlada B

    2011-01-21

    A minimal enriched P450 BM3 library was screened for the ability to oxidize inert cyclic and acyclic alkanes. The F87A/A328V mutant was found to effectively hydroxylate cyclooctane, cyclodecane and cyclododecane. F87V/A328F with high activity towards cyclooctane hydroxylated acyclic n-octane to 2-(R)-octanol (46% ee) with high regioselectivity (92%).

  17. One-pot synthesis of acyclic nucleosides from carbohydrate derivatives, by combination of tandem and sequential reactions.

    PubMed

    Boto, Alicia; Hernández, Dácil; Hernández, Rosendo; Alvarez, Eleuterio

    2007-12-07

    The design of processes which combine tandem and sequential reactions allows the transformation of readily available precursors into high-profit products. This strategy is illustrated by the one-pot synthesis of acyclic nucleosides, which are potential antiviral compounds, from readily available carbohydrates. The reaction conditions are mild, compatible with most functional groups. Depending on the starting sugar, both common and uncommon acyclic chains can be prepared. These polyhydroxylated chains can be combined with different bases to generate diversity.

  18. Three-Dimensional Stereoscopic Tracking Velocimetry and Experimental/Numerical Comparison of Directional Solidification

    NASA Technical Reports Server (NTRS)

    Lee, David; Ge, Yi; Cha, Soyoung Stephen; Ramachandran, Narayanan; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Measurement of three-dimensional (3-D) three-component velocity fields is of great importance in both ground and space experiments for understanding materials processing and fluid physics. The experiments in these fields most likely inhibit the application of conventional planar probes for observing 3-D phenomena. Here, we present the investigation results of stereoscopic tracking velocimetry (STV) for measuring 3-D velocity fields, which include diagnostic technology development, experimental velocity measurement, and comparison with analytical and numerical computation. STV is advantageous in system simplicity for building compact hardware and in software efficiency for continual near-real-time monitoring. It has great freedom in illuminating and observing volumetric fields from arbitrary directions. STV is based on stereoscopic observation of particles-Seeded in a flow by CCD sensors. In the approach, part of the individual particle images that provide data points is likely to be lost or cause errors when their images overlap and crisscross each other especially under a high particle density. In order to maximize the valid recovery of data points, neural networks are implemented for these two important processes. For the step of particle overlap decomposition, the back propagation neural network is utilized because of its ability in pattern recognition with pertinent particle image feature parameters. For the step of particle tracking, the Hopfield neural network is employed to find appropriate particle tracks based on global optimization. Our investigation indicates that the neural networks are very efficient and useful for stereoscopically tracking particles. As an initial assessment of the diagnostic technology performance, laminar water jets with and without pulsation are measured. The jet tip velocity profiles are in good agreement with analytical predictions. Finally, for testing in material processing applications, a simple directional solidification

  19. Enantioselective Heck arylations of acyclic alkenyl alcohols using a redox-relay strategy.

    PubMed

    Werner, Erik W; Mei, Tian-Sheng; Burckle, Alexander J; Sigman, Matthew S

    2012-12-14

    Progress in the development of asymmetric Heck couplings of arenes and acyclic olefins has been limited by a tenuous understanding of the factors that dictate selectivity in migratory insertion and β-hydride elimination. On the basis of key mechanistic insight recently garnered in the exploration of selective Heck reactions, we report here an enantioselective variant that delivers β-, γ-, or δ-aryl carbonyl products from acyclic alkenol substrates. The catalyst system imparts notable regioselectivity during migratory insertion and promotes the migration of the alkene's unsaturation toward the alcohol to ultimately form the ketone product. The reaction uses aryldiazonium salts as the arene source, yields enantiomeric products from opposite starting alkene configurations, and uses a readily accessible ligand. The racemic nature of the alkenol substrate does not bias the enantioselection.

  20. Cascade Cyclizations of Acyclic and Macrocyclic Alkynones: Studies toward the Synthesis of Phomactin A

    PubMed Central

    Ciesielski, Jennifer; Gandon, Vincent; Frontier, Alison J.

    2013-01-01

    A study of the reactivity and diastereoselectivity of the Lewis acid-promoted cascade cyclizations of both acyclic and macrocyclic alkynones is described. In these reactions, a β-iodoallenolate intermediate is generated via conjugate addition of iodide to an alkynone, followed by an intramolecular aldol reaction with a tethered aldehyde to afford a cyclohexenyl alcohol. The Lewis acid magnesium iodide (MgI2) was found to promote irreversible ring closure, while cyclizations using BF3·OEt2 as promoter occurred reversibly. For both acyclic and macrocyclic ynones, high diastereoselectivity was observed in the intramolecular aldol reaction. The MgI2 protocol for cyclization was applied to the synthesis of advanced intermediates relevant to the synthesis of phomactin natural products, during which a novel transannular cation-olefin cyclization was observed. DFT calculations were conducted to analyze the mechanism of this unusual MgI2-promoted process. PMID:23724905

  1. Three-dimensional application of the Johnson-King turbulence model for a boundary-layer direct method

    NASA Technical Reports Server (NTRS)

    Kavsaoglu, Mehmet S.; Kaynak, Unver; Van Dalsem, William R.

    1989-01-01

    The Johnson-King turbulence model as extended to three-dimensional flows was evaluated using finite-difference boundary-layer direct method. Calculations were compared against the experimental data of the well-known Berg-Elsenaar incompressible flow over an infinite swept-wing. The Johnson-King model, which includes the nonequilibrium effects in a developing turbulent boundary-layer, was found to significantly improve the predictive quality of a direct boundary-layer method. The improvement was especially visible in the computations with increased three-dimensionality of the mean flow, larger integral parameters, and decreasing eddy-viscosity and shear stress magnitudes in the streamwise direction; all in better agreement with the experiment than simple mixing-length methods.

  2. Three-dimensional application of the Johnson-King turbulence model for a boundary-layer direct method

    NASA Technical Reports Server (NTRS)

    Kavsaoglu, Mehmet S.; Kaynak, Unver; Van Dalsem, William R.

    1989-01-01

    The Johnson-King turbulence model as extended to three-dimensional flows was evaluated using finite-difference boundary-layer direct method. Calculations were compared against the experimental data of the well-known Berg-Elsenaar incompressible flow over an infinite swept-wing. The Johnson-King model, which includes the nonequilibrium effects in a developing turbulent boundary-layer, was found to significantly improve the predictive quality of a direct boundary-layer method. The improvement was especially visible in the computations with increased three-dimensionality of the mean flow, larger integral parameters, and decreasing eddy-viscosity and shear stress magnitudes in the streamwise direction; all in better agreement with the experiment than simple mixing-length methods.

  3. Ultra-directional source of longitudinal acoustic waves based on a two-dimensional solid/solid phononic crystal

    SciTech Connect

    Morvan, B.; Tinel, A.; Sainidou, R.; Rembert, P.; Vasseur, J. O.; Hladky-Hennion, A.-C.; Swinteck, N.; Deymier, P. A.

    2014-12-07

    Phononic crystals (PC) can be used to control the dispersion properties of acoustic waves, which are essential to direct their propagation. We use a PC-based two-dimensional solid/solid composite to demonstrate experimentally and theoretically the spatial filtering of a monochromatic non-directional wave source and its emission in a surrounding water medium as an ultra-directional beam with narrow angular distribution. The phenomenon relies on square-shaped equifrequency contours (EFC) enabling self-collimation of acoustic waves within the phononic crystal. Additionally, the angular width of collimated beams is controlled via the EFC size-shrinking when increasing frequency.

  4. A novel lithography process for 3D (three-dimensional) interconnect using an optical direct-writing exposure system

    NASA Astrophysics Data System (ADS)

    Azuma, T.; Sekiguchi, M.; Matsuo, M.; Kawasaki, A.; Hagiwara, K.; Matsui, H.; Kawamura, N.; Kishimoto, K.; Nakamura, A.; Washio, Y.

    2010-03-01

    A novel lithography process for 3D (Three-dimensional) interconnect was developed using an optical direct-writing exposure tool. A reflective IR (Infra-red) alignment system allows a direct detection of alignment marks both on front-side and back-side of wafer, and consequently allows feasible micro-fabrication for 3D interconnect using the reversed wafer. A combination of the optical direct-writing exposure tool of Dainippon Screen MFG. Co., Ltd. with the reflective IR alignment system and a high aspect chemically amplified resist of Tokyo Ohka Kogyo Co., Ltd. provides the lithography process exclusively for 12-inch wafer level 3D interconnect.

  5. Triphosgene-Pyridine Mediated Stereoselective Chlorination of Acyclic Aliphatic 1,3-Diols†

    PubMed Central

    Villalpando, Andrés; Saputra, Mirza A.; Tugwell, Thomas H.; Kartika, Rendy

    2015-01-01

    We describe a strategy to chlorinate stereocomplementary acyclic aliphatic 1,3-diols using a mixture of triphosgene and pyridine. While 1,3-anti diols readily led to 1,3-anti dichlorides, 1,3-syn diols must be converted to 1,3-syn diol monosilylethers to access the corresponding 1,3-syn dichlorides. These dichlorination protocols were operationally simple, very mild, and readily tolerated by advanced synthetic intermediates. PMID:26323232

  6. Acyclic ketones in the defensive secretion of a "daddy longlegs" (Leiobunum vittatum).

    PubMed

    Meinwald, J; Kluge, A F; Carrel, J E; Eisner, T

    1971-07-01

    The defensive secretion of the "daddy longlegs" Leiobunum vittatum was analyzed and found to contain the acyclic ketones 4-methylheptan-3-one and E-4,6-dimethyl-6-octen-3-one as its major organic components. Although 4-methylheptan-3-one has been found previously as an alarm substance in certain ant genera, the second component, whose structure is confirmed by synthesis, is new.

  7. Universal ultrafast sandpaper assisting rubbing method for room temperature fabrication of two-dimensional nanosheets directly on flexible polymer substrate

    NASA Astrophysics Data System (ADS)

    Yu, Yan; Jiang, Shenglin; Zhang, Guangzu; Zhou, Wenli; Miao, Xiangshui; Zeng, Yike; Wang, Jing; He, Jungang; Zhang, Ling

    2012-08-01

    In this letter, a universal ultrafast sandpaper assisting rubbing method was proposed to fabricate two-dimensional nanosheets (graphene, hexagonal boron nitride, tungsten disulfide, molybdenum disulfide) directly on flexible polymer substrate under room temperature. By two steps of rubbing progresses totally within 2 min, raw materials could be evolved to be thinner and to be attached onto polymer substrate. The final products showed high surface stability, which would be very useful during applications, and the physical mechanisms of surface stability were discussed. The micro-morphology evolutions of two-dimensional powders and sandpapers were tested to study the physical mechanisms of the method.

  8. An analysis of lower-dimensional approximations to the scalar dissipation rate using direct numerical simulations of plane jet flames

    SciTech Connect

    Chen, Jackie; Sankaran, Ramanan; Hawkes, Evatt R

    2009-05-01

    The difficulty of experimental measurements of the scalar dissipation rate in turbulent flames has required researchers to estimate the true three-dimensional (3D) scalar dissipation rate from one-dimensional (1D) or two-dimensional (2D) gradient measurements. In doing so, some relationship must be assumed between the true values and their lower dimensional approximations. We develop these relationships by assuming a form for the statistics of the gradient vector orientation, which enables several new results to be obtained and the true 3D scalar dissipation PDF to be reconstructed from the lower-dimensional approximations. We use direct numerical simulations (DNS) of turbulent plane jet flames to examine the orientation statistics, and verify our assumptions and final results. We develop and validate new theoretical relationships between the lower-dimensional and true moments of the scalar dissipation PDF assuming a log-normal true PDF. We compare PDFs reconstructed from lower-dimensional gradient projections with the true values and find an excellent agreement for a 2D simulated measurement and also for a 1D simulated measurement perpendicular to the mean flow variations. Comparisons of PDFs of thermal dissipation from DNS with those obtained via reconstruction from 2D experimental measurements show a very close match, indicating this PDF is not unique to a particular flame configuration. We develop a technique to reconstruct the joint PDF of the scalar dissipation and any other scalar, such as chemical species or temperature. Reconstructed conditional means of the hydroxyl mass fraction are compared with the true values and an excellent agreement is obtained.

  9. Stationary Wavelet-based Two-directional Two-dimensional Principal Component Analysis for EMG Signal Classification

    NASA Astrophysics Data System (ADS)

    Ji, Yi; Sun, Shanlin; Xie, Hong-Bo

    2017-06-01

    Discrete wavelet transform (WT) followed by principal component analysis (PCA) has been a powerful approach for the analysis of biomedical signals. Wavelet coefficients at various scales and channels were usually transformed into a one-dimensional array, causing issues such as the curse of dimensionality dilemma and small sample size problem. In addition, lack of time-shift invariance of WT coefficients can be modeled as noise and degrades the classifier performance. In this study, we present a stationary wavelet-based two-directional two-dimensional principal component analysis (SW2D2PCA) method for the efficient and effective extraction of essential feature information from signals. Time-invariant multi-scale matrices are constructed in the first step. The two-directional two-dimensional principal component analysis then operates on the multi-scale matrices to reduce the dimension, rather than vectors in conventional PCA. Results are presented from an experiment to classify eight hand motions using 4-channel electromyographic (EMG) signals recorded in healthy subjects and amputees, which illustrates the efficiency and effectiveness of the proposed method for biomedical signal analysis.

  10. Anti-EGFRvIII monoclonal antibody armed with 177Lu: in vivo comparison of macrocyclic and acyclic ligands

    PubMed Central

    Hens, Marc; Vaidyanathan, Ganesan; Zhao, Xiao-Guang; Bigner, Darell D.; Zalutsky, Michael R.

    2010-01-01

    Introduction Monoclonal antibody (mAb) L8A4 binds specifically to the epidermal growth factor receptor variant III (EGFRvIII) that is present on gliomas but not normal tissues, and is internalized rapidly after receptor binding. Because of the short range of its β-emissions, labeling this mAb with177Lu would be an attractive approach for the treatment of residual tumor margins remaining after surgical debulking of brain tumors. Materials and Methods L8A4 mAb was labeled with 177Lu using the acyclic ligands [(R)-2-Amino-3-(4-isothiocyanatophenyl)propyl]-trans-(S,S)-cyclohexane-1,2-diamine- pentaacetic acid (CHX-A″-DTPA) and 2-(4-Isothiocyanatobenzyl)-6-methyldiethylene- triaminepentaacetic acid (1B4M-DTPA), and the macrocyclic ligands S-2-(4- Isothiocyanatobenzyl)-1,4,7,10-tetraazacyclododecane-tetraacetic acid (C-DOTA) and α-(5-isothiocyanato-2-methoxyphenyl)-1,4,7,10-tetraazacyclododecane-1,4,7,10- tetraacetic acid (MeO-DOTA). Paired-label tissue distribution experiments were performed in athymic mice bearing subcutaneous EGFRvIII-expressing U87.)EGFR glioma xenografts over a period of 1 to 8 days to directly compare 177Lu-labeled L8A4 to L8A4 labeled with 125I using N-succinimidyl 4-guanidinomethyl-3-[125I]iodobenzoate ([125I]SGMIB). Results Except with C-DOTA, tumor uptake for the 177Lu-labeled mAb was significantly higher than the co-administered radioiodinated preparation; however, this was also the case for spleen, liver, bone and kidneys. Tumor:normal tissue ratios for 177Lu-1B4M-DTPA-L8A4 and to an even greater extent, 177Lu-MeO-DOTA-L8A4, were higher than those for [125I]SGMIB-L8A4 in most other tissues. Conclusions Tumor and normal tissue distribution patterns for this anti-EGFRvIII mAb were dependent on the nature of the bifunctional chelate used for 177Lu labeling. Optimal results were obtained with 1B4M-DTPA and MeO-DOTA, suggesting no clear advantage for acyclic vs. macrocyclic ligands for this application. PMID:20870149

  11. Fabrication of three-dimensional microfluidic channels inside glass using nanosecond laser direct writing.

    PubMed

    Liu, Changning; Liao, Yang; He, Fei; Shen, Yinglong; Chen, Danping; Cheng, Ya; Xu, Zhizhan; Sugioka, Koji; Midorikawa, Katsumi

    2012-02-13

    We show that fabrication of three-dimensional microfluidic channels embedded in glass can be achieved by using a Q-switched, frequency-doubled Nd:YAG laser. The processing mainly consists of two steps: (1) formation of hollow microfluidic channels in porous glass immersed in Rhodamine 6G dissolved in water by nanosecond laser ablation; and (2) postannealing of the fabricated porous glass sample at 1120 °C for consolidation of the sample. In particular, a bilayer microfluidic structure is created in glass substrate using this technique for showcasing its capability of three-dimensional structuring.

  12. Bayesian reconstruction of P(r) directly from two-dimensional detector images via a Markov chain Monte Carlo method

    PubMed Central

    Paul, Sudeshna; Friedman, Alan M.; Bailey-Kellogg, Chris; Craig, Bruce A.

    2013-01-01

    The interatomic distance distribution, P(r), is a valuable tool for evaluating the structure of a molecule in solution and represents the maximum structural information that can be derived from solution scattering data without further assumptions. Most current instrumentation for scattering experiments (typically CCD detectors) generates a finely pixelated two-dimensional image. In contin­uation of the standard practice with earlier one-dimensional detectors, these images are typically reduced to a one-dimensional profile of scattering inten­sities, I(q), by circular averaging of the two-dimensional image. Indirect Fourier transformation methods are then used to reconstruct P(r) from I(q). Substantial advantages in data analysis, however, could be achieved by directly estimating the P(r) curve from the two-dimensional images. This article describes a Bayesian framework, using a Markov chain Monte Carlo method, for estimating the parameters of the indirect transform, and thus P(r), directly from the two-dimensional images. Using simulated detector images, it is demonstrated that this method yields P(r) curves nearly identical to the reference P(r). Furthermore, an approach for evaluating spatially correlated errors (such as those that arise from a detector point spread function) is evaluated. Accounting for these errors further improves the precision of the P(r) estimation. Experimental scattering data, where no ground truth reference P(r) is available, are used to demonstrate that this method yields a scattering and detector model that more closely reflects the two-dimensional data, as judged by smaller residuals in cross-validation, than P(r) obtained by indirect transformation of a one-dimensional profile. Finally, the method allows concurrent estimation of the beam center and D max, the longest interatomic distance in P(r), as part of the Bayesian Markov chain Monte Carlo method, reducing experimental effort and providing a well defined protocol for these

  13. Bayesian reconstruction of P(r) directly from two-dimensional detector images via a Markov chain Monte Carlo method.

    PubMed

    Paul, Sudeshna; Friedman, Alan M; Bailey-Kellogg, Chris; Craig, Bruce A

    2013-04-01

    The interatomic distance distribution, P(r), is a valuable tool for evaluating the structure of a molecule in solution and represents the maximum structural information that can be derived from solution scattering data without further assumptions. Most current instrumentation for scattering experiments (typically CCD detectors) generates a finely pixelated two-dimensional image. In contin-uation of the standard practice with earlier one-dimensional detectors, these images are typically reduced to a one-dimensional profile of scattering inten-sities, I(q), by circular averaging of the two-dimensional image. Indirect Fourier transformation methods are then used to reconstruct P(r) from I(q). Substantial advantages in data analysis, however, could be achieved by directly estimating the P(r) curve from the two-dimensional images. This article describes a Bayesian framework, using a Markov chain Monte Carlo method, for estimating the parameters of the indirect transform, and thus P(r), directly from the two-dimensional images. Using simulated detector images, it is demonstrated that this method yields P(r) curves nearly identical to the reference P(r). Furthermore, an approach for evaluating spatially correlated errors (such as those that arise from a detector point spread function) is evaluated. Accounting for these errors further improves the precision of the P(r) estimation. Experimental scattering data, where no ground truth reference P(r) is available, are used to demonstrate that this method yields a scattering and detector model that more closely reflects the two-dimensional data, as judged by smaller residuals in cross-validation, than P(r) obtained by indirect transformation of a one-dimensional profile. Finally, the method allows concurrent estimation of the beam center and Dmax, the longest interatomic distance in P(r), as part of the Bayesian Markov chain Monte Carlo method, reducing experimental effort and providing a well defined protocol for these

  14. The direct field boundary impedance of two-dimensional periodic structures with application to high frequency vibration prediction.

    PubMed

    Langley, Robin S; Cotoni, Vincent

    2010-04-01

    Large sections of many types of engineering construction can be considered to constitute a two-dimensional periodic structure, with examples ranging from an orthogonally stiffened shell to a honeycomb sandwich panel. In this paper, a method is presented for computing the boundary (or edge) impedance of a semi-infinite two-dimensional periodic structure, a quantity which is referred to as the direct field boundary impedance matrix. This terminology arises from the fact that none of the waves generated at the boundary (the direct field) are reflected back to the boundary in a semi-infinite system. The direct field impedance matrix can be used to calculate elastic wave transmission coefficients, and also to calculate the coupling loss factors (CLFs), which are required by the statistical energy analysis (SEA) approach to predicting high frequency vibration levels in built-up systems. The calculation of the relevant CLFs enables a two-dimensional periodic region of a structure to be modeled very efficiently as a single subsystem within SEA, and also within related methods, such as a recently developed hybrid approach, which couples the finite element method with SEA. The analysis is illustrated by various numerical examples involving stiffened plate structures.

  15. Direct laser writing of sub-50 nm nanofluidic channels buried in glass for three-dimensional micro-nanofluidic integration.

    PubMed

    Liao, Yang; Cheng, Ya; Liu, Changning; Song, Jiangxin; He, Fei; Shen, Yinglong; Chen, Danping; Xu, Zhizhan; Fan, Zhichao; Wei, Xunbin; Sugioka, Koji; Midorikawa, Katsumi

    2013-04-21

    We report on the fabrication of nanofluidic channels directly buried in silicate glass with transverse widths down to less than 50 nm using three-dimensional (3D) femtosecond laser direct writing. Using this technique, integrated micro-nanofluidic systems have been produced by simultaneously writing micro- and nanofluidic channels arranged into various 3D configurations in glass substrates. The fabricated micro- and nanofluidic systems have been used to demonstrate DNA analysis, e.g. stretching of DNA molecules. Our technique offers new opportunities to develop novel 3D micro-nanofluidic systems for a variety of lab-on-a-chip applications.

  16. Directionality of replication fork movement determined by two-dimensional native-native DNA agarose gel electrophoresis.

    PubMed

    Ivessa, Andreas S

    2013-01-01

    The analysis of replication intermediates by the neutral-neutral two-dimensional agarose gel technique allows determining the chromosomal positions where DNA replication initiates, whether replication forks pause or stall at specific sites, or whether two DNA molecules undergo DNA recombination events. This technique does not, however, immediately tell in which direction replication forks migrate through the DNA region under investigation. Here, we describe the procedure to determine the direction of replication fork progression by carrying out a restriction enzyme digest of DNA imbedded in agarose after the completion of the first dimension of a 2D gel.

  17. Hydroxyl-directed stereoselective diboration of alkenes.

    PubMed

    Blaisdell, Thomas P; Caya, Thomas C; Zhang, Liang; Sanz-Marco, Amparo; Morken, James P

    2014-07-02

    An alkoxide-catalyzed directed diboration of alkenyl alcohols is described. This reaction occurs in a stereoselective fashion and is demonstrated with cyclic and acyclic homoallylic and bishomoallylic alcohol substrates. After oxidation, the reaction generates 1,2-diols such that the process represents a method for the stereoselective directed dihydroxylation of alkenes.

  18. Projection of two-dimensional diffusion in narrow asymmetric channels onto the longitudinal direction

    SciTech Connect

    Pineda, Inti; Dagdug, Leonardo

    2014-01-14

    Diffusive transport of particles is a ubiquitous feature of physical, chemical and biological systems. Typical structures like pores, tubes or fibers, are quasi one-dimensional, such that we need to solve 2+1 or 3+1 dimensional differential equations to describe correctly transport along them. The so-called Fick-Jacobs approach dramatically simplifies the problem if one assumes that a solute distribution in any cross-section of the channel is uniform at equilibrium. That study focuses on the mapping of the diffusion equation in a two-dimensional narrow asymmetric channel of varying cross section onto the longitudinal coordinate. We present a generalization to the case of an asymmetric channel using the projection method introduced earlier by Kalinay and Percus. We derive an expansion of the effective diffusion coefficient, which represents corrections to the Fick-Jacobs equation and contains the well-known previous results as special cases. Finally, we study numerically some specific two-dimensional asymmetric channel configurations to test and show the broader applicability of this effective diffusion coefficient formula.

  19. Projection of two-dimensional diffusion in narrow asymmetric channels onto the longitudinal direction

    NASA Astrophysics Data System (ADS)

    Pineda, Inti; Dagdug, Leonardo

    2014-01-01

    Diffusive transport of particles is a ubiquitous feature of physical, chemical and biological systems. Typical structures like pores, tubes or fibers, are quasi one-dimensional, such that we need to solve 2+1 or 3+1 dimensional differential equations to describe correctly transport along them. The so-called Fick-Jacobs approach dramatically simplifies the problem if one assumes that a solute distribution in any cross-section of the channel is uniform at equilibrium. That study focuses on the mapping of the diffusion equation in a two-dimensional narrow asymmetric channel of varying cross section onto the longitudinal coordinate. We present a generalization to the case of an asymmetric channel using the projection method introduced earlier by Kalinay and Percus. We derive an expansion of the effective diffusion coefficient, which represents corrections to the Fick-Jacobs equation and contains the well-known previous results as special cases. Finally, we study numerically some specific two-dimensional asymmetric channel configurations to test and show the broader applicability of this effective diffusion coefficient formula.

  20. Follicular characteristics and intrafollicular concentrations of nitric oxide and ascorbic acid during ovarian acyclicity in water buffalo (Bubalus bubalis).

    PubMed

    Khan, Firdous Ahmad; Das, Goutam Kumar

    2012-01-01

    The objective of this study was to examine the follicular characteristics and intrafollicular concentrations of nitric oxide and ascorbic acid during ovarian acyclicity in buffaloes. Ovaries were collected from 56 acyclic and 95 cyclic buffaloes at slaughter, surface follicle number was counted and follicles were classified into small (5.0-6.9 mm), medium (7.0-9.9 mm), and large (≥ 10.0 mm) size categories based on their diameter. Follicular fluid was aspirated and assayed for nitric oxide, ascorbic acid, estradiol, and progesterone. Acyclic buffaloes had a higher (P<0.05) number of medium-sized follicles and a lower (P<0.001) number of large follicles than the cyclic ones. In acyclic animals, the number of large follicles was lower (P<0.01) than in medium size category which in turn was lower (P<0.001) than the number of small follicles. In contrast, the number of medium and large follicles was not different (P>0.05) in the cyclic control. However, the number of small-sized follicles was higher (P<0.001) compared to the other two categories. The incidence of large-sized follicles was lower (P<0.05) in acyclic buffalo population compared to the cyclic control. Evaluation of estrogenic status demonstrated that all the follicles of acyclic buffaloes are estrogen-inactive (E (2)/P (4) ratio<1). Small- and medium-sized follicles of acyclic buffaloes had higher concentrations of nitric oxide (P<0.05 and P<0.001, respectively) and lower concentrations of ascorbic acid (P<0.05 and P<0.01, respectively) than the corresponding size estrogen-active follicles of their cyclic counterparts. In conclusion, this study indicates that follicular development continues during acyclicity in buffaloes. Although follicles in some acyclic buffaloes attain a size corresponding to morphological dominance, they are unable to achieve functional dominance, perhaps due to an altered balance of intrafollicular nitric oxide and ascorbic acid and, as a result, these follicles instead of

  1. Template-directed convective assembly of three-dimensional face-centered-cubic colloidal crystals

    NASA Astrophysics Data System (ADS)

    Zhang, Fan

    2003-03-01

    We have demonstrated that square two-dimensional grating templates can drive the growth of three-dimensional (3D), face-centered-cubic (FCC) colloidal crystals by convective assembly. The square symmetry (i.e. (100) planes parallel to the substrate) of the underlying template was transferred to the colloidal crystal and maintained throughout its growth of 50 layers. We characterized crystals grown on flat and on templated substrates using electron microscopy and small-angle x-ray scattering (SAXS). SAXS measurements of the templated samples clearly show four-fold diffraction patterns arising from FCC domains without stacking faults. The work is partially supported by NSF grants DMR-0203378, the PENN MRSEC, DMR-0079909, and NASA grant NAG8-2172.

  2. Meniscus-confined three-dimensional electrodeposition for direct writing of wire bonds.

    PubMed

    Hu, Jie; Yu, Min-Feng

    2010-07-16

    Continued progress in the electronics industry depends on downsizing, to a few micrometers, the wire bonds required for wiring integrated chips into circuit boards. We developed an electrodeposition method that exploits the thermodynamic stability of a microscale or nanoscale liquid meniscus to "write" pure copper and platinum three-dimensional structures of designed shapes and sizes in an ambient air environment. We demonstrated an automated wire-bonding process that enabled wire diameters of less than 1 micrometer and bond sizes of less than 3 micrometers, with a breakdown current density of more than 10(11) amperes per square meter for the wire bonds. The technology was used to fabricate high-density and high-quality interconnects, as well as complex three-dimensional microscale and even nanoscale metallic structures.

  3. Bacterial twitching motility is coordinated by a two-dimensional tug-of-war with directional memory

    NASA Astrophysics Data System (ADS)

    Marathe, Rahul; Meel, Claudia; Schmidt, Nora C.; Dewenter, Lena; Kurre, Rainer; Greune, Lilo; Alexander Schmidt, M.; Müller, Melanie J. I.; Lipowsky, Reinhard; Maier, Berenike; Klumpp, Stefan

    2014-05-01

    Type IV pili are ubiquitous bacterial motors that power surface motility. In peritrichously piliated species, it is unclear how multiple pili are coordinated to generate movement with directional persistence. Here we use a combined theoretical and experimental approach to test the hypothesis that multiple pili of Neisseria gonorrhoeae are coordinated through a tug-of-war. Based on force-dependent unbinding rates and pilus retraction speeds measured at the level of single pili, we build a tug-of-war model. Whereas the one-dimensional model robustly predicts persistent movement, the two-dimensional model requires a mechanism of directional memory provided by re-elongation of fully retracted pili and pilus bundling. Experimentally, we confirm memory in the form of bursts of pilus retractions. Bursts are seen even with bundling suppressed, indicating re-elongation from stable core complexes as the key mechanism of directional memory. Directional memory increases the surface range explored by motile bacteria and likely facilitates surface colonization.

  4. Direct measurements of forces induced by Bloch surface waves in a one-dimensional photonic crystal.

    PubMed

    Shilkin, Daniil A; Lyubin, Evgeny V; Soboleva, Irina V; Fedyanin, Andrey A

    2015-11-01

    An experimental study of the interaction between a single dielectric microparticle and the evanescent field of the Bloch surface wave in a one-dimensional (1D) photonic crystal is reported. The Bloch surface wave-induced forces on a 1 μm polystyrene sphere were measured by photonic force microscopy. The results demonstrate the potential of 1D photonic crystals for the optical manipulation of microparticles and suggest a novel approach for utilizing light in lab-on-a-chip devices.

  5. Two dimensional beam smoothing by spectral dispersion for direct drive inertial confinement fusion

    SciTech Connect

    Rothenberg, J.E.

    1995-07-11

    Two dimensional smoothing by spectral dispersion is analyzed by using diffraction theory calculations. It is shown that by using standard frequency modulated light one can obtain bandwidth limited smoothing over integration times relevant to inertial confinement fusion (about 1 nsec) with modest induced beam divergence. At longer integration times one can obtain bandwidth limited smoothing by increasing the divergence and/or by using more advanced phase modulation methods.

  6. Direct observation of charge state in the quasi-one-dimensional conductor Li0.9Mo6O17

    PubMed Central

    Wu, Guoqing; Ye, Xiao-shan; Zeng, Xianghua; Wu, Bing; Clark, W. G.

    2016-01-01

    The quasi-one-dimensional conductor Li0.9Mo6O17 has been of great interest because of its unusual properties. It has a conducting phase with properties different from a simple Fermi liquid, a poorly understood “insulating” phase as indicated by a metal-“insulator” crossover (a mystery for over 30 years), and a superconducting phase which may involve spin triplet Cooper pairs as a three-dimensional (p-wave) non-conventional superconductor. Recent evidence suggests a density wave (DW) gapping regarding the metal-“insulator” crossover. However, the nature of the DW, such as whether it is due to the change in the charge state or spin state, and its relationship to the dimensional crossover and to the spin triplet superconductivity, remains elusive. Here by performing 7Li-/95Mo-nuclear magnetic resonance (NMR) spectroscopy, we directly observed the charge state which shows no signature of change in the electric field gradient (nuclear quadrupolar frequency) or in the distribution of it, thus providing direct experimental evidences demonstrating that the long mysterious metal-“insulator” crossover is not due to the charge density wave (CDW) that was thought, and the nature of the DW gapping is not CDW. This discovery opens a parallel path to the study of the electron spin state and its possible connections to other unusual properties. PMID:26853454

  7. Direct-Write, Self-Aligned Electrospinning on Paper for Controllable Fabrication of Three-Dimensional Structures.

    PubMed

    Luo, Guoxi; Teh, Kwok Siong; Liu, Yumeng; Zang, Xining; Wen, Zhiyu; Lin, Liwei

    2015-12-23

    Electrospinning, a process that converts a solution or melt droplet into an ejected jet under a high electric field, is a well-established technique to produce one-dimensional (1D) fibers or two-dimensional (2D) randomly arranged fibrous meshes. Nevertheless, the direct electrospinning of fibers into controllable three-dimensional (3D) architectures is still a nascent technology. Here, we apply near-field electrospinning (NFES) to directly write arbitrarily shaped 3D structures through consistent and spatially controlled fiber-by-fiber stacking of polyvinylidene fluoride (PVDF) fibers. An element central to the success of this 3D electrospinning is the use of a printing paper placed on the grounded conductive plate and acting as a fiber collector. Once deposited on the paper, residual solvents from near-field electrospun fibers can infiltrate the paper substrate, enhancing the charge transfer between the deposited fibers and the ground plate via the fibrous network within the paper. Such charge transfer grounds the deposited fibers and turns them into locally fabricated electrical poles, which attract subsequent in-flight fibers to deposit in a self-aligned manner on top of each other. This process enables the design and controlled fabrication of electrospun 3D structures such as grids, walls, hollow cylinders, and other 3D logos. As such, this technique has the potential to advance the existing electrospinning technologies in constructing 3D structures for biomedical, microelectronics, and MEMS/NMES applications.

  8. Directed Abelian algebras and their application to stochastic models

    NASA Astrophysics Data System (ADS)

    Alcaraz, F. C.; Rittenberg, V.

    2008-10-01

    With each directed acyclic graph (this includes some D -dimensional lattices) one can associate some Abelian algebras that we call directed Abelian algebras (DAAs). On each site of the graph one attaches a generator of the algebra. These algebras depend on several parameters and are semisimple. Using any DAA, one can define a family of Hamiltonians which give the continuous time evolution of a stochastic process. The calculation of the spectra and ground-state wave functions (stationary state probability distributions) is an easy algebraic exercise. If one considers D -dimensional lattices and chooses Hamiltonians linear in the generators, in finite-size scaling the Hamiltonian spectrum is gapless with a critical dynamic exponent z=D . One possible application of the DAA is to sandpile models. In the paper we present this application, considering one- and two-dimensional lattices. In the one-dimensional case, when the DAA conserves the number of particles, the avalanches belong to the random walker universality class (critical exponent στ=3/2 ). We study the local density of particles inside large avalanches, showing a depletion of particles at the source of the avalanche and an enrichment at its end. In two dimensions we did extensive Monte-Carlo simulations and found στ=1.780±0.005 .

  9. Understanding effects of matrix protease and matrix organization on directional persistence and translational speed in three-dimensional cell migration.

    PubMed

    Zaman, Muhammad H; Matsudaira, Paul; Lauffenburger, Douglas A

    2007-01-01

    Recent studies have shown significant differences in migration mechanisms between two- and three-dimensional environments. While experiments have suggested a strong dependence of in vivo migration on both structure and proteolytic activity, the underlying biophysics of such dependence has not been studied adequately. In addition, the existing models of persistent random walk migration are primarily based on two-dimensional movement and do not account for the effect of proteolysis or matrix inhomogeneity. Using lattice Monte Carlo methods, we present a model to study the role of matrix metallo-proteases (MMPs) on directional persistence and speed. The simulations account for a given cell's ability to deform as well as to digest the matrix as the cell moves in three dimensions. Our results show a bimodal dependence of speed and persistence on matrix pore size and suggest high sensitivity on MMP activity, which is in very good agreement with experimental studies carried out in 3D matrices.

  10. Computational solutions of three-dimensional advection-diffusion equation using fourth order time efficient alternating direction implicit scheme

    NASA Astrophysics Data System (ADS)

    Saqib, Muhammad; Hasnain, Shahid; Mashat, Daoud Suleiman

    2017-08-01

    To develop an efficient numerical scheme for three-dimensional advection diffusion equation, higher order ADI method was proposed. 2nd and fourth order ADI schemes were used to handle such problem. Von Neumann stability analysis shows that Alternating Direction Implicit scheme is unconditionally stable. The accuracy and efficiency of such schemes was depicted by two test problems. Numerical results for two test problems were carried out to establish the performance of the given method and to compare it with the others Typical methods. Fourth order ADI method were found to be very efficient and stable for solving three dimensional Advection Diffusion Equation. The proposed methods can be implemented for solving non-linear problems arising in engineering and physics.

  11. A Practical Approach for Scalable Conjunctive Query Answering on Acyclic {EL}^+ Knowledge Base

    NASA Astrophysics Data System (ADS)

    Mei, Jing; Liu, Shengping; Xie, Guotong; Kalyanpur, Aditya; Fokoue, Achille; Ni, Yuan; Li, Hanyu; Pan, Yue

    Conjunctive query answering for {EL}^{++} ontologies has recently drawn much attention, as the Description Logic {EL}^{++} captures the expressivity of many large ontologies in the biomedical domain and is the foundation for the OWL 2 EL profile. In this paper, we propose a practical approach for conjunctive query answering in a fragment of {EL}^{++}, namely acyclic {EL}^+, that supports role inclusions. This approach can be implemented with low cost by leveraging any existing relational database management system to do the ABox data completion and query answering. We conducted a preliminary experiment to evaluate our approach using a large clinical data set and show our approach is practical.

  12. Next generation macrocyclic and acyclic cationic lipids for gene transfer: Synthesis and in vitro evaluation.

    PubMed

    Jubeli, Emile; Maginty, Amanda B; Abdul Khalique, Nada; Raju, Liji; Abdulhai, Mohamad; Nicholson, David G; Larsen, Helge; Pungente, Michael D; Goldring, William P D

    2015-10-01

    Previously we reported the synthesis and in vitro evaluation of four novel, short-chain cationic lipid gene delivery vectors, characterized by acyclic or macrocyclic hydrophobic regions composed of, or derived from, two 7-carbon chains. Herein we describe a revised synthesis of an expanded library of related cationic lipids to include extended chain analogues, their formulation with plasmid DNA (pDNA) and in vitro delivery into Chinese hamster ovarian (CHO-K1) cells. The formulations were evaluated against each other based on structural differences in the hydrophobic domain and headgroup. Structurally the library is divided into four sets based on lipids derived from two 7- or two 11-carbon hydrophobic chains, C7 and C11 respectively, which possess either a dimethylamine or a trimethylamine derived headgroup. Each set includes four cationic lipids based on an acyclic or macrocyclic, saturated or unsaturated hydrophobic domain. All lipids were co-formulated with the commercial cationic lipid 1,2-dimyristoyl-sn-glycero-3-ethylphosphocholine (EPC) in a 1:1 molar ratio, along with one of two distinct neutral co-lipids, cholesterol or 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) in an overall cationic-to-neutral lipid molar ratio of 3:2. Binding of lipid formulations with DNA, and packing morphology associated with the individual lipid-DNA complexes were characterized by gel electrophoresis and small angle X-ray diffraction (SAXD), respectively. As a general trend, lipoplex formulations based on mismatched binary cationic lipids, composed of a shorter C7 lipid and the longer lipid EPC (C14), were generally associated with higher transfection efficiency and lower cytotoxicity than their more closely matched C11/EPC binary lipid formulation counterparts. Furthermore, the cyclic lipids gave transfection levels as high as or greater than their acyclic counterparts, and formulations with cholesterol exhibited higher transfection and lower cytotoxicity than those

  13. Direct Observation of Mode-Coupling Instability in Two-Dimensional Plasma Crystals

    SciTech Connect

    Coueedel, L.; Nosenko, V.; Ivlev, A. V.; Zhdanov, S. K.; Thomas, H. M.; Morfill, G. E.

    2010-05-14

    Dedicated experiments on melting of two-dimensional plasma crystals were carried out. The melting was always accompanied by spontaneous growth of the particle kinetic energy, suggesting a universal plasma-driven mechanism underlying the process. By measuring three principal dust-lattice wave modes simultaneously, it is unambiguously demonstrated that the melting occurs due to the resonance coupling between two of the dust-lattice modes. The variation of the wave modes with the experimental conditions, including the emergence of the resonant (hybrid) branch, reveals exceptionally good agreement with the theory of mode-coupling instability.

  14. DNA origami-directed, discrete three-dimensional plasmonic tetrahedron nanoarchitectures with tailored optical chirality.

    PubMed

    Dai, Gaole; Lu, Xuxing; Chen, Zhong; Meng, Chun; Ni, Weihai; Wang, Qiangbin

    2014-04-23

    Discrete, three-dimensional (3D) gold nanoparticle (AuNP) tetrahedron nanoarchitectures are successfully self-assembled with DNA origami as template with high purity (>85%). A distinct plasmonic chiral response is experimentally observed from the AuNP tetrahedron nanoarchitectures and appears in a configuration-dependent manner. The chiral optical properties are then rationally engineered by modifying the structural parameters including the AuNP size and interparticle distance. Theoretical study of the AuNP tetrahedron nanoarchitectures shows the dependence of the chiral optical property on the AuNP size and interparticle distance, consistent with the ensemble averaged measurements.

  15. Regio- and stereospecific rhodium-catalyzed allylic alkylation with an acyl anion equivalent: an approach to acyclic α-ternary β,γ-unsaturated aryl ketones.

    PubMed

    Turnbull, Ben W H; Chae, Jungha; Oliver, Samuel; Evans, P Andrew

    2017-05-01

    The regio- and stereospecific rhodium-catalyzed allylic alkylation of secondary allylic carbonates with cyanohydrin pronucleophiles facilitates the direct construction of acyclic α-ternary β,γ-unsaturated aryl ketones. Interestingly, this study illustrates the impact of deaggregating agents on regiocontrol and the electronic nature of the aryl component to suppress olefin isomerization. In addition, we demonstrate that the dimethylamino substituent, which modulates the pKa of the α-ternary β,γ-unsaturated aryl ketone, provides a useful synthetic handle for further functionalization via Kumada cross-coupling of the aryl trimethylammonium salt. Finally, the stereospecific alkylation of a chiral nonracemic secondary allylic carbonate affords the enantioenriched α-ternary aryl ketone, which was employed in a formal synthesis of trichostatic acid to illustrate that the allylic alkylation proceeds with net retention of configuration.

  16. Three-dimensional direct numerical simulation of soot formation and transport in a temporally evolving nonpremixed ethylene jet flame

    SciTech Connect

    Lignell, David O.; Chen, Jacqueline H.; Smith, Philip J.

    2008-10-15

    Three-dimensional direct numerical simulation of soot formation with complex chemistry is presented. The simulation consists of a temporally evolving, planar, nonpremixed ethylene jet flame with a validated, 19-species reduced mechanism. A four-step, three-moment, semiempirical soot model is employed. Previous two-dimensional decaying turbulence simulations have shown the importance of multidimensional flame dynamical effects on soot concentration [D.O. Lignell, J.H. Chen, P.J. Smith, T. Lu, C.K. Law, Combust. Flame 151 (1-2) (2007) 2-28]. It was shown that flame curvature strongly impacts the diffusive motion of the flame relative to soot (which is essentially convected with the flow), resulting in soot being differentially transported toward or away from the flame zone. The proximity of the soot to the flame directly influences soot reactivity and radiative properties. Here, the analysis is extended to three dimensions in a temporal jet configuration with mean shear. Results show that similar local flame dynamic effects of strain and curvature are important, but that enhanced turbulent mixing of fuel and oxidizer streams has a first-order effect on transport of soot toward flame zones. Soot modeling in turbulent flames is a challenge due to the complexity of soot formation and transport processes and the lack of detailed experimental soot-flame-flow structural data. The present direct numerical simulation provides the first step toward providing such data. (author)

  17. Tissue-engineered 3-dimensional (3D) microenvironment enhances the direct reprogramming of fibroblasts into cardiomyocytes by microRNAs

    PubMed Central

    Li, Yanzhen; Dal-Pra, Sophie; Mirotsou, Maria; Jayawardena, Tilanthi M.; Hodgkinson, Conrad P.; Bursac, Nenad; Dzau, Victor J.

    2016-01-01

    We have recently shown that a combination of microRNAs, miR combo, can directly reprogram cardiac fibroblasts into functional cardiomyocytes in vitro and in vivo. Reprogramming of cardiac fibroblasts by miR combo in vivo is associated with improved cardiac function following myocardial infarction. However, the efficiency of direct reprogramming in vitro is relatively modest and new strategies beyond the traditional two-dimensional (2D) culture should be identified to improve reprogramming process. Here, we report that a tissue-engineered three-dimensional (3D) hydrogel environment enhanced miR combo reprogramming of neonatal cardiac and tail-tip fibroblasts. This was associated with significantly increased MMPs expression in 3D vs. 2D cultured cells, while pharmacological inhibition of MMPs blocked the effect of the 3D culture on enhanced miR combo mediated reprogramming. We conclude that 3D tissue-engineered environment can enhance the direct reprogramming of fibroblasts to cardiomyocytes via a MMP-dependent mechanism. PMID:27941896

  18. Direct design of aspherical lenses for extended non-Lambertian sources in three-dimensional rotational geometry

    PubMed Central

    Wu, Rengmao; Hua, Hong

    2016-01-01

    Illumination design used to redistribute the spatial energy distribution of light source is a key technique in lighting applications. However, there is still no effective illumination design method for extended sources, especially for extended non-Lambertian sources. What we present here is to our knowledge the first direct method for extended non-Lambertian sources in three-dimensional (3D) rotational geometry. In this method, both meridional rays and skew rays of the extended source are taken into account to tailor the lens profile in the meridional plane. A set of edge rays and interior rays emitted from the extended source which will take a given direction after the refraction of the aspherical lens are found by the Snell’s law, and the output intensity at this direction is then calculated to be the integral of the luminance function of the outgoing rays at this direction. This direct method is effective for both extended non-Lambertian sources and extended Lambertian sources in 3D rotational symmetry, and can directly find a solution to the prescribed design problem without cumbersome iterative illuminance compensation. Two examples are presented to demonstrate the effectiveness of the proposed method in terms of performance and capacity for tackling complex designs. PMID:26832484

  19. On Kraichnan's 'direct interaction approximation' and Kolmogoroff's theory in two-dimensional plasma turbulence

    SciTech Connect

    Kulsrud, R.M.; Sudan, R.N.

    1981-04-01

    The nonlinear damping in a strongly turbulent convecting plasma computed by Kraichnan's modified direct inteaction approximation and the power spectrum are rederived in a physically transparent form using Kolmogoroff's theory of turbulence.

  20. Direct-referencing Two-dimensional-array Digital Microfluidics Using Multi-layer Printed Circuit Board

    PubMed Central

    Gong, Jian; Kim, Chang-Jin “CJ”

    2008-01-01

    Digital (i.e. droplet-based) microfluidics, by the electrowetting-on-dielectric (EWOD) mechanism, has shown great potential for a wide range of applications, such as lab-on-a-chip. While most reported EWOD chips use a series of electrode pads essentially in one-dimensional line pattern designed for specific tasks, the desired universal chips allowing user-reconfigurable paths would require the electrode pads in two-dimensional pattern. However, to electrically access the electrode pads independently, conductive lines need to be fabricated underneath the pads in multiple layers, raising a cost issue especially for disposable chip applications. In this article, we report the building of digital microfluidic plates based on a printed-circuit-board (PCB), in which multilayer electrical access lines were created inexpensively using mature PCB technology. However, due to its surface topography and roughness and resulting high resistance against droplet movement, as-fabricated PCB surfaces require unacceptably high (~500 V) voltages unless coated with or immersed in oil. Our goal is EWOD operations of aqueous droplets not only on oil-covered but also on dry surfaces. To meet varying levels of performances, three types of gradually complex post-PCB microfabrication processes are developed and evaluated. By introducing land-grid-array (LGA) sockets in the packaging, a scalable digital microfluidics system with reconfigurable and low-cost chip is also demonstrated. PMID:19234613

  1. Concurrent photoacoustic markers for direct three-dimensional ultrasound to video registration

    NASA Astrophysics Data System (ADS)

    Cheng, Alexis; Guo, Xiaoyu; Kang, Hyun-Jae; Tavakoli, Behnoosh; Kang, Jin U.; Taylor, Russell H.; Boctor, Emad M.

    2014-03-01

    Fusion of video and other imaging modalities is common in modern surgical procedures to provide surgeons with additional information that can provide precise surgical guidance. An example of such uses interventional guidance equipment and surgical navigation systems to register the tools and devices used in surgery with each other. In this work, we focus explicitly on registering three-dimensional ultrasound with a stereocamera system. These surgical navigation systems often use optical or electromagnetic trackers. However, both of these tracking systems have various drawbacks leading to target registration errors of approximately 3mm. Previous work has shown that photoacoustic markers can be used to register three-dimensional ultrasound with video resulting in target registration errors which are much lower than the current state of the art. This work extends this idea by generating multiple photoacoustic markers concurrently as opposed to the sequential method used in the previous work. This development greatly enhances the acquisition time by a factor equal to the number of concurrently generated photoacoustic markers. This work is demonstrated on a synthetic phantom and an ex vivo porcine kidney phantom. The resulting target registration errors for these experiments ranged from 840 to 1360 μm and standard deviations from 370 to 640 μm.

  2. Multitopic ligand directed assembly of low-dimensional metal-chalcogenide organic frameworks.

    PubMed

    Liu, Yi; Ye, Kaiqi; Wang, Yue; Zhang, Qichun; Bu, Xianhui; Feng, Pingyun

    2017-01-31

    Despite tremendous progress in metal-organic frameworks, only limited success has been achieved with metal-chalcogenide organic frameworks. Metal-chalcogenide organic frameworks are desirable because they offer a promising route towards tunable semiconducting porous frameworks. Here, four novel semiconducting chalcogenide-organic hybrid compounds have been synthesized through a solvothermal method. Multitopic organic molecules, i.e., 1,2-di-(4-pyridyl)ethylene (L(1)), 1,3,5-tris(4-pyridyl-trans-ethenyl)benzene (L(2)) and tetrakis(4-pyridyloxymethylene)methane (L(3)), have been used as linkers to assemble Zn(SAr)2 or Zn2(SAr)4 units to generate different patterns of spatial organizations. Single-crystal structural analyses indicate that compounds NTU-2, NTU-3 and NTU-4 possess two-dimensional layer structures, while compound NTU-1 adopts a one-dimensional coordination framework (NTU-n, where n is the number related to a specific structure). The diffuse-reflectance spectra demonstrate that these four compounds possess indirect bandgaps and their tunable bandgaps are correlated with their compositions and crystal structures.

  3. Femtosecond laser direct writing of large-area two-dimensional metallic photonic crystal structures on tungsten surfaces.

    PubMed

    Qiao, Hongzhen; Yang, Jianjun; Wang, Fei; Yang, Yang; Sun, Julong

    2015-10-05

    Metallic photonic crystals (MPCs) and metamaterials operating in the visible spectrum are required for high-temperature nanophotonics, but they are often difficult to construct. This study demonstrates a new approach to directly write two-dimensional (2D) MPCs on tungsten surfaces through the cylindrical focusing of two collinear femtosecond laser beams with certain temporal delays and orthogonal linear polarizations. Results are physically attributed to the laser-induced transient crossed temperature grating patterns and tempo-spatial thermal correlations. Optical properties of the fabricated MPCs are characterized. Such a simple and efficient technique can be used to fabricate large-area, 2D microstructures on metal surfaces for potential applications.

  4. Alternating-direction implicit numerical solution of the time-dependent, three-dimensional, single fluid, resistive magnetohydrodynamic equations

    SciTech Connect

    Finan, C.H. III

    1980-12-01

    Resistive magnetohydrodynamics (MHD) is described by a set of eight coupled, nonlinear, three-dimensional, time-dependent, partial differential equations. A computer code, IMP (Implicit MHD Program), has been developed to solve these equations numerically by the method of finite differences on an Eulerian mesh. In this model, the equations are expressed in orthogonal curvilinear coordinates, making the code applicable to a variety of coordinate systems. The Douglas-Gunn algorithm for Alternating-Direction Implicit (ADI) temporal advancement is used to avoid the limitations in timestep size imposed by explicit methods. The equations are solved simultaneously to avoid syncronization errors.

  5. An HSS Matrix-Inspired Butterfly-Based Direct Solver for Analyzing Scattering From Two-Dimensional Objects

    NASA Astrophysics Data System (ADS)

    Liu, Yang; Guo, Han; Michielssen, Eric

    A butterfly-based fast direct integral equation solver for analyzing high-frequency scattering from two-dimensional objects is presented. The solver leverages a randomized butterfly scheme to compress blocks corresponding to near- and far-field interactions in the discretized forward and inverse electric field integral operators. The observed memory requirements and computational cost of the proposed solver scale as O(Nlog^2N) and O(N^1.5 logN), respectively. The solver is applied to the analysis of scattering from electrically large objects spanning over ten thousand of wavelengths and modeled in terms of five million unknowns.

  6. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.

    PubMed

    Small, Meagan C; Aytenfisu, Asaminew H; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D

    2017-04-01

    The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (D-allose and D-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars D-allose and D-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

  7. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

    NASA Astrophysics Data System (ADS)

    Small, Meagan C.; Aytenfisu, Asaminew H.; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D.

    2017-02-01

    The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (uc(d)-allose and uc(d)-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars uc(d)-allose and uc(d)-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

  8. A novel acyclic oligomycin A derivative formed via retro-aldol rearrangement of oligomycin A.

    PubMed

    Lysenkova, Lyudmila N; Turchin, Konstantin F; Korolev, Alexander M; Bykov, Evgenyi E; Danilenko, Valery N; Bekker, Olga B; Trenin, Alexey S; Elizarov, Sergei M; Dezhenkova, Lyubov G; Shtil, Alexander A; Preobrazhenskaya, Maria N

    2012-08-01

    The antibiotic oligomycin A in the presence of K(2)CO(3) and n-Bu(4)NHSO(4) in chloroform in phase-transfer conditions afforded a novel derivative through the initial retro-aldol fragmentation of the 8,9 bond, followed by further transformation of the intermediate aldehyde. NMR, MS and quantum chemical calculations showed that the novel compound is the acyclic oligomycin A derivative, in which the 8,9 carbon bond is disrupted and two polyfunctional branches are connected with spiroketal moiety in positions C-23 and C-25. The tri-O-acetyl derivative of the novel derivative was prepared. The acyclic oligomycin A derivative retained the ability to induce apoptosis in tumor cells at low micromolar concentrations, whereas its antimicrobial potencies decreased substantially. The derivative virtually lost the inhibitory activity against F(0)F(1) ATP synthase-containing proteoliposomes, strongly suggesting the existence of the target(s) beyond F(0)F(1) ATP synthase that is important for the antitumor potency of oligomycin A.

  9. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability.

    PubMed

    Murayama, Keiji; Asanuma, Hiroyuki

    2017-01-03

    Acyclic serinol derivatives are useful scaffolds for tethering dyes within DNA duplexes. Here we synthesised an inverse l-threoninol (il-threoninol) scaffold and compared its effect on DNA duplex stability to other acyclic artificial nucleic acid scaffolds that are based on d-threoninol, l-threoninol, and serinol. When planar trans-azobenzene was incorporated into the DNA duplex through a single bulge-like motif (the wedge), the il-threoninol scaffold stabilised the duplex most efficiently. When scaffolds were incorporated in complementary positions (dimer motif) or in three adjacent positions (cluster motif), d-threoninol was the most stabilising. CD spectra indicated that the effect of scaffold on the duplex stability was closely related to the winding induced by each scaffold. When trans-azobenzene was photo-isomerised to non-planar cis-azobenzene, il-threoninol destabilised the duplex most strongly, irrespective of the number of artificial residues incorporated. The properties of the il-threoninol scaffold make it a useful tether for dyes or other functionalities. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

    NASA Astrophysics Data System (ADS)

    Small, Meagan C.; Aytenfisu, Asaminew H.; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D.

    2017-04-01

    The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars ( d-allose and d-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars d-allose and d-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

  11. Three dimensional complex plasma structures in a combined radio frequency and direct current discharge

    NASA Astrophysics Data System (ADS)

    Mitic, S.; Klumov, B. A.; Khrapak, S. A.; Morfill, G. E.

    2013-04-01

    We report on the first detailed analysis of large three dimensional (3D) complex plasma structures in experiments performed in pure rf and combined rf+dc discharge modes. Inductively coupled plasma is generated by an rf coil wrapped around the vertically positioned cylindrical glass tube at a pressure of 0.3 mbar. In addition, dc plasma can be generated by applying voltage to the electrodes at the ends of the tube far from the rf coil. The injected monodisperse particles are levitated in the plasma below the coil. A scanning laser sheet and a high resolution camera are used to determine the 3D positions of about 105 particles. The observed bowl-shaped particle clouds reveal coexistence of various structures, including well-distinguished solid-like, less ordered liquid-like, and pronounced string-like phases. New criteria to identify string-like structures are proposed.

  12. A sparse structure learning algorithm for Gaussian Bayesian Network identification from high-dimensional data.

    PubMed

    Huang, Shuai; Li, Jing; Ye, Jieping; Fleisher, Adam; Chen, Kewei; Wu, Teresa; Reiman, Eric

    2013-06-01

    Structure learning of Bayesian Networks (BNs) is an important topic in machine learning. Driven by modern applications in genetics and brain sciences, accurate and efficient learning of large-scale BN structures from high-dimensional data becomes a challenging problem. To tackle this challenge, we propose a Sparse Bayesian Network (SBN) structure learning algorithm that employs a novel formulation involving one L1-norm penalty term to impose sparsity and another penalty term to ensure that the learned BN is a Directed Acyclic Graph--a required property of BNs. Through both theoretical analysis and extensive experiments on 11 moderate and large benchmark networks with various sample sizes, we show that SBN leads to improved learning accuracy, scalability, and efficiency as compared with 10 existing popular BN learning algorithms. We apply SBN to a real-world application of brain connectivity modeling for Alzheimer's disease (AD) and reveal findings that could lead to advancements in AD research.

  13. Two Novel Two-Stage Direction of Arrival Estimation Algorithms for Two-Dimensional Mixed Noncircular and Circular Sources.

    PubMed

    Shi, Heping; Leng, Wen; Guan, Zhiwei; Jin, Tongzhi

    2017-06-18

    This paper addresses the two-dimensional (2D) direction-of-arrival (DOA) estimation problem with two novel methods for mixed noncircular and circular signals. The first proposed method is named the two-stage direction-of-arrival matrix (TSDOAM) method, and the other is called the two-stage rank reduction (TSRARE) method. The proposed methods utilize both the circularity and the direction-of-arrival differences between the noncircular and circular sources to estimate the 2D directions-of-arrival (DOAs). The maximum detectable 2D angle parameters of the TSDOAM and TSRARE methods are twice those of the existing methods. Moreover, the TSRARE method can detect more incident signals than the TSDOAM method due to the array aperture of two parallel uniform linear arrays (ULAs) being fully utilized. Simulation results show that compared to the existing methods for the small angle separation of 2D directions-of-arrival, the two proposed methods perform well in terms of the signal-to-noise ratio (SNR) and snapshots.

  14. Ultrasound directed self-assembly of three-dimensional user-specified patterns of particles in a fluid medium

    NASA Astrophysics Data System (ADS)

    Prisbrey, M.; Greenhall, J.; Guevara Vasquez, F.; Raeymaekers, B.

    2017-01-01

    We use ultrasound directed self-assembly to organize particles dispersed in a fluid medium into a three-dimensional (3D) user-specified pattern. The technique employs ultrasound transducers that line the boundary of a fluid reservoir to create a standing ultrasound wave field. The acoustic radiation force associated with the wave field drives particles dispersed in the fluid medium into organized patterns, assuming that the particles are much smaller than the wavelength and do not interact with each other. We have theoretically derived a direct solution method to calculate the ultrasound transducer operating parameters that are required to assemble a user-specified 3D pattern of particles in a fluid reservoir of arbitrary geometry. We formulate the direct solution method as a constrained optimization problem that reduces to eigendecomposition. We experimentally validate the solution method by assembling 3D patterns of carbon nanoparticles in a water reservoir and observe good quantitative agreement between theory and experiment. Additionally, we demonstrate the versatility of the solution method by simulating ultrasound directed self-assembly of complex 3D patterns of particles. The method works for any 3D simple, closed fluid reservoir geometry in combination with any arrangement of ultrasound transducers and enables employing ultrasound directed self-assembly in a myriad of engineering applications, including biomedical and materials fabrication processes.

  15. Two Novel Two-Stage Direction of Arrival Estimation Algorithms for Two-Dimensional Mixed Noncircular and Circular Sources

    PubMed Central

    Shi, Heping; Leng, Wen; Guan, Zhiwei; Jin, Tongzhi

    2017-01-01

    This paper addresses the two-dimensional (2D) direction-of-arrival (DOA) estimation problem with two novel methods for mixed noncircular and circular signals. The first proposed method is named the two-stage direction-of-arrival matrix (TSDOAM) method, and the other is called the two-stage rank reduction (TSRARE) method. The proposed methods utilize both the circularity and the direction-of-arrival differences between the noncircular and circular sources to estimate the 2D directions-of-arrival (DOAs). The maximum detectable 2D angle parameters of the TSDOAM and TSRARE methods are twice those of the existing methods. Moreover, the TSRARE method can detect more incident signals than the TSDOAM method due to the array aperture of two parallel uniform linear arrays (ULAs) being fully utilized. Simulation results show that compared to the existing methods for the small angle separation of 2D directions-of-arrival, the two proposed methods perform well in terms of the signal-to-noise ratio (SNR) and snapshots. PMID:28629154

  16. A Low-Complexity Method for Two-Dimensional Direction-of-Arrival Estimation Using an L-Shaped Array.

    PubMed

    Wang, Qing; Yang, Hang; Chen, Hua; Dong, Yangyang; Wang, Laihua

    2017-01-19

    In this paper, a new low-complexity method for two-dimensional (2D) direction-of-arrival (DOA) estimation is proposed. Based on a cross-correlation matrix formed from the L-shaped array, the proposed algorithm obtains the automatic pairing elevation and azimuth angles without eigendecomposition, which can avoid high computational cost. In addition, the cross-correlation matrix eliminates the effect of noise, which can achieve better DOA performance. Then, the theoretical error of the algorithm is analyzed and the Cramer-Rao bound (CRB) for the direction of arrival estimation is derived . Simulation results demonstrate that, at low signal-to-noise ratios (SNRs) and with a small number of snapshots, in contrast to Tayem's algorithm and Kikuchi's algorithm, the proposed algorithm achieves better DOA performance with lower complexity, while, for Gu's algorithm, the proposed algorithm has slightly inferior DOA performance but with significantly lower complexity.

  17. Three-dimensional microfluidic channel with arbitrary length and configuration fabricated inside glass by femtosecond laser direct writing.

    PubMed

    Liao, Yang; Ju, Yongfeng; Zhang, Long; He, Fei; Zhang, Qiang; Shen, Yinglong; Chen, Danping; Cheng, Ya; Xu, Zhizhan; Sugioka, Koji; Midorikawa, Katsumi

    2010-10-01

    We demonstrate, for the first time to the best of our knowledge, fabrication of three-dimensional microfluidic channels with arbitrary lengths and configurations inside glass by femtosecond laser direct writing. The main fabrication process includes two steps: (1) direct formation of hollow microchannels in a porous glass substrate immersed in water by femtosecond laser ablation and (2) postannealing of the glass substrate at ∼1150°C by which the porous glass can be consolidated. We show that a square-wavelike channel with a total length of ∼1.4 cm and a diameter of ∼64 μm can be easily produced ∼250 μm beneath the glass surface.

  18. A Low-Complexity Method for Two-Dimensional Direction-of-Arrival Estimation Using an L-Shaped Array

    PubMed Central

    Wang, Qing; Yang, Hang; Chen, Hua; Dong, Yangyang; Wang, Laihua

    2017-01-01

    In this paper, a new low-complexity method for two-dimensional (2D) direction-of-arrival (DOA) estimation is proposed. Based on a cross-correlation matrix formed from the L-shaped array, the proposed algorithm obtains the automatic pairing elevation and azimuth angles without eigendecomposition, which can avoid high computational cost. In addition, the cross-correlation matrix eliminates the effect of noise, which can achieve better DOA performance. Then, the theoretical error of the algorithm is analyzed and the Cramer–Rao bound (CRB) for the direction of arrival estimation is derived . Simulation results demonstrate that, at low signal-to-noise ratios (SNRs) and with a small number of snapshots, in contrast to Tayem’s algorithm and Kikuchi’s algorithm, the proposed algorithm achieves better DOA performance with lower complexity, while, for Gu’s algorithm, the proposed algorithm has slightly inferior DOA performance but with significantly lower complexity. PMID:28106840

  19. Patterned and functionalized nanofiber scaffolds in three-dimensional hydrogel constructs enhance neurite outgrowth and directional control

    NASA Astrophysics Data System (ADS)

    McMurtrey, Richard J.

    2014-12-01

    Objective. Neural tissue engineering holds incredible potential to restore functional capabilities to damaged neural tissue. It was hypothesized that patterned and functionalized nanofiber scaffolds could control neurite direction and enhance neurite outgrowth. Approach. A method of creating aligned electrospun nanofibers was implemented and fiber characteristics were analyzed using environmental scanning electron microscopy. Nanofibers were composed of polycaprolactone (PCL) polymer, PCL mixed with gelatin, or PCL with a laminin coating. Three-dimensional hydrogels were then integrated with embedded aligned nanofibers to support neuronal cell cultures. Microscopic images were captured at high-resolution in single and multi-focal planes with eGFP-expressing neuronal SH-SY5Y cells in a fluorescent channel and nanofiber scaffolding in another channel. Neuronal morphology and neurite tracking of nanofibers were then analyzed in detail. Main results. Aligned nanofibers were shown to enable significant control over the direction of neurite outgrowth in both two-dimensional (2D) and three-dimensional (3D) neuronal cultures. Laminin-functionalized nanofibers in 3D hyaluronic acid (HA) hydrogels enabled significant alignment of neurites with nanofibers, enabled significant neurite tracking of nanofibers, and significantly increased the distance over which neurites could extend. Specifically, the average length of neurites per cell in 3D HA constructs with laminin-functionalized nanofibers increased by 66% compared to the same laminin fibers on 2D laminin surfaces, increased by 59% compared to 2D laminin-coated surface without fibers, and increased by 1052% compared to HA constructs without fibers. Laminin functionalization of fibers also doubled average neurite length over plain PCL fibers in the same 3D HA constructs. In addition, neurites also demonstrated tracking directly along the fibers, with 66% of neurite lengths directly tracking laminin-coated fibers in 3D HA

  20. Detailed Multi‐dimensional Modeling of Direct Internal Reforming Solid Oxide Fuel Cells

    PubMed Central

    Tseronis, K.; Fragkopoulos, I.S.; Bonis, I.

    2016-01-01

    Abstract Fuel flexibility is a significant advantage of solid oxide fuel cells (SOFCs) and can be attributed to their high operating temperature. Here we consider a direct internal reforming solid oxide fuel cell setup in which a separate fuel reformer is not required. We construct a multidimensional, detailed model of a planar solid oxide fuel cell, where mass transport in the fuel channel is modeled using the Stefan‐Maxwell model, whereas the mass transport within the porous electrodes is simulated using the Dusty‐Gas model. The resulting highly nonlinear model is built into COMSOL Multiphysics, a commercial computational fluid dynamics software, and is validated against experimental data from the literature. A number of parametric studies is performed to obtain insights on the direct internal reforming solid oxide fuel cell system behavior and efficiency, to aid the design procedure. It is shown that internal reforming results in temperature drop close to the inlet and that the direct internal reforming solid oxide fuel cell performance can be enhanced by increasing the operating temperature. It is also observed that decreases in the inlet temperature result in smoother temperature profiles and in the formation of reduced thermal gradients. Furthermore, the direct internal reforming solid oxide fuel cell performance was found to be affected by the thickness of the electrochemically‐active anode catalyst layer, although not always substantially, due to the counter‐balancing behavior of the activation and ohmic overpotentials. PMID:27570502

  1. Two-Dimensional Simulations of Plastic-Shell, Direct-Drive Implosions on OMEGA

    SciTech Connect

    Radha, P.B.; Goncharov, V.N.; Collins, T.J.B.; Delettrez, J.A.; Elbaz, Y.; Glebov, V.Yu.; Keck, R.L.; Keller, D.E.; Knauer, J.P.; Marozas, J.A.; Marshall, F.J.; McKenty, P.W.; Meyerhofer, D.D.; Regan, S.P.; Sangster, T.C.; Shvarts, D.; Skupsky, S.; Srebro, Y.; Town, R.P.J.; Stoeckl, C.

    2005-02-18

    Multidimensional hydrodynamic properties of high-adiabat direct-drive plastic-shell implosions on the OMEGA laser system are investigated using the multidimensional hydrodynamic code, DRACO. Multimode simulations including the effects of nonuniform illumination and target roughness indicate that shell stability during the acceleration phase plays a critical role in determining target performance.

  2. A concept for improving the dimensional stability of filamentary composites in one direction

    NASA Technical Reports Server (NTRS)

    Dow, N. F.; Rosen, B. W.

    1971-01-01

    Investigation of filamentary composites having high strength and stiffness and a zero thermal coefficient of expansion in one direction shows that advanced filament materials, such as boron, have substantial advantages over conventional filamentary composites. Various other results are discussed, including guidelines and analysis methods for further evaluation.

  3. Detailed Multi-dimensional Modeling of Direct Internal Reforming Solid Oxide Fuel Cells.

    PubMed

    Tseronis, K; Fragkopoulos, I S; Bonis, I; Theodoropoulos, C

    2016-06-01

    Fuel flexibility is a significant advantage of solid oxide fuel cells (SOFCs) and can be attributed to their high operating temperature. Here we consider a direct internal reforming solid oxide fuel cell setup in which a separate fuel reformer is not required. We construct a multidimensional, detailed model of a planar solid oxide fuel cell, where mass transport in the fuel channel is modeled using the Stefan-Maxwell model, whereas the mass transport within the porous electrodes is simulated using the Dusty-Gas model. The resulting highly nonlinear model is built into COMSOL Multiphysics, a commercial computational fluid dynamics software, and is validated against experimental data from the literature. A number of parametric studies is performed to obtain insights on the direct internal reforming solid oxide fuel cell system behavior and efficiency, to aid the design procedure. It is shown that internal reforming results in temperature drop close to the inlet and that the direct internal reforming solid oxide fuel cell performance can be enhanced by increasing the operating temperature. It is also observed that decreases in the inlet temperature result in smoother temperature profiles and in the formation of reduced thermal gradients. Furthermore, the direct internal reforming solid oxide fuel cell performance was found to be affected by the thickness of the electrochemically-active anode catalyst layer, although not always substantially, due to the counter-balancing behavior of the activation and ohmic overpotentials.

  4. Mapping Dimensionality and Directionality of Electronic Behavior in CeCoIn5: the Superconducting State

    NASA Astrophysics Data System (ADS)

    Feldman, Benjamin E.; Gyenis, Andras; Randeria, Mallika T.; Peterson, Gabriel A.; Aynajian, Pegor; Bauer, Eric D.; Yazdani, Ali

    Unconventional superconductors often exhibit anisotropic physical properties that arise from the directional dependence of their order parameters. A prime example is CeCoIn5, a heavy fermion d-wave superconductor with a rich low-temperature phase diagram consisting of competing and coexisting magnetic and superconducting orders. Here we present dilution refrigerator scanning tunneling microscopy of CeCoIn5 cleaved perpendicular to its basal plane. We study superconductivity on the (100) surface, whose normal vector points along the antinode of the superconducting energy gap. The gap magnitude is similar to that observed in the basal plane, with a key difference: it does not exhibit any suppression near step edges. Application of a magnetic field along the [100] direction leads to the formation of anisotropic vortices, and the vortex lattice undergoes a transition at high field before the superconducting state gives way to a pseudogap phase. Our measurements illustrate the directional dependence of the superconducting properties in CeCoIn5, and more generally, demonstrate the utility of imaging d-wave superconductors along their nodal and antinodal directions.

  5. A semi-direct solver for compressible three-dimensional rotational flow

    NASA Technical Reports Server (NTRS)

    Chang, S.-C.; Adamczyk, J. J.

    1983-01-01

    An iterative procedure is presented for solving steady inviscid 3-D subsonic rotational flow problems. The procedure combines concepts from classical secondary flow theory with an extension to 3-D of a novel semi-direct Cauchy-Riemann solver. It is developed for generalized coordinates and can be exercised using standard finite difference procedures. The stability criterion of the iterative procedure is discussed along with its ability to capture the evolution of inviscid secondary flow in a turning channel.

  6. A semi-direct solver for compressible 3-dimensional rotational flow

    NASA Technical Reports Server (NTRS)

    Chang, S. C.; Adamczyk, J. J.

    1983-01-01

    An iterative procedure is presented for solving steady inviscid 3-D subsonic rotational flow problems. The procedure combines concepts from classical secondary flow theory with an extension to 3-D of a novel semi-direct Cauchy-Riemann solver. It is developed for generalized coordinates and can be exercised using standard finite difference procedures. The stability criterion of the iterative procedure is discussed along with its ability to capture the evolution of inviscid secondary flow in a turning channel.

  7. Lévy-type diffusion on one-dimensional directed Cantor graphs.

    PubMed

    Burioni, Raffaella; Caniparoli, Luca; Lepri, Stefano; Vezzani, Alessandro

    2010-01-01

    Lévy-type walks with correlated jumps, induced by the topology of the medium, are studied on a class of one-dimensional deterministic graphs built from generalized Cantor and Smith-Volterra-Cantor sets. The particle performs a standard random walk on the sets but is also allowed to move ballistically throughout the empty regions. Using scaling relations and the mapping onto the electric network problem, we obtain the exact values of the scaling exponents for the asymptotic return probability, the resistivity, and the mean-square displacement as a function of the topological parameters of the sets. Interestingly, the system undergoes a transition from superdiffusive to diffusive behavior as a function of the filling of the fractal. The deterministic topology also allows us to discuss the importance of the choice of the initial condition. In particular, we demonstrate that local and average measurements can display different asymptotic behavior. The analytic results are compared to the numerical solution of the master equation of the process.

  8. Separation of time scales in one-dimensional directed nucleation-growth processes

    NASA Astrophysics Data System (ADS)

    Pierobon, Paolo; Miné-Hattab, Judith; Cappello, Giovanni; Viovy, Jean-Louis; Lagomarsino, Marco Cosentino

    2010-12-01

    Proteins involved in homologous recombination such as RecA and hRad51 polymerize on single- and double-stranded DNA according to a nucleation-growth kinetics, which can be monitored by single-molecule in vitro assays. The basic models currently used to extract biochemical rates rely on ensemble averages and are typically based on an underlying process of bidirectional polymerization, in contrast with the often observed anisotropic polymerization of similar proteins. For these reasons, if one considers single-molecule experiments, the available models are useful to understand observations only in some regimes. In particular, recent experiments have highlighted a steplike polymerization kinetics. The classical model of one-dimensional nucleation growth, the Kolmogorov-Avrami-Mehl-Johnson (KAMJ) model, predicts the correct polymerization kinetics only in some regimes and fails to predict the steplike behavior. This work illustrates by simulations and analytical arguments the limitation of applicability of the KAMJ description and proposes a minimal model for the statistics of the steps based on the so-called stick-breaking stochastic process. We argue that this insight might be useful to extract information on the time and length scales involved in the polymerization kinetics.

  9. Direct three-dimensional characterization and multiscale visualization of wheat straw deconstruction by white rot fungus.

    PubMed

    Liu, Li; Qian, Chen; Jiang, Lei; Yu, Han-Qing

    2014-08-19

    Microbial degradation of lignocellulose for resource and energy recovery has received increasing interest. Despite its obvious importance, the mechanism behind the biodegradation, especially the changes of morphological structure and surface characteristics, has not been fully understood. Here, we used three-dimensional (3D) characterization and multiscale visualization methods, in combination with chemical compositional analyses, to elucidate the degradation process of wheat straw by a white rot fungus, Phanerochaete chrysosporium. It was found that the fungal attack initiated from stomata. Lignin of the straw decayed in both size and quantity, and heterogeneity in the biodegradation was observed. After treatment with the fungus, the straw surface turned from hydrophobic to hydrophilic, and the adhesion of the straw surface increased in the fungal degradation. The morphology of the straw outer layer became heterogeneous and loose with the formation of many holes with various sizes. The wasp-tunnels-like structure of the collenchyma and parenchyma of the straw as well as the fungal hyphae interspersed inside the straw structure were clearly visualized in the 3D reconstruction structure. This work offers a new insight into the mechanism of lignocellulose biodegradation and demonstrates that multiscale visualization methods could be a useful tool to explore such complex processes.

  10. Microstructure Analysis and Multi-Unit Cell Model of Three Dimensionally Four-Directional Braided Composites

    NASA Astrophysics Data System (ADS)

    Xu, Kun; Qian, Xiaomei

    2015-02-01

    In this paper, a new multi-unit cell model of three dimensionally braided composites is presented on the basis of the microstructure analysis of 3D braided preforms produced by four-step 1 × 1 method. According to a new unit cell partition scheme, the multi-unit cell model possesses five kinds of unit cells, namely interior, exterior surface, interior surface, exterior corner and interior corner unit cells. Each type of the representative volume cell has unique microstructure and volume fraction in braided composites. On the basis of these five unit cell models, the structural geometry parameters of the preforms are analyzed and the relationship between the structural parameters and the braiding parameters in different regions are derived in detail, such as the braiding angles, fiber volume fraction, yarn packing factor, braiding pitch and so on. Finally, by using the multi-unit cell model, the main structural parameters of braided composites specimens are calculated to validate the effectiveness of the model. The results are in good agreement with the available experimental data. In addition, the effect of braiding angle on the squeezing condition of braiding yarn is analyzed. The variations of the volume proportion of five unit cells to the whole specimen with rows and columns are discussed, respectively. The presented multi-unit cell model can be adopted to design 3D braided composites and predict their mechanical properties.

  11. Low-field one-dimensional and direction-dependent relaxation imaging of bovine articular cartilage

    NASA Astrophysics Data System (ADS)

    Rössler, Erik; Mattea, Carlos; Mollova, Ayret; Stapf, Siegfried

    2011-12-01

    The structure of articular cartilage is separated into three layers of differently oriented collagen fibers, which is accompanied by a gradient of increasing glycosaminoglycan (GAG) and decreasing water concentration from the top layer towards the bone interface. The combined effect of these structural variations results in a change of the longitudinal and transverse relaxation times as a function of the distance from the cartilage surface. In this paper, this dependence is investigated at a magnetic field strength of 0.27 T with a one-dimensional depth resolution of 50 μm on bovine hip and stifle joint articular cartilage. By employing this method, advantage is taken of the increasing contrast of the longitudinal relaxation rate found at lower magnetic field strengths. Furthermore, evidence for an orientational dependence of relaxation times with respect to an axis normal to the surface plane is given, an observation that has recently been reported using high-field MRI and that was explained by preferential orientations of collagen bundles in each of the three cartilage zones. In order to quantify the extent of a further contrast mechanism and to estimate spatially dependent glycosaminoglycan concentrations, the data are supplemented by proton relaxation times that were acquired in bovine articular cartilage that was soaked in a 0.8 mM aqueous Gd ++ solution.

  12. Laser-guided direct writing for three-dimensional tissue engineering.

    PubMed

    Nahmias, Yaakov; Schwartz, Robert E; Verfaillie, Catherine M; Odde, David J

    2005-10-20

    One of the principal limitations to the size of an engineered tissue is oxygen and nutrient transport. Lacking a vascular bed, cells embedded in an engineered tissue will consume all available oxygen within hours while out branching blood vessels will take days to vascularize the implanted tissue. One possible solution is to directly write vascular structures within the engineered tissue prior to implantation, reconstructing the tissue according to its native architecture. The cell patterning technique, laser-guided direct writing (LGDW), can pattern multiple cells types with micrometer resolution on arbitrary surfaces, including biological gels. Here we show that LGDW can pattern human umbilical vein endothelial cells (HUVEC) in two- and three-dimensions with micrometer accuracy. By patterning HUVEC on Matrigel, we can direct their self-assembly into vascular structures along the desired pattern. Finally, co-culturing the vascular structures with hepatocytes resulted in an aggregated tubular structure similar in organization to a hepatic sinusoid. This capability can facilitate studies of tissue architecture at the single cell level, and of heterotypic interactions underlying processes such as liver and pancreas morphogenesis, differentiation, and angiogenesis. Copyright 2005 Wiley Periodicals, Inc.

  13. Enhancement of direct urea-hydrogen peroxide fuel cell performance by three-dimensional porous nickel-cobalt anode

    NASA Astrophysics Data System (ADS)

    Guo, Fen; Cao, Dianxue; Du, Mengmeng; Ye, Ke; Wang, Guiling; Zhang, Wenping; Gao, Yinyi; Cheng, Kui

    2016-03-01

    A novel three-dimensional (3D) porous nickel-cobalt (Ni-Co) film on nickel foam is successfully prepared and further used as an efficient anode for direct urea-hydrogen peroxide fuel cell (DUHPFC). By varying the cobalt/nickel mole ratios into 0%, 20%, 50%, 80% and 100%, the optimized Ni-Co/Ni foam anode with a ratio of 80% is obtained in terms of the best cell performance among five anodes. Effects of the KOH and urea concentrations, the flow rate and operation temperature on the fuel cell performance are investigated. Results show DUHPFC with the 3D Ni-Co/Ni foam anode exhibits a higher performance than those reported direct urea fuel cells. The cell gives an open circuit voltage of 0.83 V and a peak power density as high as 17.4 and 31.5 mW cm-2 at 20 °C and 70 °C, respectively, when operating on 7.0 mol L-1 KOH and 0.5 mol L-1 urea as the fuel at a flow rate of 15 mL min-1. Besides, when the human urine is directly fed as the fuel, direct urine-hydrogen peroxide fuel cell reaches a maximum power density of 7.5 mW cm-2 with an open circuit voltage of 0.80 V at 20 °C, showing a good application prospect in wastewater treatment.

  14. Future directions in 3-dimensional imaging and neurosurgery: stereoscopy and autostereoscopy.

    PubMed

    Christopher, Lauren A; William, Albert; Cohen-Gadol, Aaron A

    2013-01-01

    Recent advances in 3-dimensional (3-D) stereoscopic imaging have enabled 3-D display technologies in the operating room. We find 2 beneficial applications for the inclusion of 3-D imaging in clinical practice. The first is the real-time 3-D display in the surgical theater, which is useful for the neurosurgeon and observers. In surgery, a 3-D display can include a cutting-edge mixed-mode graphic overlay for image-guided surgery. The second application is to improve the training of residents and observers in neurosurgical techniques. This article documents the requirements of both applications for a 3-D system in the operating room and for clinical neurosurgical training, followed by a discussion of the strengths and weaknesses of the current and emerging 3-D display technologies. An important comparison between a new autostereoscopic display without glasses and current stereo display with glasses improves our understanding of the best applications for 3-D in neurosurgery. Today's multiview autostereoscopic display has 3 major benefits: It does not require glasses for viewing; it allows multiple views; and it improves the workflow for image-guided surgery registration and overlay tasks because of its depth-rendering format and tools. Two current limitations of the autostereoscopic display are that resolution is reduced and depth can be perceived as too shallow in some cases. Higher-resolution displays will be available soon, and the algorithms for depth inference from stereo can be improved. The stereoscopic and autostereoscopic systems from microscope cameras to displays were compared by the use of recorded and live content from surgery. To the best of our knowledge, this is the first report of application of autostereoscopy in neurosurgery.

  15. Three-dimensional photonic crystals created by single-step multi-directional plasma etching.

    PubMed

    Suzuki, Katsuyoshi; Kitano, Keisuke; Ishizaki, Kenji; Noda, Susumu

    2014-07-14

    We fabricate 3D photonic nanostructures by simultaneous multi-directional plasma etching. This simple and flexible method is enabled by controlling the ion-sheath in reactive-ion-etching equipment. We realize 3D photonic crystals on single-crystalline silicon wafers and show high reflectance (>95%) and low transmittance (<-15dB) at optical communication wavelengths, suggesting the formation of a complete photonic bandgap. Moreover, our method simply demonstrates Si-based 3D photonic crystals that show the photonic bandgap effect in a shorter wavelength range around 0.6 μm, where further fine structures are required.

  16. Indirect-direct band gap transition of two-dimensional arsenic layered semiconductors—cousins of black phosphorus

    NASA Astrophysics Data System (ADS)

    Luo, Kun; Chen, ShiYou; Duan, ChunGang

    2015-08-01

    The monolayer arsenic in the puckered honeycomb structure was recently predicted to be a stable two-dimensional layered semiconductor and therefore named arsenene. Unfortunately, it has an indirect band gap, which limits its practical application. Using first-principles calculations, we show that the band gaps of few-layer arsenic have an indirect-direct transition as the number of arsenic layers ( n) increases from n=1 to n=2. As n increases from n=2 to infinity, the stacking of the puckered honeycomb arsenic layers forms the orthorhombic arsenic crystal (-As, arsenolamprite), which has a similar structure to the black phosphorus and also has a direct band gap. This indirect-direct transition stems from the distinct quantum-confinement effect on the indirect and direct band-edge states with different wavefunction distribution. The strain effect on these electronic states is also studied, showing that the in-plane strains can induce very different shift of the indirect and direct band edges, and thus inducing an indirect-direct band gap transition too. The band gap dependence on strain is non-monotonic, with both positive and negative deformation potentials. Although the gap of arsenene opens between As p-p bands, the spin-orbit interaction decreases the gap by only 0.02 eV, which is much smaller than the decrease in GaAs with an s-p band gap. The calculated band gaps of arsenene and e-As using the hybrid functional are 1.4 and 0.4 eV respectively, which are comparable to those of phosphorene and black phosphorus.

  17. Enantioselective Construction of Acyclic Quaternary Carbon Stereocenters: Palladium-Catalyzed Decarboxylative Allylic Alkylation of Fully Substituted Amide Enolates.

    PubMed

    Starkov, Pavel; Moore, Jared T; Duquette, Douglas C; Stoltz, Brian M; Marek, Ilan

    2017-07-19

    We report a divergent and modular protocol for the preparation of acyclic molecular frameworks containing newly created quaternary carbon stereocenters. Central to this approach is a sequence composed of a (1) regioselective and -retentive preparation of allyloxycarbonyl-trapped fully substituted stereodefined amide enolates and of a (2) enantioselective palladium-catalyzed decarboxylative allylic alkylation reaction using a novel bisphosphine ligand.

  18. Direct E-jet printing of three-dimensional fibrous scaffold for tendon tissue engineering.

    PubMed

    Wu, Yang; Wang, Zuyong; Ying Hsi Fuh, Jerry; San Wong, Yoke; Wang, Wilson; San Thian, Eng

    2017-04-01

    Tissue engineering (TE) offers a promising strategy to restore diseased tendon tissue. However, a suitable scaffold for tendon TE has not been achieved with current fabrication techniques. Herein, we report the development of a novel electrohydrodynamic jet printing (E-jetting) for engineering 3D tendon scaffold with high porosity and orientated micrometer-size fibers. The E-jetted scaffold comprised tubular multilayered micrometer-size fibrous bundles, with interconnected spacing and geometric anisotropy along the longitudinal direction of the scaffold. Fiber diameter, stacking pattern, and interfiber distance have been observed to affect the structural stability of the scaffold, of which the enhanced mechanical strength can be obtained for scaffolds with thick fibers as the supporting layer. Human tenocytes showed a significant increase in cellular metabolism on the E-jetted scaffolds as compared to that on conventional electrospun scaffolds (2.7-, 2.8-, and 3.1-fold increase for 150, 300, and 600 µm interfiber distance, respectively; p < 0.05). Furthermore, the scaffolds provided structural support for human tenocytes to align with controlled orientation along the longitudinal direction of the scaffold, and promoted the expression of collagen type I. For the first time, E-jetting has been explored as a novel scaffolding approach for tendon TE, and offers a 3D fibrous scaffold to promote organized tissue reconstruction for potential tendon healing. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 616-627, 2017.

  19. Estimating the Illumination Direction From Three-Dimensional Texture of Brownian Surfaces

    PubMed Central

    van Doorn, Andrea J.; Koenderink, Jan J.

    2017-01-01

    We studied whether human observers can estimate the illumination direction from 3D textures of random Brownian surfaces, containing undulations over a range of scales. The locally Lambertian surfaces were illuminated with a collimated beam from random directions. The surfaces had a uniform albedo and thus texture appeared only through shading and shadowing. The data confirm earlier results with Gaussian surfaces, containing undulations of a single scale. Observers were able to accurately estimate the source azimuth. If shading dominated the images, the observers committed 180° errors. If cast shadows were present, they resolved this convex-concave-ambiguity almost completely. Thus, observers relied on second-order statistics in the shading regime and used an unidentified first-order cue in the shadow regime. The source elevations could also be estimated, which can be explained by the observers’ exploitation of the statistical homogeneity of the stimulus set. The fraction of the surface that is in shadow and the median intensity are likely cues for these elevation estimates. PMID:28491273

  20. Estimating the Illumination Direction From Three-Dimensional Texture of Brownian Surfaces.

    PubMed

    Pont, Sylvia C; van Doorn, Andrea J; Koenderink, Jan J

    2017-01-01

    We studied whether human observers can estimate the illumination direction from 3D textures of random Brownian surfaces, containing undulations over a range of scales. The locally Lambertian surfaces were illuminated with a collimated beam from random directions. The surfaces had a uniform albedo and thus texture appeared only through shading and shadowing. The data confirm earlier results with Gaussian surfaces, containing undulations of a single scale. Observers were able to accurately estimate the source azimuth. If shading dominated the images, the observers committed 180° errors. If cast shadows were present, they resolved this convex-concave-ambiguity almost completely. Thus, observers relied on second-order statistics in the shading regime and used an unidentified first-order cue in the shadow regime. The source elevations could also be estimated, which can be explained by the observers' exploitation of the statistical homogeneity of the stimulus set. The fraction of the surface that is in shadow and the median intensity are likely cues for these elevation estimates.

  1. Ruthenium-mediated cycloaromatization of acyclic enediynes and dienynes at ambient temperature.

    PubMed

    O'Connor, Joseph M; Friese, Seth J; Tichenor, Mark

    2002-04-10

    The ruthenium(II) cation, [Cp*Ru(NCMe)3]OTf (4), triggers the Bergman cycloaromatization of acyclic endiynes at room temperature in THF solvent. Treatment of 1,2-di(1-alkynynyl)cyclopentenes (13-Me, alkynyl = propynyl; 13-Prn, alkynyl = pentynyl; 13-Bui, alkynyl = 4-methyl-pent-1-ynyl) with 4 in THF solvent at room temperature gives rise to the ruthenium arene complexes: [Cp*Ru{(3a,4,5,6,7,7a-eta)-2,3-dihydro-5,6-dialkyl-1H-indene}]OTf (15-Me, alkyl = methyl, 64% yield; 15-Prn, alkyl = n-propyl, 73% yield; 15-Bui, alkyl = 4-methyl-1-pentynyl, 88% yield). In a similar fashion, the room-temperature reaction of 4 with 1-ethynyl-2-(1-propynyl)cyclopentene (11) and [2-(1-propynyl)-1-cyclopenten-1-yl]trimethylsilane (14) leads to the formation of [Cp*Ru{(3a,4,5,6,7,7a-eta)-2,3-dihydro-5-methyl-1H-indene}]OTf (12, 92% yield) and [Cp*Ru{(3a,4,5,6,7,7a-eta)-2,3-dihydro-6-methyl-1H-inden-5-yl)trimethylsilane}]OTf (16, 77% yield), respectively. The bis(TMS)-substituted enediyne (1-cyclopentene-1,2-diyldi-2,1-ethynediyl)bis(trimethylsilane) (9-TMS) and 4 underwent reaction at 100 degrees C to give [Cp*Ru{(3a,4,5,6,7,7a-eta)-2,3-dihydro-1H-inden-5-yl)trimethylsilane}]OTf (10, 69% yield). Deuterium-labeling studies rule out a mechanism that involves a ruthenium-vinylidene intermediate, and provide support for the involvement of a p-benzyne intermediate. In a similar fashion, complex 4 is shown to trigger the cycloaromatization of the conjugated dienyne, 1-ethenyl-2-(1-pentynyl)cyclopentene (19), at room temperature in chloroform-d1 solvent to give [Cp*Ru{(3a,4,5,6,7,7a-eta)-2,3-dihydro-5-(1-propyl)-1H-indene}]OTf (20, 96% yield), with no deuterium enrichment. In the absence of ruthenium the thermal cyclization reactions of unsubstituted acyclic enediynes (Bergman cycloaromatization) and acyclic conjugated dienynes (Hopf cyclization) typically require elevated temperatures (150-250 degrees C). Complexes 10 and 15-Prn were characterized structurally by X-ray crystallography.

  2. Constraints on Universal Extra-Dimensional Dark Matter from Direct Detection Results

    NASA Astrophysics Data System (ADS)

    Torpin, Trevor; Duda, Gintaras

    2011-04-01

    Detection of dark matter is one of the most challenging and important problems in astro-particle physics. One theory that produces a viable particle dark matter candidate is Universal Extra Dimensions (UED), in which the existence of a 4th spatial dimension is theorized. The extra dimension is not seen because it is compactifed on a circular orbifold whose radius is too small to be observed with current technology. What separates this theory over other Kaluza-Klein-type theories is that UED allows all standard model particles and fields to propagate in the extra dimension. The dark matter candidate in UED theories is a stable particle known as the Lightest Kaluza-Klein Particle or LKP, and the LKP can exist with sufficient relic density to serve as the dark matter. This work will present bounds on UED model parameters from direct dark matter searches such as the CDMS II.

  3. Direct manufacturing of ultrathin graphite on three-dimensional nanoscale features

    PubMed Central

    Pacios, Mercè; Hosseini, Peiman; Fan, Ye; He, Zhengyu; Krause, Oliver; Hutchison, John; Warner, Jamie H.; Bhaskaran, Harish

    2016-01-01

    There have been many successful attempts to grow high-quality large-area graphene on flat substrates. Doing so at the nanoscale has thus far been plagued by significant scalability problems, particularly because of the need for delicate transfer processes onto predefined features, which are necessarily low-yield processes and which can introduce undesirable residues. Herein we describe a highly scalable, clean and effective, in-situ method that uses thin film deposition techniques to directly grow on a continuous basis ultrathin graphite (uG) on uneven nanoscale surfaces. We then demonstrate that this is possible on a model system of atomic force probe tips of various radii. Further, we characterize the growth characteristics of this technique as well as the film’s superior conduction and lower adhesion at these scales. This sets the stage for such a process to allow the use of highly functional graphite in high-aspect-ratio nanoscale components. PMID:26939862

  4. Note: Fast compact laser shutter using a direct current motor and three-dimensional printing

    SciTech Connect

    Zhang, Grace H. Braverman, Boris; Kawasaki, Akio; Vuletić, Vladan

    2015-12-15

    We present a mechanical laser shutter design that utilizes a direct current electric motor to rotate a blade which blocks and unblocks a light beam. The blade and the main body of the shutter are modeled with computer aided design (CAD) and are produced by 3D printing. Rubber flaps are used to limit the blade’s range of motion, reducing vibrations and preventing undesirable blade oscillations. At its nominal operating voltage, the shutter achieves a switching speed of (1.22 ± 0.02) m/s with 1 ms activation delay and 10 μs jitter in its timing performance. The shutter design is simple, easy to replicate, and highly reliable, showing no failure or degradation in performance over more than 10{sup 8} cycles.

  5. Note: Fast compact laser shutter using a direct current motor and three-dimensional printing

    NASA Astrophysics Data System (ADS)

    Zhang, Grace H.; Braverman, Boris; Kawasaki, Akio; Vuletić, Vladan

    2015-12-01

    We present a mechanical laser shutter design that utilizes a direct current electric motor to rotate a blade which blocks and unblocks a light beam. The blade and the main body of the shutter are modeled with computer aided design (CAD) and are produced by 3D printing. Rubber flaps are used to limit the blade's range of motion, reducing vibrations and preventing undesirable blade oscillations. At its nominal operating voltage, the shutter achieves a switching speed of (1.22 ± 0.02) m/s with 1 ms activation delay and 10 μs jitter in its timing performance. The shutter design is simple, easy to replicate, and highly reliable, showing no failure or degradation in performance over more than 108 cycles.

  6. Direct observation of quantum phonon fluctuations in a one-dimensional Bose gas.

    PubMed

    Armijo, Julien

    2012-06-01

    We report the first direct observation of collective quantum fluctuations in a continuous field. Shot-to-shot atom number fluctuations in small subvolumes of a weakly interacting, ultracold atomic 1D cloud are studied using in situ absorption imaging and statistical analysis of the density profiles. In the cloud centers, well in the quantum quasicondensate regime, the ratio of chemical potential to thermal energy is μ/k(B)T≃4, and, owing to high resolution, up to 20% of the microscopically observed fluctuations are quantum phonons. Within a nonlocal analysis at variable observation length, we observe a clear deviation from a classical field prediction, which reveals the emergence of dominant quantum fluctuations at short length scales, as the thermodynamic limit breaks down.

  7. Three-dimensional modeling of direct-drive cryogenic implosions on OMEGA

    DOE PAGES

    Igumenshchev, I. V.; Goncharov, V. N.; Marshall, F. J.; ...

    2016-05-04

    The effects of large-scale (with Legendre modes ≲10) laser-imposed nonuniformities in direct-drive cryogenic implosions on the OMEGA laser system are investigated using three-dimension hydrodynamic simulations performed using a newly developed code ASTER. Sources of these nonuniformities include an illumination pattern produced by 60 OMEGA laser beams, capsule offsets (~10 to 20 μm), and imperfect pointing, energy balance, and timing of the beams (with typical σrms ~10 μm, 10%, and 5 ps, respectively). Two implosion designs using 26-kJ triple-picket laser pulses were studied: a nominal design, in which a 880-μm-diameter capsule is illuminated by the same-diameter beams, and a “R75” designmore » using a capsule of 900 μm in diameter and beams of 75% of this diameter. Simulations found that nonuniformities because of capsule offsets and beam imbalance have the largest effect on implosion performance. These nonuniformities lead to significant distortions of implosion cores resulting in an incomplete stagnation. The shape of distorted cores is well represented by neutron images, but loosely in x-rays. Simulated neutron spectra from perturbed implosions show large directional variations and up to ~ 2 keV variation of the hot spot temperature inferred from these spectra. The R75 design is more hydrodynamically efficient because of mitigation of crossed-beam energy transfer, but also suffers more from the nonuniformities. Furthermore, simulations predict a performance advantage of this design over the nominal design when the target offset and beam imbalance σrms are reduced to less than 5 μm and 5%, respectively.« less

  8. Three-dimensional modeling of direct-drive cryogenic implosions on OMEGA

    SciTech Connect

    Igumenshchev, I. V.; Goncharov, V. N.; Marshall, F. J.; Knauer, J. P.; Campbell, E. M.; Forrest, C. J.; Froula, D. H.; Glebov, V. Yu.; McCrory, R. L.; Regan, S. P.; Sangster, T. C.; Skupsky, S.; Stoeckl, C.

    2016-05-04

    The effects of large-scale (with Legendre modes ≲10) laser-imposed nonuniformities in direct-drive cryogenic implosions on the OMEGA laser system are investigated using three-dimension hydrodynamic simulations performed using a newly developed code ASTER. Sources of these nonuniformities include an illumination pattern produced by 60 OMEGA laser beams, capsule offsets (~10 to 20 μm), and imperfect pointing, energy balance, and timing of the beams (with typical σrms ~10 μm, 10%, and 5 ps, respectively). Two implosion designs using 26-kJ triple-picket laser pulses were studied: a nominal design, in which a 880-μm-diameter capsule is illuminated by the same-diameter beams, and a “R75” design using a capsule of 900 μm in diameter and beams of 75% of this diameter. Simulations found that nonuniformities because of capsule offsets and beam imbalance have the largest effect on implosion performance. These nonuniformities lead to significant distortions of implosion cores resulting in an incomplete stagnation. The shape of distorted cores is well represented by neutron images, but loosely in x-rays. Simulated neutron spectra from perturbed implosions show large directional variations and up to ~ 2 keV variation of the hot spot temperature inferred from these spectra. The R75 design is more hydrodynamically efficient because of mitigation of crossed-beam energy transfer, but also suffers more from the nonuniformities. Furthermore, simulations predict a performance advantage of this design over the nominal design when the target offset and beam imbalance σrms are reduced to less than 5 μm and 5%, respectively.

  9. Three-dimensional modeling of direct-drive cryogenic implosions on OMEGA

    SciTech Connect

    Igumenshchev, I. V.; Goncharov, V. N.; Marshall, F. J.; Knauer, J. P.; Campbell, E. M.; Forrest, C. J.; Froula, D. H.; Glebov, V. Yu.; McCrory, R. L.; Regan, S. P.; Sangster, T. C.; Skupsky, S.; Stoeckl, C.

    2016-05-04

    The effects of large-scale (with Legendre modes ≲10) laser-imposed nonuniformities in direct-drive cryogenic implosions on the OMEGA laser system are investigated using three-dimension hydrodynamic simulations performed using a newly developed code ASTER. Sources of these nonuniformities include an illumination pattern produced by 60 OMEGA laser beams, capsule offsets (~10 to 20 μm), and imperfect pointing, energy balance, and timing of the beams (with typical σrms ~10 μm, 10%, and 5 ps, respectively). Two implosion designs using 26-kJ triple-picket laser pulses were studied: a nominal design, in which a 880-μm-diameter capsule is illuminated by the same-diameter beams, and a “R75” design using a capsule of 900 μm in diameter and beams of 75% of this diameter. Simulations found that nonuniformities because of capsule offsets and beam imbalance have the largest effect on implosion performance. These nonuniformities lead to significant distortions of implosion cores resulting in an incomplete stagnation. The shape of distorted cores is well represented by neutron images, but loosely in x-rays. Simulated neutron spectra from perturbed implosions show large directional variations and up to ~ 2 keV variation of the hot spot temperature inferred from these spectra. The R75 design is more hydrodynamically efficient because of mitigation of crossed-beam energy transfer, but also suffers more from the nonuniformities. Furthermore, simulations predict a performance advantage of this design over the nominal design when the target offset and beam imbalance σrms are reduced to less than 5 μm and 5%, respectively.

  10. Investigation on the Bearing Abilities of Three-Dimensional Full Five-Directional Braided Composites with Cut-Edge

    NASA Astrophysics Data System (ADS)

    Wang, Yibo; Liu, Zhenguo; Lei, Bing; Huang, Xiang; Li, Xiaokang

    2017-08-01

    The longitudinal tensile experiments of cut-edge effect on the mechanical performance of three-dimensional full five-directional (3DF5D) braided composites were conducted. The specimens involved two different braiding angles and two different cutting ways. Fracture appearance of specimens without cut-edge and cutting along width direction presented flush, while explosive for specimen with cut-edge along thickness direction. The fracture of axis yarns mainly contributed to the damage of specimens. Cut-edge had little influence on the stiffness of 3DF5D braided composites and had approximately 20 % reduction in tensile strength compared with specimens without cut-edge. The periodic boundary conditions under cut-edge and uncut-edge situations were applied to the RVC to simulate the mesoscopic damage mechanism using finite element method. The stress-strain curves and damage evolution nephogram were obtained. The variation of cut-edge effect with the number of inner cells was predicted by superimposing inner cells method, the addition of inner cells could strengthen the performance of 3DF5D braided composites with cut-edge. These results will play an important role in evaluating the mechanical properties of braided materials after cutting.

  11. Fast Shear Compounding Using Robust Two-dimensional Shear Wave Speed Calculation and Multi-directional Filtering

    PubMed Central

    Song, Pengfei; Manduca, Armando; Zhao, Heng; Urban, Matthew W.; Greenleaf, James F.; Chen, Shigao

    2014-01-01

    A fast shear compounding method was developed in this study using only one shear wave push-detect cycle, such that the shear wave imaging frame rate is preserved and motion artifacts are minimized. The proposed method is composed of the following steps: 1. applying a comb-push to produce multiple differently angled shear waves at different spatial locations simultaneously; 2. decomposing the complex shear wave field into individual shear wave fields with differently oriented shear waves using a multi-directional filter; 3. using a robust two-dimensional (2D) shear wave speed calculation to reconstruct 2D shear elasticity maps from each filter direction; 4. compounding these 2D maps from different directions into a final map. An inclusion phantom study showed that the fast shear compounding method could achieve comparable performance to conventional shear compounding without sacrificing the imaging frame rate. A multi-inclusion phantom experiment showed that the fast shear compounding method could provide a full field-of-view (FOV), 2D, and compounded shear elasticity map with three types of inclusions clearly resolved and stiffness measurements showing excellent agreement to the nominal values. PMID:24613636

  12. Three-dimensional flow with elevated helicity in driven cavity by parallel walls moving in perpendicular directions

    NASA Astrophysics Data System (ADS)

    Povitsky, Alex

    2017-08-01

    The proposed flow in a 3-D cubic cavity is driven by its parallel walls moving in perpendicular directions to create a genuinely three-dimensional highly separated vortical flow, yet having simple single-block cubical geometry of computational domain. The elevated level of helicity is caused by motion of a wall in the direction of axis of primary vortex created by a parallel wall. The velocity vector field is obtained numerically by using second-order upwind scheme and 2003 grid. Helicity, magnitude of normalized helicity, and kinematic vorticity number are evaluated for Reynolds numbers ranging from 100 to 1000. Formation of two primary vortices with their axis oriented perpendicularly and patterns of secondary vortices are discussed. Computational results are compared to the well-known 3-D recirculating cavity flow case where the lid moves in the direction parallel to the cavity side walls. Also results are compared to the diagonally top-driven cavity and to the cavity flow driven by moving top and side walls. The streamlines for the proposed flow show that the particles emerging from top and bottom of the cavity do mix well. Quantitative evaluation of mixing of two fluids in the proposed cavity flow confirms that mixing occurs faster than in the benchmark case.

  13. Investigation on the Bearing Abilities of Three-Dimensional Full Five-Directional Braided Composites with Cut-Edge

    NASA Astrophysics Data System (ADS)

    Wang, Yibo; Liu, Zhenguo; Lei, Bing; Huang, Xiang; Li, Xiaokang

    2016-11-01

    The longitudinal tensile experiments of cut-edge effect on the mechanical performance of three-dimensional full five-directional (3DF5D) braided composites were conducted. The specimens involved two different braiding angles and two different cutting ways. Fracture appearance of specimens without cut-edge and cutting along width direction presented flush, while explosive for specimen with cut-edge along thickness direction. The fracture of axis yarns mainly contributed to the damage of specimens. Cut-edge had little influence on the stiffness of 3DF5D braided composites and had approximately 20 % reduction in tensile strength compared with specimens without cut-edge. The periodic boundary conditions under cut-edge and uncut-edge situations were applied to the RVC to simulate the mesoscopic damage mechanism using finite element method. The stress-strain curves and damage evolution nephogram were obtained. The variation of cut-edge effect with the number of inner cells was predicted by superimposing inner cells method, the addition of inner cells could strengthen the performance of 3DF5D braided composites with cut-edge. These results will play an important role in evaluating the mechanical properties of braided materials after cutting.

  14. Towards a three-dimensional network of direct laser written waveguides on a chip for quantum optical experiments (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Landowski, Alexander; Schmidt, Michael; Renner, Michael; von Freymann, Georg; Widera, Artur

    2016-09-01

    Waveguide networks are essential to gain control over photons on a chip-scale level, for applications in, e.g., optical communication, light routing, and even quantum simulation. Quantum simulators on a chip use highly controllable pairs of single photons to shed light onto the role of entanglement in interacting many-body systems. We build three-dimensional waveguide networks on a chip using a commercial system for direct laser writing in a low fluorescent photoresist on a silica substrate and air cladding. Due to our capability to fabricate three-dimensional structures, we use special coupling structures, that enable addressing all input and output ports of our waveguide network through the substrate via one microscope objective simultaneously. Since the photoresist shows low fluorescence for excitation at 532 nm, we will be able to integrate single quantum emitters, such as color centers in diamond, into the waveguide, acting as integrated single quantum system. Here we present our current arc shaped coupling structure, discuss the limits of the single mode-operation of the waveguides and show first beamsplitting devices. We analyze the contributions to the damping in our network, including the bend loss for bend radii smaller than 10 µm.

  15. On the direct determination of three-dimensional crystallographic phases at low resolution: crambin at 6 A.

    PubMed

    Dorset, D L

    2000-04-11

    Using a pseudo-atom approach, the three-dimensional crystallographic phases for the protein crambin (a = 40.76, b = 18.49, c = 22.33 A, beta = 90.61 degrees, space group P2(1)) were determined to 6 A by direct methods. First, the centrosymmetric h0l set was assigned phases by symbolic addition, and the initial solution was then refined by Fourier methods. Phase values of strong reflections were then permuted, and the decision to change the phase value for two of these was made by consulting a cross-correlation of the experimental density histogram to the theoretical or known histogram for the protein. The two-dimensional basis was then extended by the Sayre equation into three dimensions by assigning a phase to a third allowed hkl origin-defining reflection and an algebraic value to another axial reflection. The correct solution was again identified by the histogram correlation, yielding a solution in which the mean phase error for all 98 reflections was 61.5 degrees or 23.1 degrees for the 21 most intense reflections. A parallel study with another protein indicates this method may have general utility.

  16. On the direct determination of three-dimensional crystallographic phases at low resolution: Crambin at 6 Å

    PubMed Central

    Dorset, Douglas L.

    2000-01-01

    Using a pseudo-atom approach, the three-dimensional crystallographic phases for the protein crambin (a = 40.76, b = 18.49, c = 22.33 Å, β = 90.61°, space group P21) were determined to 6 Å by direct methods. First, the centrosymmetric h0ℓ set was assigned phases by symbolic addition, and the initial solution was then refined by Fourier methods. Phase values of strong reflections were then permuted, and the decision to change the phase value for two of these was made by consulting a cross-correlation of the experimental density histogram to the theoretical or known histogram for the protein. The two-dimensional basis was then extended by the Sayre equation into three dimensions by assigning a phase to a third allowed hkℓ origin-defining reflection and an algebraic value to another axial reflection. The correct solution was again identified by the histogram correlation, yielding a solution in which the mean phase error for all 98 reflections was 61.5° or 23.1° for the 21 most intense reflections. A parallel study with another protein indicates this method may have general utility. PMID:10725378

  17. Micro-CT Characterization on the Meso-Structure of Three-Dimensional Full Five-Directional Braided Composite

    NASA Astrophysics Data System (ADS)

    Ya, Jixuan; Liu, Zhenguo; Wang, Yuanhang

    2017-06-01

    The meso-structure is important in predicting mechanical properties of the three-dimensional (3D) braided composite. In this paper, the internal structure and porosity of three-dimensional full five-directional (3DF5D) braided composite is characterized at mesoscopic scale (the scale of the yarns) using micro-computed tomography (micro-CT) non-destructively. Glass fiber yarns as tracer are added into the sample made of carbon fiber to enhance the contrast in the sectional images. The model of tracer yarns is established with 3D reconstruction method to analyze the cross-section and path of yarns. The porosities are reconstructed and characterized in the end. The results demonstrate that the cross sections of braiding yarns and axial yarns change with the regions and the heights in one pitch of 3DF5D braided composites. The path of braiding yarns are various in the different regions while the axial yarns are always straight. Helical indentations appear on the surfaces of the axial yarns because of the squeeze from braiding yarns. Moreover, the porosities in different shapes and sizes are almost located in the matrix and between the yarns.

  18. The Acyclic Retinoid Peretinoin Inhibits Hepatitis C Virus Replication and Infectious Virus Release in Vitro

    NASA Astrophysics Data System (ADS)

    Shimakami, Tetsuro; Honda, Masao; Shirasaki, Takayoshi; Takabatake, Riuta; Liu, Fanwei; Murai, Kazuhisa; Shiomoto, Takayuki; Funaki, Masaya; Yamane, Daisuke; Murakami, Seishi; Lemon, Stanley M.; Kaneko, Shuichi

    2014-04-01

    Clinical studies suggest that the oral acyclic retinoid Peretinoin may reduce the recurrence of hepatocellular carcinoma (HCC) following surgical ablation of primary tumours. Since hepatitis C virus (HCV) infection is a major cause of HCC, we assessed whether Peretinoin and other retinoids have any effect on HCV infection. For this purpose, we measured the effects of several retinoids on the replication of genotype 1a, 1b, and 2a HCV in vitro. Peretinoin inhibited RNA replication for all genotypes and showed the strongest antiviral effect among the retinoids tested. Furthermore, it reduced infectious virus release by 80-90% without affecting virus assembly. These effects could be due to reduced signalling from lipid droplets, triglyceride abundance, and the expression of mature sterol regulatory element-binding protein 1c and fatty acid synthase. These negative effects of Peretinoin on HCV infection may be beneficial in addition to its potential for HCC chemoprevention in HCV-infected patients.

  19. Ether lipid-ester prodrugs of acyclic nucleoside phosphonates: activity against adenovirus replication in vitro.

    PubMed

    Hartline, Caroll B; Gustin, Kortney M; Wan, William B; Ciesla, Stephanie L; Beadle, James R; Hostetler, Karl Y; Kern, Earl R

    2005-02-01

    The acyclic nucleoside phosphonate cidofovir (CDV) and its closely related analogue (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)-adenine ([S]-HPMPA) have been reported to have activity against many adenovirus (AdV) serotypes. A new series of orally active ether lipid-ester prodrugs of CDV and of (S)-HPMPA that have slight differences in the structure of their lipid esters were evaluated, in tissue-culture cells, for activity against 5 AdV serotypes. The results indicated that, against several AdV serotypes, the most active compounds were 15-2500-fold more active than the unmodified parent compounds and should be evaluated further for their potential to treat AdV infections in humans.

  20. Pd-Catalyzed N-Arylation of Secondary Acyclic Amides: Catalyst Development, Scope, and Computational Study

    PubMed Central

    Hicks, Jacqueline D.; Hyde, Alan M.; Cuezva, Alberto Martinez; Buchwald, Stephen L.

    2009-01-01

    We report the efficient N-arylation of acyclic secondary amides and related nucleophiles with aryl nonaflates, triflates, and chlorides. This method allows for easy variation of the aromatic component in tertiary aryl amides. A new biaryl phosphine with P-bound 3,5-(bis)trifluoromethylphenyl groups was found to be uniquely effective for this amidation. The critical aspects of the ligand were explored through synthetic, mechanistic, and computational studies. Systematic variation of the ligand revealed the importance of (1) a methoxy group on the aromatic carbon of the “top ring” ortho to the phosphorus and (2) two highly electron-withdrawing P-bound 3,5-(bis)trifluoromethylphenyl groups. Computational studies suggest the electron-deficient nature of the ligand is important in facilitating amide binding to the LPd(II)(Ph)(X) intermediate. PMID:19886610

  1. Halogen bonding in water results in enhanced anion recognition in acyclic and rotaxane hosts

    NASA Astrophysics Data System (ADS)

    Langton, Matthew J.; Robinson, Sean W.; Marques, Igor; Félix, Vítor; Beer, Paul D.

    2014-12-01

    Halogen bonding (XB), the attractive interaction between an electron-deficient halogen atom and a Lewis base, has undergone a dramatic development as an intermolecular force analogous to hydrogen bonding (HB). However, its utilization in the solution phase remains underdeveloped. Furthermore, the design of receptors capable of strong and selective recognition of anions in water remains a significant challenge. Here we demonstrate the superiority of halogen bonding over hydrogen bonding for strong anion binding in water, to the extent that halide recognition by a simple acyclic mono-charged receptor is achievable. Quantification of iodide binding by rotaxane hosts reveals the strong binding by the XB-rotaxane is driven exclusively by favourable enthalpic contributions arising from the halogen-bonding interactions, whereas weaker association with the HB-rotaxanes is entropically driven. These observations demonstrate the unique nature of halogen bonding in water as a strong alternative interaction to the ubiquitous hydrogen bonding in molecular recognition and assembly.

  2. Acyclic N-halamine-immobilized polyurethane: Preparation and antimicrobial and biofilm-controlling functions

    PubMed Central

    Luo, Jie; Porteous, Nuala; Lin, Jiajin; Sun, Yuyu

    2015-01-01

    Hydroxyl groups were introduced onto polyurethane surfaces through 1,6-hexamethylene diisocyanate activation, followed by diethanolamine hydroxylation. Polymethacrylamide was covalently attached to the hydroxylated polyurethane through surface grafting polymerization of methacrylamide using cerium (IV) ammonium nitrate as an initiator. After bleach treatment, the amide groups of the covalently bound polymethacrylamide chains were transformed into N-halamines. The new N-halamine-immobilized polyurethane provided a total sacrifice of 107–108 colony forming units per milliliter of Staphylococcus aureus (Gram-positive bacteria), Escherichia coli (Gram-negative bacteria), and Candida albicans (fungi) within 10 min and successfully prevented bacterial and fungal biofilm formation. The antimicrobial and biofilm-controlling effects were both durable and rechargeable, pointing to great potentials of the new acyclic N-halamine-immobilized polyurethane for a broad range of related applications. PMID:26089593

  3. Acyclic Immucillin Phosphonates. Second-Generation Inhibitors of Plasmodium falciparum Hypoxanthine- Guanine-Xanthine Phosphoribosyltransferase

    SciTech Connect

    Hazelton, Keith Z.; Ho, Meng-Chaio; Cassera, Maria B.; Clinch, Keith; Crump, Douglas R.; Rosario Jr., Irving; Merino, Emilio F.; Almo, Steve C.; Tyler, Peter C.; Schramm, Vern L.

    2012-06-22

    We found that Plasmodium falciparum is the primary cause of deaths from malaria. It is a purine auxotroph and relies on hypoxanthine salvage from the host purine pool. Purine starvation as an antimalarial target has been validated by inhibition of purine nucleoside phosphorylase. Hypoxanthine depletion kills Plasmodium falciparum in cell culture and in Aotus monkey infections. Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from P. falciparum is required for hypoxanthine salvage by forming inosine 5'-monophosphate, a branchpoint for all purine nucleotide synthesis in the parasite. We present a class of HGXPRT inhibitors, the acyclic immucillin phosphonates (AIPs), and cell permeable AIP prodrugs. The AIPs are simple, potent, selective, and biologically stable inhibitors. The AIP prodrugs block proliferation of cultured parasites by inhibiting the incorporation of hypoxanthine into the parasite nucleotide pool and validates HGXPRT as a target in malaria.

  4. Two-dimensional chromatography method applied to the enantiomeric determination of lansoprazole in human plasma by direct sample injection.

    PubMed

    Gomes, Ricardo F; Cassiano, Neila M; Pedrazzoli, J; Cass, Quezia B

    2010-01-01

    A two-dimensional HPLC method based on the direct injection of biological samples has been developed and validated for the determination of lansoprazole enantiomers in human plasma. The lansoprazole enantiomers were extracted from the biological matrix using an octyl restricted access media bovine serum albumin column (C8 RAM BSA) and the enantioseparation was performed on an amylose tris(3,5-dimethoxyphenylcarbamate) chiral column using acetonitrile:water (35:65 v/v) and UV detection at 285 nm. Analysis time was 25 min with no time spent on sample preparation. The method was applied to the analysis of the plasma samples obtained from nine Brazilian volunteers who received a 30 mg oral dose of racemic lansoprazole and was able to quantify the enantiomers of lansoprazole in the clinical samples analyzed. Copyright 2009 Wiley-Liss, Inc.

  5. Three-dimensional symmetry analysis of a direct-drive irradiation scheme for the laser megajoule facility

    SciTech Connect

    Ramis, R.; Temporal, M.; Canaud, B.; Brandon, V.

    2014-08-15

    The symmetry of a Direct-Drive (DD) irradiation scheme has been analyzed by means of three-dimensional (3D) simulations carried out by the code MULTI (R. Ramis et al., Comput. Phys. Commun. 49, 475 (1988)) that includes hydrodynamics, heat transport, and 3D laser ray-tracing. The implosion phase of a target irradiated by the Laser Megajoule (LMJ) facility in the context of the Shock Ignition scheme has been considered. The LMJ facility has been designed for Indirect-Drive, and by this reason that the irradiation scheme must be modified when used for DD. Thus, to improve the implosion uniformity to acceptable levels, the beam centerlines should be realigned and the beam power balance should be adjusted. Several alternatives with different levels of complexity are presented and discussed.

  6. Iteration-based direct ellipse-specific algebraic fitting method of incomplete spots for onsite three-dimensional measurement

    NASA Astrophysics Data System (ADS)

    Wang, Zhenxing; Wu, Zhuoqi; Zhen, Xijin; Yang, Rundang; Xi, Juntong

    2015-01-01

    The direct ellipse-specific algebraic fitting (DESAF) method proposed by Fitzgibbon is a classical method to fit an ellipse from discrete points. Generally, for a complete spot, an ellipse, which coincides well with the complete contour of the spot, can be fitted by DESAF. However, for an incomplete spot damaged by some noises such as nonuniform optical surfaces, depth steps, and occlusion, DESAF would fit an incorrect ellipse which could not accurately match the complete contour of the spot. We analyze this problem encountered in the onsite three-dimensional measurement of hull plates and propose a method to remove these outlier points from the contours of incomplete spots. The experiments of computer simulated data and real data demonstrate that the proposed method can dramatically remove the outlier points from the contour and improve the detection accuracy of the center of the incomplete spot.

  7. A direct and quantitative three-dimensional reconstruction of the internal structure of disordered mesoporous carbon with tailored pore size.

    PubMed

    Balach, Juan; Soldera, Flavio; Acevedo, Diego F; Mücklich, Frank; Barbero, César A

    2013-06-01

    A new technique that allows direct three-dimensional (3D) investigations of mesopores in carbon materials and quantitative characterization of their physical properties is reported. Focused ion beam nanotomography (FIB-nt) is performed by a serial sectioning procedure with a dual beam FIB-scanning electron microscopy instrument. Mesoporous carbons (MPCs) with tailored mesopore size are produced by carbonization of resorcinol-formaldehyde gels in the presence of a cationic surfactant as a pore stabilizer. A visual 3D morphology representation of disordered porous carbon is shown. Pore size distribution of MPCs is determined by the FIB-nt technique and nitrogen sorption isotherm methods to compare both results. The obtained MPCs exhibit pore sizes of 4.7, 7.2, and 18.3 nm, and a specific surface area of ca. 560 m(2)/g.

  8. Clustering and fluidization in a one-dimensional granular system: molecular dynamics and direct-simulation Monte Carlo method.

    PubMed

    Pasini, J M; Cordero, P

    2001-04-01

    We study a one-dimensional granular gas of pointlike particles not subject to gravity between two walls at temperatures T(left) and T(right). The system exhibits two distinct regimes, depending on the normalized temperature difference Delta=(T(right)-T(left))/(T(right)+T(left)): one completely fluidized and one in which a cluster coexists with the fluidized gas. When Delta is above a certain threshold, cluster formation is fully inhibited, obtaining a completely fluidized state. The mechanism that produces these two phases is explained. In the fluidized state the velocity distribution function exhibits peculiar non-Gaussian features. For this state, comparison between integration of the Boltzmann equation using the direct-simulation Monte Carlo method and results stemming from microscopic Newtonian molecular dynamics gives good coincidence, establishing that the non-Gaussian features observed do not arise from the onset of correlations.

  9. Direct-numerical simulation of the glottal jet and vocal-fold dynamics in a three-dimensional laryngeal model

    PubMed Central

    Zheng, X.; Mittal, R.; Xue, Q.; Bielamowicz, S.

    2011-01-01

    An immersed-boundary method based flow solver coupled with a finite-element solid dynamics solver is employed in order to conduct direct-numerical simulations of phonatory dynamics in a three-dimensional model of the human larynx. The computed features of the glottal flow including mean and peak flow rates, and the open and skewness quotients are found to be within the normal physiological range. The flow-induced vibration pattern shows the classical “convergent-divergent” glottal shape, and the vibration amplitude is also found to be typical for human phonation. The vocal fold motion is analyzed through the method of empirical eigenfunctions and this analysis indicates a 1:1 modal entrainment between the “adduction-abduction” mode and the “mucosal wave” mode. The glottal jet is found to exhibit noticeable cycle-to-cycle asymmetric deflections and the mechanism underlying this phenomenon is examined. PMID:21786908

  10. Direct numerical simulation of three-dimensional Navier Stokes equations for a slit nozzle free jet and experimental verification

    NASA Astrophysics Data System (ADS)

    Yuu, Shiichi; Nishioka, Toshifumi; Umekage, Toshihiko

    1993-02-01

    The third-order upwind finite difference scheme is applied to the convective terms in three-dimensional Navier-Stokes equations to directly simulate the free jet flow emitted from a slit nozzle. The calculated flow field ranges from the nozzle exit to the fully developed turbulent region. The calculated results of turbulent characteristics (mean velocity distributions, turbulent intensity distributions, velocity autocorrelations and power spectra) are compared with the experimental data. The mesh size is roughly ten times the Kolmogorov microscale; however, the calculated turbulent characteristics represent fairly well the experimental ones, except that the data are strongly dependent upon small-scale eddies. This means that the simulation documents well the motion of large-scale eddies which play an important role in the flow-field formation. Neglecting the small-scale eddies in the third-order upwind finite difference scheme does not greatly affect the calculated results of large-scale eddy motions.

  11. A PARALIND Decomposition-Based Coherent Two-Dimensional Direction of Arrival Estimation Algorithm for Acoustic Vector-Sensor Arrays

    PubMed Central

    Zhang, Xiaofei; Zhou, Min; Li, Jianfeng

    2013-01-01

    In this paper, we combine the acoustic vector-sensor array parameter estimation problem with the parallel profiles with linear dependencies (PARALIND) model, which was originally applied to biology and chemistry. Exploiting the PARALIND decomposition approach, we propose a blind coherent two-dimensional direction of arrival (2D-DOA) estimation algorithm for arbitrarily spaced acoustic vector-sensor arrays subject to unknown locations. The proposed algorithm works well to achieve automatically paired azimuth and elevation angles for coherent and incoherent angle estimation of acoustic vector-sensor arrays, as well as the paired correlated matrix of the sources. Our algorithm, in contrast with conventional coherent angle estimation algorithms such as the forward backward spatial smoothing (FBSS) estimation of signal parameters via rotational invariance technique (ESPRIT) algorithm, not only has much better angle estimation performance, even for closely-spaced sources, but is also available for arbitrary arrays. Simulation results verify the effectiveness of our algorithm. PMID:23604030

  12. Clustering and fluidization in a one-dimensional granular system: Molecular dynamics and direct-simulation Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Pasini, José Miguel; Cordero, Patricio

    2001-04-01

    We study a one-dimensional granular gas of pointlike particles not subject to gravity between two walls at temperatures Tleft and Tright. The system exhibits two distinct regimes, depending on the normalized temperature difference Δ=(Tright- Tleft)/(Tright+Tleft): one completely fluidized and one in which a cluster coexists with the fluidized gas. When Δ is above a certain threshold, cluster formation is fully inhibited, obtaining a completely fluidized state. The mechanism that produces these two phases is explained. In the fluidized state the velocity distribution function exhibits peculiar non-Gaussian features. For this state, comparison between integration of the Boltzmann equation using the direct-simulation Monte Carlo method and results stemming from microscopic Newtonian molecular dynamics gives good coincidence, establishing that the non-Gaussian features observed do not arise from the onset of correlations.

  13. Three-dimensional direct numerical simulation of turbulent lean premixed methane combustion with detailed kinetics

    DOE PAGES

    Aspden, A. J.; Day, M. S.; Bell, J. B.

    2016-02-18

    The interaction of maintained homogeneous isotropic turbulence with lean premixed methane flames is investigated using direct numerical simulation with detailed chemistry. The conditions are chosen to be close to those found in atmospheric laboratory experiments. As the Karlovitz number is increased from 1 to 36, the preheat zone becomes thickened, while the reaction zone remains largely unaffected. A negative correlation of fuel consumption with mean flame surface curvature is observed. With increasing turbulence intensity, the chemical composition in the preheat zone tends towards that of an idealised unity Lewis number flame, which we argue is the onset of the transitionmore » to distributed burning, and the response of the various chemical species is shown to fall into broad classes. Smaller-scale simulations are used to isolate the specific role of species diffusion at high turbulent intensities. Diffusion of atomic hydrogen is shown to be related to the observed curvature correlations, but does not have significant consequential impact on the thickening of the preheat zone. It is also shown that susceptibility of the preheat zone to thickening by turbulence is related to the 'global' Lewis number (the Lewis number of the deficient reactant); higher global Lewis number flames tend to be more prone to thickening.« less

  14. Three-dimensional direct numerical simulation of turbulent lean premixed methane combustion with detailed kinetics

    SciTech Connect

    Aspden, A. J.; Day, M. S.; Bell, J. B.

    2016-02-18

    The interaction of maintained homogeneous isotropic turbulence with lean premixed methane flames is investigated using direct numerical simulation with detailed chemistry. The conditions are chosen to be close to those found in atmospheric laboratory experiments. As the Karlovitz number is increased from 1 to 36, the preheat zone becomes thickened, while the reaction zone remains largely unaffected. A negative correlation of fuel consumption with mean flame surface curvature is observed. With increasing turbulence intensity, the chemical composition in the preheat zone tends towards that of an idealised unity Lewis number flame, which we argue is the onset of the transition to distributed burning, and the response of the various chemical species is shown to fall into broad classes. Smaller-scale simulations are used to isolate the specific role of species diffusion at high turbulent intensities. Diffusion of atomic hydrogen is shown to be related to the observed curvature correlations, but does not have significant consequential impact on the thickening of the preheat zone. It is also shown that susceptibility of the preheat zone to thickening by turbulence is related to the 'global' Lewis number (the Lewis number of the deficient reactant); higher global Lewis number flames tend to be more prone to thickening.

  15. Three-Dimensional Nanometer Features of Direct Current Electrical Trees in Low-Density Polyethylene.

    PubMed

    Pallon, Love K H; Nilsson, Fritjof; Yu, Shun; Liu, Dongming; Diaz, Ana; Holler, Mirko; Chen, Xiangrong R; Gubanski, Stanislaw; Hedenqvist, Mikael S; Olsson, Richard T; Gedde, Ulf W

    2017-03-08

    Electrical trees are one reason for the breakdown of insulating materials in electrical power systems. An understanding of the growth of electrical trees plays a crucial role in the development of reliable high voltage direct current (HVDC) power grid systems with transmission voltages up to 1 MV. A section that contained an electrical tree in low-density polyethylene (LDPE) has been visualized in three dimensions (3D) with a resolution of 92 nm by X-ray ptychographic tomography. The 3D imaging revealed prechannel-formations with a lower density with the width of a couple of hundred nanometers formed around the main branch of the electrical tree. The prechannel structures were partially connected with the main tree via paths through material with a lower density, proving that the tree had grown in a step-by-step manner via the prestep structures formed in front of the main channels. All the prechannel structures had a size well below the limit of the Paschen law and were thus not formed by partial discharges. Instead, it is suggested that the prechannel structures were formed by electro-mechanical stress and impact ionization, where the former was confirmed by simulations to be a potential explanation with electro-mechanical stress tensors being almost of the same order of magnitude as the short-term modulus of low-density polyethylene.

  16. Direct three dimensional observation of the microstructure and chemistry of C3S hydration

    NASA Astrophysics Data System (ADS)

    Hu, Qinang

    Although portland cement has been used for over a hundred years as the binder in concrete, the basic mechanism of hydration is still not well understood. Progress has been halted for the fact that it is challenging for most current experimental techniques to give direct observation of the hydration process in-situ and provide quantitative measurement on the microstructure and chemistry at the nano-length scale. Recent advances of nano scale X-ray imaging make nano-tomography and nano-X-ray fluorescence reality. The nano-scale X-ray beams in these techniques allow the sample to be imaged nondestructively and provide a high transmission of signal that penetrate through both sample materials and a possible solution environment, which could make themselves in-situ techniques. Moreover, these techniques can be combined to enrich both datasets to become a more powerful technique. In this dissertation, the applications of both techniques have been established from micron lab scale experiment to nano-synchrotron investigation for studying cementitious materials. The progresses have been shown from first application on 3D chemical characterization of fly ash particles at the nanoscale to later updated versions of in-situ experiments for studying cement hydration, which allow quantitative measurements on 3D structure, chemistry and mass density of hydration products at different hydration periods. These unprecedented discoveries could lead to a breakthrough for both nanoscale analysis of any material and cement hydration research.

  17. Direct observation of many-body charge density oscillations in a two-dimensional electron gas

    NASA Astrophysics Data System (ADS)

    Sessi, Paolo; Silkin, Vyacheslav M.; Nechaev, Ilya A.; Bathon, Thomas; El-Kareh, Lydia; Chulkov, Evgueni V.; Echenique, Pedro M.; Bode, Matthias

    2015-10-01

    Quantum interference is a striking manifestation of one of the basic concepts of quantum mechanics: the particle-wave duality. A spectacular visualization of this effect is the standing wave pattern produced by elastic scattering of surface electrons around defects, which corresponds to a modulation of the electronic local density of states and can be imaged using a scanning tunnelling microscope. To date, quantum-interference measurements were mainly interpreted in terms of interfering electrons or holes of the underlying band-structure description. Here, by imaging energy-dependent standing-wave patterns at noble metal surfaces, we reveal, in addition to the conventional surface-state band, the existence of an `anomalous' energy band with a well-defined dispersion. Its origin is explained by the presence of a satellite in the structure of the many-body spectral function, which is related to the acoustic surface plasmon. Visualizing the corresponding charge oscillations provides thus direct access to many-body interactions at the atomic scale.

  18. Direct laser writing of three-dimensional network structures as templates for disordered photonic materials

    NASA Astrophysics Data System (ADS)

    Haberko, Jakub; Muller, Nicolas; Scheffold, Frank

    2013-10-01

    In the present article we substantially expand on our recent study about the fabrication of mesoscale polymeric templates of disordered photonic network materials [Haberko and Scheffold, Opt. Expr.OPEXFF1094-408710.1364/OE.21.001057 21, 1057 (2013)]. We present a detailed analysis and discussion of important technical aspects related to the fabrication and characterization of these fascinating materials. Compared to our initial report we were able to reduce the typical structural length scale of the seed pattern from a=3.3μm to a=2μm, bringing it closer to the technologically relevant fiber-optic communications wavelength range around λ˜1.5μm. We have employed scanning electron microscopy coupled with focused ion beam cutting to look inside the bulk of the samples of different heights. Moreover, we demonstrate the use of laser scanning confocal microscopy to assess the real space structure of the samples fabricated by direct laser writing. We address in detail questions about scalability, finite size effects, and geometrical distortions. We also study the effect of the lithographic voxel shape, that is, the ellipsoidal shape of the laser pen used in the fabrication process. To this end we employ detailed numerical modeling of the scattering function using a discrete dipole approximation scheme.

  19. Strategies for directing the structure and function of three-dimensional collagen biomaterials across length scales.

    PubMed

    Walters, B D; Stegemann, J P

    2014-04-01

    Collagen type I is a widely used natural biomaterial that has found utility in a variety of biological and medical applications. Its well-characterized structure and role as an extracellular matrix protein make it a highly relevant material for controlling cell function and mimicking tissue properties. Collagen type I is abundant in a number of tissues, and can be isolated as a purified protein. This review focuses on hydrogel biomaterials made by reconstituting collagen type I from a solubilized form, with an emphasis on in vitro studies in which collagen structure can be controlled. The hierarchical structure of collagen from the nanoscale to the macroscale is described, with an emphasis on how structure is related to function across scales. Methods of reconstituting collagen into hydrogel materials are presented, including molding of macroscopic constructs, creation of microscale modules and electrospinning of nanoscale fibers. The modification of collagen biomaterials to achieve the desired structures and functions is also addressed, with particular emphasis on mechanical control of collagen structure, creation of collagen composite materials and crosslinking of collagenous matrices. Biomaterials scientists have made remarkable progress in rationally designing collagen-based biomaterials and in applying them both to the study of biology and for therapeutic benefit. This broad review illustrates recent examples of techniques used to control collagen structure and thereby to direct its biological and mechanical functions.

  20. Three dimensional mapping of Fe dopants in ceria nanocrystals using direct spectroscopic electron tomography.

    PubMed

    Goris, Bart; Meledina, Maria; Turner, Stuart; Zhong, Zhichao; Batenburg, K Joost; Bals, Sara

    2016-12-01

    Electron tomography is a powerful technique for the 3D characterization of the morphology of nanostructures. Nevertheless, resolving the chemical composition of complex nanostructures in 3D remains challenging and the number of studies in which electron energy loss spectroscopy (EELS) is combined with tomography is limited. During the last decade, dedicated reconstruction algorithms have been developed for HAADF-STEM tomography using prior knowledge about the investigated sample. Here, we will use the prior knowledge that the experimental spectrum of each reconstructed voxel is a linear combination of a well-known set of references spectra in a so-called direct spectroscopic tomography technique. Based on a simulation experiment, it is shown that this technique provides superior results in comparison to conventional reconstruction methods for spectroscopic data, especially for spectrum images containing a relatively low signal to noise ratio. Next, this technique is used to investigate the spatial distribution of Fe dopants in Fe:Ceria nanoparticles in 3D. It is shown that the presence of the Fe(2+) dopants is correlated with a reduction of the Ce atoms from Ce(4+) towards Ce(3+). In addition, it is demonstrated that most of the Fe dopants are located near the voids inside the nanoparticle.

  1. New acyclic secondary metabolites from the biologically active fraction of Albizia lebbeck flowers.

    PubMed

    Al-Massarani, Shaza M; El Gamal, Ali A; Abd El Halim, Mohamed F; Al-Said, Mansour S; Abdel-Kader, Maged S; Basudan, Omer A; Alqasoumi, Saleh I

    2017-01-01

    The total extract of Albizia lebbeck flowers was examined in vivo for its possible hepatoprotective activity in comparison with the standard drug silymarin at two doses. The higher dose expressed promising activity especially in reducing the levels of AST, ALT and bilirubin. Fractionation via liquid-liquid partition and reexamination of the fractions revealed that the n-butanol fraction was the best in improving liver biochemical parameters followed by the n-hexane fraction. However, serum lipid parameters were best improved with CHCl3 fraction. The promising biological activity results initiated an intensive chromatographic purification of A. lebbeck flowers fractions. Two compounds were identified from natural source for the first time, the acyclic farnesyl sesquiterpene glycoside1-O-[6-O-α-l-arabinopyranosyl-β-d-glucopyranoside]-(2E,6E-)-farnesol (6) and the squalene derivative 2,3-dihydroxy-2,3-dihydrosqualene (9), in addition to eight compounds reported here for the first time from the genus Albizia; two benzyl glycosides, benzyl 1-O-β-d-glucopyranoside (1) and benzyl 6-O-α-l-arabinopyranosyl β-d-glucopyranoside (2); three acyclic monoterpene glycosides, linalyl β-d-glucopyranoside (3) and linalyl 6-O-α-l-arabinopyranosyl-β-d-glucopyranoside (4); (2E)-3,7-dimethylocta-2,6-dienoate-6-O-α-l arabinopyranosyl-β-d-glucopyranoside (5), two oligoglycosides, n-hexyl-α-l arabinopyranosyl-(1 → 6)-β-d-glucopyranoside (creoside) (7) and n-octyl α-l-arabinopyranosyl-(1 → 6)-β-d-glucopyranoside (rhodiooctanoside) (8); and ethyl fructofuranoside (10). The structures of the isolated compounds were elucidated based on extensive examination of their spectroscopic 1D and 2D-NMR, MS, UV, and IR data. It is worth mentioning that, some of the isolated linalol glycoside derivatives were reported as aroma precursors.

  2. Directional migration and differentiation of neural stem cells within three-dimensional microenvironments.

    PubMed

    Shamloo, Amir; Heibatollahi, Motahare; Mofrad, Mohammad R K

    2015-03-01

    Harnessing neural stem cells to repair neuronal damage is a promising potential treatment for neuronal diseases. To enable future therapeutic efficacy, the survival, proliferation, migration and differentiation of neural stem/progenitor cells (NPCs) should be accurately studied and optimized in in vitro platforms before transplanting these cells into the body for treatment purposes. Such studies can determine the appropriate quantities of the biochemical and biomechanical factors needed to control and optimize NPC behavior in vivo. In this study, NPCs were cultured within a microfluidic device while being encapsulated within the collagen matrix. The migration and differentiation of NPCs were studied in response to varying concentrations of nerve growth factor (NGF) and within varying densities of collagen matrices. It was shown that the migration and differentiation of NPCs can be significantly improved by providing the appropriate range of NGF concentrations while encapsulating the cells within the collagen matrix of optimal density. In particular, it was observed that within collagen matrices of intermediate density (0.9 mg ml(-1)), NPCs have a higher ability to migrate farther and in a collective manner while their differentiation into neurons is significantly higher and the cells can form protrusions and connections with their neighboring cells. Within collagen matrices with higher densities (1.8 mg ml(-1)), the cells did not migrate significantly as compared to the ones within lower matrix densities; within the matrices with lower collagen densities (0.45 mg ml(-1)) most of the cells migrated in an individual manner. However, no significant differentiation into neurons was observed for these two cases. It was also found that depending on the collagen matrix density, a minimum concentration of NGF caused a collective migration of NPCs, and a minimum concentration gradient of this factor stimulated the directional navigation of the cells. The results of this

  3. Palladium(II)-catalyzed direct alkenylation of nonaromatic enamides.

    PubMed

    Gigant, Nicolas; Gillaizeau, Isabelle

    2012-07-06

    A mild and efficient method for the direct alkenylation of nonaromatic enamides was achieved through a palladium(II)-catalyzed C-H functionalization. The reaction scope includes cyclic and acyclic enamides and a range of activated alkenes. This approach represents the first successful direct C(3)-functionalization of nonaromatic cyclic enamides.

  4. Direct reconstruction in CT-analogous pharmacokinetic diffuse fluorescence tomography: two-dimensional simulative and experimental validations

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Zhang, Yanqi; Zhang, Limin; Li, Jiao; Zhou, Zhongxing; Zhao, Huijuan; Gao, Feng

    2016-04-01

    We present a generalized strategy for direct reconstruction in pharmacokinetic diffuse fluorescence tomography (DFT) with CT-analogous scanning mode, which can accomplish one-step reconstruction of the indocyanine-green pharmacokinetic-rate images within in vivo small animals by incorporating the compartmental kinetic model into an adaptive extended Kalman filtering scheme and using an instantaneous sampling dataset. This scheme, compared with the established indirect and direct methods, eliminates the interim error of the DFT inversion and relaxes the expensive requirement of the instrument for obtaining highly time-resolved date-sets of complete 360 deg projections. The scheme is validated by two-dimensional simulations for the two-compartment model and pilot phantom experiments for the one-compartment model, suggesting that the proposed method can estimate the compartmental concentrations and the pharmacokinetic-rates simultaneously with a fair quantitative and localization accuracy, and is well suitable for cost-effective and dense-sampling instrumentation based on the highly-sensitive photon counting technique.

  5. Application of three-dimensional reduced graphene oxide-gold composite modified electrode for direct electrochemistry and electrocatalysis of myoglobin.

    PubMed

    Shi, Fan; Xi, Jingwen; Hou, Fei; Han, Lin; Li, Guangjiu; Gong, Shixing; Chen, Chanxing; Sun, Wei

    2016-01-01

    In this paper a three-dimensional (3D) reduced graphene oxide (RGO) and gold (Au) composite was synthesized by electrodeposition and used for the electrode modification with carbon ionic liquid electrode (CILE) as the substrate electrode. Myoglobin (Mb) was further immobilized on the surface of 3D RGO-Au/CILE to obtain an electrochemical sensing platform. Direct electrochemistry of Mb on the modified electrode was investigated with a pair of well-defined redox waves appeared on cyclic voltammogram, indicating the realization of direct electron transfer of Mb with the modified electrode. The results can be ascribed to the presence of highly conductive 3D RGO-Au composite on the electrode surface that accelerate the electron transfer rate between the electroactive center of Mb and the electrode. The Mb modified electrode showed excellent electrocatalytic activity to the reduction of trichloroacetic acid in the concentration range from 0.2 to 36.0 mmol/L with the detection limit of 0.06 mmol/L (3σ). Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Direct method of three-dimensional imaging using the multiple-wavelength range-gated active imaging principle.

    PubMed

    Matwyschuk, Alexis

    2016-05-10

    The tomography executed with mono-wavelength active imaging systems uses the recording of several images to restore a three-dimensional (3D) scene. Thus, in order to show the depth in the scene, a different color is attributed to each recorded image. Therefore, the 3D restoration depends on the video frame rate of the camera. By using a multiple-wavelength range-gated active imaging system, it is possible to restore the 3D scene directly in a single image at the moment of recording with a video camera. Each emitted light pulse with a different wavelength corresponds to a visualized zone at a different distance in the scene. The camera shutter opens just once during the emission of light pulses with the different wavelengths. Thus, the restoration can be executed in real time with regard to the video frame rate of the camera. From an analytical model and from a graphical approach, we demonstrated the feasibility of this new method of 3D restoration. The non-overlapping conditions between two consecutive visualized zones are analyzed. The experimental test results confirm these different conditions and validate the theoretical principle to directly restore the 3D scene in a color image with a multiple-wavelength laser source, an RGB filter, and a triggerable intensified camera.

  7. Application of a Three-Dimensional Shell Theory to the Free Vibration of Shells Arbitrarily Deep in One Direction

    NASA Astrophysics Data System (ADS)

    YOUNG, P. G.

    2000-11-01

    A three-dimensional shell theory is presented which is applicable to doubly curved thick open shells which are arbitrarily deep (have a large side-length to radius of curvature ratio) in one principal direction but are shallow in the other direction. The strain-displacement equations for the proposed “deep-shallow” shell theory are expressed in Cartesian co-ordinates and the limits of applicability of these equations are discussed. These equations are then used in a Ritz variational formulation with algebraic polynomials as trial functions to solve for the natural frequencies of a number of doubly curved shell problems. A novel approach is also proposed in which penalty functions are introduced to enforce continuity of displacements at two opposite ends of a shell of rectangular platform, increasing the range of problems which can be treated to include closed shells, such as cylinders, barrels, cooling-tower-type structures, toroids, rings, etc. (a sub-class of shells of revolution).

  8. Vasoinhibin, an N-terminal Prolactin Fragment, Directly Inhibits Cardiac Angiogenesis in Three-dimensional Heart Culture

    PubMed Central

    Nakajima, Ryojun; Nakamura, Eri; Harigaya, Toshio

    2017-01-01

    Vasoinhibins (Vi) are fragments of the growth hormone/prolactin (PRL) family and have antiangiogenic functions in many species. It is considered that Vi derived from PRL are involved in the pathogenesis of peripartum cardiomyopathy (PPCM). However, the pathogenic mechanism of PPCM, as well as heart angiogenesis, is not yet clear. Therefore, the aim of the present study is to clarify whether Vi act directly on angiogenesis inhibition in heart blood vessels. Endothelial cell viability was decreased by Vi treatment in a culture experiment. Furthermore, expression of proangiogenic genes, such as vascular endothelial growth factor, endothelial nitric oxide synthase, and VE-cadherin, were decreased. On the other hand, apoptotic factor gene, caspase 3, and inflammatory factor genes, tumor necrosis factor α and interleukin 6, were increased by Vi treatment. In three-dimensional left ventricular wall angiogenesis assay in mice, Vi treatment also inhibited cell migration, neovessel sprouting, and growth toward collagen gel. These data demonstrate that Vi treatment directly suppresses angiogenesis of the heart and support the hypothesis that Vi induce PPCM. PMID:28163696

  9. Overland flow computations in urban and industrial catchments from direct precipitation data using a two-dimensional shallow water model.

    PubMed

    Cea, L; Garrido, M; Puertas, J; Jácome, A; Del Río, H; Suárez, J

    2010-01-01

    This paper presents the experimental validation and the application to a real industrial catchment of a two-dimensional depth-averaged shallow water model used for the computation of rainfall-runoff transformation from direct precipitation data. Instead of using the common approach in flood inundation modelling, which consists in computing the water depth and velocity fields given the water discharge, in this study the rainfall intensity is imposed directly in the model, the surface runoff being generated automatically. The model considers infiltration losses simultaneously with flow simulation. Gullies are also included in the model, although the coupling between the surface runoff and the sewer network is not considered. Experimental validation of the model is presented in several simplified laboratory configurations of urban catchments, in which the surface runoff has been measured for different hyetographs. The application to a real industrial catchment includes a sewer network flow component, which is solved with the SWMM model. The numerical predictions of the discharge hydrograph generated by a 12 hours storm event are compared with field measurements, providing encouraging results.

  10. Direct reconstruction in CT-analogous pharmacokinetic diffuse fluorescence tomography: two-dimensional simulative and experimental validations.

    PubMed

    Wang, Xin; Zhang, Yanqi; Zhang, Limin; Li, Jiao; Zhou, Zhongxing; Zhao, Huijuan; Gao, Feng

    2016-04-30

    We present a generalized strategy for direct reconstruction in pharmacokinetic diffuse fluorescence tomography (DFT) with CT-analogous scanning mode, which can accomplish one-step reconstruction of the indocyanine-green pharmacokinetic-rate images within in vivo small animals by incorporating the compartmental kinetic model into an adaptive extended Kalman filtering scheme and using an instantaneous sampling dataset. This scheme, compared with the established indirect and direct methods, eliminates the interim error of the DFT inversion and relaxes the expensive requirement of the instrument for obtaining highly time-resolved date-sets of complete 360 deg projections. The scheme is validated by two-dimensional simulations for the two-compartment model and pilot phantom experiments for the one-compartment model, suggesting that the proposed method can estimate the compartmental concentrations and the pharmacokinetic-rates simultaneously with a fair quantitative and localization accuracy, and is well suitable for cost-effective and dense-sampling instrumentation based on the highly-sensitive photon counting technique.

  11. Direct experimental visualization of the global Hamiltonian progression of two-dimensional Lagrangian flow topologies from integrable to chaotic state

    SciTech Connect

    Baskan, O.; Clercx, H. J. H; Speetjens, M. F. M.; Metcalfe, G.

    2015-10-15

    Countless theoretical/numerical studies on transport and mixing in two-dimensional (2D) unsteady flows lean on the assumption that Hamiltonian mechanisms govern the Lagrangian dynamics of passive tracers. However, experimental studies specifically investigating said mechanisms are rare. Moreover, they typically concern local behavior in specific states (usually far away from the integrable state) and generally expose this indirectly by dye visualization. Laboratory experiments explicitly addressing the global Hamiltonian progression of the Lagrangian flow topology entirely from integrable to chaotic state, i.e., the fundamental route to efficient transport by chaotic advection, appear non-existent. This motivates our study on experimental visualization of this progression by direct measurement of Poincaré sections of passive tracer particles in a representative 2D time-periodic flow. This admits (i) accurate replication of the experimental initial conditions, facilitating true one-to-one comparison of simulated and measured behavior, and (ii) direct experimental investigation of the ensuing Lagrangian dynamics. The analysis reveals a close agreement between computations and observations and thus experimentally validates the full global Hamiltonian progression at a great level of detail.

  12. Synergistic effects of acyclic retinoid and OSI-461 on growth inhibition and gene expression in human hepatoma cells.

    PubMed

    Shimizu, Masahito; Suzui, Masumi; Deguchi, Atsuko; Lim, Jin T E; Xiao, Danhua; Hayes, Julia H; Papadopoulos, Kyriakos P; Weinstein, I Bernard

    2004-10-01

    Hepatoma is one of the most frequently occurring cancers worldwide. However, effective chemotherapeutic agents for this disease have not been developed. Acyclic retinoid, a novel synthetic retinoid, can reduce the incidence of postsurgical recurrence of hepatoma and improve the survival rate. OSI-461, a potent derivative of exisulind, can increase intracellular levels of cyclic GMP, which leads to activation of protein kinase G and induction of apoptosis in cancer cells. In the present study, we examined the combined effects of acyclic retinoid plus OSI-461 in the HepG2 human hepatoma cell line. We found that the combination of as little as 1.0 micromol/L acyclic retinoid and 0.01 micromol/L OSI-461 exerted synergistic inhibition of the growth of HepG2 cells. Combined treatment with low concentrations of these two agents also acted synergistically to induce apoptosis in HepG2 cells through induction of Bax and Apaf-1, reduction of Bcl-2 and Bcl-xL, and activation of caspase-3, -8, and -9. OSI-461 enhanced the G0-G1 arrest caused by acyclic retinoid, and the combination of these agents caused a synergistic decrease in the levels of expression of cyclin D1 protein and mRNA, inhibited cyclin D1 promoter activity, decreased the level of hyperphosphorylated forms of the Rb protein, induced increased cellular levels of the p21(CIP1) protein and mRNA, and stimulated p21(CIP1) promoter activity. Moreover, OSI-461 enhanced the ability of acyclic retinoid to induce increased cellular levels of retinoic acid receptor beta and to stimulate retinoic acid response element-chloramphenicol acetyltransferase activity. A hypothetical model involving concerted effects on p21(CIP1) and retinoic acid receptor beta expression is proposed to explain these synergistic effects. Our results suggest that the combination of acyclic retinoid plus OSI-461 might be an effective regimen for the chemoprevention and chemotherapy of human hepatoma and possibly other malignancies.

  13. Ultralow flexural properties of copper microhelices fabricated via electrodeposition-based three-dimensional direct-writing technology.

    PubMed

    Yi, Zhiran; Lei, Yu; Zhang, Xianyun; Chen, Yining; Guo, Jianjun; Xu, Gaojie; Yu, Min-Feng; Cui, Ping

    2017-08-31

    Helical metallic micro/nanostructures as functional components have considerable potential for future miniaturized devices, based on their unique mechanical and electrical properties. Thus, understanding and controlling the mechanical properties of metallic helices is desirable for their practical application. Herein, we implemented a direct-writing technique based on the electrodeposition method to grow copper microhelices with well-defined and programmable three-dimensional (3D) features. The mechanical properties of the 3D helical structures were studied by the electrically induced quasistatic and dynamic electromechanical resonance technique. These methods mainly explored the static pull-in process and the dynamic electromechanical response, respectively. It was found that the center-symmetric and vertical double copper microhelix structure with 1.2 μm wire diameter has a flexural rigidity of 0.9 × 10(-14) N m(2) and the single vertical copper microhelix structure with 1.1 μm wire diameter has a flexural rigidity of 0.5989 × 10(-14) N m(2). By comparing with microwires and other reported micro/nanohelices, we found that the copper microhelices reported here had an ultralow stiffness (about 0.13 ± 0.01 N m(-1)). It is found that the experimental results agree well with the finite element calculations. The proposed method can be used to fabricate and measure the flexural properties of three-dimensional complex micro/nanowire structures, and may have a profound effect on the application of microhelices in various useful microdevices such as helix-based microelectromechanical switches, sensors and actuators based on their unique mechanical properties.

  14. Bi-directional-bi-dimensionality alignment of self-supporting Mn3O4 nanorod and nanotube arrays with different bacteriostasis and magnetism.

    PubMed

    Chen, Qun; Wei, Chengzhen; Gao, Feng; Pang, Huan; Lu, Qingyi

    2013-12-21

    Self-supported Mn3O4 patterns of aligned nanorods and nanotubes were synthesized through a bi-directional-bi-dimensionality growth model by using sodium gluconate and urea as additives under mild hydrothermal conditions without the use of any substrates. In one direction, Mn3O4 grows to form one-dimensional nanorods or nanotubes, while in the other direction Mn3O4 grows into two-dimensional nanoplates to support the nanorods or nanotubes to align into arrays. These two kinds of new nanostructures, a nanotube pattern and a nanorod pattern, show similar and good bacteriostasis for Gram positive bacteria, but for Gram negative bacteria the nanotube pattern shows much better bacterial restraint than the nanorod pattern. Magnetic studies show that the nanorod arrays display similar magnetic properties to the commercial Mn3O4, while the nanotube arrays show different ferromagnetic behaviors with enhanced remnant magnetization and saturation magnetization (Ms) at low temperature.

  15. Bi-directional-bi-dimensionality alignment of self-supporting Mn3O4 nanorod and nanotube arrays with different bacteriostasis and magnetism

    NASA Astrophysics Data System (ADS)

    Chen, Qun; Wei, Chengzhen; Gao, Feng; Pang, Huan; Lu, Qingyi

    2013-11-01

    Self-supported Mn3O4 patterns of aligned nanorods and nanotubes were synthesized through a bi-directional-bi-dimensionality growth model by using sodium gluconate and urea as additives under mild hydrothermal conditions without the use of any substrates. In one direction, Mn3O4 grows to form one-dimensional nanorods or nanotubes, while in the other direction Mn3O4 grows into two-dimensional nanoplates to support the nanorods or nanotubes to align into arrays. These two kinds of new nanostructures, a nanotube pattern and a nanorod pattern, show similar and good bacteriostasis for Gram positive bacteria, but for Gram negative bacteria the nanotube pattern shows much better bacterial restraint than the nanorod pattern. Magnetic studies show that the nanorod arrays display similar magnetic properties to the commercial Mn3O4, while the nanotube arrays show different ferromagnetic behaviors with enhanced remnant magnetization and saturation magnetization (Ms) at low temperature.Self-supported Mn3O4 patterns of aligned nanorods and nanotubes were synthesized through a bi-directional-bi-dimensionality growth model by using sodium gluconate and urea as additives under mild hydrothermal conditions without the use of any substrates. In one direction, Mn3O4 grows to form one-dimensional nanorods or nanotubes, while in the other direction Mn3O4 grows into two-dimensional nanoplates to support the nanorods or nanotubes to align into arrays. These two kinds of new nanostructures, a nanotube pattern and a nanorod pattern, show similar and good bacteriostasis for Gram positive bacteria, but for Gram negative bacteria the nanotube pattern shows much better bacterial restraint than the nanorod pattern. Magnetic studies show that the nanorod arrays display similar magnetic properties to the commercial Mn3O4, while the nanotube arrays show different ferromagnetic behaviors with enhanced remnant magnetization and saturation magnetization (Ms) at low temperature. Electronic supplementary

  16. Three-dimensional direct numerical simulation of electromagnetically driven multiscale shallow layer flows: Numerical modeling and physical properties

    NASA Astrophysics Data System (ADS)

    Lardeau, Sylvain; Ferrari, Simone; Rossi, Lionel

    2008-12-01

    Three-dimensional (3D) direct numerical simulations of a flow driven by multiscale electromagnetic forcing are performed in order to reproduce with maximum accuracy the quasi-two-dimensional (2D) flow generated by the same multiscale forcing in the laboratory. The method presented is based on a 3D description of the flow and the electromagnetic forcing. Very good agreements between our simulations and the experiments are found both on velocity and acceleration field, this last comparison being, to our knowledge, done for the first time. Such agreement requires that both experiments and simulations are carefully performed and, more importantly, that the underlying simplification to model the experiments and the multiscale electromagnetic forcing do not introduce significant errors. The results presented in this paper differ significantly from previous 2D direct numerical simulation in which a classical linear Rayleigh friction modeling term was used to mimic the effect of the wall-normal friction. Indeed, purely 2D simulations are found to underestimate the Reynolds number and, due to the dominance of nonhomogeneous bottom friction, lead to the wrong physical mechanism. For the range of conditions presented in this paper, the Reynolds number, defined by the ratio between acceleration and viscous terms, remains the order of unity, and the Hartmann number, defined by the ratio between electromagnetic force terms and viscous terms, is about 2. The main conclusion is that 3D simulations are required to model the (3D) electromagnetic forces and the wall-normal shear. Indeed, even if the flow is quasi-2D in terms of energy, a full 3D approach is required to simulate these shallow layer flows driven by multiscale electromagnetic forcing. In the range of forcing intensity investigated in this paper, these multiscale flows remain quasi-2D, with negligible energy in the wall-normal velocity component. It is also shown that the driving terms are the electromagnetic forcing and

  17. Accuracy of three-dimensional versus two-dimensional echocardiography for quantification of aortic regurgitation and validation by three-dimensional three-directional velocity-encoded magnetic resonance imaging.

    PubMed

    Ewe, See Hooi; Delgado, Victoria; van der Geest, Rob; Westenberg, Jos J M; Haeck, Marlieke L A; Witkowski, Tomasz G; Auger, Dominique; Marsan, Nina Ajmone; Holman, Eduard R; de Roos, Albert; Schalij, Martin J; Bax, Jeroen J; Sieders, Allard; Siebelink, Hans-Marc J

    2013-08-15

    Quantitative assessment of aortic regurgitation (AR) remains challenging. The present study evaluated the accuracy of 2-dimensional (2D) and 3-dimensional (3D) transthoracic echocardiography (TTE) for AR quantification, using 3D 3-directional velocity-encoded magnetic resonance imaging (VE-MRI) as the reference method. Thirty-two AR patients were included. With color Doppler TTE, 2D effective regurgitant orifice area (EROA) was calculated using the proximal isovelocity surface area method. From the 3D TTE multiplanar reformation data, 3D-EROA was calculated by planimetry of the vena contracta. Regurgitant volumes (RVol) were obtained by multiplying the 2D-EROA and 3D-EROA by the velocity-time integral of AR jet and compared with that obtained using VE-MRI. For the entire population, 3D TTE RVol demonstrated a strong correlation and good agreement with VE-MRI RVol (r = 0.94 and -13.6 to 15.6 ml/beat, respectively), whereas 2D TTE RVol showed a modest correlation and large limits of agreement with VE-MRI (r = 0.70 and -22.2 to 32.8 ml/beat, respectively). Eccentric jets were noted in 16 patients (50%). In these patients, 3D TTE demonstrated an excellent correlation (r = 0.95) with VE-MRI, a small bias (0.1 ml/beat) and narrow limits of agreement (-18.7 to 18.8 ml/beat). Finally, the kappa agreement between 3D TTE and VE-MRI for grading of AR severity was good (k = 0.96), whereas the kappa agreement between 2D TTE and VE-MRI was suboptimal (k = 0.53). In conclusion, AR RVol quantification using 3D TTE is accurate, and its advantage over 2D TTE is particularly evident in patients with eccentric jets.

  18. The preparation and intra- and intermolecular addition reactions of acyclic N-acylimines: application to the synthesis of (+/-)-sertraline.

    PubMed

    DeNinno, M P; Eller, C; Etienne, J B

    2001-10-19

    Intramolecular endo-cyclization reactions of N-acyliminium ions have seen wide application for the synthesis of heterocyclic compounds. The corresponding exocyclic variant, which would provide 1-aminotetralin derivatives, for example, has little precedent. We have discovered that acyclic N-acylcarbamates can be readily reduced to the corresponding N-acylhemiaminal derivatives in high yield using DIBAL as the reducing agent. These intermediates are remarkably stable and, if desired, can be purified and stored. The acyclic N-acylhemiaminals undergo both intra- and intermolecular nucleophilic addition reactions mediated by strong Lewis acids, such as TiCl(4). Diastereoselectivity, induced either by a substituent on the newly formed ring, or by utilizing a chiral ester on the carbamic acid, was disappointingly low. This methodology was successfully applied to the synthesis of the racemic form of the marketed antidepressant sertraline.

  19. The synthesis and antiviral properties of acyclic nucleoside analogues with a phosphonomethoxy fragment in the side chain.

    PubMed

    Khandazhinskaya, A; Yasko, M; Shirokova, E

    2006-01-01

    Acyclic nucleoside analogues bearing phosphonomethoxy residues in the side chain (ANP) attract much attention due to a very beneficial combination of biological properties. Intensive work of organic chemists during the last two decades resulted in a large panel of new compounds that were evaluated as potential antiviral drugs. Herein, we present an overview of major chemical structures within the group of acyclic nucleoside analogues containing phosphonomethoxy side fragments and describe main aspects of their synthesis and antiviral potential. We also describe progress in "prodrug" approaches applied to this chemical group to improve pharmacokinetic profiles of the potential candidates. Chemical modifications in the molecule of parental ANP aimed at blocking of phosphonate charges resulted in a set of promising derivatives, two of which have been recently approved for treatment of hepatits B (Hepsera) and HIV (Viread). The preparation, antiviral properties and some aspects of metabolic transformations and pharmacokinetics of ANP prodrugs are discussed.

  20. Quantitative Three-Dimensional Characterization of Block Copolymer Directed Self-Assembly on Combined Chemical and Topographical Prepatterned Templates.

    PubMed

    Segal-Peretz, Tamar; Ren, Jiaxing; Xiong, Shisheng; Khaira, Gurdaman; Bowen, Alec; Ocola, Leonidas E; Divan, Ralu; Doxastakis, Manolis; Ferrier, Nicola J; de Pablo, Juan; Nealey, Paul F

    2017-02-28

    Characterization of the three-dimensional (3D) structure in directed self-assembly (DSA) of block copolymers is crucial for understanding the complex relationships between the guiding template and the resulting polymer structure so DSA could be successfully implemented for advanced lithography applications. Here, we combined scanning transmission electron microscopy (STEM) tomography and coarse-grain simulations to probe the 3D structure of P2VP-b-PS-b-P2VP assembled on prepatterned templates using solvent vapor annealing. The templates consisted of nonpreferential background and raised guiding stripes that had PS-preferential top surfaces and P2VP-preferential sidewalls. The full 3D characterization allowed us to quantify the shape of the polymer domains and the interface between domains as a function of depth in the film and template geometry and offered important insights that were not accessible with 2D metrology. Sidewall guiding was advantageous in promoting the alignment and lowering the roughness of the P2VP domains over the sidewalls, but incommensurate confinement from the increased topography could cause roughness and intermittent dislocations in domains over the background region at the bottom of the film. The 3D characterization of bridge structures between domains over the background and breaks within domains on guiding lines sheds light on possible origins of common DSA defects. The positional fluctuations of the PS/P2VP interface between domains showed a depth-dependent behavior, with high levels of fluctuations near both the free surface of the film and the substrate and lower fluctuation levels in the middle of the film. This research demonstrates how 3D characterization offers a better understanding of DSA processes, leading to better design and fabrication of directing templates.

  1. Quantitative three-dimensional characterization of block copolymer directed self-assembly on combined chemical and topographical prepatterned templates

    DOE PAGES

    Segal-Peretz, Tamar; Ren, Jiaxing; Xiong, Shisheng; ...

    2016-12-22

    Characterization of the three-dimensional (3D) structure in directed self-assembly (DSA) of block copolymers is crucial for understanding the complex relationships between the guiding template and the resulting polymer structure so DSA could be successfully implemented for advanced lithography applications. Here, we combined scanning transmission electron microscopy (STEM) tomography and coarse-grain simulations to probe the 3D structure of P2VP-b-PS-b-P2VP assembled on prepatterned templates using solvent vapor annealing. The templates consisted of nonpreferential background and raised guiding stripes that had PS-preferential top surfaces and P2VP-preferential sidewalls. The full 3D characterization allowed us to quantify the shape of the polymer domains and themore » interface between domains as a function of depth in the film and template geometry and offered important insights that were not accessible with 2D metrology. Sidewall guiding was advantageous in promoting the alignment and lowering the roughness of the P2VP domains over the sidewalls, but incommensurate confinement from the increased topography could cause roughness and intermittent dislocations in domains over the background region at the bottom of the film. The 3D characterization of bridge structures between domains over the background and breaks within domains on guiding lines sheds light on possible origins of common DSA defects. The positional fluctuations of the PS/P2VP interface between domains showed a depth-dependent behavior, with high levels of fluctuations near both the free surface of the film and the substrate and lower fluctuation levels in the middle of the film. As a result, this research demonstrates how 3D characterization offers a better understanding of DSA processes, leading to better design and fabrication of directing templates.« less

  2. Quantitative three-dimensional characterization of block copolymer directed self-assembly on combined chemical and topographical prepatterned templates

    SciTech Connect

    Segal-Peretz, Tamar; Ren, Jiaxing; Xiong, Shisheng; Khaira, Gurdaman; Bowen, Alec; Ocola, Leonidas E.; Divan, Ralu N. S.; Doxastakis, Manolis; Ferrier, Nicola J.; de Pablo, Juan; Nealey, Paul F.

    2016-12-22

    Characterization of the three-dimensional (3D) structure in directed self-assembly (DSA) of block copolymers is crucial for understanding the complex relationships between the guiding template and the resulting polymer structure so DSA could be successfully implemented for advanced lithography applications. Here, we combined scanning transmission electron microscopy (STEM) tomography and coarse-grain simulations to probe the 3D structure of P2VP-b-PS-b-P2VP assembled on prepatterned templates using solvent vapor annealing. The templates consisted of nonpreferential background and raised guiding stripes that had PS-preferential top surfaces and P2VP-preferential sidewalls. The full 3D characterization allowed us to quantify the shape of the polymer domains and the interface between domains as a function of depth in the film and template geometry and offered important insights that were not accessible with 2D metrology. Sidewall guiding was advantageous in promoting the alignment and lowering the roughness of the P2VP domains over the sidewalls, but incommensurate confinement from the increased topography could cause roughness and intermittent dislocations in domains over the background region at the bottom of the film. The 3D characterization of bridge structures between domains over the background and breaks within domains on guiding lines sheds light on possible origins of common DSA defects. The positional fluctuations of the PS/P2VP interface between domains showed a depth-dependent behavior, with high levels of fluctuations near both the free surface of the film and the substrate and lower fluctuation levels in the middle of the film. As a result, this research demonstrates how 3D characterization offers a better understanding of DSA processes, leading to better design and fabrication of directing templates.

  3. Towards a three-dimensional framework of centrally regulated and goal-directed exercise behaviour: a narrative review.

    PubMed

    Venhorst, Andreas; Micklewright, Dominic; Noakes, Timothy D

    2017-08-23

    The Central Governor Model (CGM) ignited a paradigm shift from concepts of catastrophic failure towards central regulation of exercise performance. However, the CGM has focused on the central integration of afferent feedback in homeostatic control. Accordingly, it neglected the important role of volitional self-regulatory control and the integration of affective components inherently attached to all physiological cues. Another limitation is the large reliance on the Gestalt phenomenon of perceived exertion. Thus, progress towards a comprehensive multidimensional model of perceived fatigability and exercise regulation is needed. Drawing on Gate Control Theory of pain, we propose a three-dimensional framework of centrally regulated and goal-directed exercise behaviour, which differentiates between sensory, affective and cognitive processes shaping the perceptual milieu during exercise. We propose that: (A) perceived mental strain and perceived physical strain are primary determinants of pacing behaviour reflecting sensory-discriminatory processes necessary to align planned behaviour with current physiological state, (B) core affect plays a primary and mediatory role in exercise and performance regulation, and its underlying two dimensions hedonicity and arousal reflect affective-motivational processes triggering approach and avoidance behaviour, and (C) the mindset-shift associated with an action crisis plays a primary role in volitional self-regulatory control reflecting cognitive-evaluative processes between further goal-pursuit and goal-disengagement. The proposed framework has the potential to enrich theory development in centrally regulated and goal-directed exercise behaviour by emphasising the multidimensional dynamic processes underpinning perceived fatigability and provides a practical outline for investigating the complex interplay between the psychophysiological determinants of pacing and performance during prolonged endurance exercise. © Article author

  4. Three-dimensional construction and omni-directional rolling analysis of a novel frame-like lattice modular robot

    NASA Astrophysics Data System (ADS)

    Ding, Wan; Wu, Jianxu; Yao, Yan'an

    2015-07-01

    Lattice modular robots possess diversity actuation methods, such as electric telescopic rod, gear rack, magnet, robot arm, etc. The researches on lattice modular robots mainly focus on their hardware descriptions and reconfiguration algorithms. Meanwhile, their design architectures and actuation methods perform slow telescopic and moving speeds, relative low actuation force verse weight ratio, and without internal space to carry objects. To improve the mechanical performance and reveal the locomotion and reconfiguration binary essences of the lattice modular robots, a novel cube-shaped, frame-like, pneumatic-based reconfigurable robot module called pneumatic expandable cube(PE-Cube) is proposed. The three-dimensional(3D) expanding construction and omni-directional rolling analysis of the constructed robots are the main focuses. The PE-Cube with three degrees of freedom(DoFs) is assembled by replacing the twelve edges of a cube with pneumatic cylinders. The proposed symmetric construction condition makes the constructed robots possess the same properties in each supporting state, and a binary control strategy cooperated with binary actuator(pneumatic cylinder) is directly adopted to control the PE-Cube. Taking an eight PE-Cube modules' construction as example, its dynamic rolling simulation, static rolling condition, and turning gait are illustrated and discussed. To testify telescopic synchronization, respond speed, locomotion feasibility, and repeatability and reliability of hardware system, an experimental pneumatic-based robotic system is built and the rolling and turning experiments of the eight PE-Cube modules' construction are carried out. As an extension, the locomotion feasibility of a thirty-two PE-Cube modules' construction is analyzed and proved, including dynamic rolling simulation, static rolling condition, and dynamic analysis in free tipping process. The proposed PE-Cube module, construction method, and locomotion analysis enrich the family of the

  5. DIRECT INTEGRATION OF THE COLLISIONLESS BOLTZMANN EQUATION IN SIX-DIMENSIONAL PHASE SPACE: SELF-GRAVITATING SYSTEMS

    SciTech Connect

    Yoshikawa, Kohji; Umemura, Masayuki; Yoshida, Naoki

    2013-01-10

    We present a scheme for numerical simulations of collisionless self-gravitating systems which directly integrates the Vlasov-Poisson equations in six-dimensional phase space. Using the results from a suite of large-scale numerical simulations, we demonstrate that the present scheme can simulate collisionless self-gravitating systems properly. The integration scheme is based on the positive flux conservation method recently developed in plasma physics. We test the accuracy of our code by performing several test calculations, including the stability of King spheres, the gravitational instability, and the Landau damping. We show that the mass and the energy are accurately conserved for all the test cases we study. The results are in good agreement with linear theory predictions and/or analytic solutions. The distribution function keeps the property of positivity and remains non-oscillatory. The largest simulations are run on 64{sup 6} grids. The computation speed scales well with the number of processors, and thus our code performs efficiently on massively parallel supercomputers.

  6. Comprehensive one-dimensional, semi-analytical, mathematical model for liquid-feed polymer electrolyte membrane direct methanol fuel cells

    NASA Astrophysics Data System (ADS)

    Kareemulla, D.; Jayanti, S.

    Polymer electrolyte membrane direct methanol fuel cells (PEM-DMFCs) have several advantages over hydrogen-fuelled PEM fuel cells; but sluggish methanol electrochemical oxidation and methanol crossover from the anode to the cathode through the PEM are two major problems with these cells. In the present work, a comprehensive one-dimensional, single phase, isothermal mathematical model is developed for a liquid-feed PEM-DMFC, taking into account all the necessary mass transport and electrochemical phenomena. Diffusion and convective effects are considered for methanol transport on the anode side and in the PEM, whereas only diffusional transport of species is considered on the cathode side. A multi-step reaction mechanism is used to describe the electrochemical oxidation of methanol at the anode. Stefan-Maxwell equations are used to describe multi-component diffusion on the cathode side and Tafel type of kinetics is used to describe the simultaneous methanol oxidation and oxygen reduction reactions at the cathode. The model fully accounts for the mixed potential effect caused by methanol crossover at the cathode. It shows excellent agreement with literature data of the limiting current density for different low methanol feed concentrations at different operating temperatures. At high methanol feed concentrations, oxygen depletion on the cathode side, due to excessive methanol crossover, results in mass-transport limitations. The model can be used to optimize the geometric and physical parameters with a view to extracting the highest current density while still keeping a tolerably low methanol crossover.

  7. Characteristics and generation of elastic turbulence in a three-dimensional parallel plate channel using direct numerical simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Hong-Na; Li, Feng-Chen; Li, Xiao-Bin; Li, Dong-Yang; Cai, Wei-Hua; Yu, Bo

    2016-09-01

    Direct numerical simulations (DNSs) of purely elastic turbulence in rectilinear shear flows in a three-dimensional (3D) parallel plate channel were carried out, by which numerical databases were established. Based on the numerical databases, the present paper analyzed the structural and statistical characteristics of the elastic turbulence including flow patterns, the wall effect on the turbulent kinetic energy spectrum, and the local relationship between the flow motion and the microstructures’ behavior. Moreover, to address the underlying physical mechanism of elastic turbulence, its generation was presented in terms of the global energy budget. The results showed that the flow structures in elastic turbulence were 3D with spatial scales on the order of the geometrical characteristic length, and vortex tubes were more likely to be embedded in the regions where the polymers were strongly stretched. In addition, the patterns of microstructures’ elongation behave like a filament. From the results of the turbulent kinetic energy budget, it was found that the continuous energy releasing from the polymers into the main flow was the main source of the generation and maintenance of the elastic turbulent status. Project supported by the National Natural Science Foundation of China (Grant Nos. 51276046 and 51506037), the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (Grant No. 51421063), the China Postdoctoral Science Foundation (Grant No. 2016M591526), the Heilongjiang Postdoctoral Fund, China (Grant No. LBH-Z15063), and the China Postdoctoral International Exchange Program.

  8. Low-dimensional transport and large thermoelectric power factors in bulk semiconductors by band engineering of highly directional electronic states.

    PubMed

    Bilc, Daniel I; Hautier, Geoffroy; Waroquiers, David; Rignanese, Gian-Marco; Ghosez, Philippe

    2015-04-03

    Thermoelectrics are promising for addressing energy issues but their exploitation is still hampered by low efficiencies. So far, much improvement has been achieved by reducing the thermal conductivity but less by maximizing the power factor. The latter imposes apparently conflicting requirements on the band structure: a narrow energy distribution and a low effective mass. Quantum confinement in nanostructures and the introduction of resonant states were suggested as possible solutions to this paradox, but with limited success. Here, we propose an original approach to fulfill both requirements in bulk semiconductors. It exploits the highly directional character of some orbitals to engineer the band structure and produce a type of low-dimensional transport similar to that targeted in nanostructures, while retaining isotropic properties. Using first-principle calculations, the theoretical concept is demonstrated in Fe2YZ Heusler compounds, yielding power factors 4 to 5 times larger than in classical thermoelectrics at room temperature. Our findings are totally generic and rationalize the search of alternative compounds with similar behavior. Beyond thermoelectricity, these might be relevant also in the context of electronic, superconducting, or photovoltaic applications.

  9. WSJointInv2D-MT-DCR: An efficient joint two-dimensional magnetotelluric and direct current resistivity inversion

    NASA Astrophysics Data System (ADS)

    Amatyakul, Puwis; Vachiratienchai, Chatchai; Siripunvaraporn, Weerachai

    2017-05-01

    An efficient joint two-dimensional direct current resistivity (DCR) and magnetotelluric (MT) inversion, referred to as WSJointInv2D-MT-DCR, was developed with FORTRAN 95 based on the data space Occam's inversion algorithm. Our joint inversion software can be used to invert just the MT data or the DCR data, or invert both data sets simultaneously to get the electrical resistivity structures. Since both MT and DCR surveys yield the same resistivity structures, the two data types enhance each other leading to a better interpretation. Two synthetic and a real field survey are used here to demonstrate that the joint DCR and MT surveys can help constrain each other to reduce the ambiguities occurring when inverting the DCR or MT alone. The DCR data increases the lateral resolution of the near surface structures while the MT data reveals the deeper structures. When the MT apparent resistivity suffers from the static shift, the DCR apparent resistivity can serve as a replacement for the estimation of the static shift factor using the joint inversion. In addition, we also used these examples to show the efficiency of our joint inversion code. With the availability of our new joint inversion software, we expect the number of joint DCR and MT surveys to increase in the future.

  10. Three-dimensional bio-printing of hepatic structures with direct-converted hepatocyte-like cells.

    PubMed

    Kang, Kyojin; Kim, Yohan; Lee, Seung Bum; Kim, Ji Sook; Park, Sua; Kim, Wan-Doo; Yang, Heung-Mo; Kim, Sung-Joo; Jeong, Jaemin; Choi, Dongho

    2017-07-20

    Three-dimensional (3D) bio-printing technology is a promising new technology in the field of bio-artificial organ generation with regard to overcoming the limitations of organ supply. The cell source for bio-printing is very important. Here, we generated 3D hepatic scaffold with mouse induced hepatocyte-like cells (miHeps), and investigated whether their function was improved after transplantation in vivo. To generate miHeps, mouse embryonic fibroblasts were transformed with pMX retroviruses individually expressing hepatic transcription factors Hnf4a and Foxa3. After 8-10 days, MEFs formed rapidly-growing hepatocyte-like colonies. For 3D bio-printing, miHeps were mixed with a 3% alginate hydrogel and extruded by nozzle pressure. After seven days, they were transplanted into the omentum of Jo2-treated NSG mice as a liver damage model. Real-time PCR and immunofluorescence analyses were conducted to evaluate hepatic function. The 3D bio-printed hepatic scaffold (25 x 25 mm) expressed albumin, and ASGR1 and HNF4a expression gradually increased for 28 days in vitro. When transplanted in vivo, the cells in the hepatic scaffold grew more and exhibited higher albumin expression than in vitro scaffold. Therefore, combining 3D bio-printing with direct conversion technology appears to be an effective option for liver therapy.

  11. Modelling the two-dimensional flow between an estuary and lake connected by a bi-directional hydraulic structure

    NASA Astrophysics Data System (ADS)

    Zigic, Sasha; King, Brian; Lemckert, Charles

    2005-04-01

    A method to model the influence of a hydraulic structure connecting two water bodies is presented. This method was incorporated into an existing two-dimensional (depth-averaged) hydrodynamic model. Specifically, the flow in and out of a cell (used to represent the hydraulic structure) is calculated using a broad crested weir formula and is determined from the time-varying head difference between the two systems. An example application of the method is also presented. In this example the hydraulic structure cell was used to model the flow through an automated bi-directional hydraulic structure connecting an estuary to an artificial lake system. The gates of this hydraulic structure are programmed to open four times each day (once during each semi-diurnal tidal phase) and remain open for a period of 2 hours, allowing alternative and partial exchange between the two water bodies. Hence, the model setup involved the specification of the opening and closing times of the gates and the calibration of the discharge coefficient. Tests indicated that these were the most sensitive parameters which ensured the correct volume of water exchange between the two systems. Finally, the model-predicted results were compared with available surface elevation observations at two sites within the lake. The comparison showed a good agreement (RMS error <0.09), quantifying the ability of the hydraulic structure cells to simulate the flux between the estuary and lake for each opening.

  12. Hierarchically structured one-dimensional TiO2 for protein immobilization, direct electrochemistry, and mediator-free glucose sensing.

    PubMed

    Si, Peng; Ding, Shujiang; Yuan, Jun; Lou, Xiong Wen David; Kim, Dong-Hwan

    2011-09-27

    A novel one-dimensional hierarchically structured TiO(2) (1DHS TiO(2)) was synthesized by a solvothermal method using multiwalled carbon nanotubes (MWCNTs) as a template and evaluated for the immobilization of protein and biosensing applications. Characterization studies showed that the 1DHS TiO(2) possessed an anatase crystalline structure and a large surface area with narrow pore size distribution. Fast direct electron transfer was observed for glucose oxidase (GOx) immobilized on the 1DHS TiO(2), and excellent electrocatalytic performance for glucose detection can be obtained without a mediator. The glucose sensor based on the GOx/1DHS TiO(2)-modified electrode had a high sensitivity of 9.90 μA mM(-1) cm(-2) and a low detection limit of 1.29 μM. The fabricated biosensor displayed good selectivity and long-term stability, indicating that the novel structured TiO(2) is a promising material for the immobilization of biomolecules and the fabrication of third-generation biosensors. © 2011 American Chemical Society

  13. Three-dimensional direct observation of Gouy phase shift in a terajet produced by a dielectric cuboid

    SciTech Connect

    Nguyen Pham, Hai Huy Hisatake, Shintaro Nagatsuma, Tadao; Minin, I. V. Minin, O. V.

    2016-05-09

    The generation of the terajet at the terahertz (THz) frequency with the capability of subwavelength beam-compression has been attracting increasing research interest, as did the generation of the nanojet at the optical frequency. In particular, a terajet generated from a dielectric cuboid was not previously studied experimentally in the THz region. We here experimentally demonstrate three-dimensional visualizations and characterization of a terajet generated from a dielectric cuboid with a refractive index of n = 1.46 at 125 GHz. The subwavelength compressed beam and the Gouy phase shift phenomena of the terajet are directly observed. It is also found out that a calculation model of Gouy phase shift based on focused Gaussian beam by a lens cannot explain the Gouy phase shift of compressed beam by the terajet. The intensity enhancement of about 7.4 dB and full width at half maximum of 0.6λ are obtained at the distance 0.5λ from the cuboid.

  14. Accessing Three-Dimensional Crystals with Incorporated Guests through Metal-Directed Coiled-Coil Peptide Assembly.

    PubMed

    Nepal, Manish; Sheedlo, Michael J; Das, Chittaranjan; Chmielewski, Jean

    2016-08-31

    Obtaining three-dimensional (3D) protein and peptide crystals on demand requires a precisely orchestrated hierarchical assembly of biopolymer building blocks. In this work, we disclose a metal-ion-mediated strategy to assemble trimeric coiled-coil peptides in a head-to-tail fashion into linear strands with interstrand interactions. This design led to hexagonal 3D peptide crystal formation within 30 min in the presence of divalent metal ions. The crystal morphology could be controlled by varying the metal ion/peptide ratio, resulting in hexagonal discs to rods. Diffraction studies elucidated the head-to-tail arrangement of the coiled-coil linear strands and their hexagonal, antiparallel packing within the crystal. Unsatisfied ligands at the hexagonal ends of the crystals were harnessed as a powerful means to direct His-tagged fluorophores to distinct locations within the crystals. Overall, the designed hierarchical assembly provides a facile means to obtain 3D peptide crystals and incorporate His-tag-based cargoes and may have potential use in drug delivery and sensor design.

  15. Bearing Abilities and Progressive Damage Analysis of Three Dimensional Four-Directional Braided Composites with Cut-Edge

    NASA Astrophysics Data System (ADS)

    Lei, Bing; Liu, Zhenguo; Ya, Jixuan; Wang, Yibo; Li, Xiaokang

    2016-08-01

    Cut-edge is a kind of damage for the three-dimensional four-directional (3D4d) braided composites which is inevitable because of machining to meet requisite shape and working in the abominable environment. The longitudinal tensile experiment of the 3D4d braided composites with different braiding angles between cut-edge and the ones without cut-edge was conducted. Then representative volume cell (RVC) with interface zones was established to analyze the tensile properties through the fracture and damage mechanics. The periodic boundary conditions under the cut-edge and uncut-edge conditions were imposed to simulate the failure mechanism. Stress-strain distribution and the damage evolution nephogram in cut-edge condition were conducted. Numerical results were coincident with the experimental results. Finally the variation of cut-edge effect with the specimen thickness was simulated by superimposing inner cells. The consequence showed that thickness increase can effectively reduce cut-edge influence on longitudinal strength for 3D4d braided composites. Cut-edge simulation of braided composites has guiding significance on the actual engineering application.

  16. Nanoscale surface chemistry directs the tunable assembly of silver octahedra into three two-dimensional plasmonic superlattices

    PubMed Central

    Lee, Yih Hong; Shi, Wenxiong; Lee, Hiang Kwee; Jiang, Ruibin; Phang, In Yee; Cui, Yan; Isa, Lucio; Yang, Yijie; Wang, Jianfang; Li, Shuzhou; Ling, Xing Yi

    2015-01-01

    A major challenge in nanoparticle self-assembly is programming the large-area organization of a single type of anisotropic nanoparticle into distinct superlattices with tunable packing efficiencies. Here we utilize nanoscale surface chemistry to direct the self-assembly of silver octahedra into three distinct two-dimensional plasmonic superlattices at a liquid/liquid interface. Systematically tuning the surface wettability of silver octahedra leads to a continuous superlattice structural evolution, from close-packed to progressively open structures. Notably, silver octahedra standing on vertices arranged in a square lattice is observed using hydrophobic particles. Simulations reveal that this structural evolution arises from competing interfacial forces between the particles and both liquid phases. Structure-to-function characterizations reveal that the standing octahedra array generates plasmonic ‘hotstrips', leading to nearly 10-fold more efficient surface-enhanced Raman scattering compared with the other more densely packed configurations. The ability to assemble these superlattices on the wafer scale over various platforms further widens their potential applications. PMID:25923409

  17. Macro- and micro-designed chitosan-alginate scaffold architecture by three-dimensional printing and directional freezing.

    PubMed

    Reed, Stephanie; Lau, Grace; Delattre, Benjamin; Lopez, David Don; Tomsia, Antoni P; Wu, Benjamin M

    2016-01-07

    While many tissue-engineered constructs aim to treat cartilage defects, most involve chondrocyte or stem cell seeding on scaffolds. The clinical application of cell-based techniques is limited due to the cost of maintaining cellular constructs on the shelf, potential immune response to allogeneic cell lines, and autologous chondrocyte sources requiring biopsy from already diseased or injured, scarce tissue. An acellular scaffold that can induce endogenous influx and homogeneous distribution of native stem cells from bone marrow holds great promise for cartilage regeneration. This study aims to develop such an acellular scaffold using designed, channeled architecture that simultaneously models the native zones of articular cartilage and subchondral bone. Highly porous, hydrophilic chitosan-alginate (Ch-Al) scaffolds were fabricated in three-dimensionally printed (3DP) molds designed to create millimeter scale macro-channels. Different polymer preform casting techniques were employed to produce scaffolds from both negative and positive 3DP molds. Macro-channeled scaffolds improved cell suspension distribution and uptake overly randomly porous scaffolds, with a wicking volumetric flow rate of 445.6 ± 30.3 mm(3) s(-1) for aqueous solutions and 177 ± 16 mm(3) s(-1) for blood. Additionally, directional freezing was applied to Ch-Al scaffolds, resulting in lamellar pores measuring 300 μm and 50 μm on the long and short axes, thus creating micrometer scale micro-channels. After directionally freezing Ch-Al solution cast in 3DP molds, the combined macro- and micro-channeled scaffold architecture enhanced cell suspension uptake beyond either macro- or micro-channels alone, reaching a volumetric flow rate of 1782.1 ± 48 mm(3) s(-1) for aqueous solutions and 440.9 ± 0.5 mm(3) s(-1) for blood. By combining 3DP and directional freezing, we can control the micro- and macro-architecture of Ch-Al to drastically improve cell influx into and distribution within the scaffold

  18. Integrating Remote Sensing Data with Directional Two- Dimensional Wavelet Analysis and Open Geospatial Techniques for Efficient Disaster Monitoring and Management.

    PubMed

    Lin, Yun-Bin; Lin, Yu-Pin; Deng, Dong-Po; Chen, Kuan-Wei

    2008-02-19

    In Taiwan, earthquakes have long been recognized as a major cause oflandslides that are wide spread by floods brought by typhoons followed. Distinguishingbetween landslide spatial patterns in different disturbance regimes is fundamental fordisaster monitoring, management, and land-cover restoration. To circumscribe landslides,this study adopts the normalized difference vegetation index (NDVI), which can bedetermined by simply applying mathematical operations of near-infrared and visible-redspectral data immediately after remotely sensed data is acquired. In real-time disastermonitoring, the NDVI is more effective than using land-cover classifications generatedfrom remotely sensed data as land-cover classification tasks are extremely time consuming.Directional two-dimensional (2D) wavelet analysis has an advantage over traditionalspectrum analysis in that it determines localized variations along a specific direction whenidentifying dominant modes of change, and where those modes are located in multi-temporal remotely sensed images. Open geospatial techniques comprise a series ofsolutions developed based on Open Geospatial Consortium specifications that can beapplied to encode data for interoperability and develop an open geospatial service for sharing data. This study presents a novel approach and framework that uses directional 2Dwavelet analysis of real-time NDVI images to effectively identify landslide patterns andshare resulting patterns via open geospatial techniques. As a case study, this study analyzedNDVI images derived from SPOT HRV images before and after the ChiChi earthquake(7.3 on the Richter scale) that hit the Chenyulan basin in Taiwan, as well as images aftertwo large typhoons (Xangsane and Toraji) to delineate the spatial patterns of landslidescaused by major disturbances. Disturbed spatial patterns of landslides that followed theseevents were successfully delineated using 2D wavelet analysis, and results of patternrecognitions of landslides were

  19. Toward three-dimensional microelectronic systems: directed self-assembly of silicon microcubes via DNA surface functionalization.

    PubMed

    Lämmerhardt, Nico; Merzsch, Stephan; Ledig, Johannes; Bora, Achyut; Waag, Andreas; Tornow, Marc; Mischnick, Petra

    2013-07-02

    The huge and intelligent processing power of three-dimensional (3D) biological "processors" like the human brain with clock speeds of only 0.1 kHz is an extremely fascinating property, which is based on a massively parallel interconnect strategy. Artificial silicon microprocessors are 7 orders of magnitude faster. Nevertheless, they do not show any indication of intelligent processing power, mostly due to their very limited interconnectivity. Massively parallel interconnectivity can only be realized in three dimensions. Three-dimensional artificial processors would therefore be at the root of fabricating artificially intelligent systems. A first step in this direction would be the self-assembly of silicon based building blocks into 3D structures. We report on the self-assembly of such building blocks by molecular recognition, and on the electrical characterization of the formed assemblies. First, planar silicon substrates were functionalized with self-assembling monolayers of 3-aminopropyltrimethoxysilane for coupling of oligonucleotides (single stranded DNA) with glutaric aldehyde. The oligonucleotide immobilization was confirmed and quantified by hybridization with fluorescence-labeled complementary oligonucleotides. After the individual processing steps, the samples were analyzed by contact angle measurements, ellipsometry, atomic force microscopy, and fluorescence microscopy. Patterned DNA-functionalized layers were fabricated by microcontact printing (μCP) and photolithography. Silicon microcubes of 3 μm edge length as model objects for first 3D self-assembly experiments were fabricated out of silicon-on-insulator (SOI) wafers by a combination of reactive ion etching (RIE) and selective wet etching. The microcubes were then surface-functionalized using the same protocol as on planar substrates, and their self-assembly was demonstrated both on patterned silicon surfaces (88% correctly placed cubes), and to cube aggregates by complementary DNA

  20. Executive Summary of Ares V: Lunar Capabilities Concept Review Through Phase A-Cycle 3

    NASA Technical Reports Server (NTRS)

    Holladay, J. B.; Baggett, K. E.; Feldman, S. M.

    2011-01-01

    This Technical Memorandum (TM) was generated as an overall Ares V summary from the Lunar Capabilities Concept Review (LCCR) through Phase A-Cycle 3 (PA-C3) with the intent that it may be coupled with separately published appendices for a more detailed, integrated narrative. The Ares V has evolved from the initial point of departure (POD) 51.00.48 LCCR configuration to the current candidate POD, PA-C3D, and the family of vehicles concept that contains vehicles PA-C3A through H. The logical progression from concept to POD vehicles is summarized in this TM and captures the trade space and performance of each. The family-of-vehicles concept was assessed during PA-C3 and offered flexibility in the path forward with the ability to add options deemed appropriate. A description of each trade space is given in addition to a summary of each Ares V element. The Ares V contributions to a Mars campaign are also highlighted with the goal of introducing Ares V capabilities within the trade space. The assessment of the Ares V vehicle as it pertains to Mars missions remained locked to the architecture presented in Mars Design Reference Authorization 5.0 using the PA-C3D vehicle configuration to assess Mars transfer vehicle options, in-space EDS capabilities, docking adaptor and propellant transfer assessments, and lunar and Mars synergistic potential.

  1. Bifurcatriol, a New Antiprotozoal Acyclic Diterpene from the Brown Alga Bifurcaria bifurcata.

    PubMed

    Smyrniotopoulos, Vangelis; Merten, Christian; Kaiser, Marcel; Tasdemir, Deniz

    2017-08-02

    Linear diterpenes that are commonly found in brown algae are of high chemotaxonomic and ecological importance. This study reports bifurcatriol (1), a new linear diterpene featuring two stereogenic centers isolated from the Irish brown alga Bifurcariabifurcata. The gross structure of this new natural product was elucidated based on its spectroscopic data (IR, 1D and 2D-NMR, HRMS). Its absolute configuration was identified by experimental and computational vibrational circular dichroism (VCD) spectroscopy, combined with the calculation of (13)C-NMR chemical shielding constants. Bifurcatriol (1) was tested for in vitro antiprotozoal activity towards a small panel of parasites (Plasmodium falciparum, Trypanosoma brucei rhodesiense, T. cruzi, and Leishmania donovani) and cytotoxicity against mammalian primary cells. The highest activity was exerted against the malaria parasite P. falciparum (IC50 value 0.65 μg/mL) with low cytotoxicity (IC50 value 56.6 μg/mL). To our knowledge, this is the first successful application of VCD and DP4 probability analysis of the calculated (13)C-NMR chemical shifts for the simultaneous assignment of the absolute configuration of multiple stereogenic centers in a long-chain acyclic natural product.

  2. Amino acids of the Murchison meteorite. I - Six carbon acyclic primary alpha-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, J. R.; Gandy, W. E.; Pizzarello, S.

    1981-01-01

    Six of the seven chain isomers of six-carbon acyclic primary alpha-amino alkanoic acids (leucine isomers) have been either identified or confirmed in hot-water extracts of the Murchison meteorite using combined gas chromatography-mass spectrometry (GC-MS) and ion exchange chromatography. 2-Amino-2-ethylbutyric acid, 2-amino-2,3-dimethylbutyric acid, pseudoleucine, and 2-methylnorvaline were positively identified by GC-MS. These amino acids have not been previously reported to occur in natural materials and may be uniquely meteoritic in origin. The presence of leucine and isoleucine (including the diastereoisomer, alloisoleucine) was confirmed. Peaks corresponding to norleucine were seen by ion-exchange and gas chromatography but characteristic mass spectra were not obtained. The alpha-branched chain isomers in this series are quantitatively the most significant. These results are compared with literature data on amino acid synthesis by electrical discharge and Fischer-Tropsch-type catalysis. Neither model system produces an amino acid suite that is completely comparable to that found in the Murchison meteorite.

  3. Amino acids of the Murchison meteorite. III - Seven carbon acyclic primary alpha-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, John R.; Pizzarello, Sandra

    1986-01-01

    All of the eighteen possible seven-carbon acyclic primary alpha-amino alkanoic acids have been positively identified in a hot-water extract of the Murchison meteorite by the combined use of gas chromatography-mass spectrometry, ion exchange chromatography and reversed-phase chromatography. None of these amino acids has previously been found in meteorites or in any other natural material. They range in concentration from less than or equal to 0.5 to 5.3 nmol/g. Configuration assignments were made for 2-amino-3,4-dimethylpentanoic acid and allo-2-amino-3,4-dimethylpentanoic acid and the diasteromer ratio was determined. Fifty-five amino acids have now been positively identified in the Murchison meteorite, 36 of which are unknown in terrestrial materials. This unique suite of amino acids is characterized by the occurrence of all structural isomers within the two major classes of amino acids represented, by the predominance of branched chain isomers, and by an exponential decline in amount with increasing carbon chain length within homologous series. These characteristics of the Murchison amino acids are suggestive of synthesis before incorporation into a parent body.

  4. Enhanced topical and transdermal delivery of antineoplastic and antiviral acyclic nucleoside phosphonate cPr-PMEDAP.

    PubMed

    Vávrová, Kateřina; Kovaříková, Petra; Skolová, Barbora; Líbalová, Martina; Roh, Jaroslav; Cáp, Robert; Holý, Antonín; Hrabálek, Alexandr

    2011-12-01

    Acyclic nucleoside phosphonates possess unique antiviral and antineoplastic activities; however, their polar phosphonate moiety is associated with low ability to cross biological membranes. We explored the potential of transdermal and topical delivery of 2,6-diaminopurine derivative cPr-PMEDAP. In vitro diffusion of cPr-PMEDAP was investigated using formulations at different pH and concentration and with permeation enhancer through porcine and human skin. Ability of 0.1-5% cPr-PMEDAP to cross human skin barrier was very low with flux values ~40 ng/cm(2)/h, the majority of compound found in the stratum corneum. The highest permeation rates were found at pH 6; increased donor concentration had no influence. The permeation enhancer dodecyl 6-dimethylaminohexanoate (DDAK, 1%) increased flux of cPr-PMEDAP (up to 61 times) and its concentration in nucleated epidermis (up to ~0.5 mg of cPr-PMEDAP/g of the tissue). No deamination of cPr-PMEDAP into PMEG occurred during permeation studies, but N-dealkylation into PMEDAP mediated by skin microflora was observed. Transdermal or topical application of cPr-PMEDAP enabled by the permeation enhancer DDAK may provide an attractive alternative route of administration of this potent antitumor and antiviral compound.

  5. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.

    PubMed

    He, Xibing; Lopes, Pedro E M; Mackerell, Alexander D

    2013-10-01

    A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments resulting in significant improvement in the treatment of the conformational energies and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules.

  6. Solution-phase parallel synthesis of acyclic nucleoside libraries of purine, pyrimidine, and triazole acetamides.

    PubMed

    Pathak, Ashish K; Pathak, Vibha; Reynolds, Robert C

    2014-09-08

    Molecular diversity plays a pivotal role in modern drug discovery against phenotypic or enzyme-based targets using high throughput screening technology. Under the auspices of the Pilot Scale Library Program of the NIH Roadmap Initiative, we produced and report herein a diverse library of 181 purine, pyrimidine, and 1,2,4-triazole-N-acetamide analogues which were prepared in a parallel high throughput solution-phase reaction format. A set of assorted amines were reacted with several nucleic acid N-acetic acids utilizing HATU as the coupling reagent to produce diverse acyclic nucleoside N-acetamide analogues. These reactions were performed using 24 well reaction blocks and an automatic reagent-dispensing platform under inert atmosphere. The targeted compounds were purified on an automated purification system using solid sample loading prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS, and were analyzed for purity by HPLC before submission to the Molecular Libraries Small Molecule Repository (MLSMR) at NIH. Initial screening through the Molecular Libraries Probe Production Centers Network (MLPCN) program, indicates that several analogues showed diverse and interesting biological activities.

  7. A chemical biosynthesis design for an antiatherosclerosis drug by acyclic tocopherol intermediate analogue based on "isoprenomics".

    PubMed

    Uto, Yoshihiro; Koyama, Daisuke; Otsuki, Mamoru; Otomo, Naoki; Shirai, Tadashi; Abe, Chiaki; Nakata, Eiji; Nagasawa, Hideko; Hori, Hitoshi

    2009-01-01

    Phytyl quinols, namely acyclic tocopherols, are key intermediates of tocopherol biosynthesis, but their biological activities remain unclear. We therefore investigated the structure-activity relationship of phytyl quinols to apply a chemical biosynthesis design for an antiatherosclerosis drug based on isoprenomics. We have achieved the biosynthesis-oriented design and synthesis of alpha- (TX-2254) and beta-(TX-2247) phytyl quinol as an unnatural intermediate, other gamma- (TX-2242) and delta-(TX-2231) phytyl quinol as a natural one. Geometry optimization and Molecular orbital (MO) calculation of TX-2254 showed a unique right-angle structure; however, MO energy of TX-2254 and d-alpha-tocopherol were very similar. Radical reactivity of TX-2231 was equal to dl-alpha-tocopherol, whereas TX-2254, TX-2247, and TX-2231 showed lower reactivity than dl-alpha-tocopherol. All four phytyl quinols showed almost the same moderate inhibitory activity against low-density lipoprotein (LDL) oxidation instead of their different degree of C-methylation with character different from tocopherols. In vivo toxicities of phytyl quinols against chick embryo chorioallantoic membrane (CAM) vasculature were hardly observed. We proposed phytyl quinols were possible antioxidants in plants and animals, like vitamin E.

  8. Flotation properties of some oxygen-containing compounds of the acyclic series

    SciTech Connect

    Shreider, E.M.; Para, S.F.; Galanov, M.E.; Trachik, T.L.; Lagutina, L.V.

    1981-01-01

    In the monatomic alcohols series, maximum flotation activity is reached at 6 to 8 carbon atoms in the radical. It was decided to investigate the reagent properties of some other substances containing hydroxyl radicals which have not previously been considered. Oxygen-containing compounds in the acyclic series were examined, including alcohols: I - ethanol, ethylene-glycol, glycerol, pentaerythrytol, D-mannitol; II - dulcitol, D-sorbitol, D-mannitol, xylitol; glycols - monoethyleneglycol, diethyleneglycol, triethyleneglycol, polyethyleneglycol; and ethanolamines - ethanolamine, triethanolamine. The flotation properties of the reagents were determined in a Mekhanobr laboratory flotation machine with a chamber volume of 1.5 liter and an impeller speed of 1800 rpm. The materials tested were the <1 mm size fractions from run-of-plant charge and slurry from the radial thickeners. The samples were first dried and averaged. The pulp density was 200 g/l. The reagent conditions were kept constant throughout (50% of the total added at the start of a test, 25% after 2 min and 25% after 4 min from the start). The reagent additions were 1.0 to 1.4 kg/ton. All of these compounds had a very weak flotation activity.

  9. Polarizable Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical Drude Oscillator

    PubMed Central

    He, Xibing; Lopes, Pedro E. M.; MacKerell, Alexander D.

    2014-01-01

    A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments, results in significant improvement in the treatment of the conformational energies, and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules. PMID:23703219

  10. A direct in vivo measurement of the three-dimensional orientation of the occlusal plane and of the sagittal discrepancy of the jaws.

    PubMed

    Ferrario, Virgilio F.; Sforza, Chiarella; Serrao, Graziano; Ciusa, Veronica

    2000-02-01

    The aim of the present investigation was to three dimensionally assess craniofacial relationships in vivo. Specifically, by using a non-invasive direct technique, the following measurements were made: 1) natural head position relative to the ground; 2) orientation of the occlusal plane relative to the subject's intrinsic facial planes; and 3) anteroposterior discrepancy of the dental bases, taking into consideration all the facial hard- and soft-tissue structures. Several dental and soft-tissue facial landmarks were directly digitized from 24 adult healthy volunteers with Angle Class I occlusions by means of an electromagnetic three-dimensional computerized digitizer. In natural head position, the three-dimensional orientation of Camper's, occlusal, and mandibular planes were measured along with the anteroposterior maxillo-mandibular discrepancies. In the frontal plane projection, all the measured planes appeared about horizontal. In the lateral plane projection, on average, Camper's plane deviated from the true horizontal by approximately 18 degrees (in a 'head flexed' direction). The occlusal plane deviated from the same horizontal by about 14 degrees, while the mandibular plane had a steeper inclination (about 30 degrees ); both planes were significantly correlated to Camper's plane. The measurements of anteroposterior jaw discrepancy revealed a wide range of sagittal relationships in the analyzed subjects. The method was found to be repeatable and fast. This direct three-dimensional in vivo assessment of the orientation of occlusal plane relative to the other facial planes could allow for a more comprehensive analysis of maxillo-mandibular sagittal discrepancies.

  11. Evaluation of automated direct sample introduction with comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry for the screening analysis of dioxins of fish oil

    USDA-ARS?s Scientific Manuscript database

    An automated direct sample introduction technique coupled to comprehensive two-dimensional gas chromatography-time of flight mass spectrometry (DSI-GC×GC/TOF-MS) was applied for the development of a relatively fast and easy analytical screening method for 17 polychlorinated dibenzo-p-dioxins/dibenzo...

  12. Static fluctuations of a thick one-dimensional interface in the 1+1 directed polymer formulation: numerical study.

    PubMed

    Agoritsas, Elisabeth; Lecomte, Vivien; Giamarchi, Thierry

    2013-06-01

    We study numerically the geometrical and free-energy fluctuations of a static one-dimensional (1D) interface with a short-range elasticity, submitted to a quenched random-bond Gaussian disorder of finite correlation length ξ>0 and at finite temperature T. Using the exact mapping from the static 1D interface to the 1+1 directed polymer (DP) growing in a continuous space, we focus our analysis on the disorder free energy of the DP end point, a quantity which is strictly zero in the absence of disorder and whose sample-to-sample fluctuations at a fixed growing time t inherit the statistical translation invariance of the microscopic disorder explored by the DP. Constructing a new numerical scheme for the integration of the Kardar-Parisi-Zhang evolution equation obeyed by the free energy, we address numerically the time and temperature dependence of the disorder free-energy fluctuations at fixed finite ξ. We examine, on one hand, the amplitude D[over ̃](t) and effective correlation length ξ[over ̃](t) of the free-energy fluctuations and, on the other hand, the imprint of the specific microscopic disorder correlator on the large-time shape of the free-energy two-point correlator. We observe numerically the crossover to a low-temperature regime below a finite characteristic temperature T(c)(ξ), as previously predicted by Gaussian variational method computations and scaling arguments and extensively investigated analytically in [Phys. Rev. E 87, 042406 (2013)]. Finally, we address numerically the time and temperature dependence of the roughness B(t), which quantifies the DP end point transverse fluctuations, and we show how the amplitude D[over ̃](∞)(T,ξ) controls the different regimes experienced by B(t)-in agreement with the analytical predictions of a DP toy model approach.

  13. Four-dimensional intensity-modulated radiation therapy planning for dynamic tracking using a direct aperture deformation (DAD) method

    SciTech Connect

    Gui Minzhi; Feng Yuanming; Yi Byongyong; Dhople, Anil Arvind; Yu, Cedric

    2010-05-15

    Purpose: Planning for the delivery of intensity-modulated radiation therapy (IMRT) to a moving target, referred to as four-dimensional (4D) IMRT planning, is a crucial step for achieving the treatment objectives for sites that move during treatment delivery. The authors proposed a simplistic method that accounts for both rigid and nonrigid respiration-induced target motion based on 4D computed tomography (4DCT) data sets. Methods: A set of MLC apertures and weights was first optimized on a reference phase of a 4DCT data set. At each beam angle, the apertures were morphed from the reference phase to each of the remaining phases according to the relative shape changes in the beam's eye view of the target. Three different planning schemes were evaluated for two lung cases and one pancreas patient: (1) Individually optimizing each breathing phase; (2) optimizing the reference phase and shifting the optimized apertures to other breathing phases based on a rigid-body image registration; and (3) optimizing the reference phase and deforming the optimized apertures to the other phases based on the deformation and translation of target contours. Planning results using scheme 1 serves as the ''gold standard'' for plan quality assessment; scheme 2 is the method previously proposed in the literature; and scheme 3 is the method the authors proposed in this article. The optimization results were compared between the three schemes for all three cases. Results: The proposed scheme 3 is comparable to scheme 1 in plan quality, and provides improved target coverage and conformity with similar normal tissue dose compared with scheme 2. Conclusions: Direct aperture deformation method for 4D IMRT planning improves upon methods that only consider rigid-body motion and achieves a plan quality close to that optimized for each of the phases.

  14. Facial Sketch Synthesis Using Two-dimensional Direct Combined Model-based Face-Specific Markov Network.

    PubMed

    Tu, Ching-Ting; Chan, Yu-Hsien; Chen, Yi-Chung

    2016-05-20

    A facial sketch synthesis system is proposed featuring a two-dimensional direct combined model (2DDCM)-based facespecific Markov network. In contrast to existing facial sketch synthesis systems, the proposed scheme aims to synthesize sketches which reproduce the unique drawing style of a particular artist, where this drawing style is learned from a dataset consisting of a large number of image/sketch pairwise training samples. The synthesis system comprises three modules, namely a global module, a local module, and an enhancement module. The global module applies a 2DDCM approach to synthesize the global facial geometry and texture of the input image. The detailed texture is then added to the synthesized sketch in a local patch-based manner using a parametric 2DDCM model and a non-parametric Markov random field (MRF) network. Notably, the MRF approach gives the synthesized results an appearance more consistent with the drawing style of the training samples, while the 2DDCM approach enables the synthesis of outcomes with a more derivative style. As a result, the similarity between the synthesized sketches and the input images is greatly improved. Finally, a post-processing operation is performed to enhance the shadowed regions of the synthesized image by adding strong lines or curves to emphasize the lighting conditions. The experimental results confirm that the synthesized facial images are in good qualitative and quantitative agreement with the input images as well as the ground-truth sketches provided by the same artist. The representing power of the proposed framework is demonstrated by synthesizing facial sketches from input images with a wide variety of facial poses, lighting conditions, and races even when such images are not included in the training dataset. Moreover, the practical applicability of the proposed framework is demonstrated by means of automatic facial recognition tests.

  15. High-resolution computer-generated reflection holograms with three-dimensional effects written directly on a silicon surface by a femtosecond laser.

    PubMed

    Wædegaard, Kristian J; Balling, Peter

    2011-02-14

    An infrared femtosecond laser has been used to write computer-generated holograms directly on a silicon surface. The high resolution offered by short-pulse laser ablation is employed to write highly detailed holograms with resolution up to 111 kpixels/mm2. It is demonstrated how three-dimensional effects can be realized in computer-generated holograms. Three-dimensional effects are visualized as a relative motion between different parts of the holographic reconstruction, when the hologram is moved relative to the reconstructing laser beam. Potential security applications are briefly discussed.

  16. Time-domain measurement of terahertz frequency magnetoplasmon resonances in a two-dimensional electron system by the direct injection of picosecond pulsed currents

    NASA Astrophysics Data System (ADS)

    Wu, Jingbo; Sydoruk, Oleksiy; Mayorov, Alexander S.; Wood, Christopher D.; Mistry, Divyang; Li, Lianhe; Linfield, Edmund H.; Giles Davies, A.; Cunningham, John E.

    2016-02-01

    We have investigated terahertz (THz) frequency magnetoplasmon resonances in a two-dimensional electron system through the direct injection of picosecond duration current pulses. The evolution of the time-domain signals was measured as a function of magnetic field, and the results were found to be in agreement with calculations using a mode-matching approach for four modes observed in the frequency range above 0.1 THz. This introduces a generic technique suitable for sampling ultrafast carrier dynamics in low-dimensional semiconductor nanostructures at THz frequencies.

  17. Time-domain measurement of terahertz frequency magnetoplasmon resonances in a two-dimensional electron system by the direct injection of picosecond pulsed currents

    SciTech Connect

    Wu, Jingbo; Mayorov, Alexander S.; Wood, Christopher D.; Mistry, Divyang; Li, Lianhe; Linfield, Edmund H.; Giles Davies, A.; Cunningham, John E.; Sydoruk, Oleksiy

    2016-02-29

    We have investigated terahertz (THz) frequency magnetoplasmon resonances in a two-dimensional electron system through the direct injection of picosecond duration current pulses. The evolution of the time-domain signals was measured as a function of magnetic field, and the results were found to be in agreement with calculations using a mode-matching approach for four modes observed in the frequency range above 0.1 THz. This introduces a generic technique suitable for sampling ultrafast carrier dynamics in low-dimensional semiconductor nanostructures at THz frequencies.

  18. Mesh generation for two-dimensional regions using the Tektronix DVST (direct view storage tube) graphics terminal

    NASA Technical Reports Server (NTRS)

    Gabrielson, V. K.

    1975-01-01

    The computer program DVMESH and the use of the Tektronix DVST graphics terminal were described for applications of preparing mesh data for use in various two-dimensional axisymmetric finite element stress analysis and heat transfer codes.

  19. Cell Tracking Accuracy Measurement Based on Comparison of Acyclic Oriented Graphs

    PubMed Central

    Sorokin, Dmitry V.; Matula, Petr; Ortiz-de-Solórzano, Carlos; Kozubek, Michal

    2015-01-01

    Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal relationships between them. Such a representation maintains the knowledge of all important cellular events within a captured field of view, such as migration, division, death, and transit through the field of view. The increasing number of cell tracking algorithms calls for comparison of their performance. However, the lack of a standardized cell tracking accuracy measure makes the comparison impracticable. This paper defines and evaluates an accuracy measure for objective and systematic benchmarking of cell tracking algorithms. The measure assumes the existence of a ground-truth reference, and assesses how difficult it is to transform a computed graph into the reference one. The difficulty is measured as a weighted sum of the lowest number of graph operations, such as split, delete, and add a vertex and delete, add, and alter the semantics of an edge, needed to make the graphs identical. The measure behavior is extensively analyzed based on the tracking results provided by the participants of the first Cell Tracking Challenge hosted by the 2013 IEEE International Symposium on Biomedical Imaging. We demonstrate the robustness and stability of the measure against small changes in the choice of weights for diverse cell tracking algorithms and fluorescence microscopy datasets. As the measure penalizes all possible errors in the tracking results and is easy to compute, it may especially help developers and analysts to tune their algorithms according to their needs. PMID:26683608

  20. Ester prodrugs of acyclic nucleoside thiophosphonates compared to phosphonates: synthesis, antiviral activity and decomposition study.

    PubMed

    Roux, Loïc; Priet, Stéphane; Payrot, Nadine; Weck, Clément; Fournier, Maëlenn; Zoulim, Fabien; Balzarini, Jan; Canard, Bruno; Alvarez, Karine

    2013-05-01

    9-[2-(Thiophosphonomethoxy)ethyl]adenine [S-PMEA, 8] and (R)-9-[2-(Thiophosphonomethoxy)propyl]adenine [S-PMPA, 9] are acyclic nucleoside thiophosphonates we described recently that display the same antiviral spectrum (DNA viruses) as approved and potent phosphonates PMEA and (R)-PMPA. Here, we describe the synthesis, antiviral activities in infected cell cultures and decomposition study of bis(pivaloyloxymethoxy)-S-PMEA [Bis-POM-S-PMEA, 13] and bis(isopropyloxymethylcarbonyl)-S-PMPA [Bis-POC-S-PMPA, 14] as orally bioavailable prodrugs of the S-PMEA 8 and S-PMPA 9, in comparison to the equivalent "non-thio" derivatives [Bis-POM-PMEA, 11] and [Bis-POC-PMPA, 12]. Compounds 11, 12, 13 and 14 were evaluated for their in vitro antiviral activity against HIV-1-, HIV-2-, HBV- and a broad panel of DNA viruses, and found to exhibit moderate to potent antiviral activity. In order to determine the decomposition pathway of the prodrugs 11, 12, 13 and 14 into parent compounds PMEA, PMPA, 8 and 9, kinetic data and decomposition pathways in several media are presented. As expected, bis-POM-S-PMEA 13 and bis-POC-S-PMPA 14 behaved as prodrugs of S-PMEA 8 and S-PMPA 9. However, thiophosphonates 8 and 9 were released very smoothly in cell extracts, in contrast to the release of PMEA and PMPA from "non-thio" prodrugs 11 and 12. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  1. Cell Tracking Accuracy Measurement Based on Comparison of Acyclic Oriented Graphs.

    PubMed

    Matula, Pavel; Maška, Martin; Sorokin, Dmitry V; Matula, Petr; Ortiz-de-Solórzano, Carlos; Kozubek, Michal

    2015-01-01

    Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal relationships between them. Such a representation maintains the knowledge of all important cellular events within a captured field of view, such as migration, division, death, and transit through the field of view. The increasing number of cell tracking algorithms calls for comparison of their performance. However, the lack of a standardized cell tracking accuracy measure makes the comparison impracticable. This paper defines and evaluates an accuracy measure for objective and systematic benchmarking of cell tracking algorithms. The measure assumes the existence of a ground-truth reference, and assesses how difficult it is to transform a computed graph into the reference one. The difficulty is measured as a weighted sum of the lowest number of graph operations, such as split, delete, and add a vertex and delete, add, and alter the semantics of an edge, needed to make the graphs identical. The measure behavior is extensively analyzed based on the tracking results provided by the participants of the first Cell Tracking Challenge hosted by the 2013 IEEE International Symposium on Biomedical Imaging. We demonstrate the robustness and stability of the measure against small changes in the choice of weights for diverse cell tracking algorithms and fluorescence microscopy datasets. As the measure penalizes all possible errors in the tracking results and is easy to compute, it may especially help developers and analysts to tune their algorithms according to their needs.

  2. Methoxymethyl (MOM) group nitrogen protection of pyrimidines bearing C-6 acyclic side-chains.

    PubMed

    Kraljević, Tatjana Gazivoda; Petrović, Martina; Krištafor, Svjetlana; Makuc, Damjan; Plavec, Janez; Ross, Tobias L; Ametamey, Simon M; Raić-Malić, Silvana

    2011-06-20

    Novel N-methoxymethylated (MOM) pyrimidine (4-13) and pyrimidine-2,4-diones (15-17) nucleoside mimetics in which an isobutyl side-chain is attached at the C-6 position of the pyrimidine moiety were synthesized. Synthetic methods via O-persilylated or N-anionic uracil derivatives have been evaluated for the synthesis of N-1- and/or N-3-MOM pyrimidine derivatives with C-6 acyclic side-chains. A synthetic approach using an activated N-anionic pyrimidine derivative afforded the desired N,N-1,3-diMOM and N-1-MOM pyrimidines 4 and 5 in good yield. Introduction of fluorine into the side-chain was performed with DAST as the fluorinating reagent to give a N,N-1,3-diMOM pyrimidine 13 with a 1-fluoro-3-hydroxyisobutyl moiety at C-6. Conformational study of the monotritylated N-1-MOM pyrimidine 12 by the use of the NOE experiments revealed the predominant conformation of the compound to be one where the hydroxymethyl group in the C-6 side-chain is close to the N-1-MOM moiety, while the OMTr is in proximity to the CH(3)-5 group. Contrary to this no NOE enhancements between the N-1-MOM group and hydroxymethyl or fluoromethyl protons in 13 were observed, which suggested a nonrestricted rotation along the C-6 side-chain. Fluorinated N,N-1,3-diMOM pyrimidine 13 emerged as a model compound for development of tracer molecules for non-invasive imaging of gene expression using positron emission tomography (PET).

  3. Synergistic growth inhibition by acyclic retinoid and vitamin K2 in human hepatocellular carcinoma cells.

    PubMed

    Kanamori, Toh; Shimizu, Masahito; Okuno, Masataka; Matsushima-Nishiwaki, Rie; Tsurumi, Hisashi; Kojima, Soichi; Moriwaki, Hisataka

    2007-03-01

    Hepatocellular carcinoma (HCC) is one of the most prevalent cancers worldwide. However, effective chemopreventive and chemotherapeutic agents for this cancer have not yet been developed. In clinical trials acyclic retinoid (ACR) and vitamin K(2) (VK(2)) decreased the recurrence rate of HCC. In the present study we examined the possible combined effects of ACR or another retinoid 9-cis retinoic acid (9cRA) plus VK(2) in the HuH7 human HCC cell line. We found that the combination of 1.0 microM ACR or 1.0 microM 9cRA plus 10 microM VK(2) synergistically inhibited the growth of HuH7 cells without affecting the growth of Hc normal human hepatocytes. The combined treatment with ACR plus VK(2) also acted synergistically to induce apoptosis in HuH7 cells. Treatment with VK(2) alone inhibited phosphorylation of the retinoid X receptor (RXR)alpha protein, which is regarded as a critical factor for liver carcinogenesis, through inhibition of Ras activation and extracellular signal-regulated kinase phosphorylation. Moreover, the inhibition of RXRalpha phosphorylation by VK(2) was enhanced when the cells were cotreated with ACR. The combination of retinoids plus VK(2) markedly increased both the retinoic acid receptor responsive element and retinoid X receptor responsive element promoter activities in HuH7 cells. Our results suggest that retinoids (especially ACR) and VK(2) cooperatively inhibit activation of the Ras/MAPK signaling pathway, subsequently inhibiting the phosphorylation of RXRalpha and the growth of HCC cells. This combination might therefore be effective for the chemoprevention and chemotherapy of HCC.

  4. A defocus-information-free autostereoscopic three-dimensional (3D) digital reconstruction method using direct extraction of disparity information (DEDI)

    NASA Astrophysics Data System (ADS)

    Li, Da; Cheung, Chifai; Zhao, Xing; Ren, Mingjun; Zhang, Juan; Zhou, Liqiu

    2016-10-01

    Autostereoscopy based three-dimensional (3D) digital reconstruction has been widely applied in the field of medical science, entertainment, design, industrial manufacture, precision measurement and many other areas. The 3D digital model of the target can be reconstructed based on the series of two-dimensional (2D) information acquired by the autostereoscopic system, which consists multiple lens and can provide information of the target from multiple angles. This paper presents a generalized and precise autostereoscopic three-dimensional (3D) digital reconstruction method based on Direct Extraction of Disparity Information (DEDI) which can be used to any transform autostereoscopic systems and provides accurate 3D reconstruction results through error elimination process based on statistical analysis. The feasibility of DEDI method has been successfully verified through a series of optical 3D digital reconstruction experiments on different autostereoscopic systems which is highly efficient to perform the direct full 3D digital model construction based on tomography-like operation upon every depth plane with the exclusion of the defocused information. With the absolute focused information processed by DEDI method, the 3D digital model of the target can be directly and precisely formed along the axial direction with the depth information.

  5. Zirconocene-assisted remote cleavage of C-C and C-O bonds: application to acyclic stereodefined metalated hydrocarbons.

    PubMed

    Bruffaerts, J; Pierrot, D; Marek, I

    2016-11-08

    The molding of molecules through remote functionalisation has increasingly become popular as it provides original and flexible synthetic alternatives to classical retrosynthetic analysis. In this Perspective article, we summarise more than a decade of studies in the specific field of remote activation of inert C-C and C-O bonds using the unique abilities of organozirconocene species mainly from our own research group. By demonstrating that these reactions represent novel and powerful entries towards acyclic stereodefined reactive organometallic species, we aim to show the vast opportunities this concept-driven methodology discovery offers.

  6. Amino acids of the Murchison meteorite. II - Five carbon acyclic primary beta-, gamma-, and delta-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, J. R.; Pizzarello, S.; Yuen, G. U.

    1985-01-01

    The five-carbon acyclic primary beta, gamma, and delta amino alkanoic acids of the Murchison meteorite are studied using gas chromatography-mass spectrometry and ion exchange chromatography. The chromatograms reveal that alpha is the most abundant monoamino alkanoic acid followed by gamma and beta, and an exponential increase in the amount of amino acid is observed as the carbon number increases in the homologous series. The influence of frictional heating, spontaneous thermal decomposition, and radiation of the synthesis of amino acids is examined. The data obtained support an amino acid synthesis process involving random combination of single-carbon precursors.

  7. Acyclic phosphonate nucleotides and human adenylate kinases: impact of a borano group on alpha-P position.

    PubMed

    Topalis, D; Alvarez, K; Barral, K; Munier-Lehmann, H; Schneider, B; Véron, M; Guerreiro, C; Mulard, L; El-Amri, C; Canard, B; Deville-Bonne, D

    2008-04-01

    Adenylate kinases are involved in the activation of antiviral drugs such as the acyclic phosphonates analogs PMEA and (R)PMPA. We examine the in vitro phosphorylation of PMEA and PMPA bearing a borano- or a H- group on the phosphorus atom. The alpha-borano or alpha-H on PMEA and PMPA were detrimental to the activity of recombinant human AMP kinases 1 and 2. Docking PMEA to the active site of AMP kinase 1 indicated that the borano group may prevent two conserved critical Arg interactions with the alpha-phosphate, resulting in substrate bad positioning.

  8. Asymmetric conjugate addition of alkylzirconium reagents to α,β-unsaturated thioesters: access to fragrances and acyclic stereochemical arrays.

    PubMed

    Gao, Zhenbo; Fletcher, Stephen P

    2017-09-01

    Copper-catalyzed asymmetric conjugate addition of alkylzirconium species to α,β-unsaturated thioesters is reported. A variety of functionalized alkyl nucleophiles were introduced with yields around 70% and ee's over 92%. The method was applied to the straightforward syntheses of the commercially important fragrances phenoxanol (both enantiomers 97% ee), and hydroxycitronellal (98% ee). The 1,4-addition products can be converted to enantiomerically enriched linear building blocks bearing a terminal functional group. Formation of further α,β-unsaturated thioesters provides an iterative route for the stereocontrolled synthesis of functionalized acyclic arrays and we demonstrate almost complete catalyst control in the formation of additional stereocentres.

  9. Full-Scale Direct Numerical Simulation of Two- and Three-Dimensional Instabilities and Rivulet Formulation in Heated Falling Films

    NASA Technical Reports Server (NTRS)

    Krishnamoorthy, S.; Ramaswamy, B.; Joo, S. W.

    1995-01-01

    A thin film draining on an inclined plate has been studied numerically using finite element method. Three-dimensional governing equations of continuity, momentum and energy with a moving boundary are integrated in an arbitrary Lagrangian Eulerian frame of reference. Kinematic equation is solved to precisely update interface location. Rivulet formation based on instability mechanism has been simulated using full-scale computation. Comparisons with long-wave theory are made to validate the numerical scheme. Detailed analysis of two- and three-dimensional nonlinear wave formation and spontaneous rupture forming rivulets under the influence of combined thermocapillary and surface-wave instabilities is performed.

  10. Method for estimating the propagation direction of a coherent plasma structure using a one-dimensional diagnostic array.

    PubMed

    Kobayashi, T; Birkenmeier, G; Wolfrum, E; Laggner, F M; Willensdorfer, M; Stroth, U; Inagaki, S; Itoh, S-I; Itoh, K

    2014-08-01

    This article proposes a new method to evaluate basic characteristics of the dynamics of a coherent plasma structure (blob). With this method, one can evaluate the propagation angle of a blob in a two-dimensional plasma cross section as well as the blob velocity, size, and amplitude from one-dimensional data. The method is applied to blob measurements from the Lithium beam emission spectroscopy system in ASDEX-Upgrade. Statistical features of the observed blob velocities, angles of propagation, blob sizes, and amplitudes are discussed. The validity of the method is examined by comparing two values of the propagation angle that are evaluated in an independent manner.

  11. Method for estimating the propagation direction of a coherent plasma structure using a one-dimensional diagnostic array

    SciTech Connect

    Kobayashi, T.; Birkenmeier, G.; Wolfrum, E.; Stroth, U.; Laggner, F. M.; Willensdorfer, M.; Inagaki, S.; Itoh, S.-I.; Itoh, K.

    2014-08-15

    This article proposes a new method to evaluate basic characteristics of the dynamics of a coherent plasma structure (blob). With this method, one can evaluate the propagation angle of a blob in a two-dimensional plasma cross section as well as the blob velocity, size, and amplitude from one-dimensional data. The method is applied to blob measurements from the Lithium beam emission spectroscopy system in ASDEX-Upgrade. Statistical features of the observed blob velocities, angles of propagation, blob sizes, and amplitudes are discussed. The validity of the method is examined by comparing two values of the propagation angle that are evaluated in an independent manner.

  12. Direct time integration of Maxwell's equations in two-dimensional dielectric waveguides for propagation and scattering of femtosecond electromagnetic solitons

    NASA Technical Reports Server (NTRS)

    Joseph, Rose M.; Goorjian, Peter M.; Taflove, Allen

    1993-01-01

    We present what are to our knowledge first-time calculations from vector nonlinear Maxwell's equations of femtosecond soliton propagation and scattering, including carrier waves, in two-dimensional dielectric waveguides. The time integration efficiently implements linear and nonlinear convolutions for the electric polarization, and the nonlinear convolution accounts for two quantum effects, the Kerr and Raman interactions. By retaining the optical carrier, the new method solves for fundamental quantities - optical electric and magnetic fields in space and time - rather than a nonphysical envelope function. It has the potential to provide an unprecedented two- and three-dimensional modeling capability for millimeter-scale integrated-optical circuits with submicrometer engineered inhomogeneities.

  13. Estimation of Item Dimensional Measurement Direction Using Conditional Covariance Patterns. Computerized Testing Report. LSAC Research Report Series.

    ERIC Educational Resources Information Center

    Bolt, Daniel; Roussos, Louis; Stout, William

    Several nonparametric dimensionality assessment tools have demonstrated the usefulness of item pair conditional covariances as building blocks for investigating multidimensional test structure. Recently, J. Zhang and W. Stout (1999) have related the structural properties of conditional covariances in a generalized compensatory framework to a test…

  14. The Effect of Acyclic Retinoid on the Metabolomic Profiles of Hepatocytes and Hepatocellular Carcinoma Cells

    PubMed Central

    Qin, Xian-Yang; Wei, Feifei; Tanokura, Masaru; Ishibashi, Naoto; Shimizu, Masahito; Moriwaki, Hisataka; Kojima, Soichi

    2013-01-01

    Background/Purpose Acyclic retinoid (ACR) is a promising chemopreventive agent for hepatocellular carcinoma (HCC) that selectively inhibits the growth of HCC cells (JHH7) but not normal hepatic cells (Hc). To better understand the molecular basis of the selective anti-cancer effect of ACR, we performed nuclear magnetic resonance (NMR)-based and capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS)-based metabolome analyses in JHH7 and Hc cells after treatment with ACR. Methodology/Principal Findings NMR-based metabolomics revealed a distinct metabolomic profile of JHH7 cells at 18 h after ACR treatment but not at 4 h after ACR treatment. CE-TOFMS analysis identified 88 principal metabolites in JHH7 and Hc cells after 24 h of treatment with ethanol (EtOH) or ACR. The abundance of 71 of these metabolites was significantly different between EtOH-treated control JHH7 and Hc cells, and 49 of these metabolites were significantly down-regulated in the ACR-treated JHH7 cells compared to the EtOH-treated JHH7 cells. Of particular interest, the increase in adenosine-5′-triphosphate (ATP), the main cellular energy source, that was observed in the EtOH-treated control JHH7 cells was almost completely suppressed in the ACR-treated JHH7 cells; treatment with ACR restored ATP to the basal levels observed in both EtOH-control and ACR-treated Hc cells (0.72-fold compared to the EtOH control-treated JHH7 cells). Moreover, real-time PCR analyses revealed that ACR significantly increased the expression of pyruvate dehydrogenase kinases 4 (PDK4), a key regulator of ATP production, in JHH7 cells but not in Hc cells (3.06-fold and 1.20-fold compared to the EtOH control, respectively). Conclusions/Significance The results of the present study suggest that ACR may suppress the enhanced energy metabolism of JHH7 cells but not Hc cells; this occurs at least in part via the cancer-selective enhancement of PDK4 expression. The cancer-selective metabolic pathways identified in

  15. Radiolabeling, stability studies, and pharmacokinetic evaluation of thulium-170-labeled acyclic and cyclic polyaminopolyphosphonic acids.

    PubMed

    Vats, Kusum; Das, Tapas; Sarma, Haladhar D; Banerjee, Sharmila; Pillai, M R A

    2013-12-01

    Thulium-170 [T1/2=128.4 days, Eβ(max)=968 keV, and Eγ=84 keV (3.26%)] could be considered an easily producible and cost-effective alternative to (89)Sr for the preparation of radiopharmaceuticals for palliation of bone pain arising due to skeletal metastases. Multidentate aminomethylene polyphosphonic acids have already been proven to be effective as carrier moieties for developing radiolabeled bone pain palliation agents using lanthanide radionuclides. Therefore, an attempt was made to evaluate the potential of a series of (170)Tm-labeled acyclic (diethylenetriaminepentamethylene phosphonic acid and triethylenetetraminehexamethylene phosphonic acid) and cyclic polyaminopolyphosphonic acids (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetramethylene phosphonic acid [DOTMP] and 1,4,8,11-tetraazacyclotetradecane-1,4,8,11-tetramethylene phosphonic acid [CTMP]) toward their use as alternative bone pain palliation agents. Thulium-170 was produced by irradiating the natural Tm2O3 target at a thermal neutron flux of 7×10(13) n·cm(-2)·s(-1) for a period of 60 days. All the phosphonic acid ligands were synthesized and characterized in-house. The protocols for radiolabeling the phosphonic acids with (170)Tm were standardized. Biological evaluation of the (170)Tm-labeled phosphonic acids were carried out in normal Wistar rats by biodistribution as well as by scintigraphic studies. Thulium-170 was produced with adequate specific activity (173 Ci/g, 6.41 TBq/g) and high radionuclidic purity (99.62%). All the (170)Tm-labeled phosphonic acids, except (170)Tm-CTMP, were prepared with very high radiochemical purity (>98%) under optimized reaction conditions and exhibited high stability. All the agents showed selective skeletal accumulation with insignificant uptake in other vital organs/tissues and major clearance through renal pathway. These findings were also substantiated by scintigraphic studies. Although all the (170)Tm-labeled phosphonic acids showed significant and

  16. In vitro validation of real-time three-dimensional color Doppler echocardiography for direct measurement of proximal isovelocity surface area in mitral regurgitation.

    PubMed

    Little, Stephen H; Igo, Stephen R; Pirat, Bahar; McCulloch, Marti; Hartley, Craig J; Nosé, Yukihiko; Zoghbi, William A

    2007-05-15

    The 2-dimensional (2D) color Doppler (2D-CD) proximal isovelocity surface area (PISA) method assumes a hemispheric flow convergence zone to estimate transvalvular flow. Recently developed 3-dimensional (3D)-CD can directly visualize PISA shape and surface area without geometric assumptions. To validate a novel method to directly measure PISA using real-time 3D-CD echocardiography, a circulatory loop with an ultrasound imaging chamber was created to model mitral regurgitation (MR). Thirty-two different regurgitant flow conditions were tested using symmetric and asymmetric flow orifices. Three-dimensional-PISA was reconstructed from a hand-held real-time 3D-CD data set. Regurgitant volume was derived using both 2D-CD and 3D-CD PISA methods, and each was compared against a flow-meter standard. The circulatory loop achieved regurgitant volume within the clinical range of MR (11 to 84 ml). Three-dimensional-PISA geometry reflected the 2D geometry of the regurgitant orifice. Correlation between the 2D-PISA method regurgitant volume and actual regurgitant volume was significant (r(2) = 0.47, p <0.001). Mean 2D-PISA regurgitant volume underestimate was 19.1 +/- 25 ml (2 SDs). For the 3D-PISA method, correlation with actual regurgitant volume was significant (r(2) = 0.92, p <0.001), with a mean regurgitant volume underestimate of 2.7 +/- 10 ml (2 SDs). The 3D-PISA method showed less regurgitant volume underestimation for all orifice shapes and regurgitant volumes tested. In conclusion, in an in vitro model of MR, 3D-CD was used to directly measure PISA without geometric assumption. Compared with conventional 2D-PISA, regurgitant volume was more accurate when derived from 3D-PISA across symmetric and asymmetric orifices within a broad range of hemodynamic flow conditions.

  17. Seven-coordinate iron and manganese complexes with acyclic and rigid pentadentate chelates and their superoxide dismutase activity.

    PubMed

    Liu, Gao-Feng; Filipović, Milos; Heinemann, Frank W; Ivanović-Burmazović, Ivana

    2007-10-15

    The reactions of seven-coordinate [Fe(III)(dapsox)(H(2)O)(2)]ClO(4).H(2)O (1), [Fe(II)(H(2)dapsox)(H(2)O)(2)](NO(3))(2).H(2)O (2), and [Mn(II)(H(2)dapsox)(CH(3)OH)(H(2)O)](ClO4)2(H2O) (3) complexes of the acyclic and rigid pentadentate H(2)dapsox ligand [H2dapsox = 2,6-diacetylpyridinebis(semioxamazide)] with superoxide have been studied spectrophotometrically, electrochemically, and by a submillisecond mixing UV/vis stopped-flow in dimethyl sulfoxide (DMSO). The same studies were performed on the seven-coordinate [Mn(II)(Me(2)[15]pyridinaneN(5))(H(2)O)(2)]Cl(2).H(2)O (4) complex with the flexible macrocyclic Me(2)[15]pyridinaneN(5) ligand (Me(2)[15]pyridinaneN(5) = trans-2,13-dimethyl-3,6,9,12,18-pentaazabicyclo[12.3.1]octadeca-1(18),14,16-triene), which belongs to the class of proven superoxide dismutase (SOD) mimetics. The X-ray crystal structures of 2-4 were determined. All complexes possess pentagonal-bipyramidal geometry with the pentadentate ligand in the equatorial plane and solvent molecules in the axial positions. The stopped-flow experiments in DMSO (0.06% of water) reveal that all four metal complexes catalyze the fast disproportionation of superoxide under the applied experimental conditions, and the catalytic rate constants are found to be (3.7 +/- 0.5) x 10(6), (3.9 +/- 0.5) x 10(6), (1.2 +/- 0.3) x 10(7), and (5.3 +/- 0.8) x 10(6) M(-1) s(-1) for 1-4, respectively. The cytochrome c McCord-Fridovich (McCF) assay in an aqueous solution at pH = 7.8 resulted in the IC(50) values (and corresponding kMcCF constants) for 3 and 4, 0.013 +/- 0.001 microM (1.9 +/- 0.2 x 10(8) M(-1) s(-1)) and 0.024 +/- 0.001 microM (1.1 +/- 0.3 x 10(8) M(-1) s(-1)), respectively. IC(50) values from a nitroblue tetrazolium assay are found to be 6.45 +/- 0.02 and 1.36 +/- 0.03 microM for 1 and 4, respectively. The data have been compared with those obtained by direct stopped-flow measurements and discussed in terms of the side reactions that occur under the conditions of

  18. Catalytic enantioselective aza-Diels-Alder reactions of unactivated acyclic 1,3-dienes with aryl-, alkenyl-, and alkyl-substituted imines.

    PubMed

    Hatanaka, Yasuo; Nantaku, Shuuto; Nishimura, Yuhki; Otsuka, Tomoyuki; Sekikaw, Tohru

    2017-08-08

    A catalytic enantioselective aza-Diels-Alder reaction of unactivated acyclic dienes with aryl-, alkenyl-, and alkyl-substituted imines is described. With 5-10 mol% loadings of a new Brønsted acid catalyst, the aza-Diels-Alder reaction of unactivated acyclic dienes proceeded to give the corresponding aza-Diels-Alder adducts in high yields (up to 98%) with excellent enantioselectivity (up to 98% ee). Preliminary DFT calculations suggest that the reaction proceeds through a chiral ion pair intermediate.

  19. GRASr2 evaluation of aliphatic acyclic and alicyclic terpenoid tertiary alcohols and structurally related substances used as flavoring ingredients.

    PubMed

    Marnett, Lawrence J; Cohen, Samuel M; Fukushima, Shoji; Gooderham, Nigel J; Hecht, Stephen S; Rietjens, Ivonne M C M; Smith, Robert L; Adams, Timothy B; Bastaki, Maria; Harman, Christie L; McGowen, Margaret M; Taylor, Sean V

    2014-04-01

    This publication is the 1st in a series of publications by the Expert Panel of the Flavor and Extract Manufacturers Assoc. summarizing the Panel's 3rd re-evaluation of Generally Recognized as Safe (GRAS) status referred to as the GRASr2 program. In 2011, the Panel initiated a comprehensive program to re-evaluate the safety of more than 2700 flavor ingredients that have previously met the criteria for GRAS status under conditions of intended use as flavor ingredients. Elements that are fundamental to the safety evaluation of flavor ingredients include exposure, structural analogy, metabolism, pharmacokinetics, and toxicology. Flavor ingredients are evaluated individually and in the context of the available scientific information on the group of structurally related substances. Scientific data relevant to the safety evaluation of the use of aliphatic acyclic and alicyclic terpenoid tertiary alcohols and structurally related substances as flavoring ingredients are evaluated. The group of aliphatic acyclic and alicyclic terpenoid tertiary alcohols and structurally related substances was reaffirmed as GRAS (GRASr2) based, in part, on their rapid absorption, metabolic detoxication, and excretion in humans and other animals; their low level of flavor use; the wide margins of safety between the conservative estimates of intake and the no-observed-adverse effect levels determined from subchronic studies and the lack of significant genotoxic and mutagenic potential.

  20. Synthesis and Evaluation of Novel Acyclic Nucleoside Phosphonates as Inhibitors of Plasmodium falciparum and Human 6-Oxopurine Phosphoribosyltransferases.

    PubMed

    Kaiser, Martin M; Hocková, Dana; Wang, Tzu-Hsuan; Dračínský, Martin; Poštová-Slavětínská, Lenka; Procházková, Eliška; Edstein, Michael D; Chavchich, Marina; Keough, Dianne T; Guddat, Luke W; Janeba, Zlatko

    2015-10-01

    Acyclic nucleoside phosphonates (ANPs) are a promising class of antimalarial therapeutic drug leads that exhibit a wide variety of Ki values for Plasmodium falciparum (Pf) and human hypoxanthine-guanine-(xanthine) phosphoribosyltransferases [HG(X)PRTs]. A novel series of ANPs, analogues of previously reported 2-(phosphonoethoxy)ethyl (PEE) and (R,S)-3-hydroxy-2-(phosphonomethoxy)propyl (HPMP) derivatives, were designed and synthesized to evaluate their ability to act as inhibitors of these enzymes and to extend our ongoing antimalarial structure-activity relationship studies. In this series, (S)-3-hydroxy-2-(phosphonoethoxy)propyl (HPEP), (S)-2-(phosphonomethoxy)propanoic acid (CPME), or (S)-2-(phosphonoethoxy)propanoic acid (CPEE) are the acyclic moieties. Of this group, (S)-3-hydroxy-2-(phosphonoethoxy)propylguanine (HPEPG) exhibits the highest potency for PfHGXPRT, with a Ki value of 0.1 μM and a Ki value for human HGPRT of 0.6 μM. The crystal structures of HPEPG and HPEPHx (where Hx=hypoxanthine) in complex with human HGPRT were obtained, showing specific interactions with active site residues. Prodrugs for the HPEP and CPEE analogues were synthesized and tested for in vitro antimalarial activity. The lowest IC50 value (22 μM) in a chloroquine-resistant strain was observed for the bis-amidate prodrug of HPEPG. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.

    PubMed

    Abrishami, V; Bilbao-Castro, J R; Vargas, J; Marabini, R; Carazo, J M; Sorzano, C O S

    2015-10-01

    We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Three-dimensional analysis of root canal curvature and direction of maxillary lateral incisors by using cone-beam computed tomography.

    PubMed

    Park, Pan-Soo; Kim, Kee-Deog; Perinpanayagam, Hiran; Lee, Jong-Ki; Chang, Seok Woo; Chung, Shin Hye; Kaufman, Blythe; Zhu, Qiang; Safavi, Kamran E; Kum, Kee-Yeon

    2013-09-01

    Root canal curvature can affect the technical quality of endodontic treatment. Prior studies measured canal curvature mainly by 2-dimensional radiography. The aim of this study was to measure the 3-dimensional (3D) root canal curvature and canal direction of maxillary lateral incisors by using cone-beam computed tomography (CBCT) and mathematical modeling. The CBCT images of 186 maxillary lateral incisors from 110 patients were used to measure 3D root canal curvature by using V-works and kappa software. In addition, the direction of each root canal was determined by measuring the orientation of the apical one-third with respect to the coronal two-thirds. All 186 maxillary lateral incisors were found to have canal curvature that was mainly oriented in the disto-palatal direction. The point of maximum curvature was located 0.5 mm from the root apex. Maxillary lateral incisors have 3D canal curvature that is maximal near the root apex, oriented in the disto-palatal direction. These CBCT analyses provide valuable information for root canal instrumentation of maxillary lateral incisors. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  3. Fast reconfiguration algorithm of computer generated holograms for adaptive view direction change in holographic three-dimensional display.

    PubMed

    Cho, Jaebum; Hahn, Joonku; Kim, Hwi

    2012-12-17

    Reconfiguration is a computational algorithm of adaptively updating computer generated holograms (CGHs) for the positional change of an observer's viewing window with low computational load by efficiently using pre-calculated elementary CGHs. A fast reconfiguration algorithm of CGHs for three-dimensional mesh objects is proposed. Remarkable improvement is achieved in the computation speed of CGHs, which is at least 20-times faster than repetitive re-computation of CGHs. The image quality of reconfigured CGHs is analyzed.

  4. Direct Conversion of Equine Adipose-Derived Stem Cells into Induced Neuronal Cells Is Enhanced in Three-Dimensional Culture.

    PubMed

    Petersen, Gayle F; Hilbert, Bryan J; Trope, Gareth D; Kalle, Wouter H J; Strappe, Padraig M

    2015-12-01

    The ability to culture neurons from horses may allow further investigation into equine neurological disorders. In this study, we demonstrate the generation of induced neuronal cells from equine adipose-derived stem cells (EADSCs) using a combination of lentiviral vector expression of the neuronal transcription factors Brn2, Ascl1, Myt1l (BAM) and NeuroD1 and a defined chemical induction medium, with βIII-tubulin-positive induced neuronal cells displaying a distinct neuronal morphology of rounded and compact cell bodies, extensive neurite outgrowth, and branching of processes. Furthermore, we investigated the effects of dimensionality on neuronal transdifferentiation, comparing conventional two-dimensional (2D) monolayer culture against three-dimensional (3D) culture on a porous polystyrene scaffold. Neuronal transdifferentiation was enhanced in 3D culture, with evenly distributed cells located on the surface and throughout the scaffold. Transdifferentiation efficiency was increased in 3D culture, with an increase in mean percent conversion of more than 100% compared to 2D culture. Additionally, induced neuronal cells were shown to transit through a Nestin-positive precursor state, with MAP2 and Synapsin 2 expression significantly increased in 3D culture. These findings will help to increase our understanding of equine neuropathogenesis, with prospective roles in disease modeling, drug screening, and cellular replacement for treatment of equine neurological disorders.

  5. Encapsulation of Adipose Stromal Vascular Fraction Cells in Alginate Hydrogel Spheroids Using a Direct-Write Three-Dimensional Printing System

    PubMed Central

    Touroo, Jeremy S.; Church, Kenneth H.; Hoying, James B.

    2013-01-01

    Abstract The study of tissue function in vitro has been aided by the development of three-dimensional culture systems that more accurately duplicate the complex cell components of tissues and organs. Bioprinting of cells provides a rapid tissue fabrication technique that can be used to evaluate normal and pathologic conditions in vitro as well as to construct complex three-dimensional tissue structures for implantation in regenerative medicine therapies. Studies were performed using a direct write three-dimensional bioprinting system to fabricate adipose-derived stromal vascular fraction cell spheroids. Human fat–derived stromal vascular fraction cells were mixed in 1.5% (w/v) alginate solutions, and fabrication conditions were varied to produce an array of spheroids. The spheroids were placed in spinner culture, and spheroid integrity and encapsulated cell viability were assessed for 16 days. Results establish the ability to tightly control adipose SVF spheroids in the range of 800–1500 μm. Fabrication conditions were used to control spheroid size, and the results illustrate the ability to construct spheroids of precise size and shape. The adipose SVF cell population remains viable and the spheroid integrity was maintained for 16 days in suspension culture. The direct-write printing of adipose stromal vascular fraction cell containing spheroids provides a rapid fabrication technology to support in vitro microphysiologic system studies. PMID:24380055

  6. A system of fast one-dimensional X-ray cinema with direct registration and accumulation of images by a matrix CCD

    NASA Astrophysics Data System (ADS)

    Fedotov, M. G.; Panchenko, V. E.

    1995-02-01

    A recording system on the basis of a matrix CCD and the first results of its testing are described. The system is intended for fast registration (from 10 up to 100 μs per image) of the limited (100 through 500) series of one-dimensional X-ray images. Here the CCD is used for direct registration of X-rays as well as for the accumulation and short-time storage of one-dimensional bulk images. After the registration is complete, the accumulated images are transformed into a digitized electric signal, which is read out by a computer. Our consideration also deals with the system speed main restrictions, which are due to both the electric parameters of a matrix CCD and the charge-diffusion effects in the substratum. Besides, the methods for diminishing these restrictions are discussed.

  7. Mask-free construction of three-dimensional silicon structures by dry etching assisted gray-scale femtosecond laser direct writing

    NASA Astrophysics Data System (ADS)

    Liu, Xue-Qing; Yu, Lei; Chen, Qi-Dai; Sun, Hong-Bo

    2017-02-01

    A mask-free micro/nano fabrication method is proposed for constructing arbitrary gradient height structures on silicon, combining gray-scale femtosecond laser direct writing (GS-FsLDW) with subsequent dry etching. Arbitrary two-dimensional patterns with a gradient concentration of oxygen atoms can be fabricated on the surface of undoped silicon wafer by FsLDW in air. After dry etching, various three-dimensional (3D) gradient height silicon structures are fabricated by controlling the laser power, scanning step, etching time, and etching power. As an example, a well-defined 3D Fresnel zone plate was fabricated on silicon wafer, which shows excellent focusing and imaging properties. The combination of high precision from dry etching and 3D fabrication ability on non-planar substrates of FsLDW, may broaden its applications in microelectronics, micro-optics, and microelectromechanical systems.

  8. Direct simulation of melting a cryogenic surface with a two-dimensional axisymmetric turbulent superheated vapor jet

    NASA Astrophysics Data System (ADS)

    Baran, Adam J.

    This dissertation presents original research into the melting process of a downward facing cryogenic solid hydrogen surface subject to a two dimensional axisymmetric jet impingement flow of superheated hydrogen vapor. The motivation for the study is to investigate concepts of storing rocket propellants as a solid and rapidly melting the solid for liquid propellant delivery to a rocket engine. The present study considers a more favorable liquid removal arrangement than prior (1970s) experiments which melted solid hydrogen at the bottom of a cryostat. This is a numerical study that involves computation fluid dynamic (CFD) simulation of four distinct physical phenomena: (1) melting, (2) jet impingement heat transfer (JIHT), (3) multiphase transport, and (4) film breakup/droplet formation. The volume of fluid (VOF) method is used with the V2F turbulence model in a commercial CFD Navier-Stokes solver (FLUENT) to investigate the multiphase nature of melt transport and its interaction with the vapor stream; i.e., the phenomena relevant to effective heat transfer between the vapor and the melting interface. The goal of the research is: (1) to develop a numerical method to study the problem and (2) evaluate several simple configurations to begin investigating relevant phenomena for the purpose of enhancing melting rate. Many options exist for the vapor to interact with the solid surface. The scope of this initial research is limited to a steady jet of single phase superheated hydrogen vapor at fixed jet exit conditions (T = 525 R and Re = 11,000) at a fixed jet standoff ( H/D = 1.0). Condensation/vaporization are not considered. Although film breakup/droplet formation is a phenomenon where two dimensional features evolve into three dimensional events, this phenomenon is approximated as two dimensional to allow a computationally tractable problem for this initial study. Calculations are performed validating the numerical method for melting and JIHT against known results

  9. Direct evidence for a three-dimensional magnetic flux rope flanked by two active magnetic reconnection X lines at Earth's magnetopause.

    PubMed

    Øieroset, M; Phan, T D; Eastwood, J P; Fujimoto, M; Daughton, W; Shay, M A; Angelopoulos, V; Mozer, F S; McFadden, J P; Larson, D E; Glassmeier, K-H

    2011-10-14

    We report the direct detection by three THEMIS spacecraft of a magnetic flux rope flanked by two active X lines producing colliding plasma jets near the center of the flux rope. The observed density depletion and open magnetic field topology inside the flux rope reveal important three-dimensional effects. There was also evidence for nonthermal electron energization within the flux rope core where the fluxes of 1-4 keV superthermal electrons were higher than those in the converging reconnection jets. The observed ion and electron energizations differ from current theoretical predictions.

  10. Recurrence of hyperprolactinemia and continuation of ovarian acyclicity in captive African elephants (Loxodonta africana) treated with cabergoline.

    PubMed

    Morfeld, Kari A; Ball, Ray L; Brown, Janine L

    2014-09-01

    Hyperprolactinemia is associated with reproductive acyclicity in zoo African elephants (Loxodonta africana) and may contribute to the non-self-sustainability of the captive population in North America. It is a common cause of infertility in women and other mammals and can be treated with the dopamine agonist cabergoline. The objectives of this study were to assess prolactin responses to cabergoline treatment in hyperprolactinemic, acyclic African elephants and to determine the subsequent impact on ovarian cyclic activity. Five elephants, diagnosed as hyperprolactinemic (>11 ng/ml prolactin) and acyclic (maintenance of baseline progestagens for at least 1 yr), were treated with 1-2 mg cabergoline orally twice weekly for 16-82 wk. Cabergoline reduced (P < 0.05) serum prolactin concentrations during the treatment period compared to pretreatment levels in four of five elephants (11.5 +/- 3.2 vs. 9.1 +/- 3.4 ng/ml; 20.3 +/- 16.7 vs. 7.9 +/- 9.8 ng/ml; 26.4 +/- 15.0 vs. 6.8 +/- 1.5 ng/ml; 42.2 +/- 22.6 vs. 18.6 +/- 8.9 ng/ml). However, none of the females resumed ovarian cyclicity based on serum progestagen analyses up to 1 yr posttreatment. In addition, within 1 to 6 wk after cessation of oral cabergoline, serum prolactin concentrations returned to concentrations that were as high as or higher than before treatment (P < 0.05). One elephant that exhibited the highest pretreatment prolactin concentration (75.2 +/- 10.5 ng/ml) did not respond to cabergoline and maintained elevated levels throughout the study. Thus, oral cabergoline administration reduced prolactin concentrations in elephants with hyperprolactinemia, but there was no resumption of ovarian cyclicity, and a significant prolactin rebound effect was observed. It is possible that higher doses or longer treatment intervals may be required for cabergoline treatment to result in permanent suppression of prolactin secretion and to mitigate associated ovarian cycle problems.

  11. 3-dimensional magnetotelluric inversion including topography using deformed hexahedral edge finite elements and direct solvers parallelized on symmetric multiprocessor computers - Part II: direct data-space inverse solution

    NASA Astrophysics Data System (ADS)

    Kordy, M.; Wannamaker, P.; Maris, V.; Cherkaev, E.; Hill, G.

    2016-01-01

    Following the creation described in Part I of a deformable edge finite-element simulator for 3-D magnetotelluric (MT) responses using direct solvers, in Part II we develop an algorithm named HexMT for 3-D regularized inversion of MT data including topography. Direct solvers parallelized on large-RAM, symmetric multiprocessor (SMP) workstations are used also for the Gauss-Newton model update. By exploiting the data-space approach, the computational cost of the model update becomes much less in both time and computer memory than the cost of the forward simulation. In order to regularize using the second norm of the gradient, we factor the matrix related to the regularization term and apply its inverse to the Jacobian, which is done using the MKL PARDISO library. For dense matrix multiplication and factorization related to the model update, we use the PLASMA library which shows very good scalability across processor cores. A synthetic test inversion using a simple hill model shows that including topography can be important; in this case depression of the electric field by the hill can cause false conductors at depth or mask the presence of resistive structure. With a simple model of two buried bricks, a uniform spatial weighting for the norm of model smoothing recovered more accurate locations for the tomographic images compared to weightings which were a function of parameter Jacobians. We implement joint inversion for static distortion matrices tested using the Dublin secret model 2, for which we are able to reduce nRMS to ˜1.1 while avoiding oscillatory convergence. Finally we test the code on field data by inverting full impedance and tipper MT responses collected around Mount St Helens in the Cascade volcanic chain. Among several prominent structures, the north-south trending, eruption-controlling shear zone is clearly imaged in the inversion.

  12. Proline isomerism leads to multiple folded conformations of calbindin D9k: direct evidence from two-dimensional 1H NMR spectroscopy.

    PubMed Central

    Chazin, W J; Kördel, J; Drakenberg, T; Thulin, E; Brodin, P; Grundström, T; Forsén, S

    1989-01-01

    A complete analysis of calbindin D9k by two-dimensional 1H nuclear magnetic resonance spectroscopy has established the existence of two conformations for the folded protein in solution. Well-resolved major and minor resonances in a ratio of 3:1 are observed throughout the 1H NMR spectrum. Two-dimensional exchange experiments show that the major and minor species are related by an equilibrium process. Analysis of short proton-proton distances along the peptide backbone, identified by two-dimensional nuclear Overhauser effect spectroscopy, provides unambiguous evidence that the two forms of the folded protein differ only in the isomerization state of the peptide bond between Gly-42 and Pro-43. Cis-trans isomerism of Pro-43 is thereby directly identified as the cause of multiple conformations for the folded protein in solution. In addition, when Pro-43 is mutated to a glycine residue there is no indication of multiple conformations. These results provide evidence for the possibility of conformational heterogeneity in the native state of globular proteins. PMID:2928325

  13. Multiplexed dual second-dimension column comprehensive two-dimensional gas chromatography (GC × 2GC) using thermal modulation and contra-directional second-dimension columns.

    PubMed

    Savareear, Benjamin; Shellie, Robert A

    2013-11-25

    A multiplexed dual-secondary column comprehensive two-dimensional gas chromatography approach (GC×2GC) designed for complex sample analysis is introduced. The approach splits the first-dimension column effluent into two second-dimension columns with different stationary phases, and recombines the two streams into one detector post-separation. The approach produces two single two-dimensional chromatograms for each injection. Careful manipulation of thermal modulator timing parameters combined with a novel contra-directional modulation regime facilitates this approach. A selection of 34 laboratory reference compounds containing n-alkanes, alcohols, aromatic hydrocarbons, ketones, esters and halogenated hydrocarbons were analysed to demonstrate the approach. The dual two-dimensional chromatogram from this single detector system provides complementary information due to the unique selectivity of the three separation columns. The results of this proof-of-principle investigation provide significant impetus for further development of GC×2GC-MS methodology. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Direct Comparisons of the Morphology, Migration, Cell Adhesions, and Actin Cytoskeleton of Fibroblasts in Four Different Three-Dimensional Extracellular Matrices

    PubMed Central

    Hakkinen, Kirsi M.; Harunaga, Jill S.; Doyle, Andrew D.

    2011-01-01

    Interactions between cells and the extracellular matrix are at the core of tissue engineering and biology. However, most studies of these interactions have used traditional two-dimensional (2D) tissue culture, which is less physiological than three-dimensional (3D) tissue culture. In this study, we compared cell behavior in four types of commonly used extracellular matrix under 2D and 3D conditions. Specifically, we quantified parameters of cell adhesion and migration by human foreskin fibroblasts in cell-derived matrix or hydrogels of collagen type I, fibrin, or basement membrane extract (BME). Fibroblasts in 3D were more spindle shaped with fewer lateral protrusions and substantially reduced actin stress fibers than on 2D matrices; cells failed to spread in 3D BME. Cell–matrix adhesion structures were detected in all matrices. Although the shapes of these cell adhesions differed, the total area per cell occupied by cell–matrix adhesions in 2D and 3D was nearly identical. Fibroblasts migrated most rapidly in cell-derived 3D matrix and collagen and migrated minimally in BME, with highest migration directionality in cell-derived matrix. This identification of quantitative differences in cellular responses to different matrix composition and dimensionality should help guide the development of customized 3D tissue culture and matrix scaffolds for tissue engineering. PMID:20929283

  15. Magnetron sputtering based direct fabrication of three dimensional CdTe hierarchical nanotrees exhibiting stable superhydrophobic property

    NASA Astrophysics Data System (ADS)

    Luo, Bingwei; Deng, Yuan; Wang, Yao; Shi, Yongming; Cao, Lili; Zhu, Wei

    2013-09-01

    Three dimensional CdTe hierarchical nanotrees are initially prepared by a simple one-step magnetron sputtering method without any templates or additives. The CdTe hierarchical nanotrees are constructed by the spear-like vertical trunks and horizontal branches with the diameters of about 100 nm at bottom and became cuspidal on the top. The particular nanostructure imparts these materials superhydrophobic property, and this property can be preserved after placing in air for 90 days, and is stable even after the ultraviolet light and X-ray irradiation, respectively. This study provides a simple strategy to achieve superhydrophobic properties for CdTe materials at lower temperature, which opens a new potential for CdTe solar cell with self-cleaning property.

  16. Three-dimensional, sharp-tipped electrodes concentrate applied fields to enable direct electrical release of intact biomarkers from cells.

    PubMed

    Poudineh, Mahla; Mohamadi, Reza M; Sage, Andrew; Mahmoudian, Laili; Sargent, Edward H; Kelley, Shana O

    2014-05-21

    Biomarkers such as proteins and nucleic acids released from human cells, bacteria, and viruses offer a wealth of information pertinent to diagnosis and treatment ranging from cancer to infectious disease. The release of these molecules from within cells is a crucial step in biomarker analysis. Here we show that purely electric-field-driven lysis can be achieved, inline, within a microfluidic channel; that it can produce highly efficient lysis and biomarker release; and, further, that it can do so with minimal degradation of the released biomarkers. Central to this new technology is the use of three-dimensional sharp-tipped electrodes (3DSTEs) in lysis, which we prove using experiment and finite-element modeling produce the electric field concentration necessary for efficient cell wall rupture.

  17. Micro-fabrication by laser radiation forces: a direct route to reversible free-standing three-dimensional structures.

    PubMed

    Athanasekos, Loukas; Vasileiadis, Miltiadis; Mantzaridis, Christos; Karoutsos, Vagelis C; Koutselas, Ioannis; Pispas, Stergios; Vainos, Nikolaos A

    2012-10-22

    The origins and first demonstration of structurally stable solids formed by use of radiation forces are presented. By experimentally proving that radiation forces can indeed produce stable solid material forms, a novel method enabling two- and three-dimensional (2d and 3d) microfabrication is introduced: An optical, non-contact single-step physical operation, reversible with respect to materials nature, based on the sole use of radiation forces. The present innovation is elucidated by the formation of polyisoprene and polybutadiene micro-solids, as well as plasmonic and fluorescent hybrids, respectively comprising Au nanoparticles and CdS quantum dots, together with novel concepts of polymeric fiber-drawing by radiation forces.

  18. Three-dimensional direct numerical simulations of co/counter-current vertical gas-Liquid annular flows

    NASA Astrophysics Data System (ADS)

    Farhaoui, Asma; Kahouadji, Lyes; Chergui, Jalel; Juric, Damir; Shin, Seungwon; Craster, Richard; Matar, Omar

    2016-11-01

    We carry out three-dimensional numerical simulations of co/counter current Gas-Liquid annular flows using the parallel code, BLUE, based on a projection method for the resolution of the Navier-Stokes equations and a hybrid Front-Tracking/Level-Set method for the interface advection. Gas-Liquid annular flows and falling films in a pipe are present in a broad range of industrial processes. This configuration consists of an important multiphase flow regime where the liquid occupies the area adjacent to the internal circumference of the pipe and the gas flows in the pipe core. Experimentally, four distinctive flow regimes were identified ('dual-wave', 'thick ripple', 'disturbance wave' and 'regular wave' regimes), that we attempt to simulate. In order to visualize these different regimes, various liquid (water) and gas (air) flow-rates are investigated. EPSRC UK Programme Grant EP/K003976/1.

  19. Direct visualization of a two-dimensional topological insulator in the single-layer 1 T'-WT e2

    NASA Astrophysics Data System (ADS)

    Jia, Zhen-Yu; Song, Ye-Heng; Li, Xiang-Bing; Ran, Kejing; Lu, Pengchao; Zheng, Hui-Jun; Zhu, Xin-Yang; Shi, Zhi-Qiang; Sun, Jian; Wen, Jinsheng; Xing, Dingyu; Li, Shao-Chun

    2017-07-01

    We have grown nearly freestanding single-layer 1 T'-WT e2 on graphitized 6 H -SiC(0001) by using molecular beam epitaxy (MBE), and characterized its electronic structure with scanning tunneling microscopy/spectroscopy (STM/STS). The existence of topological edge states at the periphery of single-layer WT e2 islands was confirmed. Surprisingly, a bulk band gap at the Fermi level and insulating behaviors were also found in single-layer WT e2 at low temperature, which are likely associated with an incommensurate charge order transition. The realization of two-dimensional topological insulators (2D TIs) in single-layer transition-metal dichalcogenide provides a promising platform for further exploration of the 2D TIs' physics and related applications.

  20. Three-dimensional motion aftereffects reveal distinct direction-selective mechanisms for binocular processing of motion through depth

    PubMed Central

    Czuba, Thaddeus B.; Rokers, Bas; Guillet, Kyle; Huk, Alexander C.; Cormack, Lawrence K.

    2013-01-01

    Motion aftereffects are historically considered evidence for neuronal populations tuned to specific directions of motion. Despite a wealth of motion aftereffect studies investigating 2D (frontoparallel) motion mechanisms, there is a remarkable dearth of psychophysical evidence for neuronal populations selective for the direction of motion through depth (i.e., tuned to 3D motion). We compared the effects of prolonged viewing of unidirectional motion under dichoptic and monocular conditions and found large 3D motion aftereffects that could not be explained by simple inheritance of 2D monocular aftereffects. These results (1) demonstrate the existence of neurons tuned to 3D motion as distinct from monocular 2D mechanisms, (2) show that distinct 3D direction selectivity arises from both interocular velocity differences and changing disparities over time, and (3) provide a straightforward psychophysical tool for further probing 3D motion mechanisms. PMID:21945967

  1. Three-dimensional optical micro-angiography maps directional blood perfusion deep within microcirculation tissue beds in vivo

    NASA Astrophysics Data System (ADS)

    Wang, Ruikang K.

    2007-12-01

    Optical micro-angiography (OMAG) is a recently developed method of imaging localized blood perfusion at capillary level resolution within microcirculatory beds. This paper reports that the OMAG is capable of directional blood perfusion mapping in vivo. This is achieved simply by translating the mirror located in the reference arm back and forth while 3D imaging is performed. The mirror which moves toward the incident beam gives the blood perfusion that flows away from the beam direction and vice versa. The approach is experimentally demonstrated by imaging of a flow phantom and then cerebro-vascular perfusion of a live mouse with cranium intact.

  2. A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.; Fleming, Graham R.

    2015-09-01

    Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

  3. A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

    PubMed

    Lewis, Nicholas H C; Dong, Hui; Oliver, Thomas A A; Fleming, Graham R

    2015-09-28

    Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

  4. A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

    SciTech Connect

    Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.; Fleming, Graham R.

    2015-09-28

    Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

  5. The role of minerals in the thermal alteration of organic matter--IV. Generation of n-alkanes, acyclic isoprenoids, and alkenes in laboratory experiments.

    PubMed

    Huizinga, B J; Tannenbaum, E; Kaplan, I R

    1987-01-01

    A series of pyrolysis experiments, utilizing two different immature oil-prone kerogens ("type I": Green River Formation kerogen; "Type II": Monterey Formation kerogen) mixed with common sedimentary minerals (calcite, illite, or Na-montmorillonite), was conducted to study the effects of minerals on the generation of n-alkanes, acyclic isoprenoids, and alkenes during laboratory-simulated catagenesis of kerogen. The influence of clay minerals on the aliphatic hydrocarbons is critically dependent on the water concentration during laboratory thermal maturation. Under extremely low contents of water (i.e., dry pyrolysis, where only pyrolysate water is present), C12(+) -range n-alkanes and acyclic isoprenoids are mostly destroyed by montmorillonite but undergo only minor alteration with illite. Both clay minerals significantly reduce alkene formation during dry pyrolysis. Under hydrous conditions (mineral/water = 2:1), the effects of the clay minerals are substantially reduced. In addition, the dry pyrolysis experiments show that illite and montmorillonite preferentially retain large amounts of the polar constituents of bitumen, but not n-alkanes or acyclic isoprenoids. Therefore, bitumen fractionation according to polarity differences occurs in the presence of these clay minerals. By this process, n-alkanes and acyclic isoprenoids are concentrated in the bitumen fraction that is not strongly adsorbed on the clay matrices. The extent of these concentrations effects is greatly diminished during hydrous pyrolysis. In contrast, calcite has no significant influence on the thermal evolution of the hydrocarbons. In addition, calcite is incapable of retaining bitumen. Therefore, the fractionation of n-alkanes or acyclic isoprenoids relative to the polar constituents of bitumen is insignificant in the presence of calcite.

  6. Synthesis, spectroscopic characterization and crystal structure of novel NNNN-donor μ-bis(bidentate) tetraaza acyclic Schiff base ligands.

    PubMed

    Habibi, Mohammad Hossein; Shojaee, Elahe; Nichol, Gary S

    2012-12-01

    Novel NNNN-donor μ-bis(bidentate) tetraaza acyclic Schiff base ligands with different substituents (CF(3), N(CH(3))(2) or OH groups) were synthesized by the condensation reaction of triethylenetetramine with 4-substituted benzaldehydes. Triethylenetetramine tris(4-trifluoromethylbenzylidene) (TTFMB), triethylenetetramine tris(4-dimethylaminobenzylidene) (TTDMB) and triethylenetetramine tris(2,4-dihydroxybenzylidene) (TTDHB) were formed as N(4) donor ligands. The formation of a five-membered imidazolidine ring from the ethylenediamine backbone as a spacer-cumbridging unit gives rise to a new type of imidazolidine ligand. The structure of the TTFMB and TTDMB were determined by single crystal X-ray crystallography. The synthesized ligands have been characterized on the basis of the results of cyclic voltammetry (CV) and spectroscopic studies viz. FT-IR spectroscopy (FT-IR), mass spectroscopy (MS) and UV-Vis spectroscopy (UV-Vis). Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Selective sorption of alkali-metal cations by carboxylic acid resins containing acyclic or cyclic polyether units

    SciTech Connect

    Hayashita, Takashi; Goo, Mija; Lee, Jong Chan; Kim, Jong Seung; Krzykawski, J.; Bartsch, R.A. )

    1990-11-01

    Novel ion-exchange resins have been prepared by condensation polymerization with formaldehyde in formic acid of three polyether carboxylic acids which possess two benzo group substituents. The selectivities and efficiencies of competitive alkali-metal cation sorption from aqueous solutions by these polyether carboxylic acid resins are strongly influenced by (1) the pH of the aqueous solution, (2) the acyclic or cyclic nature of the polyether unit, and (3) the conformational positioning of the carboxylic acid group in the resins derived from cyclic polyether (crown ether) compounds. Good sorption selectivity for Na{sup +} was observed for dibenzo-16-crown-5 resin 3 in which the pendant carboxylic acid group is oriented over the polyether cavity. Resin 3 was utilized as a stationary phase for selective column concentration of Na{sup +} from dilute aqueous solution.

  8. Identification and geochemical significance of cyclic di-and trisulphides with linear and acyclic isoprenoid carbon skeletons in immature sediments

    NASA Astrophysics Data System (ADS)

    Kohnen, Math E. L.; Sinninghe Damsté, Jaap S.; ten Haven, H. L.; Van Dalen, A. C. Kock; Schouten, Stefan; De Leeuw, Jan W.

    1991-12-01

    Homologous series (C 15-C 24) of novel 3- n-alkyl-1,2-dithianes and 3- n-alkyl-6-methyl-1,2-di-thianes have been identified in immature sediments. The identification of these compounds was based on comparison of mass spectra and Chromatographie data with those of synthesized 3-methyl-6-tridecyll, 2-dithiane. In addition, 4-methyl-3-(3,7,11-trimethyldodecyl)-1,2-dithiane, 4-(4,8,12-trimethyltridecyl)-1,2-dithiane, 5-methyl-4-(3,7,11-trimethyldodecyl)-1,2,3-trithiepane, and a 1,2-dithiane possessing a pentakishomohopane carbon skeleton were tentatively assigned on the basis of mass spectral characteristics, selective chemolysis, and desulphurisation. The occurrence of these cyclic di-and trisulphides with linear, acyclic isoprenoid and hopanoid carbon skeletons in thermally immature sediments indicates that inorganic polysulphides are incorporated into functionalised lipids during the early stages of diagenesis.

  9. Design, synthesis and evaluation of a series of acyclic fleximer nucleoside analogues with anti-coronavirus activity.

    PubMed

    Peters, Hannah L; Jochmans, Dirk; de Wilde, Adriaan H; Posthuma, Clara C; Snijder, Eric J; Neyts, Johan; Seley-Radtke, Katherine L

    2015-08-01

    A series of doubly flexible nucleoside analogues were designed based on the acyclic sugar scaffold of acyclovir and the flex-base moiety found in the fleximers. The target compounds were evaluated for their antiviral potential and found to inhibit several coronaviruses. Significantly, compound 2 displayed selective antiviral activity (CC50 >3× EC50) towards human coronavirus (HCoV)-NL63 and Middle East respiratory syndrome-coronavirus, but not severe acute respiratory syndrome-coronavirus. In the case of HCoV-NL63 the activity was highly promising with an EC50 <10 μM and a CC50 >100 μM. As such, these doubly flexible nucleoside analogues are viewed as a novel new class of drug candidates with potential for potent inhibition of coronaviruses.

  10. Enantioselective Lewis acid-catalyzed Mukaiyama-Michael reactions of acyclic enones. Catalysis by allo-threonine-derived oxazaborolidinones.

    PubMed

    Wang, Xiaowei; Adachi, Shinya; Iwai, Hiroyoshi; Takatsuki, Hiroshi; Fujita, Katsuhiro; Kubo, Mikako; Oku, Akira; Harada, Toshiro

    2003-12-26

    allo-Threonine-derived O-aroyl-B-phenyl-N-tosyl-1,3,2-oxazaborolidin-5-ones 1g,n catalyze the asymmetric Mukaiyama-Michael reaction of acyclic enones with a trimethylsilyl ketene S,O-acetal in high enantioselectivity. A range of alkenyl methyl ketones is successfully employed as Michael acceptors affording ee values of 85-90% by using 10 mol % of the catalyst. The use of 2,6-diisopropylphenol and tert-butyl methyl ether as additives is found to be essential to achieve high enantioselectivity in these reactions. The effects of the additives are discussed in terms of the retardation of an Si(+)-catalyzed racemic pathway, which seriously deteriorates the enantioselectivity of asymmetric Mukaiyama-Michael reactions. A working model for asymmetric induction is proposed based on correlation between catalyst structures and enantioselectivities.

  11. A new technique for studying directional cell migration in a hydrogel-based three-dimensional matrix for tissue engineering model systems.

    PubMed

    Topman, Gil; Shoham, Naama; Sharabani-Yosef, Orna; Lin, Feng-Huei; Gefen, Amit

    2013-08-01

    Cell migration has a key role in biological processes, e.g. malignancy, wound healing, immune response and morphogenesis. Studying migration and factors that influence it is beneficial, e.g. for developing drugs to suppress metastasis, heal wounds faster or enhance the response to infection. Though the majority of the literature describes two-dimensional (2D) migration studies in culture dishes, a more realistic approach is to study migration in three-dimensional (3D) constructs. However, simple-to-implement, straight-forward standardized quantitative techniques for analysis of migration rates of cell colonies in 3D are still required in the field. Here, we describe a new model system for quantifying directional migration of colonies in a hyaluronic acid (oxi-HA) and adipic acid dihydrazide (ADH) hydrogel-based 3D matrix. We further demonstrate that our previously reported image processing technique for measuring migration in 2D (Topman et al., 2011, 2012) is extendable for analyzing the rates of migration of cells that directionally migrate in the hydrogel and are fluorescently stained with a 4',6-diamidino-2-phenylindole (DAPI) nuclear stain. Together, the present experimental setup and image processing algorithm provide a standard test bench for measuring migration rates in a fully automated, robust assay which is useful for high-throughput screening in large-scale drug evaluations, where effects on migration in a 3D matrix are sought.

  12. Two-dimensional direct-current resistivity survey to supplement borehole data in ground-water models of the former Blaine Naval Ammunition Depot, Hastings, Nebraska, September 2003

    USGS Publications Warehouse

    Kress, Wade H.; Ball, Lyndsay B.; Teeple, Andrew; Turco, Michael J.

    2006-01-01

    The former Blaine Naval Ammunition Depot located immediately southeast of Hastings, Nebraska, was an ammunition facility during World War II and the Korean Conflict. Waste-management practices during operation and decommissioning of the former Depot resulted in soil and ground-water contamination. Ground-water models have been used by the U.S. Army Corps of Engineers to provide information on the fate and transport of contaminants on the former Depot site. During September 2003, the U.S. Geological Survey, in cooperation with the U.S. Army Corps of Engineers, Kansas City District, conducted a pilot study to collect two-dimensional direct-current resistivity data on the site along six profiles near existing monitoring wells. The inversion results of field data from five of the six two-dimensional direct-current resistivity profiles display distinct electrical stratigraphy consistent with three resistivity units (low resistivity, high resistivity, and low resistivity). These three resistivity units correlate with rock-stratigraphic or hydrogeologic units described prior to this study. To interpret the resistivity profiles, additional data extending through the lower confining unit into the underlying Niobrara Formation could be used with the existing data to construct forward models for data analysis and interpretation.

  13. The Use of Total Human Bone Marrow Fraction in a Direct Three-Dimensional Expansion Approach for Bone Tissue Engineering Applications: Focus on Angiogenesis and Osteogenesis

    PubMed Central

    Oliveira, Hugo; Catros, Sylvain; Siadous, Robin; Derkaoui, Sidi-Mohammed; Bareille, Reine; Letourneur, Didier; Amédée, Joëlle

    2015-01-01

    Current approaches in bone tissue engineering have shown limited success, mostly owing to insufficient vascularization of the construct. A common approach consists of co-culture of endothelial cells and osteoblastic cells. This strategy uses cells from different sources and differentiation states, thus increasing the complexity upstream of a clinical application. The source of reparative cells is paramount for the success of bone tissue engineering applications. In this context, stem cells obtained from human bone marrow hold much promise. Here, we analyzed the potential of human whole bone marrow cells directly expanded in a three-dimensional (3D) polymer matrix and focused on the further characterization of this heterogeneous population and on their ability to promote angiogenesis and osteogenesis, both in vitro and in vivo, in a subcutaneous model. Cellular aggregates were formed within 24 h and over the 12-day culture period expressed endothelial and bone-specific markers and a specific junctional protein. Ectopic implantation of the tissue-engineered constructs revealed osteoid tissue and vessel formation both at the periphery and within the implant. This work sheds light on the potential clinical use of human whole bone marrow for bone regeneration strategies, focusing on a simplified approach to develop a direct 3D culture without two-dimensional isolation or expansion. PMID:25333855

  14. A Unified Direct-Inverse Procedure for Two-Dimensional Boundary Layers Using Spline/Finite Difference Discretization.

    DTIC Science & Technology

    1987-02-01

    pt. 50 20 7 Potential 3b I-A 3 pt. 47 20 7 Potential 3c D 3 pt. 40 20 7 Hiemenz Fit 3d I-A 3 pt. 36 20 7 Hiemenz Fit V _ _ _ _ _ _ _ 4...the Hiemenz polynomial fit of the edge velocity for viscous flow. This case is included to test the ability of the direct and inverse methods to

  15. Comment on ``Simulation of a two-dimensional Rayleigh-Benard system using the direct simulation Monte Carlo method``

    SciTech Connect

    Garcia, A.L.; Baras, F.; Mansour, M.M.

    1994-06-30

    In a recent paper, Watanabe, {ital et. al.} used direct simulation Monte Carlo to study Rayleigh-B{acute e}nard convection. They reported that, using stress-free boundary conditions, the onset of convection in the simulation occurred at a Rayleigh number much larger than the critical Rayleigh number predicted by linear stability analysis. We show that the source of their discrepancy is their failure to include the temperature jump effect in the calculation of Rayleigh number.

  16. Toward Metal-Organic Framework-Based Solar Cells: Enhancing Directional Exciton Transport by Collapsing Three-Dimensional Film Structures.

    PubMed

    Goswami, Subhadip; Ma, Lin; Martinson, Alex B F; Wasielewski, Michael R; Farha, Omar K; Hupp, Joseph T

    2016-11-16

    Owing to their ability to act as light-harvesting scaffolds, porphyrin-containing metal-organic frameworks (MOFs) are in the forefront of research on the application of highly ordered molecular materials to problems in solar-energy conversion. In this work, solvent-assisted linker exchange (SALE) is performed on a pillared paddlewheel porphyrin containing MOF thin film to collapse a 3D framework to a 2D framework. The change in dimensionality of the framework is confirmed by a decrease in the film thickness, the magnitude of which is in agreement with crystallographic parameters for related bulk materials. Furthermore, NMR spectroscopy performed on the digested sample suggests a similar change in geometry is achieved in bulk MOF samples. The decreased distance between the porphyrin chromophores in the 2D MOF film compared to the 3D film results in enhanced energy transfer through the film. The extent of energy transport was probed by assembling MOF thin film where the outermost layers are palladium porphyrin (P2) units, which act as energy traps and fluorescence quenchers. Steady-state emission spectroscopy together with time-resolved emission spectroscopy indicates that excitons can travel through about 9-11 layers (porphyrin layers) in 2D films, whereas in 3D films energy transfer occurs through no more than about 6-8 layers. The results are difficult to understand if only changes in MOF interlayer spacing are considered but become much more understandable if dipole-dipole coupling distances are considered.

  17. Toward Metal–Organic Framework-Based Solar Cells: Enhancing Directional Exciton Transport by Collapsing Three-Dimensional Film Structures

    SciTech Connect

    Goswami, Subhadip; Ma, Lin; Martinson, Alex B. F.; Wasielewski, Michael R.; Farha, Omar K.; Hupp, Joseph T.

    2016-11-16

    Owing to their ability to act as light-harvesting scaffolds, porphyrin-containing metal-organic frameworks (MOFs) are in the forefront of research on the application of highly ordered molecular materials to problems in solar-energy conversion. In this work, solvent-assisted linker exchange (SALE) is performed on a pillared paddlewheel porphyrin containing MOF thin film to collapse a 3D framework to a 2D framework. The change in dimensionality of the framework is confirmed by a decrease in the film thickness, the magnitude of which is in agreement with crystallographic parameters for related bulk materials. Furthermore, NMR spectroscopy performed on the digested sample suggests a similar change in geometry is achieved in bulk MOF samples. The decreased distance between the porphyrin chromophores in the 2D MOF film compared to the 3D film results in enhanced energy transfer through the film. The extent of energy transport was probed by assembling MOF thin film where the outermost layers are palladium porphyrin (P2) units, which act as energy traps and fluorescence quenchers. Steady-state emission spectroscopy together with time-resolved emission spectroscopy indicates that excitons can travel through about 9-11 layers (porphyrin layers) in 2D films, whereas in 3D films energy transfer occurs through no more than about 6-8 layers. The results are difficult to understand if only changes in MOF interlayer spacing are considered but become much more understandable if dipole-dipole coupling distances are considered.

  18. Three-dimensional system enabling the maintenance and directed differentiation of pluripotent stem cells under defined conditions

    PubMed Central

    Zujur, Denise; Kanke, Kosuke; Lichtler, Alexander C.; Hojo, Hironori; Chung, Ung-il; Ohba, Shinsuke

    2017-01-01

    The development of in vitro models for the maintenance and differentiation of pluripotent stem cells (PSCs) is an active area of stem cell research. The strategies used so far are based mainly on two-dimensional (2D) cultures, in which cellular phenotypes are regulated by soluble factors. We show that a 3D culture system with atelocollagen porous scaffolds can significantly improve the outcome of the current platforms intended for the maintenance and lineage specification of mouse PSCs (mPSCs). Unlike 2D conditions, the 3D conditions maintained the undifferentiated state of mouse embryonic stem cells (mESCs) without exogenous stimulation and also supported endoderm, mesoderm, and ectoderm differentiation of mESCs under serum-free conditions. Moreover, 3D mPSC–derived mesodermal cells showed accelerated osteogenic differentiation, giving rise to functional osteoblast-osteocyte populations within calcified structures. The present strategy offers a 3D platform suitable for the formation of organoids that mimic in vivo organs containing various cell types, and it may be adaptable to the generation of ectoderm-, mesoderm-, and endoderm-derived tissues when combined with appropriate differentiation treatments. PMID:28508073

  19. Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions.

    PubMed

    Fraley, Stephanie I; Wu, Pei-Hsun; He, Lijuan; Feng, Yunfeng; Krisnamurthy, Ranjini; Longmore, Gregory D; Wirtz, Denis

    2015-10-01

    Multiple attributes of the three-dimensional (3D) extracellular matrix (ECM) have been independently implicated as regulators of cell motility, including pore size, crosslink density, structural organization, and stiffness. However, these parameters cannot be independently varied within a complex 3D ECM protein network. We present an integrated, quantitative study of these parameters across a broad range of complex matrix configurations using self-assembling 3D collagen and show how each parameter relates to the others and to cell motility. Increasing collagen density resulted in a decrease and then an increase in both pore size and fiber alignment, which both correlated significantly with cell motility but not bulk matrix stiffness within the range tested. However, using the crosslinking enzyme Transglutaminase II to alter microstructure independently of density revealed that motility is most significantly predicted by fiber alignment. Cellular protrusion rate, protrusion orientation, speed of migration, and invasion distance showed coupled biphasic responses to increasing collagen density not predicted by 2D models or by stiffness, but instead by fiber alignment. The requirement of matrix metalloproteinase (MMP) activity was also observed to depend on microstructure, and a threshold of MMP utility was identified. Our results suggest that fiber topography guides protrusions and thereby MMP activity and motility.

  20. Three-dimensional active microcatheter combining shape memory alloy actuators and direct-drive tubular electrostatic micromotors

    NASA Astrophysics Data System (ADS)

    Bourbon, Gilles; Minotti, Patrice; Langlet, Philippe; Masuzawa, Takahisa; Fujita, Hiroyuki

    1998-09-01

    This paper investigates 3D active microcatheters having millimeter size outer diameters. The proposed architectures combine mechanical cells which involve new direct-drive tubular electrostatic micromotors and conventional shape memory alloy actuators. The tubular electrostatic motors are actuated by silicon surface micromachined flexible stators. The polysilicon stators integrate up to several thousands of direct-drive electrostatic microactuators. However, they have been designed in order to provide a gap compensation at the rotor/motor frame interface. Multiple stator/rotor contact interactions involve a significant speed reduction that allow a large torque amplification, as a consequence of the torque/speed duality. These mechanical interactions allow the rotor to be moved with respect to the motor frame through direct-drive contact mechanisms, therefore allowing high torque/low speed characteristics to be performed. In such a way to get a 3D behavior, the microcatheter combines tubular electrostatic motors having flexible rotors. The rotors integrate Ti-Ni shape memory alloy wires which actuate a 2D bending motion on each mechanical cell. The 3D global behavior of the catheter is provided by the relative rotation of each cell, with respect to the other ones. The proposed architecture is particularly convenient with respect to the electric power supply which is, usually, the major problem in designing active microcatheters. A (Phi) 1 mm 3D active catheter is given as an example, but external diameters less than one millimeter can be easily expected, opening therefore numerous applications in the near future.

  1. Laser-guided direct writing for three-dimensional tissue engineering: Analysis and application of radiation forces

    NASA Astrophysics Data System (ADS)

    Nahmias, Yaakov Koby

    Tissue Engineering aims for the creation of functional tissues or organs using a combination of biomaterials and living cells. Artificial tissues can be implanted in patients to restore tissue function that was lost due to trauma, disease, or genetic disorder. Tissue equivalents may also be used to screen the effects of drugs and toxins, reducing the use of animals in research. One of the principle limitations to the size of engineered tissue is oxygen and nutrient transport. Lacking their own vascular bed, cells embedded in the engineered tissue will consume all available oxygen within hours while out branching blood vessels will take days to vascularize the implanted tissue. Establishing capillaries within the tissue prior to implantation can potentially eliminate this limitation. One approach to establishing capillaries within the tissue is to directly write endothelial cells with micrometer accuracy as it is being built. The patterned endothelial cells will then self-assemble into vascular structures within the engineering tissue. The cell patterning technique known as laser-guided direct writing can confine multiple cells in a laser beam and deposit them as a steady stream on any non-absorbing surface with micrometer scale accuracy. By applying the generalized Lorenz-Mie theory for light scattering on laser-guided direct writing we were able to accurately predict the behavior of with various cells and particles in the focused laser. In addition, two dimensionless parameters were identified for general radiation-force based system design. Using laser-guided direct writing we were able to direct the assembly of endothelial vascular structures with micrometer accuracy in two and three dimensions. The patterned vascular structures provided the backbone for subsequent in vitro liver morphogenesis. Our studies show that hepatocytes migrate toward and adhere to endothelial vascular structures in response to endothelial-secreted hepatocyte growth factor (HGF). Our

  2. Theory of substrate-directed heat dissipation for single-layer graphene and other two-dimensional crystals

    NASA Astrophysics Data System (ADS)

    Ong, Zhun-Yong; Cai, Yongqing; Zhang, Gang

    2016-10-01

    We present a theory of the phononic thermal (Kapitza) resistance at the interface between graphene or another single-layer two-dimensional (2D) crystal (e.g., MoS2) and a flat substrate, based on a modified version of the cross-plane heat transfer model by Persson, Volokitin, and Ueba [J. Phys.: Condens. Matter 23, 045009 (2011), 10.1088/0953-8984/23/4/045009]. We show how intrinsic flexural phonon damping is necessary for obtaining a finite Kapitza resistance and also generalize the theory to encased single-layer 2D crystals with a superstrate. We illustrate our model by computing the thermal boundary conductance (TBC) for bare and SiO2-encased single-layer graphene and MoS2 on a SiO2 substrate, using input parameters from first-principles calculation. The estimated room temperatures TBC for bare (encased) graphene and MoS2 on SiO2 are 34.6 (105) and 3.10 (5.07) MWK -1m-2 , respectively. The theory predicts the existence of a phonon frequency crossover point, below which the low-frequency flexural phonons in the bare 2D crystal do not dissipate energy efficiently to the substrate. We explain within the framework of our theory how the encasement of graphene with a top SiO2 layer introduces new low-frequency transmission channels, which significantly reduce the graphene-substrate Kapitza resistance. We emphasize that the distinction between bare and encased 2D crystals must be made in the analysis of cross-plane heat dissipation to the substrate.

  3. Directing three-dimensional multicellular morphogenesis by self-organization of vascular mesenchymal cells in hyaluronic acid hydrogels.

    PubMed

    Zhu, Xiaolu; Gojgini, Shiva; Chen, Ting-Hsuan; Fei, Peng; Dong, Siyan; Ho, Chih-Ming; Segura, Tatiana

    2017-01-01

    Physical scaffolds are useful for supporting cells to form three-dimensional (3D) tissue. However, it is non-trivial to develop a scheme that can robustly guide cells to self-organize into a tissue with the desired 3D spatial structures. To achieve this goal, the rational regulation of cellular self-organization in 3D extracellular matrix (ECM) such as hydrogel is needed. In this study, we integrated the Turing reaction-diffusion mechanism with the self-organization process of cells and produced multicellular 3D structures with the desired configurations in a rational manner. By optimizing the components of the hydrogel and applying exogenous morphogens, a variety of multicellular 3D architectures composed of multipotent vascular mesenchymal cells (VMCs) were formed inside hyaluronic acid (HA) hydrogels. These 3D architectures could mimic the features of trabecular bones and multicellular nodules. Based on the Turing reaction-diffusion instability of morphogens and cells, a theoretical model was proposed to predict the variations observed in 3D multicellular structures in response to exogenous factors. It enabled the feasibility to obtain diverse types of 3D multicellular structures by addition of Noggin and/or BMP2. The morphological consistency between the simulation prediction and experimental results probably revealed a Turing-type mechanism underlying the 3D self-organization of VMCs in HA hydrogels. Our study has provided new ways to create a variety of self-organized 3D multicellular architectures for regenerating biomaterial and tissues in a Turing mechanism-based approach.

  4. Direct Fabrication of Functional Ultrathin Single-Crystal Nanowires from Quasi-One-Dimensional van der Waals Crystals.

    PubMed

    Liu, Xue; Liu, Jinyu; Antipina, Liubov Yu; Hu, Jin; Yue, Chunlei; Sanchez, Ana M; Sorokin, Pavel B; Mao, Zhiqiang; Wei, Jiang

    2016-10-12

    Micromechanical exfoliation of two-dimensional (2D) van der Waals materials has triggered an explosive interest in 2D material research. The extension of this idea to 1D van der Waals materials, possibly opening a new arena for 1D material research, has not yet been realized. In this paper, we demonstrate that 1D nanowire with sizes as small as six molecular ribbons, can be readily achieved in the Ta2(Pd or Pt)3Se8 system by simple micromechanical exfoliation. Exfoliated Ta2Pd3Se8 nanowires are n-type semiconductors, whereas isostructural Ta2Pt3Se8 nanowires are p-type semiconductors. Both types of nanowires show excellent electrical switching performance as the channel material for a field-effect transistor. Low-temperature transport measurement reveals a defect level inherent to Ta2Pd3Se8 nanowires, which enables the observed electrical switching behavior at high temperature (above 140 K). A functional logic gate consisting of both n-type Ta2Pd3Se8 and p-type Ta2Pt3Se8 field-effect transistors has also been successfully achieved. By taking advantage of the high crystal quality derived from the parent van der Waals bulk compound, our findings about the exfoliated Ta2(Pd or Pt)3Se8 nanowires demonstrate a new pathway to access single-crystal 1D nanostructures for the study of their fundamental properties and the exploration of their applications in electronics, optoelectronics, and energy harvesting.

  5. Detection and extraction of orientation-and-scale-dependent information from two-dimensional GPR data with tuneable directional wavelet filters

    NASA Astrophysics Data System (ADS)

    Tzanis, Andreas

    2013-02-01

    The Ground Probing Radar (GPR) is a valuable tool for near surface geological, geotechnical, engineering, environmental, archaeological and other work. GPR images of the subsurface frequently contain geometric information (constant or variable-dip reflections) from various structures such as bedding, cracks, fractures, etc. Such features are frequently the target of the survey; however, they are usually not good reflectors and they are highly localized in time and in space. Their scale is therefore a factor significantly affecting their detectability. At the same time, the GPR method is very sensitive to broadband noise from buried small objects, electromagnetic anthropogenic activity and systemic factors, which frequently blurs the reflections from such targets. This paper introduces a method to de-noise GPR data and extract geometric information from scale-and-dip dependent structural features, based on one-dimensional B-Spline Wavelets, two-dimensional directional B-Spline Wavelet (BSW) Filters and two-dimensional Gabor Filters. A directional BSW Filter is built by sidewise arranging s identical one-dimensional wavelets of length L, tapering the s-parallel direction (span) with a suitable window function and rotating the resulting matrix to the desired orientation. The length L of the wavelet defines the temporal and spatial scale to be isolated and the span determines the length over which to smooth (spatial resolution). The Gabor Filter is generated by multiplying an elliptical Gaussian by a complex plane wave; at any orientation the temporal or spatial scale(s) to be isolated are determined by the wavelength. λ of the plane wave and the spatial resolution by the spatial aspect ratio γ, which specifies the ellipticity of the support of the Gabor function. At any orientation, both types of filter may be tuned at any frequency or spatial wavenumber by varying the length or the wavelength respectively. The filters can be applied directly to two-dimensional

  6. Directional asymmetry of the nonlinear wave phenomena in a three-dimensional granular phononic crystal under gravity.

    PubMed

    Merkel, A; Tournat, V; Gusev, V

    2014-08-01

    We report the experimental observation of the gravity-induced asymmetry for the nonlinear transformation of acoustic waves in a noncohesive granular phononic crystal. Because of the gravity, the contact precompression increases with depth inducing space variations of not only the linear and nonlinear elastic moduli but also of the acoustic wave dissipation. We show experimentally and explain theoretically that, in contrast to symmetric propagation of linear waves, the amplitude of the nonlinearly self-demodulated wave depends on whether the propagation of the waves is in the direction of the gravity or in the opposite direction. Among the observed nonlinear processes, we report frequency mixing of the two transverse-rotational modes belonging to the optical band of vibrations and propagating with negative phase velocities, which results in the excitation of a longitudinal wave belonging to the acoustic band of vibrations and propagating with positive phase velocity. We show that the measurements of the gravity-induced asymmetry in the nonlinear acoustic phenomena can be used to compare the in-depth distributions of the contact nonlinearity and of acoustic absorption.

  7. The direct-to-indirect band gap crossover in two-dimensional van der Waals Indium Selenide crystals

    PubMed Central

    Mudd, G. W.; Molas, M. R.; Chen, X.; Zólyomi, V.; Nogajewski, K.; Kudrynskyi, Z. R.; Kovalyuk, Z. D.; Yusa, G.; Makarovsky, O.; Eaves, L.; Potemski, M.; Fal’ko, V. I.; Patanè, A.

    2016-01-01

    The electronic band structure of van der Waals (vdW) layered crystals has properties that depend on the composition, thickness and stacking of the component layers. Here we use density functional theory and high field magneto-optics to investigate the metal chalcogenide InSe, a recent addition to the family of vdW layered crystals, which transforms from a direct to an indirect band gap semiconductor as the number of layers is reduced. We investigate this direct-to-indirect bandgap crossover, demonstrate a highly tuneable optical response from the near infrared to the visible spectrum with decreasing layer thickness down to 2 layers, and report quantum dot-like optical emissions distributed over a wide range of energy. Our analysis also indicates that electron and exciton effective masses are weakly dependent on the layer thickness and are significantly smaller than in other vdW crystals. These properties are unprecedented within the large family of vdW crystals and demonstrate the potential of InSe for electronic and photonic technologies. PMID:28008964

  8. The direct-to-indirect band gap crossover in two-dimensional van der Waals Indium Selenide crystals

    NASA Astrophysics Data System (ADS)

    Mudd, G. W.; Molas, M. R.; Chen, X.; Zólyomi, V.; Nogajewski, K.; Kudrynskyi, Z. R.; Kovalyuk, Z. D.; Yusa, G.; Makarovsky, O.; Eaves, L.; Potemski, M.; Fal’Ko, V. I.; Patanè, A.

    2016-12-01

    The electronic band structure of van der Waals (vdW) layered crystals has properties that depend on the composition, thickness and stacking of the component layers. Here we use density functional theory and high field magneto-optics to investigate the metal chalcogenide InSe, a recent addition to the family of vdW layered crystals, which transforms from a direct to an indirect band gap semiconductor as the number of layers is reduced. We investigate this direct-to-indirect bandgap crossover, demonstrate a highly tuneable optical response from the near infrared to the visible spectrum with decreasing layer thickness down to 2 layers, and report quantum dot-like optical emissions distributed over a wide range of energy. Our analysis also indicates that electron and exciton effective masses are weakly dependent on the layer thickness and are significantly smaller than in other vdW crystals. These properties are unprecedented within the large family of vdW crystals and demonstrate the potential of InSe for electronic and photonic technologies.

  9. Directional asymmetry of the nonlinear wave phenomena in a three-dimensional granular phononic crystal under gravity

    NASA Astrophysics Data System (ADS)

    Merkel, A.; Tournat, V.; Gusev, V.

    2014-08-01

    We report the experimental observation of the gravity-induced asymmetry for the nonlinear transformation of acoustic waves in a noncohesive granular phononic crystal. Because of the gravity, the contact precompression increases with depth inducing space variations of not only the linear and nonlinear elastic moduli but also of the acoustic wave dissipation. We show experimentally and explain theoretically that, in contrast to symmetric propagation of linear waves, the amplitude of the nonlinearly self-demodulated wave depends on whether the propagation of the waves is in the direction of the gravity or in the opposite direction. Among the observed nonlinear processes, we report frequency mixing of the two transverse-rotational modes belonging to the optical band of vibrations and propagating with negative phase velocities, which results in the excitation of a longitudinal wave belonging to the acoustic band of vibrations and propagating with positive phase velocity. We show that the measurements of the gravity-induced asymmetry in the nonlinear acoustic phenomena can be used to compare the in-depth distributions of the contact nonlinearity and of acoustic absorption.

  10. Time-multiplexed three-dimensional displays based on directional backlights with fast-switching liquid-crystal displays.

    PubMed

    Chien, Ko-Wei; Shieh, Han-Ping D

    2006-05-01

    An autostereoscopic display using a directional backlight with a fast-switching liquid-crystal (LC) display was designed and fabricated to obtain a better perception of 3D images by enhanced resolution and brightness. A grooved light guide in combination with an asymmetric focusing foil was utilized to redirect the emitting cones of light to the left and right eyes, respectively. By designing the groove structures of the focusing foil with rotation from -1.5 degrees to 1.5 degrees in the gradient and having the pitch ratio of the grooved light guide to the focusing foil of less than 3, the boundary angle then shifts from normal viewing and the moiré phenomenon can be suppressed. Cross talk of less than 6% and a LC response time of faster than 7.1 ms further improve the stereoscopic image perception. Additionally, 2D-3D compatibility is provided.

  11. An initial assessment of three-dimensional polar direct drive capsule asymmetries for implosions at the National Ignition Facility

    SciTech Connect

    Krasheninnikova, Natalia S.; Finnegan, Sean M.; Schmitt, Mark J.

    2012-01-15

    The National Ignition Facility (NIF) provides a unique opportunity to study implosion physics with nuclear yield. The use of polar direct drive (PDD) [A. M. Cok, R. S. Craxton, and P. W. McKenty, Phys. Plasmas 15, 082705 (2008)] provides a simple platform for the experimental studies without expensive optics upgrades to NIF. To determine the optimum PDD laser pointing geometry on NIF and provide a baseline for validating inertial confinement fusion codes against experiments for symmetric and asymmetric implosions, computer simulations using the 3D radiation-hydrodynamics code hydra[M. M. Marinak, R. E. Tipton, O. L. Landen, T. J. Murphy, P. Amendt, S. W. Haan, S. P. Hatchett, C. J. Keane, R. McEachern, and R. Wallace, Phys. Plasmas 3, 2070 (1996)] were preformed. The upper hemisphere of a DT-filled CH capsule was imploded by 96 NIF beams in a PDD configuration. Asymmetries in both polar and equatorial directions around the capsule were observed, with the former dominating the latter. Analysis of the simulation results indicates that the lack of symmetry in the initial power density profile (during the first 200 ps of the implosion) is a primary cause of late-time asymmetry in the implosion as well as decreased yield. By adjusting the laser pointings, the symmetry and total neutron yield were improved. Simulations with dropped quads (four of the NIF laser system's 192 beamlines) without repointing worsen the overall symmetry by a factor of 10 (with respect to rms radial variation around the capsule) and reduce neutron yield by a factor of 2. Both of these degraded implosion characteristics are restored by azimuthal repointing of the remaining quads.

  12. Three-dimensional direct numerical simulation study of conditioned moments associated with front propagation in turbulent flows

    NASA Astrophysics Data System (ADS)

    Yu, R.; Lipatnikov, A. N.; Bai, X. S.

    2014-08-01

    In order to gain further insight into (i) the use of conditioned quantities for characterizing turbulence within a premixed flame brush and (ii) the influence of front propagation on turbulent scalar transport, a 3D Direct Numerical Simulation (DNS) study of an infinitely thin front that self-propagates in statistically stationary, homogeneous, isotropic, forced turbulence was performed by numerically integrating Navier-Stokes and level set equations. While this study was motivated by issues relevant to premixed combustion, the density was assumed to be constant in order (i) to avoid the influence of the front on the flow and, therefore, to know the true turbulence characteristics as reference quantities for assessment of conditioned moments and (ii) to separate the influence of front propagation on turbulent transport from the influence of pressure gradient induced by heat release. Numerical simulations were performed for two turbulence Reynolds numbers (50 and 100) and four ratios (1, 2, 5, and 10) of the rms turbulent velocity to the front speed. Obtained results show that, first, the mean front thickness is decreased when a ratio of the rms turbulent velocity to the front speed is decreased. Second, although the gradient diffusion closure yields the right direction of turbulent scalar flux obtained in the DNS, the diffusion coefficient Dt determined using the DNS data depends on the mean progress variable. Moreover, Dt is decreased when the front speed is increased, thus, indicating that the front propagation affects turbulent scalar transport even in a constant-density case. Third, conditioned moments of the velocity field differ from counterpart mean moments, thus, disputing the use of conditioned velocity moments for characterizing turbulence when modeling premixed turbulent combustion. Fourth, computed conditioned enstrophies are close to the mean enstrophy in all studied cases, thus, suggesting the use of conditioned enstrophy for characterizing turbulence

  13. The association between environmental lead exposure with aggressive behavior, and dimensionality of direct and indirect aggression during mid-adolescence: Birth to Twenty Plus cohort.

    PubMed

    Nkomo, Palesa; Naicker, Nisha; Mathee, Angela; Galpin, Jacky; Richter, Linda M; Norris, Shane A

    2017-08-30

    Chronic lead exposure is associated with neurological ill-health including anti-social behavior such as aggressive behavior. The main aim of this study was to examine the association between lead exposure at 13years old and dimensions of aggressive behavior during mid-adolescence. The study sample included 508 males and 578 females in mid-adolescence (age 14 to 15years) from the Birth to Twenty Plus cohort in Johannesburg, South Africa. Blood samples collected at age 13years were used to measure blood lead levels. Seventeen items characterizing aggression from the Youth Self Report questionnaire were used to examine aggressive behavior. Principal Component Analysis was used to derive composite variables from the original data for aggressive behavior; and data were examined for an association between blood lead levels and dimensionality of direct and indirect aggression and disobedience during mid-adolescence. We also examined the dimensions of aggression during mid-adolescence in relation to gender and socio-demographic factors. Blood lead levels ranged from 1 to 28.1μg/dL. Seventy two percent of males and 47.7% of females in the study had blood lead levels ≥5μg/dL. There was a positive association between elevated blood lead levels and direct aggression (p<0.05). Being male was positively associated with direct aggression (p<0.001) but, negatively associated with indirect aggression (p<0.001). Maternal education and age at birth were negatively associated with direct aggression during mid-adolescence. The significant association between elevated blood lead levels and direct aggressive behavior observed in this study may shed light on a possible environmental toxicological contribution to aggressive behavior in South African youth; and most importantly the type of aggressive behavior associated to lead exposure. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Direct design of freeform surfaces and freeform imaging systems with a point-by-point three-dimensional construction-iteration method.

    PubMed

    Yang, Tong; Zhu, Jun; Wu, Xiaofei; Jin, Guofan

    2015-04-20

    In this paper, we proposed a general direct design method for three-dimensional freeform surfaces and freeform imaging systems based on a construction-iteration process. In the preliminary surfaces-construction process, the coordinates as well as the surface normals of the data points on the multiple freeform surfaces can be calculated directly considering the rays of multiple fields and different pupil coordinates. Then, an iterative process is employed to significantly improve the image quality or achieve a better mapping relationship of the light rays. Three iteration types which are normal iteration, negative feedback and successive approximation are given. The proposed construction-iteration method is applied in the design of an easy aligned, low F-number off-axis three-mirror system. The primary and tertiary mirrors can be fabricated on a single substrate and form a single element in the final system. The secondary mirror is simply a plane mirror. With this configuration, the alignment difficulty of a freeform system can be greatly reduced. After the preliminary surfaces-construction stage, the freeform surfaces in the optical system can be generated directly from an initial planar system. Then, with the iterative process, the average RMS spot diameter decreased by 75.4% compared with the system before iterations, and the maximum absolute distortion decreased by 94.2%. After further optimization with optical design software, good image quality which is closed to diffraction-limited is achieved.

  15. Three-directional motion compensation-based novel-look-up-table for video hologram generation of three-dimensional objects freely maneuvering in space.

    PubMed

    Dong, Xiao-Bin; Kim, Seung-Cheol; Kim, Eun-Soo

    2014-07-14

    A new three-directional motion compensation-based novel-look-up-table (3DMC-NLUT) based on its shift-invariance and thin-lens properties, is proposed for video hologram generation of three-dimensional (3-D) objects moving with large depth variations in space. The input 3-D video frames are grouped into a set of eight in sequence, where the first and remaining seven frames in each set become the reference frame (RF) and general frames (GFs), respectively. Hence, each 3-D video frame is segmented into a set of depth-sliced object images (DOIs). Then x, y, and z-directional motion vectors are estimated from blocks and DOIs between the RF and each of the GFs, respectively. With these motion vectors, object motions in space are compensated. Then, only the difference images between the 3-directionally motion-compensated RF and each of the GFs are applied to the NLUT for hologram calculation. Experimental results reveal that the average number of calculated object points and the average calculation time of the proposed method have been reduced compared to those of the conventional NLUT, TR-NLUT and MPEG-NLUT by 38.14%, 69.48%, and 67.41% and 35.30%, 66.39%, and 64.46%, respectively.

  16. Two dimensional joint inversion of direct current resistivity, radio-magnetotelluric and seismic refraction data: An application from Bafra Plain, Turkey

    NASA Astrophysics Data System (ADS)

    Demirci, İsmail; Candansayar, Mehmet Emin; Vafidis, Antonis; Soupios, Pantelis

    2017-04-01

    Direct current resistivity, radio-magnetotelluric and seismic refraction methods are widely used in the identification of near surface structures with collected data generally being interpreted separately. In recent decades, the use of joint inversion algorithms in geosciences has become widespread to identify near surface structures. However, there is no developed joint inversion algorithm using direct current resistivity, radio-magnetotelluric and seismic refraction methods. In this study, we developed a new two-dimensional joint inversion algorithm for direct current resistivity, radio-magnetotelluric and seismic refraction data based on a cross gradient approach. In addition, we proposed a new data weighting matrix to stabilize the convergence behavior of the joint inversion algorithms. We used synthetic data to show the advantage of the algorithm. The developed joint inversion algorithm found resistivity and velocity models that are better than the individual inversion of each data set. We also tested an algorithm with the field data collected in the Bafra Plain (Samsun, Turkey) to investigate saltwater intrusion. In comparing the field data inversion results with the sounding log, it can be seen that the developed joint inversion algorithm with the proposed data weighting matrix recovered the resistivity and velocity model better than the individual inversion and classical joint inversion of each data set. Our results showed that a more unique hydrogeological scenario might be obtained, especially in highly conductive media, with the joint usage of these methods.

  17. Palladium catalyzed Csp2-H activation for direct aryl hydroxylation: the unprecedented role of 1,4-dioxane as a source of hydroxyl radicals.

    PubMed

    Seth, Kapileswar; Nautiyal, Manesh; Purohit, Priyank; Parikh, Naisargee; Chakraborti, Asit K

    2015-01-04

    A novel strategy for direct aryl hydroxylation via Pd-catalysed Csp(2)-H activation through an unprecedented hydroxyl radical transfer from 1,4-dioxane, used as a solvent, is reported with bio relevant and sterically hindered heterocycles and various acyclic functionalities as versatile directing groups.

  18. Estrogenic and dioxin-like compounds in sediment from Zierikzee harbour identified with CALUX assay-directed fractionation combined with one and two dimensional gas chromatography analyses.

    PubMed

    Houtman, Corine J; Booij, Petra; Jover, Eric; Pascual del Rio, David; Swart, Kees; van Velzen, Martin; Vreuls, Rene; Legler, Juliette; Brouwer, Abraham; Lamoree, Marja H

    2006-12-01

    The identity of compounds responsible for estrogenic and dioxin-like activities in sediment from the harbour of the small town Zierikzee in Zeeland, The Netherlands, was investigated using a bioassay directed fractionation approach with the in vitro estrogen and dioxin responsive reporter gene assays ER- and DR-CALUX. For identification of compounds exhibiting activity in the bioassays, either one or two-dimensional GC in combination with quadrupole (MSD), ion trap (ITD) or time-of-flight mass spectrometric detection (ToF-MS) was used, depending on the biological and chemical characteristics and the complexity of the fractions. The natural estrogenic hormone 17-beta-estradiol and its metabolite estrone were identified with GC-ITD as the main contributors to the estrogenic activity. After successive rounds of fractionation, the dioxin-like activity could be explained by the presence of various polycyclic aromatic hydrocarbons identified with GC-MSD and two-dimensional comprehensive GC x GC-ToF-MS. Some estrogenic activity of a relatively non-polar nature remained unidentified.

  19. Three-dimensional numerical simulations of lamellar structure via two-step surface-directed phase separation in polymer blend films.

    PubMed

    Yan, Li-Tang; Li, Jialin; Xie, Xu-Ming

    2008-06-14

    Lamellar structure via two-step surface-directed phase separation in polymer blend films is numerically investigated in three-dimensional (3D) space, which is more physically appropriate for the experimental situation than that in two-dimensional (2D) space [L.-T. Yan and X. M. Xie, J. Chem. Phys. 128, 034901 (2008)]. The 3D phase morphology and its evolution dynamics in both critical and off-critical conditions have been studied. The wetting layer formation mechanism during the second quench has been concerned. The effects of noise on the ordered phase structures have also been examined. The simulated results in 3D space give a more certain evidence that the lamellar structure can be induced by the surface or interface when the system is in the equilibration state with very shallow quench depth first and then imposed on a further quench depth in the unstable region of the phase diagram. It is found that the lamellar structure can also be induced in the polymer blends with off-critical condition. The simulated results demonstrate that the formation of the lamellar structure can present two basic processes and obey logarithmic growth law at the initial and metaphase stages. The results also show that a stronger thermal noise corresponds to a smaller region with the lamellar structure.

  20. Direct comparison between a two-dimensional magneto-optical trap and a Zeeman slower as sources of cold sodium atoms

    NASA Astrophysics Data System (ADS)

    Pedrozo-Peñafiel, E.; Vivanco, F.; Castilho, P.; Paiva, R. R.; Farias, K. M.; Bagnato, V. S.

    2016-06-01

    The atom source is a relevant component in many atomic molecular optics experiments. The compactness and efficiency of the source are fundamental issues, acquiring more importance as the complexity of the experiments increases. Characterizing new techniques to produce high atom flux is necessary to know the efficiency and peculiarities of each one. This allows choosing the most suitable source for a specific experiment. In this work, we show a direct comparison between a two-dimensional magneto-optical trap (2D-MOT) and a Zeeman slower (ZS) as source of cold sodium atoms to load a standard three-dimensional magneto-optical trap. The optimum parameters for each case are obtained by observing the loading rate and the final number of atoms in the 3D-MOT. We conclude that the 2D-MOT provides a high flux of atoms comparable with that produced by the ZS, but with an enormous advantage with respect to the size of the apparatus.