Shapes of interacting RNA complexes
DEFF Research Database (Denmark)
Fu, Benjamin Mingming; Reidys, Christian
2014-01-01
Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops.This shape-projection preserves the topological core of the RNA complex and for fixed topological...... genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows to compute the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform...... sampling algorithm for shapes of RNA complexes of fixed topological genus....
Abstract shape analysis of RNA.
Janssen, Stefan; Giegerich, Robert
2014-01-01
Abstract shape analysis abstract shape analysis is a method to learn more about the complete Boltzmann ensemble of the secondary structures of a single RNA molecule. Abstract shapes classify competing secondary structures into classes that are defined by their arrangement of helices. It allows us to compute, in addition to the structure of minimal free energy, a set of structures that represents relevant and interesting structural alternatives. Furthermore, it allows to compute probabilities of all structures within a shape class. This allows to ensure that our representative subset covers the complete Boltzmann ensemble, except for a portion of negligible probability. This chapter explains the main functions of abstract shape analysis, as implemented in the tool RNA shapes. RNA shapes It reports on some other types of analysis that are based on the abstract shapes idea and shows how you can solve novel problems by creating your own shape abstractions.
Exact sum rules for quantum billiards of arbitrary shape
Amore, Paolo
2018-01-01
We have derived explicit expressions for the sum rules of order one of the eigenvalues of the negative Laplacian on two dimensional domains of arbitrary shape. Taking into account the leading asymptotic behavior of these eigenvalues, as given from Weyl's law, we show that it is possible to define sum rules that are finite, using different prescriptions. We provide the explicit expressions and test them on a number of non trivial examples, comparing the exact results with precise numerical results.
Dynamics of an Imperfect Microbeam Considering its Exact Shape
Bataineh, Ahmad M.
2014-08-17
We study the static and dynamic behavior of electrically actuated micromachined arches. First, we conduct experiments on micromachined polysilicon beams by driving them electrically and varying their amplitude and frequency of voltage loads. The results reveal several interesting nonlinear phenomena of jumps, hysteresis, and softening behaviors. Next, we conduct analytical and theoretical investigation to understand the experiments. First, we solve the Eigen value problem analytically. We study the effect of the initial rise on the natural frequency and mode shapes, and use a Galerkin-based procedure to derive a reduced order model, which is then used to solve both the static and dynamic responses. We use two symmetric modes in the reduced order model to have accurate and converged results. We use long time integration to solve the nonlinear ordinary differential equations, and then modify our model using effective length to match experimental results. To further improve the matching with the experimental data, we curve-fit the exact profile of the microbeam to match the experimentally measured profile and use it in the reduced-order model to generate frequency-response curves. Finally, we use another numerical technique, the shooting technique, to solve the nonlinear ordinary differential equations. By using shooting and the curve fitted function, we found that we get good agreement with the experimental data.
RNA Structural Analysis by Evolving SHAPE Chemistry
Spitale, Robert C.; Flynn, Ryan A.; Torre, Eduardo A.; Kool, Eric T.; Chang, Howard Y.
2017-01-01
RNA is central to the flow of biological information. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. Hence the information content in RNA is not simply its linear sequence of bases, but is also encoded in complex folding of RNA molecules. A general chemical functionality that all RNAs have is a 2’-hydroxyl group in the ribose ring, and the reactivity of the 2'-hydroxyl in RNA is gated by local nucleotide flexibility. In other words, the 2'-hydroxyl is reactive at single-stranded and conformationally flexible positions but is unreactive at nucleotides constrained by base pairing. Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2’ hydroxyl group flexibility. Such RNA structure probing techniques can be read out by primer extension in experiments termed RNA SHAPE (Selective 2’ Hydroxyl Acylation and Primer Extension). Herein we describe the efforts devoted to the design and utilization of SHAPE probes for characterizing RNA structure. We also describe current technological advances that are being used to utilize SHAPE chemistry with deep sequencing to probe many RNAs in parallel. The merger of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function. PMID:25132067
SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data
DEFF Research Database (Denmark)
Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R
2015-01-01
transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES...
SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data
Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R.; Krogh, Anders; Vinther, Jeppe
2015-01-01
Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA–RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing. PMID:25805860
Directory of Open Access Journals (Sweden)
Anja Fischer
2015-06-01
Full Text Available One fundamental problem of bioinformatics is the computational recognition of DNA and RNA binding sites. Given a set of short DNA or RNA sequences of equal length such as transcription factor binding sites or RNA splice sites, the task is to learn a pattern from this set that allows the recognition of similar sites in another set of DNA or RNA sequences. Permuted Markov (PM models and permuted variable length Markov (PVLM models are two powerful models for this task, but the problem of finding an optimal PM model or PVLM model is NP-hard. While the problem of finding an optimal PM model or PVLM model of order one is equivalent to the traveling salesman problem (TSP, the problem of finding an optimal PM model or PVLM model of order two is equivalent to the quadratic TSP (QTSP. Several exact algorithms exist for solving the QTSP, but it is unclear if these algorithms are capable of solving QTSP instances resulting from RNA splice sites of at least 150 base pairs in a reasonable time frame. Here, we investigate the performance of three exact algorithms for solving the QTSP for ten datasets of splice acceptor sites and splice donor sites of five different species and find that one of these algorithms is capable of solving QTSP instances of up to 200 base pairs with a running time of less than two days.
Sloma, Michael F; Mathews, David H
2016-12-01
RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. © 2016 Sloma and Mathews; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Size, Shape, and Sequence-Dependent Immunogenicity of RNA Nanoparticles
Directory of Open Access Journals (Sweden)
Sijin Guo
2017-12-01
Full Text Available RNA molecules have emerged as promising therapeutics. Like all other drugs, the safety profile and immune response are important criteria for drug evaluation. However, the literature on RNA immunogenicity has been controversial. Here, we used the approach of RNA nanotechnology to demonstrate that the immune response of RNA nanoparticles is size, shape, and sequence dependent. RNA triangle, square, pentagon, and tetrahedron with same shape but different sizes, or same size but different shapes were used as models to investigate the immune response. The levels of pro-inflammatory cytokines induced by these RNA nanoarchitectures were assessed in macrophage-like cells and animals. It was found that RNA polygons without extension at the vertexes were immune inert. However, when single-stranded RNA with a specific sequence was extended from the vertexes of RNA polygons, strong immune responses were detected. These immunostimulations are sequence specific, because some other extended sequences induced little or no immune response. Additionally, larger-size RNA square induced stronger cytokine secretion. 3D RNA tetrahedron showed stronger immunostimulation than planar RNA triangle. These results suggest that the immunogenicity of RNA nanoparticles is tunable to produce either a minimal immune response that can serve as safe therapeutic vectors, or a strong immune response for cancer immunotherapy or vaccine adjuvants.
RNA interference-mediated simultaneous silencing of four genes using cross-shaped RNA.
Lee, Tae Yeon; Chang, Chan Il; Lee, Dooyoung; Hong, Sun Woo; Shin, Chanseok; Li, Chiang J; Kim, Soyoun; Haussecker, Dirk; Lee, Dong-Ki
2013-04-01
The structural flexibility of RNA interference (RNAi)-triggering nucleic acids suggests that the design of unconventional RNAi trigger structures with novel features is possible. Here, we report a cross-shaped RNA duplex structure, termed quadruple interfering RNA (qiRNA), with multiple target gene silencing activity. qiRNA triggers the simultaneous down-regulation of four cellular target genes via an RNAi mechanism. In addition, qiRNA shows enhanced intracellular delivery and target gene silencing over conventional siRNA when complexed with jetPEI, a linear polyethyleneimine (PEI). We also show that the long antisense strand of qiRNA is incorporated intact into an RNA-induced silencing complex (RISC). This novel RNA scaffold further expands the repertoire of RNAi-triggering molecular structures and could be used in the development of therapeutics for various diseases including viral infections and cancer.
RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence.
Masliah, Grégoire; Barraud, Pierre; Allain, Frédéric H-T
2013-06-01
The double-stranded RNA binding domain (dsRBD) is a small protein domain of 65-70 amino acids adopting an αβββα fold, whose central property is to bind to double-stranded RNA (dsRNA). This domain is present in proteins implicated in many aspects of cellular life, including antiviral response, RNA editing, RNA processing, RNA transport and, last but not least, RNA silencing. Even though proteins containing dsRBDs can bind to very specific dsRNA targets in vivo, the binding of dsRBDs to dsRNA is commonly believed to be shape-dependent rather than sequence-specific. Interestingly, recent structural information on dsRNA recognition by dsRBDs opens the possibility that this domain performs a direct readout of RNA sequence in the minor groove, allowing a global reconsideration of the principles describing dsRNA recognition by dsRBDs. We review in this article the current structural and molecular knowledge on dsRBDs, emphasizing the intricate relationship between the amino acid sequence, the structure of the domain and its RNA recognition capacity. We especially focus on the molecular determinants of dsRNA recognition and describe how sequence discrimination can be achieved by this type of domain.
DEFF Research Database (Denmark)
Garde, Henrik
2018-01-01
. For a fair comparison, exact matrix characterizations are used when probing the monotonicity relations to avoid errors from numerical solution to PDEs and numerical integration. Using a special factorization of the Neumann-to-Dirichlet map also makes the non-linear method as fast as the linear method......Detecting inhomogeneities in the electrical conductivity is a special case of the inverse problem in electrical impedance tomography, that leads to fast direct reconstruction methods. One such method can, under reasonable assumptions, exactly characterize the inhomogeneities based on monotonicity...... properties of either the Neumann-to-Dirichlet map (non-linear) or its FrÃ©chet derivative (linear). We give a comparison of the non-linear and linear approach in the presence of measurement noise, and show numerically that the two methods give essentially the same reconstruction in the unit disk domain...
Efficient Reactive Navigation with Exact Collision Determination for 3D Robot Shapes
Directory of Open Access Journals (Sweden)
Mariano Jaimez
2015-05-01
Full Text Available This paper presents a reactive navigator for wheeled mobile robots moving on a flat surface which takes into account both the actual 3D shape of the robot and the 3D surrounding obstacles. The robot volume is modelled by a number of prisms consecutive in height, and the detected obstacles, which can be provided by different kinds of range sensor, are segmented into these heights. Then, the reactive navigation problem is tackled by a number of concurrent 2D navigators, one for each prism, which are consistently and efficiently combined to yield an overall solution. Our proposal for each 2D navigator is based on the concept of the “Parameterized Trajectory Generator” which models the robot shape as a polygon and embeds its kinematic constraints into different motion models. Extensive testing has been conducted in office-like and real house environments, covering a total distance of 18.5 km, to demonstrate the reliability and effectiveness of the proposed method. Moreover, additional experiments are performed to highlight the advantages of a 3D-aware reactive navigator. The implemented code is available under an open-source licence.
Li, Chung-I; Su, Pei-Fang; Shyr, Yu
2013-12-06
Sample size calculation is an important issue in the experimental design of biomedical research. For RNA-seq experiments, the sample size calculation method based on the Poisson model has been proposed; however, when there are biological replicates, RNA-seq data could exhibit variation significantly greater than the mean (i.e. over-dispersion). The Poisson model cannot appropriately model the over-dispersion, and in such cases, the negative binomial model has been used as a natural extension of the Poisson model. Because the field currently lacks a sample size calculation method based on the negative binomial model for assessing differential expression analysis of RNA-seq data, we propose a method to calculate the sample size. We propose a sample size calculation method based on the exact test for assessing differential expression analysis of RNA-seq data. The proposed sample size calculation method is straightforward and not computationally intensive. Simulation studies to evaluate the performance of the proposed sample size method are presented; the results indicate our method works well, with achievement of desired power.
How Amino Acids and Peptides Shaped the RNA World
P.T.S. van der Gulik (Peter); D. Speijer (Dave)
2015-01-01
htmlabstractThe “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein
How amino acids and peptides shaped the RNA world
van der Gulik, Peter T. S.; Speijer, Dave
2015-01-01
The "RNA world" hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this
Investigation of RNA Structure by High-Throughput SHAPE-Based Probing Methods
DEFF Research Database (Denmark)
Poulsen, Line Dahl
of highthroughput SHAPE-based approaches to investigate RNA structure based on novel SHAPE reagents that permit selection of full-length cDNAs. The SHAPE Selection (SHAPES) method is applied to the foot-and-mouth disease virus (FMDV) plus strand RNA genome, and the data is used to construct a genome-wide structural...... map of the virus. I have used the data to discover stable structures de novo, including previously characterized structural elements, such as the internal ribosome entry site (IRES), and I show that three of the novel structures have been conserved through evolution, indicating...... that they are functional. The SHAPES method is further applied to the hepatitis C virus (HCV), where the data is used to refine known and predicted structures. Over the past years, the interest of studying RNA structure in their native environment has been increased, and to allow studying RNA structure inside living cells...
Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.
Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B
2016-01-29
Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
DEFF Research Database (Denmark)
López-Aenlle, Manuel; Brincker, Rune; Pelayo, F.
2012-01-01
When operational modal analysis (OMA) is used to estimate modal parameters, mode shapes cannot be mass normalized. In the past few years, some equations have been proposed to scale mode shapes using the mass-change method, which consists of repeating modal testing after changing the mass at diffe...
Khisamutdinov, Emil F.; Li, Hui; Jasinski, Daniel L.; Chen, Jiao; Fu, Jian; Guo, Peixuan
2014-01-01
Modulation of immune response is important in cancer immunotherapy, vaccine adjuvant development and inflammatory or immune disease therapy. Here we report the development of new immunomodulators via control of shape transition among RNA triangle, square and pentagon. Changing one RNA strand in polygons automatically induced the stretching of the interior angle from 60° to 90° or 108°, resulting in self-assembly of elegant RNA triangles, squares and pentagons. When immunological adjuvants were incorporated, their immunomodulation effect for cytokine TNF-α and IL-6 induction was greatly enhanced in vitro and in animals up to 100-fold, while RNA polygon controls induced unnoticeable effect. The RNA nanoparticles were delivered to macrophages specifically. The degree of immunostimulation greatly depended on the size, shape and number of the payload per nanoparticles. Stronger immune response was observed when the number of adjuvants per polygon was increased, demonstrating the advantage of shape transition from triangle to pentagon. PMID:25092921
Comparison of SHAPE reagents for mapping RNA structures inside living cells.
Lee, Byron; Flynn, Ryan A; Kadina, Anastasia; Guo, Jimmy K; Kool, Eric T; Chang, Howard Y
2017-02-01
Recent advances in SHAPE technology have converted the classic primer extension method to next-generation sequencing platforms, allowing transcriptome-level analysis of RNA secondary structure. In particular, icSHAPE and SHAPE-MaP, using NAI-N3 and 1M7 reagents, respectively, are methods that claim to measure in vivo structure with high-throughput sequencing. However, these compounds have not been compared on an unbiased, raw-signal level. Here, we directly compare several in vivo SHAPE acylation reagents using the simple primer extension assay. We conclude that while multiple SHAPE technologies are effective at measuring purified RNAs in vitro, acylimidazole reagents NAI and NAI-N3 give markedly greater signals with lower background than 1M7 for in vivo measurement of the RNA structurome. © 2017 Lee et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
The C. elegans mRNA decapping enzyme shapes morphology of cilia.
Adachi, Takeshi; Nagahama, Keigo; Izumi, Susumu
2017-11-04
Cilia and flagella are evolutionarily conserved organelles that protrude from cell surfaces. Most cilia and flagella are single rod-shaped but some cilia show a variety of shapes. For example, human airway epithelial cells are multiciliated, flagella of crayfish spermatozoon are star-like shaped, and fruit fly spermatozoon extends long flagella. In Caenorhabditis elegans, cilia display morphological diversity of shapes (single, dual rod-type and wing-like and highly-branched shapes). Here we show that DCAP-1 and DCAP-2, which are the homologues of mammalian DCP1 and DCP2 mRNA decapping enzymes, respectively, are involved in formation of dual rod-type and wing-like shaped cilia in C. elegans. mRNA decapping enzyme catalyzes hydrolysis of 5' cap structure of mRNA, which leads to degradation of mRNA. Rescue experiments showed that DCAP-2 acts not in glial cells surrounding cilia but in neurons. This is the first evidence to demonstrate that mRNA decapping is involved in ciliary shape formation. Copyright © 2017 Elsevier Inc. All rights reserved.
Detection of RNA-Protein Interactions in Living Cells with SHAPE.
Smola, Matthew J; Calabrese, J Mauro; Weeks, Kevin M
2015-11-24
SHAPE-MaP is unique among RNA structure probing strategies in that it both measures flexibility at single-nucleotide resolution and quantifies the uncertainties in these measurements. We report a straightforward analytical framework that incorporates these uncertainties to allow detection of RNA structural differences between any two states, and we use it here to detect RNA-protein interactions in healthy mouse trophoblast stem cells. We validate this approach by analysis of three model cytoplasmic and nuclear ribonucleoprotein complexes, in 2 min in-cell probing experiments. In contrast, data produced by alternative in-cell SHAPE probing methods correlate poorly (r = 0.2) with those generated by SHAPE-MaP and do not yield accurate signals for RNA-protein interactions. We then examine RNA-protein and RNA-substrate interactions in the RNase MRP complex and, by comparing in-cell interaction sites with disease-associated mutations, characterize these noncoding mutations in terms of molecular phenotype. Together, these results reveal that SHAPE-MaP can define true interaction sites and infer RNA functions under native cellular conditions with limited preexisting knowledge of the proteins or RNAs involved.
Aouadi, O.; Fayache, M. S.
2017-11-01
In this paper, we solve analytically the (3+1)-dimensional Dirac oscillator in the presence of a chain of delta-function-shaped shell potentials introduced as either a scalar or a vector coupling interaction depending on its behavior under Lorentz transformations. The transfer matrix method was used for the determination of the quantization energy condition and some particular cases were presented as detailed examples.
Khisamutdinov, Emil F; Li, Hui; Jasinski, Daniel L; Chen, Jiao; Fu, Jian; Guo, Peixuan
2014-09-01
Modulation of immune response is important in cancer immunotherapy, vaccine adjuvant development and inflammatory or immune disease therapy. Here we report the development of new immunomodulators via control of shape transition among RNA triangle, square and pentagon. Changing one RNA strand in polygons automatically induced the stretching of the interior angle from 60° to 90° or 108°, resulting in self-assembly of elegant RNA triangles, squares and pentagons. When immunological adjuvants were incorporated, their immunomodulation effect for cytokine TNF-α and IL-6 induction was greatly enhanced in vitro and in animals up to 100-fold, while RNA polygon controls induced unnoticeable effect. The RNA nanoparticles were delivered to macrophages specifically. The degree of immunostimulation greatly depended on the size, shape and number of the payload per nanoparticles. Stronger immune response was observed when the number of adjuvants per polygon was increased, demonstrating the advantage of shape transition from triangle to pentagon. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
SHAPE analysis of the htrA RNA thermometer from Salmonella enterica.
Choi, Edric K; Ulanowicz, Kelsey A; Nguyen, Yen Anh H; Frandsen, Jane K; Mitton-Fry, Rachel M
2017-10-01
RNA thermometers regulate expression of some genes involved in virulence of pathogenic bacteria such as Yersinia, Neisseria, and Salmonella They often function through temperature-dependent conformational changes that alter accessibility of the ribosome-binding site. The 5'-untranslated region (UTR) of the htrA mRNA from Salmonella enterica contains a very short RNA thermometer. We have systematically characterized the structure and dynamics of this thermometer at single-nucleotide resolution using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) assays. Our results confirm that the htrA thermometer adopts the predicted hairpin conformation at low temperatures, with conformational change occurring over a physiological temperature regime. Detailed SHAPE melting curves for individual nucleotides suggest that the thermometer unfolds in a cooperative fashion, with nucleotides from both upper and lower portions of the stem gaining flexibility at a common transition temperature. Intriguingly, analysis of an extended htrA 5' UTR sequence revealed not only the presence of the RNA thermometer, but also an additional, stable upstream structure. We generated and analyzed point mutants of the htrA thermometer, revealing elements that modulate its stability, allowing the hairpin to melt under the slightly elevated temperatures experienced during the infection of a warm-blooded host. This work sheds light on structure-function relationships in htrA and related thermometers, and it also illustrates the utility of SHAPE assays for detailed study of RNA thermometer systems. © 2017 Choi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Takahashi, Melissa K; Watters, Kyle E; Gasper, Paul M; Abbott, Timothy R; Carlson, Paul D; Chen, Alan A; Lucks, Julius B
2016-06-01
Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure-function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart structural flexibility. We further observe hairpin flexibility in the cellular structures of natural RNA mechanisms that use antisense RNA interactions to repress translation, confirming earlier results from in vitro studies. Finally, we design new transcriptional attenuators in silico using an interior loop as a structural requirement and show that they function as desired in vivo. This work establishes interior loops as an important structural element for designing synthetic RNA gene regulators. We anticipate that the coupling of experimental measurement of cellular RNA structure and function with computational modeling will enable rapid discovery of structure-function design principles for a diverse array of natural and synthetic RNA regulators. © 2016 Takahashi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species.
Di Giallonardo, Francesca; Schlub, Timothy E; Shi, Mang; Holmes, Edward C
2017-04-15
Viruses use the cellular machinery of their hosts for replication. It has therefore been proposed that the nucleotide and dinucleotide compositions of viruses should match those of their host species. If this is upheld, it may then be possible to use dinucleotide composition to predict the true host species of viruses sampled in metagenomic surveys. However, it is also clear that different taxonomic groups of viruses tend to have distinctive patterns of dinucleotide composition that may be independent of host species. To determine the relative strength of the effect of host versus virus family in shaping dinucleotide composition, we performed a comparative analysis of 20 RNA virus families from 15 host groupings, spanning two animal phyla and more than 900 virus species. In particular, we determined the odds ratios for the 16 possible dinucleotides and performed a discriminant analysis to evaluate the capability of virus dinucleotide composition to predict the correct virus family or host taxon from which it was isolated. Notably, while 81% of the data analyzed here were predicted to the correct virus family, only 62% of these data were predicted to their correct subphylum/class host and a mere 32% to their correct mammalian order. Similarly, dinucleotide composition has a weak predictive power for different hosts within individual virus families. We therefore conclude that dinucleotide composition is generally uniform within a virus family but less well reflects that of its host species. This has obvious implications for attempts to accurately predict host species from virus genome sequences alone. IMPORTANCE Determining the processes that shape virus genomes is central to understanding virus evolution and emergence. One question of particular importance is why nucleotide and dinucleotide frequencies differ so markedly between viruses. In particular, it is currently unclear whether host species or virus family has the biggest impact on dinucleotide frequencies and
Takahashi, Melissa K.; Watters, Kyle E.; Gasper, Paul M.; Abbott, Timothy R.; Carlson, Paul D.; Chen, Alan A.
2016-01-01
Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure–function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart structural flexibility. We further observe hairpin flexibility in the cellular structures of natural RNA mechanisms that use antisense RNA interactions to repress translation, confirming earlier results from in vitro studies. Finally, we design new transcriptional attenuators in silico using an interior loop as a structural requirement and show that they function as desired in vivo. This work establishes interior loops as an important structural element for designing synthetic RNA gene regulators. We anticipate that the coupling of experimental measurement of cellular RNA structure and function with computational modeling will enable rapid discovery of structure–function design principles for a diverse array of natural and synthetic RNA regulators. PMID:27103533
Kanna, T; Lakshmanan, M
2003-04-01
The different dynamical features underlying soliton interactions in coupled nonlinear Schrödinger equations, which model multimode wave propagation under varied physical situations in nonlinear optics, are studied. In this paper, by explicitly constructing multisoliton solutions (up to four-soliton solutions) for two-coupled and arbitrary N-coupled nonlinear Schrödinger equations using the Hirota bilinearization method, we bring out clearly the various features underlying the fascinating shape changing (intensity redistribution) collisions of solitons, including changes in amplitudes, phases and relative separation distances, and the very many possibilities of energy redistributions among the modes of solitons. However, in this multisoliton collision process the pairwise collision nature is shown to be preserved in spite of the changes in the amplitudes and phases of the solitons. Detailed asymptotic analysis also shows that when solitons undergo multiple collisions, there exists the exciting possibility of shape restoration of at least one soliton during interactions of more than two solitons represented by three- and higher-order soliton solutions. From an application point of view, we have shown from the asymptotic expressions how the amplitude (intensity) redistribution can be written as a generalized linear fractional transformation for the N-component case. Also we indicate how the multisolitons can be reinterpreted as various logic gates for suitable choices of the soliton parameters, leading to possible multistate logic. In addition, we point out that the various recently studied partially coherent solitons are just special cases of the bright soliton solutions exhibiting shape-changing collisions, thereby explaining their variable profile and shape variation in collision process.
Energy Technology Data Exchange (ETDEWEB)
Luque, A., E-mail: a.luque@upm.es [Instituto de Energía Solar, Universidad Politécnica de Madrid (Spain); Mellor, A.; Tobías, I.; Antolín, E.; Linares, P.G.; Ramiro, I.; Martí, A. [Instituto de Energía Solar, Universidad Politécnica de Madrid (Spain)
2013-03-15
The effective mass Schrödinger equation of a QD of parallelepipedic shape with a square potential well is solved by diagonalizing the exact Hamiltonian matrix developed in a basis of separation-of-variables wavefunctions. The expected below bandgap bound states are found not to differ very much from the former approximate calculations. In addition, the presence of bound states within the conduction band is confirmed. Furthermore, filamentary states bounded in two dimensions and extended in one dimension and layered states with only one dimension bounded, all within the conduction band—which are similar to those originated in quantum wires and quantum wells—coexist with the ordinary continuum spectrum of plane waves. All these subtleties are absent in spherically shaped quantum dots, often used for modeling.
Directory of Open Access Journals (Sweden)
Marc Brunel
2015-04-01
Full Text Available We present the development of a numerical simulator for digital in-line holography applications. In-line holograms of arbitrarily shaped and arbitrarily located objects are calculated using generalized Huygens-Fresnel integrals. The objects are 2D opaque or phase objects. The optical set-up is described by its optical transfer matrix. A wide variety of optical systems, involving windows, spherical or cylindrical lenses, can thus be taken into account. It makes the simulator applicable for design and description of in situ experiments. We discuss future applications of this simulator for detection of nanoparticles in droplets, or calibration of airborne instruments that detect and measure ice crystals in the atmosphere.
Energy Technology Data Exchange (ETDEWEB)
Han, Yu; Li, Qiang; Lau, Kei May, E-mail: eekmlau@ust.hk [Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Chang, Shih-Pang; Hsu, Wen-Da [National Nano Device Laboratories, Narlabs, Hsinchu 300, Taiwan (China)
2016-06-13
We report InGaAs quasi-quantum wires embedded in planar InP nanowires grown on (001) silicon emitting in the 1550 nm communication band. An array of highly ordered InP nanowire with semi-rhombic cross-section was obtained in pre-defined silicon V-grooves through selective-area hetero-epitaxy. The 8% lattice mismatch between InP and Si was accommodated by an ultra-thin stacking disordered InP/GaAs nucleation layer. X-ray diffraction and transmission electron microscope characterizations suggest excellent crystalline quality of the nanowires. By exploiting the morphological evolution of the InP and a self-limiting growth process in the V-grooves, we grew embedded InGaAs quantum-wells and quasi-quantum-wires with tunable shape and position. Room temperature analysis reveals substantially improved photoluminescence in the quasi-quantum wires as compared to the quantum-well reference, due to the reduced intrusion defects and enhanced quantum confinement. These results show great promise for integration of III-V based long wavelength nanowire lasers on the well-established (001) Si platform.
Lavender, Christopher A; Lorenz, Ronny; Zhang, Ge; Tamayo, Rita; Hofacker, Ivo L; Weeks, Kevin M
2015-05-01
Discovery and characterization of functional RNA structures remains challenging due to deficiencies in de novo secondary structure modeling. Here we describe a dynamic programming approach for model-free sequence comparison that incorporates high-throughput chemical probing data. Based on SHAPE probing data alone, ribosomal RNAs (rRNAs) from three diverse organisms--the eubacteria E. coli and C. difficile and the archeon H. volcanii--could be aligned with accuracies comparable to alignments based on actual sequence identity. When both base sequence identity and chemical probing reactivities were considered together, accuracies improved further. Derived sequence alignments and chemical probing data from protein-free RNAs were then used as pseudo-free energy constraints to model consensus secondary structures for the 16S and 23S rRNAs. There are critical differences between these experimentally-informed models and currently accepted models, including in the functionally important neck and decoding regions of the 16S rRNA. We infer that the 16S rRNA has evolved to undergo large-scale changes in base pairing as part of ribosome function. As high-quality RNA probing data become widely available, structurally-informed sequence alignment will become broadly useful for de novo motif and function discovery.
Directory of Open Access Journals (Sweden)
Christopher A Lavender
2015-05-01
Full Text Available Discovery and characterization of functional RNA structures remains challenging due to deficiencies in de novo secondary structure modeling. Here we describe a dynamic programming approach for model-free sequence comparison that incorporates high-throughput chemical probing data. Based on SHAPE probing data alone, ribosomal RNAs (rRNAs from three diverse organisms--the eubacteria E. coli and C. difficile and the archeon H. volcanii--could be aligned with accuracies comparable to alignments based on actual sequence identity. When both base sequence identity and chemical probing reactivities were considered together, accuracies improved further. Derived sequence alignments and chemical probing data from protein-free RNAs were then used as pseudo-free energy constraints to model consensus secondary structures for the 16S and 23S rRNAs. There are critical differences between these experimentally-informed models and currently accepted models, including in the functionally important neck and decoding regions of the 16S rRNA. We infer that the 16S rRNA has evolved to undergo large-scale changes in base pairing as part of ribosome function. As high-quality RNA probing data become widely available, structurally-informed sequence alignment will become broadly useful for de novo motif and function discovery.
Messenger RNA Fluctuations and Regulatory RNAs Shape the Dynamics of Negative Feedback Loop
Martínez, María Rodríguez; Tlusty, Tsvi; Pilpel, Yitzhak; Furman, Itay; 10.1103/PhysRevE.81.031924
2010-01-01
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while individual cells may show sustained oscillations in the concentrations of some proteins, such oscillations may appear damped in the population average. In this paper we investigate the role of RNA stochastic fluctuations as a leading force to produce a sustained excitatory behavior at the single cell level. Opposed to some previous models, we build a fully stochastic model of a negative feedback loop that explicitly takes into account the RNA stochastic dynamics. We find that messenger RNA random fluctuations can be amplified during translation and produce sustained pulses of protein expression. Motivated by the recent appreciation of the importance of non--coding regulatory RNAs in post--transcription regulation, we also consider the possibility that a regulatory RNA transcri...
Smola, Matthew J.; Rice, Greggory M.; Busan, Steven; Siegfried, Nathan A.; Weeks, Kevin M.
2016-01-01
SHAPE chemistries exploit small electrophilic reagents that react with the 2′-hydroxyl group to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues based on the ability of reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as for simple model RNAs. This protocol describes the experimental steps, implemented over three days, required to perform SHAPE probing and construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. These steps include RNA folding and SHAPE structure probing, mutational profiling by reverse transcription, library construction, and sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides useful troubleshooting information, often within an hour. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures, and visualize probable and alternative helices, often in under a day. We illustrate these algorithms with the E. coli thiamine pyrophosphate riboswitch, E. coli 16S rRNA, and HIV-1 genomic RNAs. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles, and entire transcriptomes. The straightforward MaP strategy greatly expands the number, length, and complexity of analyzable RNA structures. PMID:26426499
Alu elements shape the primate transcriptome by cis-regulation of RNA editing
2014-01-01
Background RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures – a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated. Results We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors. Conclusions We propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought. PMID:24485196
López-Carrasco, Amparo; Flores, Ricardo
2017-07-01
Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE). Both approaches resulted in predominant rod-like secondary structures without tertiary interactions, with the mc (+) RNA being more compact than its (-) counterpart as revealed by non-denaturing polyacryamide gel electrophoresis. Moreover, in vivo SHAPE showed that the mc ASBVd (+) form accumulates in avocado leaves as a free RNA adopting a similar rod-shaped conformation unprotected by tightly bound host proteins. Hence, the mc ASBVd (+) RNA behaves in planta like the previously studied mc (+) RNA of potato spindle tuber viroid, the type member of nuclear viroids (family Pospiviroidae), indicating that two different viroids replicating and accumulating in distinct subcellular compartments, have converged into a common structural solution. Circularity and compact secondary structures confer to these RNAs, and probably to all viroids, the intrinsic stability needed to survive in their natural habitats. However, in vivo SHAPE has not revealed the (possibly transient or loose) interactions of the mc ASBVd (+) RNA with two host proteins observed previously by UV irradiation of infected avocado leaves.
Energy Technology Data Exchange (ETDEWEB)
Singleton, Robert Jr. [Los Alamos National Laboratory; Israel, Daniel M. [Los Alamos National Laboratory; Doebling, Scott William [Los Alamos National Laboratory; Woods, Charles Nathan [Los Alamos National Laboratory; Kaul, Ann [Los Alamos National Laboratory; Walter, John William Jr [Los Alamos National Laboratory; Rogers, Michael Lloyd [Los Alamos National Laboratory
2016-05-09
For code verification, one compares the code output against known exact solutions. There are many standard test problems used in this capacity, such as the Noh and Sedov problems. ExactPack is a utility that integrates many of these exact solution codes into a common API (application program interface), and can be used as a stand-alone code or as a python package. ExactPack consists of python driver scripts that access a library of exact solutions written in Fortran or Python. The spatial profiles of the relevant physical quantities, such as the density, fluid velocity, sound speed, or internal energy, are returned at a time specified by the user. The solution profiles can be viewed and examined by a command line interface or a graphical user interface, and a number of analysis tools and unit tests are also provided. We have documented the physics of each problem in the solution library, and provided complete documentation on how to extend the library to include additional exact solutions. ExactPack’s code architecture makes it easy to extend the solution-code library to include additional exact solutions in a robust, reliable, and maintainable manner.
Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates
Paz-Yaacov, Nurit; Levanon, Erez Y.; Nevo, Eviatar; Kinar, Yaron; Harmelin, Alon; Jacob-Hirsch, Jasmine; Amariglio, Ninette; Eisenberg, Eli; Rechavi, Gideon
2010-01-01
Human and chimpanzee genomes are almost identical, yet humans express higher brain capabilities. Deciphering the basis for this superiority is a long sought-after challenge. Adenosine-to-inosine (A-to-I) RNA editing is a widespread modification of the transcriptome. The editing level in humans is significantly higher compared with nonprimates, due to exceptional editing within the primate-specific Alu sequences, but the global editing level of nonhuman primates has not been studied so far. Here we report the sequencing of transcribed Alu sequences in humans, chimpanzees, and rhesus monkeys. We found that, on average, the editing level in the transcripts analyzed is higher in human brain compared with nonhuman primates, even where the genomic Alu structure is unmodified. Correlated editing is observed for pairs and triplets of specific adenosines along the Alu sequences. Moreover, new editable species-specific Alu insertions, subsequent to the human–chimpanzee split, are significantly enriched in genes related to neuronal functions and neurological diseases. The enhanced editing level in the human brain and the association with neuronal functions both hint at the possible contribution of A-to-I editing to the development of higher brain function. We show here that combinatorial editing is the most significant contributor to the transcriptome repertoire and suggest that Alu editing adapted by natural selection may therefore serve as an alternate information mechanism based on the binary A/I code. PMID:20566853
Endom, Joerg
2014-05-01
Having a look into geophysical text books, you will find for all the described methods detailed lists of good practice. The variety of annotations specifies how to perform a reliable, trusty and plausible geophysical survey. Much space is used for considerations about all the necessary parameters like target depth, contrast, frequency, sampling, resolution and many other boundary conditions that account for a high quality report. But you will find rather fewer comments on locating and positioning. It seems to be self-evident in times of GNSS (Global Navigation Satellite Systems) and high performance laser total stations that positioning is a solved issue. This seems to apply for all geophysical methods that operate at walking speed or slower and for typical geoscientific or environmental investigation sites like brownfields, wasteland or archaeological spots, usually of nearly rectangular size. Using of measuring tapes, ropes and ranging poles here is also good practice. In civil engineering applications we observe lots of rectangular shaped inspection areas too but we as well get many linear structures like elongated bridge decks, dikes, railway tracks, runways and roads. Surveying of an archaeological place of 60 m by 82 m width requires a different positioning technology than surveying 5000 m along a highway although both sites have the same areal extent of around 5000 m2. If we furthermore take into account that during the last years GPR evolved into one of the fastest investigation methods in geophysics, survey speed becomes an important item. While examining railway tracks or roads today it is common to make use of these high speed capabilities. GPR services are typically performed at speeds of 80 km/h or even with higher velocities. Standard positioning methods do not longer apply to this problem. With speeds of more than 22 m/sec the internal latency of surveying systems gets quite relevant and even the effect of rounding within survey wheel systems is not
DEFF Research Database (Denmark)
Hansen, Kristoffer Arnsfelt; Podolskii, Vladimir V.
2010-01-01
with the well-studied corresponding hierarchies defined using ordinary threshold gates. A major open problem in Boolean circuit complexity is to provide an explicit super-polynomial lower bound for depth two threshold circuits. We identify the class of depth two exact threshold circuits as a natural subclass...
Exact Relativistic `Antigravity' Propulsion
Felber, Franklin S.
2006-01-01
The Schwarzschild solution is used to find the exact relativistic motion of a payload in the gravitational field of a mass moving with constant velocity. At radial approach or recession speeds faster than 3-1/2 times the speed of light, even a small mass gravitationally repels a payload. At relativistic speeds, a suitable mass can quickly propel a heavy payload from rest nearly to the speed of light with negligible stresses on the payload.
Mao, Yanfei; Wu, Feijie; Yu, Xiang; Bai, Jinjuan; Zhong, Weili; He, Yuke
2014-02-01
Leafy heads of cabbage (Brassica oleracea), Chinese cabbage (Brassica rapa), and lettuce (Lactuca sativa) are composed of extremely incurved leaves. The shape of these heads often dictates the quality, and thus the commercial value, of these crops. Using quantitative trait locus mapping of head traits within a population of 150 recombinant inbred lines of Chinese cabbage, we investigated the relationship between expression levels of microRNA-targeted Brassica rapa ssp. pekinensis TEOSINTE BRANCHED1, cycloidea, and PCF transcription factor4 (BrpTCP4) genes and head shape. Here, we demonstrate that a cylindrical head shape is associated with relatively low BrpTCP4-1 expression, whereas a round head shape is associated with high BrpTCP4-1 expression. In the round-type Chinese cabbage, microRNA319 (miR319) accumulation and BrpTCP4-1 expression decrease from the apical to central regions of leaves. Overexpression of BrpMIR319a2 reduced the expression levels of BrpTCP4 and resulted in an even distribution of BrpTCP4 transcripts within all leaf regions. Changes in temporal and spatial patterns of BrpTCP4 expression appear to be associated with excess growth of both apical and interveinal regions, straightened leaf tips, and a transition from the round to the cylindrical head shape. These results suggest that the miR319a-targeted BrpTCP gene regulates the round shape of leafy heads via differential cell division arrest in leaf regions. Therefore, the manipulation of miR319a and BrpTCP4 genes is a potentially important tool for use in the genetic improvement of head shape in these crops.
Efficient exact motif discovery.
Marschall, Tobias; Rahmann, Sven
2009-06-15
The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been satisfactorily solved in an exact and efficient manner. This is partly due to the large number of possibilities of defining the motif search space and the notion of over-representation. Even for well-defined formalizations, the problem is frequently solved in an ad hoc manner with heuristics that do not guarantee to find the best motif. We show how to solve the motif discovery problem (almost) exactly on a practically relevant space of IUPAC generalized string patterns, using the p-value with respect to an i.i.d. model or a Markov model as the measure of over-representation. In particular, (i) we use a highly accurate compound Poisson approximation for the null distribution of the number of motif occurrences. We show how to compute the exact clump size distribution using a recently introduced device called probabilistic arithmetic automaton (PAA). (ii) We define two p-value scores for over-representation, the first one based on the total number of motif occurrences, the second one based on the number of sequences in a collection with at least one occurrence. (iii) We describe an algorithm to discover the optimal pattern with respect to either of the scores. The method exploits monotonicity properties of the compound Poisson approximation and is by orders of magnitude faster than exhaustive enumeration of IUPAC strings (11.8 h compared with an extrapolated runtime of 4.8 years). (iv) We justify the use of the proposed scores for motif discovery by showing our method to outperform other motif discovery algorithms (e.g. MEME, Weeder) on benchmark datasets. We also propose new motifs on Mycobacterium tuberculosis. The method has been implemented in Java. It can be obtained from http://ls11-www.cs.tu-dortmund.de/people/marschal/paa_md/.
AbouEisha, Hassan M.
2014-01-01
The problem of attribute reduction is an important problem related to feature selection and knowledge discovery. The problem of finding reducts with minimum cardinality is NP-hard. This paper suggests a new algorithm for finding exact reducts with minimum cardinality. This algorithm transforms the initial table to a decision table of a special kind, apply a set of simplification steps to this table, and use a dynamic programming algorithm to finish the construction of an optimal reduct. I present results of computer experiments for a collection of decision tables from UCIML Repository. For many of the experimented tables, the simplification steps solved the problem.
Directory of Open Access Journals (Sweden)
Jérôme Chenal
2009-09-01
Full Text Available © Benoît Vollmer, sans titre, Nouakchott, 2007. Le travail scientifique a toujours entretenu un rapport étroit avec l’image. Dans le domaine de la médecine, l’imagerie passe aujourd’hui pour être indispensable à la plupart des interventions sur les corps ; les scanners, irm et autres procédés montrent une utilisation possible de l’image dans le monde des sciences exactes. La police scientifique que popularisent Ncis ou Les Experts , qu’ils soient de Miami, de Manhattan ...
Lau, Su-Ee; Schwarzacher, Trude; Othman, Rofina Yasmin; Harikrishna, Jennifer Ann
2015-08-11
The R2R3-MYB genes regulate pigmentation and morphogenesis of flowers, including flower and cell shape, and therefore have importance in the development of new varieties of orchids. However, new variety development is limited by the long breeding time required in orchids. In this study, we identified a cDNA, DhMYB1, that is expressed during flower development in a hybrid orchid, Dendrobium hybrida (Dendrobium bobby messina X Dendrobium chao phraya) then used the direct application of dsRNA to observe the effect of gene silencing on flower phenotype and floral epidermal cell shape. Flower bud development in the Dendrobium hybrid was characterised into seven stages and the time of meiosis was determined as between stages 3 to 5 when the bud is approximately half of the mature size. Scanning electron microscopy characterisation of adaxial epidermal cells of the flower perianth, showed that the petals and sepals each are divided into two distinct domains based on cell shape and size, while the labellum comprises seven domains. Thirty-two partial cDNA fragments representing R2R3-MYB gene sequences were isolated from D. hybrida. Phylogenetic analysis revealed that nine of the translated sequences were clustered with MYB sequences that are known to be involved in cell shape development and from these, DhMYB1 was selected for full length cDNA cloning and functional study. Direct application of a 430 bp dsRNA from the 3' region of DhMYB1 to emerging orchid flower buds reduced expression of DhMYB1 RNA compared with untreated control. Scanning electron microscopy of adaxial epidermal cells within domain one of the labellum of flowers treated with DhMYB1 dsRNA showed flattened epidermal cells whilst those of control flowers were conical. DhMYB1 is expressed throughout flower bud development and is involved in the development of the conical cell shape of the epidermal cells of the Dendrobium hybrida flower labellum. The direct application of dsRNA changed the phenotype of
Exact Solutions to Maccari's System
Pan, Jun-Ting; Gong, Lun-Xun
2007-07-01
Based on the generalized Riccati relation, an algebraic method to construct a series of exact solutions to nonlinear evolution equations is proposed. Being concise and straightforward, the method is applied to Maccari's system, and some exact solutions of the system are obtained. The method is of important significance in exploring exact solutions for other nonlinear evolution equations.
Gyorfy, Zsuzsanna; Draskovits, Gabor; Vernyik, Viktor; Blattner, Frederick F; Gaal, Tamas; Posfai, Gyorgy
2015-02-18
Ribosomal RNA (rrn) operons, characteristically present in several copies in bacterial genomes (7 in E. coli), play a central role in cellular physiology. We investigated the factors determining the optimal number of rrn operons in E. coli by constructing isogenic variants with 5-10 operons. We found that the total RNA and protein content, as well as the size of the cells reflected the number of rrn operons. While growth parameters showed only minor differences, competition experiments revealed a clear pattern: 7-8 copies were optimal under conditions of fluctuating, occasionally rich nutrient influx and lower numbers were favored in stable, nutrient-limited environments. We found that the advantages of quick adjustment to nutrient availability, rapid growth and economic regulation of ribosome number all contribute to the selection of the optimal rrn operon number. Our results suggest that the wt rrn operon number of E. coli reflects the natural, 'feast and famine' life-style of the bacterium, however, different copy numbers might be beneficial under different environmental conditions. Understanding the impact of the copy number of rrn operons on the fitness of the cell is an important step towards the creation of functional and robust genomes, the ultimate goal of synthetic biology. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Liu, Tao; Wu, Xidong; Wang, Yigang; Zhang, Tao; Wu, Ting; Liu, Fang; Wang, Wansong; Jiang, Gang; Xie, Minqiang
2016-01-01
The co-delivery of drug and gene has become the primary strategy in cancer therapy. Based on our previous work, to co-deliver docetaxel (DOC) and MMP-9 siRNA more efficiently for HNE-1 nasopharyngeal carcinoma therapy, a folate-modified star-shaped copolymer (FA-CD-PLLD) consisting of ?-cyclodextrin (CD) and poly(L-lysine) dendron (PLLD) was synthesized, and then used for DOC and MMP-9 co-delivery. Different from commonly used amphiphilic copolymers micelles, the obtained CD derivative could ...
Huang, Yan; Wang, Wenqian; Wu, Tingting; Xu, Li-Ping; Wen, Yongqiang; Zhang, Xueji
2016-11-01
A rapid, sensitive, and accurate detection strategy for microRNA 16 (miR-16) was developed, which combined the convenience of lateral flow biosensors (LFBs), the design flexibility of Y-shaped junction DNA probe, and the enhancement ability of endonuclease-assisted target recycling amplification. The system is composed of a molecular beacon (MB) probe, an assistant probe, and endonuclease Nt.BbvCI, which plays the role of signal translation and amplification. In the presence of the target microRNAs (miRNAs), three chains of nucleic acid could hybridize with each other to form a Y-shaped junction structure, which could be recognized by the endonuclease Nt.BbvCI. The MB probe was efficiently cleaved by endonuclease and produced two new DNA fragments, while the regenerated assistant probe and target were hybridized to another MB probe and entered into the next cycle of the amplification. In this way, the detection of the readily biodegradable miRNA was turned into the detection of two DNA fragments in the LFB. Meanwhile, the detection of two different DNAs would improve the accuracy and effectively avoid false results. The amplified products containing DNA fragments were then applied to the lateral flow nucleic acid biosensor (LFNAB) with two test zones, on which specific DNA probes were designed. The formed DNA-DNA/gold nanoparticle (GNP) conjugates were captured and accumulated to produce two red bands in two test zones. The logic judgment of the two test zones provided more accurate and convincing results. Under optimal conditions, the visual detection limit of miR-16 in aqueous solutions was 0.1 pM, which is 100-1000 times lower than that of visual or colorimetric methods in the literature. It could be used for on-field and point-of-care testing and meet the urgent demand of sensitive and selective miRNA detection in remote rural areas without costly equipment. The system displayed good universality, compatibility, high specificity, and stability of miRNA
The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection
Kong, Yimeng; Pan, Bohu; Chen, Longxian; Wang, Hongbing; Hao, Pei; Li, Xuan
2016-01-01
The hydrolytic deamination of adenosine to inosine (A-to-I editing) in precursor mRNA induces variable gene products at the post-transcription level. How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution, and very little is known about the selective constraints that drive the evolution of RNA editing events. Here we present a study on A-to-I RNA editing, by generating a global profile of A-to-I editing for a phylogeny of seven Drosophila species, a model system spanning an evolutionary timeframe of approximately 45 million years. Of totally 9281 editing events identified, 5150 (55.5%) are located in the coding sequences (CDS) of 2734 genes. Phylogenetic analysis places these genes into 1,526 homologous families, about 5% of total gene families in the fly lineages. Based on conservation of the editing sites, the editing events in CDS are categorized into three distinct types, representing events on singleton genes (type I), and events not conserved (type II) or conserved (type III) within multi-gene families. While both type I and II events are subject to purifying selection, notably type III events are positively selected, and highly enriched in the components and functions of the nervous system. The tissue profiles are documented for three editing types, and their critical roles are further implicated by their shifting patterns during holometabolous development and in post-mating response. In conclusion, three A-to-I RNA editing types are found to have distinct evolutionary dynamics. It appears that nervous system functions are mainly tested to determine if an A-to-I editing is beneficial for an organism. The coding plasticity enabled by A-to-I editing creates a new class of binary variations, which is a superior alternative to maintain heterozygosity of expressed genes in a diploid mating system. PMID:27467689
Jin, Emma Yu; Nebel, Markus E
2016-02-01
Various tools used to predict the secondary structure for a given RNA sequence are based on dynamic programming used to compute a conformation of minimum free energy. For structures without pseudoknots, a worst-case runtime proportional to n3, with n being the length of the sequence, results since a table of dimension n2 has to be filled in while a single entry gives rise to a linear computational effort. However, it was recently observed that reformulating the corresponding dynamic programming recursion together with the bookkeeping of potential folding alternatives (a technique called sparsification) may reduce the runtime to n2 on average, assuming that nucleotides of distance d form a hydrogen bond (i..e., are paired) with probability b/d(c) for some constants b > 0, c > 1. The latter is called the polymer-zeta model and plays a crucial role in speeding up the above mentioned algorithm. In this paper we discuss the application of the polymer-zeta property for the analysis of sparsification, showing that it must be applied conditionally on first and last positions to pair. Afterwards, we will investigate the combinatorics of RNA secondary structures assuming that the corresponding conditional probabilities behave according to a polymer-zeta probability model. We show that even if some of the structural parameters exhibit an almost realistic behavior on average, the expected shape of a folding in that model must be assumed to highly differ from those observed in nature. More precisely, we prove our polymer-zeta model to be appropriate for mRNA molecules but to fail in connection with almost every other family of RNA. Those findings explain the huge speedup of the dynamic programming algorithm observed empirically by Wexler et al. when applying sparsification in connection with mRNA data.
Su, Shao; Wu, Yan; Zhu, Dan; Chao, Jie; Liu, Xingfen; Wan, Ying; Su, Yan; Zuo, Xiaolei; Fan, Chunhai; Wang, Lianhui
2016-07-01
The performance for biomolecular detection is closely associated with the interfacial structure of a biosensor, which profoundly affects both thermodynamics and kinetics of the assembly, binding and signal transduction of biomolecules. Herein, it is reported on a one-step and template-free on-electrode synthesis method for making shape-controlled gold nanostructures on indium tin oxide substrates, which provide an electrochemical sensing platform for ultrasensitive detection of nucleic acids. Thus-prepared hierarchical flower-like gold nanostructures (HFGNs) possess large surface area that can readily accommodate the assembly of DNA probes for subsequent hybridization detection. It is found that the sensitivity for electrochemical DNA sensing is critically dependent on the morphology of HFGNs. By using this new strategy, a highly sensitive electrochemical biosensor is developed for label-free detection of microRNA-21 (miRNA-21), a biomarker for lung cancers. Importantly, it is demonstrated that this biosensor can be employed to measure the miRNA-21 expression level from human lung cancer cell (A549) lysates and worked well in 100% serum, suggesting its potential for applications in clinical diagnosis and a wide range of bioanalysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
The maximal family of exactly solvable chaos
Umeno, K
1996-01-01
A new two-parameter family of ergordic transformations with non-uniform invariant measures on the unit interval (I=[0,1]) is found here. The family has a special property that their invariant measures can be explicitly written in terms of algebraic functions of parameters and a dynamical variable. Furthermore, it is also proven here that this family is the most generalized class of exactly solvable chaos on (I) including the Ulam=Neumann map (y=4x(1-x)). Unpredictably, by choosing certain parameters, the maximal class of exactly solvable chaos is found to describe the asymmetric shape of the experimentally obtained first return maps of the Beloussof-Zhabotinski chemical reaction.
Exact piecewise flat gravitational waves
van de Meent, M.|info:eu-repo/dai/nl/314007067
2011-01-01
We generalize our previous linear result (van de Meent 2011 Class. Quantum Grav 28 075005) in obtaining gravitational waves from our piecewise flat model for gravity in 3+1 dimensions to exact piecewise flat configurations describing exact planar gravitational waves. We show explicitly how to
Directory of Open Access Journals (Sweden)
Olga Gutierrez
Full Text Available BACKGROUND: Thyrotroph embryonic factor (TEF, a member of the PAR bZIP family of transcriptional regulators, has been involved in neurotransmitter homeostasis, amino acid metabolism, and regulation of apoptotic proteins. In spite of its relevance, nothing is known about the regulation of TEF. PRINCIPAL FINDINGS: p53-dependent genotoxic agents have been shown to be much more harmful for PAR bZIP-deficient mice as compared to wild type animals. Here we demonstrate that TEF expression is controlled by p53 through upregulation of microRNA-125b, as determined by both regulating the activity of p53 and transfecting cells with microRNA-125b precursors. We also describe a novel role for TEF in controlling actin distribution and cell shape in mouse fibroblasts. Lack of TEF is accompanied by dramatic increase of cell area and decrease of elongation (bipolarity and dispersion (multipolarity. Staining of actin cytoskeleton also showed that TEF (-/- cells are characterized by appearance of circumferential actin bundles and disappearance of straight fibers. Interestingly, transfection of TEF (-/- fibroblasts with TEF induced a wild type-like phenotype. Consistent with our previous findings, transfection of wild type fibroblasts with miR-125b promoted a TEF (-/--like phenotype, and a similar but weaker effect was observed following exogenous expression of p53. CONCLUSIONS/SIGNIFICANCE: These findings provide the first evidence of TEF regulation, through a miR-125b-mediated pathway, and describes a novel role of TEF in the maintenance of cell shape in fibroblasts.
An exact factorization perspective on quantum interferences in nonadiabatic dynamics.
Curchod, Basile F E; Agostini, Federica; Gross, E K U
2016-07-21
Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of the exact factorization of the molecular wavefunction. In particular, we focus our attention on the shape of the time-dependent potential energy surface-the exact surface on which the nuclear dynamics takes place. We use a one-dimensional exactly solvable model to reproduce different conditions for quantum interferences, whose characteristic features already appear in one-dimension. The time-dependent potential energy surface develops complex features when strong interferences are present, in clear contrast to the observed behavior in simple nonadiabatic crossing cases. Nevertheless, independent classical trajectories propagated on the exact time-dependent potential energy surface reasonably conserve a distribution in configuration space that mimics one of the exact nuclear probability densities.
Exact cosmological solutions for MOG
Energy Technology Data Exchange (ETDEWEB)
Roshan, Mahmood [Ferdowsi University of Mashhad, Department of Physics, P.O. Box 1436, Mashhad (Iran, Islamic Republic of)
2015-09-15
We find some new exact cosmological solutions for the covariant scalar-tensor-vector gravity theory, the so-called modified gravity (MOG). The exact solution of the vacuum field equations has been derived. Also, for non-vacuum cases we have found some exact solutions with the aid of the Noether symmetry approach. More specifically, the symmetry vector and also the Noether conserved quantity associated to the point-like Lagrangian of the theory have been found. Also we find the exact form of the generic vector field potential of this theory by considering the behavior of the relevant point-like Lagrangian under the infinitesimal generator of the Noether symmetry. Finally, we discuss the cosmological implications of the solutions. (orig.)
Exact solution for generalized pairing
Pan, Feng; Draayer, J. P.
1997-01-01
An infinite dimensional algebra, which is useful for deriving exact solutions of the generalized pairing problem, is introduced. A formalism for diagonalizing the corresponding Hamiltonian is also proposed. The theory is illustrated with some numerical examples.
de Cooman, Gert; Troffaes, Matthias C. M.; Miranda, Enrique
2008-11-01
We study n-monotone functionals, which constitute a generalisation of n-monotone set functions. We investigate their relation to the concepts of exactness and natural extension, which generalise coherence and natural extension in the behavioural theory of imprecise probabilities. We improve upon a number of results in the literature, and prove among other things a representation result for exact n-monotone functionals in terms of Choquet integrals.
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA
Smith, Cameron; Heyne, Steffen; Richter, Andreas S.; Will, Sebastian; Backofen, Rolf
2010-01-01
The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA?RNA interaction, exact RNA matching and alignment of RNA, respectively. The Freiburg RNA tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informatik.uni-freiburg.de.
Exact discretization by Fourier transforms
Tarasov, Vasily E.
2016-08-01
A discretization of differential and integral operators of integer and non-integer orders is suggested. New type of differences, which are represented by infinite series, is proposed. A characteristic feature of the suggested differences is an implementation of the same algebraic properties that have the operator of differentiation (property of algebraic correspondence). Therefore the suggested differences are considered as an exact discretization of derivatives. These differences have a property of universality, which means that these operators do not depend on the form of differential equations and the parameters of these equations. The suggested differences operators allows us to have difference equations whose solutions are equal to the solutions of corresponding differential equations. The exact discretization of the derivatives of integer orders is given by the suggested differences of the same integer orders. Similarly, the exact discretization of the Riesz derivatives and integrals of integer and non-integer order is given by the proposed fractional differences of the same order.
Exact analysis of discrete data
Hirji, Karim F
2005-01-01
Researchers in fields ranging from biology and medicine to the social sciences, law, and economics regularly encounter variables that are discrete or categorical in nature. While there is no dearth of books on the analysis and interpretation of such data, these generally focus on large sample methods. When sample sizes are not large or the data are otherwise sparse, exact methods--methods not based on asymptotic theory--are more accurate and therefore preferable.This book introduces the statistical theory, analysis methods, and computation techniques for exact analysis of discrete data. After reviewing the relevant discrete distributions, the author develops the exact methods from the ground up in a conceptually integrated manner. The topics covered range from univariate discrete data analysis, a single and several 2 x 2 tables, a single and several 2 x K tables, incidence density and inverse sampling designs, unmatched and matched case -control studies, paired binary and trinomial response models, and Markov...
When 'exact recovery' is exact recovery in compressed sensing simulation
DEFF Research Database (Denmark)
Sturm, Bob L.
2012-01-01
In a simulation of compressed sensing (CS), one must test whether the recovered solution \\(\\vax\\) is the true solution \\(\\vx\\), i.e., ``exact recovery.'' Most CS simulations employ one of two criteria: 1) the recovered support is the true support; or 2) the normalized squared error is less than...
Computational Contact Mechanics Geometrically Exact Theory for Arbitrary Shaped Bodies
Konyukhov, Alexander
2013-01-01
This book contains a systematical analysis of geometrical situations leading to contact pairs -- point-to-surface, surface-to-surface, point-to-curve, curve-to-curve and curve-to-surface. Each contact pair is inherited with a special coordinate system based on its geometrical properties such as a Gaussian surface coordinate system or a Serret-Frenet curve coordinate system. The formulation in a covariant form allows in a straightforward fashion to consider various constitutive relations for a certain pair such as anisotropy for both frictional and structural parts. Then standard methods well known in computational contact mechanics such as penalty, Lagrange multiplier methods, combination of both and others are formulated in these coordinate systems. Such formulations require then the powerful apparatus of differential geometry of surfaces and curves as well as of convex analysis. The final goals of such transformations are then ready-for-implementation numerical algorithms within the finite e...
Liu, Tao; Xue, Wei; Ke, Bo; Xie, Min-Qiang; Ma, Dong
2014-04-01
A new cyclodextrin derivative (CD-PLLD) consisting of a β-cyclodextrin core and poly(l-lysine) dendron arms was prepared by the click conjugation of per-6-azido-b-cyclodextrin with propargyl focal point poly(l-lysine) dendron of third generation, and then used for docetaxel (DOC) and the best siRNA plasmid targeting MMP-9 (pMR3) co-delivery. Different from commonly used amphiphilic copolymers with cationic character, the as obtained cyclodextrin derivative may be used directly for the combinatorial delivery of nucleic acid and lipophilic anticancer drugs without a complicated micellization process. It was found that CD-PLLD/pMR3 nanocomplex showed a good gene transfection efficiency in vitro, and could mediate the reduce of MMP-9 protein in HNE-1 cells. For co-delivery analysis, the obtained CD-PLLD/DOC/pMR3 complexes could induce a more significant apoptosis than DOC or pMR3 used only, and decreased invasive capacity of HNE-1 cells. Moreover, the star-shaped copolymer exhibited better blood compatibility and lower cytotoxicity compared to PEI-25k in the hemolysis and MTT assays, which should be encouraged in nasopharyngeal cancer therapy. Copyright © 2014 Elsevier Ltd. All rights reserved.
Liu, Tao; Wu, Xidong; Wang, Yigang; Zhang, Tao; Wu, Ting; Liu, Fang; Wang, Wansong; Jiang, Gang; Xie, Minqiang
2016-07-05
The co-delivery of drug and gene has become the primary strategy in cancer therapy. Based on our previous work, to co-deliver docetaxel (DOC) and MMP-9 siRNA more efficiently for HNE-1 nasopharyngeal carcinoma therapy, a folate-modified star-shaped copolymer (FA-CD-PLLD) consisting of β-cyclodextrin (CD) and poly(L-lysine) dendron (PLLD) was synthesized, and then used for DOC and MMP-9 co-delivery. Different from commonly used amphiphilic copolymers micelles, the obtained CD derivative could be used directly for the combinatorial delivery of nucleic acid and hydrophobic DOC without a complicated micellization process. In vitro and in vivo assays are carried out to confirm the effectiveness of the target strategy and combined treatment. It was found that the conjugation of CD-PLLD with FA could enhance the DOC/MMP-9 delivery effect obviously, inducing a more significant apoptosis and decreasing invasive capacity of HEN-1 cells. In vivo assays showed that FA-CD-PLLD/DOC/MMP-9 could inhibit HNE-1 tumor growth and decrease PCNA expression effectively, indicating a promising strategy for nasopharyngeal carcinoma therapy. Moreover, the in vivo distribution of DOC and MMP-9, blood compatibility and toxicity are also explored.
Zhou, Xiaoyan; Zheng, Qianqian; Wang, Changyong; Xu, Jiake; Wu, Jian-Ping; Kirk, Thomas Brett; Ma, Dong; Xue, Wei
2016-05-25
The drug/gene codelivery is a promising strategy for cancer treatment. Herein, to realize the codelivery of docetaxel and MMP-9 siRNA plasmid efficiently into tumor cells, a star-shaped amphiphilic copolymer consisting of hyperbranched polyglycerol derivative (HPG-C18) and dendritic poly(l-lysine) (PLLD) was synthesized by the click reaction between azido-modified HPG-C18 and propargyl focal point PLLD. The obtained HPG-C18-PLLD could form the nanocomplexes with docetaxel and MMP-9, and the complexes showed good gene delivery ability in vitro by inducing an obvious decrease in MMP-9 protein expression in MCF-7 cells. The apoptosis assay showed that the complex could induce a more significant apoptosis to breast cancer cells than that of docetaxel or MMP-9 used alone. In vivo assay indicated that the codelivery strategy displayed a better effect on tumor inhibition. Moreover, HPG-C18-PLLD displayed lower toxicity as well as better blood compatibility compared to polyethylenimine PEI-25k, which may be the result of that HPG-C18-PLLD showed the comparative MMP-9 delivery ability in vivo compared with PEI-25k even if it showed the slight lower transfection efficiency in vitro. Therefore, HPG-C18-PLLD is a safe and effective carrier for the codelivery of drug/gene, which should be encouraged in tumor therapy.
Energy Technology Data Exchange (ETDEWEB)
Voss, L.
1986-01-01
The accuracy can be improved, and the risk of complications can be reduced in the case of cytodiagnostic lung puncture, if one optimises the method whereby the puncture needle is inserted into the lesion. The author describes such a procedure incorporating the use of technical aids for marking the exact puncture point of the cannula. At the same time the procedure results in a reduction of radiation exposure of both doctor and patient.
Exact constants in approximation theory
Korneichuk, N
1991-01-01
This book is intended as a self-contained introduction for non-specialists, or as a reference work for experts, to the particular area of approximation theory that is concerned with exact constants. The results apply mainly to extremal problems in approximation theory, which in turn are closely related to numerical analysis and optimization. The book encompasses a wide range of questions and problems: best approximation by polynomials and splines; linear approximation methods, such as spline-approximation; optimal reconstruction of functions and linear functionals. Many of the results are base
Weights of Exact Threshold Functions
DEFF Research Database (Denmark)
Babai, László; Hansen, Kristoffer Arnsfelt; Podolskii, Vladimir V.
2010-01-01
We consider Boolean exact threshold functions defined by linear equations, and in general degree d polynomials. We give upper and lower bounds on the maximum magnitude (absolute value) of the coefficients required to represent such functions. These bounds are very close and in the linear case...... and the Boolean cube {0,1} n . In the process we construct new families of ill-conditioned matrices. We further stratify the problem (in the linear case) in terms of the dimension k of the affine subspace spanned by the solutions, and give upper and lower bounds in this case as well. Our bounds here in terms of k...
AESS: Accelerated Exact Stochastic Simulation
Jenkins, David D.; Peterson, Gregory D.
2011-12-01
The Stochastic Simulation Algorithm (SSA) developed by Gillespie provides a powerful mechanism for exploring the behavior of chemical systems with small species populations or with important noise contributions. Gene circuit simulations for systems biology commonly employ the SSA method, as do ecological applications. This algorithm tends to be computationally expensive, so researchers seek an efficient implementation of SSA. In this program package, the Accelerated Exact Stochastic Simulation Algorithm (AESS) contains optimized implementations of Gillespie's SSA that improve the performance of individual simulation runs or ensembles of simulations used for sweeping parameters or to provide statistically significant results. Program summaryProgram title: AESS Catalogue identifier: AEJW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: University of Tennessee copyright agreement No. of lines in distributed program, including test data, etc.: 10 861 No. of bytes in distributed program, including test data, etc.: 394 631 Distribution format: tar.gz Programming language: C for processors, CUDA for NVIDIA GPUs Computer: Developed and tested on various x86 computers and NVIDIA C1060 Tesla and GTX 480 Fermi GPUs. The system targets x86 workstations, optionally with multicore processors or NVIDIA GPUs as accelerators. Operating system: Tested under Ubuntu Linux OS and CentOS 5.5 Linux OS Classification: 3, 16.12 Nature of problem: Simulation of chemical systems, particularly with low species populations, can be accurately performed using Gillespie's method of stochastic simulation. Numerous variations on the original stochastic simulation algorithm have been developed, including approaches that produce results with statistics that exactly match the chemical master equation (CME) as well as other approaches that approximate the CME. Solution
Ferreira, L. A.; Shnir, Ya.
2017-09-01
We introduce a Skyrme type model with the target space being the sphere S3 and with an action possessing, as usual, quadratic and quartic terms in field derivatives. The novel character of the model is that the strength of the couplings of those two terms are allowed to depend upon the space-time coordinates. The model should therefore be interpreted as an effective theory, such that those couplings correspond in fact to low energy expectation values of fields belonging to a more fundamental theory at high energies. The theory possesses a self-dual sector that saturates the Bogomolny bound leading to an energy depending linearly on the topological charge. The self-duality equations are conformally invariant in three space dimensions leading to a toroidal ansatz and exact self-dual Skyrmion solutions. Those solutions are labelled by two integers and, despite their toroidal character, the energy density is spherically symmetric when those integers are equal and oblate or prolate otherwise.
Directory of Open Access Journals (Sweden)
L.A. Ferreira
2017-09-01
Full Text Available We introduce a Skyrme type model with the target space being the sphere S3 and with an action possessing, as usual, quadratic and quartic terms in field derivatives. The novel character of the model is that the strength of the couplings of those two terms are allowed to depend upon the space–time coordinates. The model should therefore be interpreted as an effective theory, such that those couplings correspond in fact to low energy expectation values of fields belonging to a more fundamental theory at high energies. The theory possesses a self-dual sector that saturates the Bogomolny bound leading to an energy depending linearly on the topological charge. The self-duality equations are conformally invariant in three space dimensions leading to a toroidal ansatz and exact self-dual Skyrmion solutions. Those solutions are labelled by two integers and, despite their toroidal character, the energy density is spherically symmetric when those integers are equal and oblate or prolate otherwise.
Azbel‧, Mark Ya.
2005-08-01
The exact law of mortality dynamics in changing populations and environment is derived. It includes no explicit characteristics of animal-environment interactions (metabolism, etc.) which are a must for life; it is universal for all animals, from single-cell yeast to humans, with their drastically different biology, evolutionary history, and complexity; it is rapidly (within few percent of life span) reversible. Such a law is unique for live systems with their homeostatic self-adjustment to environment (cf. thermodynamics of liquids and glasses). The law which is valid for all live, and only live, systems is their specific natural law. Mortality is an instrument of natural selection and biological diversity. Its law, which is preserved in evolution of all species, is a conservation law of mortality, selection, evolution, biology. The law implies new kinds of intrinsic mortality and adaptation which dominate in evolutionary unprecedented protected populations and, in contrast to species-specific natural selection, proceed via universal stepwise rungs and reduce to universal cellular mechanism. The law demonstrates that intrinsic mortality and at least certain aspects of aging are disposable evolutionary byproducts, and directed genetic and/or biological changes may yield healthy and vital Methuselah lifespan. This is consistent with experiments. Universality implies that single-cell yeast may provide a master key to the cellular mechanism of universal mortality, aging, selection, evolution, and its regulation in all animals. One may look for its manifestations in animal cells also, e.g., in their replicative senescence and cancer. Evolutionary origin and genetic nature of universality are suggested.
Exact Solutions in Modified Gravity Models
Directory of Open Access Journals (Sweden)
Valery V. Obukhov
2012-06-01
Full Text Available We review the exact solutions in modified gravity. It is one of the main problems of mathematical physics for the gravity theory. One can obtain an exact solution if the field equations reduce to a system of ordinary differential equations. In this paper we consider a number of exact solutions obtained by the method of separation of variables. Some applications to Cosmology and BH entropy are briefly mentioned.
DEFF Research Database (Denmark)
Jin, Emma Yu; Nebel, M. E.
2016-01-01
algorithm. In this paper we discuss the application of the polymer-zeta property for the analysis of sparsification, showing that it must be applied conditionally on first and last positions to pair. Afterwards, we will investigate the combinatorics of RNA secondary structures assuming...
An Exact Fluctuating 1/2-BPS Configuration
Bellucci, Stefano
2009-01-01
This work explores the role of thermodynamic fluctuations in the two parameter giant and superstar configurations characterized by an ensemble of arbitrary liquid droplets or irregular shaped fuzzballs. Our analysis illustrates that the chemical and state-space geometric descriptions exhibit an intriguing set of exact pair correction functions and the global correlation lengths. The first principle of statistical mechanics shows that the possible canonical fluctuations may precisely be ascertained without any approximation. Interestingly, our intrinsic geometric study exemplifies that there exist exact fluctuating 1/2-BPS statistical configurations which involve an ensemble of microstates describing the liquid droplets or fuzzballs. The Gaussian fluctuations over an equilibrium chemical and state-space configurations accomplish a well-defined, non-degenerate, curved and regular intrinsic Riemannian manifolds for all physically admissible domains of black hole parameters. An explicit computation demonstrates t...
Quasi exact solution of the Rabi Hamiltonian
Koç, R; Tuetuencueler, H
2002-01-01
A method is suggested to obtain the quasi exact solution of the Rabi Hamiltonian. It is conceptually simple and can be easily extended to other systems. The analytical expressions are obtained for eigenstates and eigenvalues in terms of orthogonal polynomials. It is also demonstrated that the Rabi system, in a particular case, coincides with the quasi exactly solvable Poeschl-Teller potential.
Quantum algorithm for exact Monte Carlo sampling
Destainville, Nicolas; Georgeot, Bertrand; Giraud, Olivier
2010-01-01
We build a quantum algorithm which uses the Grover quantum search procedure in order to sample the exact equilibrium distribution of a wide range of classical statistical mechanics systems. The algorithm is based on recently developed exact Monte Carlo sampling methods, and yields a polynomial gain compared to classical procedures.
Exact, almost and delayed fault detection
DEFF Research Database (Denmark)
Niemann, Hans Henrik; Saberi, Ali; Stoorvogel, Anton A.
1999-01-01
Considers the problem of fault detection and isolation while using zero or almost zero threshold. A number of different fault detection and isolation problems using exact or almost exact disturbance decoupling are formulated. Solvability conditions are given for the formulated design problems....... The l-step delayed fault detection problem is also considered for discrete-time systems....
New exact wave solutions for Hirota equation
Indian Academy of Sciences (India)
... integrals in polynomial form with a high accuracy for two-dimensional plane autonomous systems. Exact soliton solution is constructed through the established first integrals. This method is a powerful tool for searching exact travelling solutions of nonlinear partial differential equations (NPDEs) in mathematical physics.
Hattori, Hiroyoshi; Janky, Rekin's; Nietfeld, Wilfried; Aerts, Stein; Madan Babu, M; Venkitaraman, Ashok R
2014-01-01
The human DNA damage response (DDR) triggers profound changes in gene expression, whose nature and regulation remain uncertain. Although certain micro-(mi)RNA species including miR34, miR-18, miR-16 and miR-143 have been implicated in the DDR, there is as yet no comprehensive description of genome-wide changes in the expression of miRNAs triggered by DNA breakage in human cells. We have used next-generation sequencing (NGS), combined with rigorous integrative computational analyses, to describe genome-wide changes in the expression of miRNAs during the human DDR. The changes affect 150 of 1523 miRNAs known in miRBase v18 from 4-24 h after the induction of DNA breakage, in cell-type dependent patterns. The regulatory regions of the most-highly regulated miRNA species are enriched in conserved binding sites for p53. Indeed, genome-wide changes in miRNA expression during the DDR are markedly altered in TP53-/- cells compared to otherwise isogenic controls. The expression levels of certain damage-induced, p53-regulated miRNAs in cancer samples correlate with patient survival. Our work reveals genome-wide and cell type-specific alterations in miRNA expression during the human DDR, which are regulated by the tumor suppressor protein p53. These findings provide a genomic resource to identify new molecules and mechanisms involved in the DDR, and to examine their role in tumor suppression and the clinical outcome of cancer patients.
Exact Tests for Hardy-Weinberg Proportions
National Research Council Canada - National Science Library
Engels, William R
2009-01-01
Exact conditional tests are often required to evaluate statistically whether a sample of diploids comes from a population with Hardy-Weinberg proportions or to confirm the accuracy of genotype assignments...
Fast Exact Euclidean Distance (FEED) Transformation
Schouten, Theo; Kittler, J.; van den Broek, Egon; Petrou, M.; Nixon, M.
2004-01-01
Fast Exact Euclidean Distance (FEED) transformation is introduced, starting from the inverse of the distance transformation. The prohibitive computational cost of a naive implementation of traditional Euclidean Distance Transformation, is tackled by three operations: restriction of both the number
Exact Test of Independence Using Mutual Information
Directory of Open Access Journals (Sweden)
Shawn D. Pethel
2014-05-01
Full Text Available Using a recently discovered method for producing random symbol sequences with prescribed transition counts, we present an exact null hypothesis significance test (NHST for mutual information between two random variables, the null hypothesis being that the mutual information is zero (i.e., independence. The exact tests reported in the literature assume that data samples for each variable are sequentially independent and identically distributed (iid. In general, time series data have dependencies (Markov structure that violate this condition. The algorithm given in this paper is the first exact significance test of mutual information that takes into account the Markov structure. When the Markov order is not known or indefinite, an exact test is used to determine an effective Markov order.
Exact Algorithms for Solving Stochastic Games
DEFF Research Database (Denmark)
Hansen, Kristoffer Arnsfelt; Koucky, Michal; Lauritzen, Niels
2012-01-01
Shapley's discounted stochastic games, Everett's recursive games and Gillette's undiscounted stochastic games are classical models of game theory describing two-player zero-sum games of potentially infinite duration. We describe algorithms for exactly solving these games.......Shapley's discounted stochastic games, Everett's recursive games and Gillette's undiscounted stochastic games are classical models of game theory describing two-player zero-sum games of potentially infinite duration. We describe algorithms for exactly solving these games....
Mixed Poisson distributions in exact solutions of stochastic autoregulation models.
Iyer-Biswas, Srividya; Jayaprakash, C
2014-11-01
In this paper we study the interplay between stochastic gene expression and system design using simple stochastic models of autoactivation and autoinhibition. Using the Poisson representation, a technique whose particular usefulness in the context of nonlinear gene regulation models we elucidate, we find exact results for these feedback models in the steady state. Further, we exploit this representation to analyze the parameter spaces of each model, determine which dimensionless combinations of rates are the shape determinants for each distribution, and thus demarcate where in the parameter space qualitatively different behaviors arise. These behaviors include power-law-tailed distributions, bimodal distributions, and sub-Poisson distributions. We also show how these distribution shapes change when the strength of the feedback is tuned. Using our results, we reexamine how well the autoinhibition and autoactivation models serve their conventionally assumed roles as paradigms for noise suppression and noise exploitation, respectively.
Barycentric Interpolation and Exact Integration Formulas for the Finite Volume Element Method
Voitovich, Tatiana V.; Vandewalle, Stefan
2008-09-01
This contribution concerns with the construction of a simple and effective technology for the problem of exact integration of interpolation polynomials arising while discretizing partial differential equations by the finite volume element method on simplicial meshes. It is based on the element-wise representation of the local shape functions through barycentric coordinates (barycentric interpolation) and the introducing of classes of integration formulas for the exact integration of generic monomials of barycentric coordinates over the geometrical shapes defined by a barycentric dual mesh. Numerical examples are presented that illustrate the validity of the technology.
Landscape of the exact energy functional
Cohen, Aron J
2015-01-01
One of the great challenges of electronic structure theory is the search for the exact functional of density functional theory (DFT). Its existence is undoubted but it is hard to even conceptualize it as it is a surface in a massively multidimensional space. However, the asymmetric two-site Hubbard model has a two-dimensional universe of density matrices and the exact functional simply becomes a function of two variables whose landscape can be calculated, visualized and explored. This one unique surface contains all the possible physics of any system in this universe. A walk on this landscape, moved to the angle of any one-electron Hamiltonian, gives a valley whose minimum is the exact total energy. We show concrete examples of pure-state density matrices that are not v-representable due to the underlying non-convex nature of the exact functional. Using the Perdew, Parr, Levy and Balduz extension to fractional ensembles we calculate the exact functional for all numbers of electrons. The derivative discontinui...
Exact solutions in three-dimensional gravity
Garcia-Diaz, Alberto A
2017-01-01
A self-contained text, systematically presenting the determination and classification of exact solutions in three-dimensional Einstein gravity. This book explores the theoretical framework and general physical and geometrical characteristics of each class of solutions, and includes information on the researchers responsible for their discovery. Beginning with the physical character of the solutions, these are identified and ordered on the basis of their geometrical invariant properties, symmetries, and algebraic classifications, or from the standpoint of their physical nature, for example electrodynamic fields, fluid, scalar field, or dilaton. Consequently, this text serves as a thorough catalogue on 2+1 exact solutions to the Einstein equations coupled to matter and fields, and on vacuum solutions of topologically massive gravity with a cosmological constant. The solutions are also examined from different perspectives, enabling a conceptual bridge between exact solutions of three- and four-dimensional gravit...
Exact and approximate calculation of giant resonances
Energy Technology Data Exchange (ETDEWEB)
Vertse, T. [Magyar Tudomanyos Akademia, Debrecen (Hungary). Atommag Kutato Intezete; Liotta, R.J. [Royal Inst. of Tech., Stockholm (Sweden); Maglione, E. [Padua Univ. (Italy). Ist. di Fisica
1995-02-13
Energies, sum rules and partial decay widths of giant resonances in {sup 208}Pb are calculated solving exactly the continuum RPA equations corresponding to a central Woods-Saxon potential. For comparison an approximate treatment of those quantities in terms of pole expansions of the Green function (Berggren and Mittag-Leffler) is also performed. It is found that the approximated results agree well with the exact ones. Comparison with experimental data is made and a search for physically meaningful resonances is carried out. ((orig.))
Exact Asymptotics of Bivariate Scale Mixture Distributions
Hashorva, Enkelejd
2009-01-01
Let (RU_1, R U_2) be a given bivariate scale mixture random vector, with R>0 being independent of the bivariate random vector (U_1,U_2). In this paper we derive exact asymptotic expansions of the tail probability P{RU_1> x, RU_2> ax}, a \\in (0,1] as x tends infintiy assuming that R has distribution function in the Gumbel max-domain of attraction and (U_1,U_2) has a specific tail behaviour around some absorbing point. As a special case of our results we retrieve the exact asymptotic behaviour ...
Verbal Interference Suppresses Exact Numerical Representation
Frank, Michael C.; Fedorenko, Evelina; Lai, Peter; Saxe, Rebecca; Gibson, Edward
2012-01-01
Language for number is an important case study of the relationship between language and cognition because the mechanisms of non-verbal numerical cognition are well-understood. When the Piraha (an Amazonian hunter-gatherer tribe who have no exact number words) are tested in non-verbal numerical tasks, they are able to perform one-to-one matching…
The Exact Renormalization Group -- renormalization theory revisited --
Sonoda, Hidenori
2007-01-01
We overview the entire renormalization theory, both perturbative and non-perturbative, by the method of the exact renormalization group (ERG). We emphasize particularly on the perturbative application of the ERG to the phi4 theory and QED in the four dimensional euclidean space.
Python for Education: The Exact Cover Problem
Directory of Open Access Journals (Sweden)
2011-06-01
Full Text Available
Python implementation of Algorithm X by Knuth is presented.
Algorithm X finds all solutions to the exact cover problem.
The exemplary results for pentominoes, Latin squares and Sudoku
are given.
On exact solutions of the Bogoyavlenskii equation
Indian Academy of Sciences (India)
Abstract. Exact solutions for the Bogoyavlenskii equation are studied by the travelling wave method and the singular manifold method. It is found that the linear superposition of the shock wave solution and the complex solitary wave solution for the physical field is still a solution of the equation of interest, except for a ...
Compiling Relational Bayesian Networks for Exact Inference
DEFF Research Database (Denmark)
Jaeger, Manfred; Chavira, Mark; Darwiche, Adnan
2004-01-01
We describe a system for exact inference with relational Bayesian networks as defined in the publicly available \\primula\\ tool. The system is based on compiling propositional instances of relational Bayesian networks into arithmetic circuits and then performing online inference by evaluating and ...
Exact Optimum Design of Segmented Thermoelectric Generators
Directory of Open Access Journals (Sweden)
M. Zare
2016-01-01
Full Text Available A considerable difference between experimental and theoretical results has been observed in the studies of segmented thermoelectric generators (STEGs. Because of simplicity, the approximate methods are widely used for design and optimization of the STEGs. This study is focused on employment of exact method for design and optimization of STEGs and comparison of exact and approximate results. Thus, using new highly efficient thermoelectric materials, four STEGs are proposed to operate in the temperature range of 300 to 1300 kelvins. The proposed STEGs are optimally designed to achieve maximum efficiency. Design and performance characteristics of the optimized generators including maximum conversion efficiency and length of elements are calculated through both exact and approximate methods. The comparison indicates that the approximate method can cause a difference up to 20% in calculation of some design characteristics despite its appropriate results in efficiency calculation. The results also show that the maximum theoretical efficiency of 23.08% is achievable using the new proposed STEGs. Compatibility factor of the selected materials for the proposed STEGs is also calculated using both exact and approximate methods. The comparison indicates a negligible difference in calculation of compatibility factor, despite the considerable difference in calculation of reduced efficiency (temperature independence efficiency.
Exact solutions for the biadjoint scalar field
Energy Technology Data Exchange (ETDEWEB)
White, C.D., E-mail: Christopher.White@glasgow.ac.uk [School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Centre for Research in String Theory, Queen Mary University of London, London E1 4NS (United Kingdom)
2016-12-10
Biadjoint scalar theories are novel field theories that arise in the study of non-abelian gauge and gravity amplitudes. In this short paper, we present exact nonperturbative solutions of the field equations, and compare their properties with monopole-like solutions in non-abelian gauge theory. Our results may pave the way for nonperturbative studies of the double copy.
New exact wave solutions for Hirota equation
Indian Academy of Sciences (India)
Nonlinear partial differential equations (NPDEs) of mathematical physics are major sub- jects in physical science. With the development of soliton theory, many useful methods for obtaining exact solutions of NPDEs have been presented. Some of them are: the (G /G)- expansion method [1–4], the simplest equation method ...
Calculation of exact vibration modes for plane grillages by the dynamic stiffness method
Hallauer, W. L., Jr.; Liu, R. Y. L.
1982-01-01
A dynamic stiffness method is developed for the calculation of the exact modal parameters for plane grillages which consist of straight and uniform beams with coincident elastic and inertial axes. Elementary bending-torsion beam theory is utilized, and bending translation is restricted to one direction. The exact bending-torsion dynamic stiffness matrix is obtained for a straight and uniform beam element with coincident elastic and inertial axes. The element stiffness matrices are assembled using the standard procedure of the static stiffness method to form the dynamic stiffness matrix of the complete grillage. The exact natural frequencies, mode shapes, and generalized masses of the grillage are then calculated by solving a nonlinear eigenvalue problem based on the dynamic stiffness matrix. The exact modal solutions for an example grillage are calculated and compared with the approximate solutions obtained by using the finite element method.
An exact dynamic stiffness matrix for axially loaded double-beam ...
Indian Academy of Sciences (India)
An exact dynamic stiffness method is presented in this paper to determine the natural frequencies and mode shapes of the axially loaded double-beam systems,which consist of two homogeneous and prismatic beams with a distributed spring in parallel between them.The effects of the axial force, shear deformation and ...
Welchman, Rosamond; Urso, Josephine
2000-01-01
Emphasizes the importance of children exploring hands-on and minds-on mathematics. Presents a midpoint shape activity for students to explore the midpoint shape of familiar quadrilaterals, such as squares and rectangles. (KHR)
Frank-Kamenetskii, Maxim D.
2013-01-01
A new variety on non-coding RNA has been discovered by several groups: circular RNA (circRNA). This discovery raises intriguing questions about the possibility of the existence of knotted RNA molecules and the existence of a new class of enzymes changing RNA topology, RNA topoisomerases.
Model checking exact cost for attack scenarios
DEFF Research Database (Denmark)
Aslanyan, Zaruhi; Nielson, Flemming
2017-01-01
Attack trees constitute a powerful tool for modelling security threats. Many security analyses of attack trees can be seamlessly expressed as model checking of Markov Decision Processes obtained from the attack trees, thus reaping the benefits of a coherent framework and a mature tool support....... However, current model checking does not encompass the exact cost analysis of an attack, which is standard for attack trees. Our first contribution is the logic erPCTL with cost-related operators. The extended logic allows to analyse the probability of an event satisfying given cost bounds and to compute...... the exact cost of an event. Our second contribution is the model checking algorithm for erPCTL. Finally, we apply our framework to the analysis of attack trees....
Exact solution to fractional logistic equation
West, Bruce J.
2015-07-01
The logistic equation is one of the most familiar nonlinear differential equations in the biological and social sciences. Herein we provide an exact solution to an extension of this equation to incorporate memory through the use of fractional derivatives in time. The solution to the fractional logistic equation (FLE) is obtained using the Carleman embedding technique that allows the nonlinear equation to be replaced by an infinite-order set of linear equations, which we then solve exactly. The formal series expansion for the initial value solution of the FLE is shown to be expressed in terms of a series of weighted Mittag-Leffler functions that reduces to the well known analytic solution in the limit where the fractional index for the derivative approaches unity. The numerical integration to the FLE provides an excellent fit to the analytic solution. We propose this approach as a general technique for solving a class of nonlinear fractional differential equations.
Exact Relativistic Magnetized Haloes around Rotating Disks
Directory of Open Access Journals (Sweden)
Antonio C. Gutiérrez-Piñeres
2015-01-01
Full Text Available The study of the dynamics of magnetic fields in galaxies is one of important problems in formation and evolution of galaxies. In this paper, we present the exact relativistic treatment of a rotating disk surrounded by a magnetized material halo. The features of the halo and disk are described by the distributional energy-momentum tensor of a general fluid in canonical form. All the relevant quantities and the metric and electromagnetic potentials are exactly determined by an arbitrary harmonic function only. For instance, the generalized Kuzmin-disk potential is used. The particular class of solutions obtained is asymptotically flat and satisfies all the energy conditions. Moreover, the motion of a charged particle on the halo is described. As far as we know, this is the first relativistic model describing analytically the magnetized halo of a rotating disk.
Exact solutions for helical magnetohydrodynamic equilibria
Energy Technology Data Exchange (ETDEWEB)
Villata, M. (Istituto di Fisica Generale, Universita di Torino, Via Pietro Giuria 1, I-10125 Torino (Italy)); Tsinganos, K. (Department of Physics, University of Crete and Research Center of Crete, GR-71409, Heraklion, Crete (Greece))
1993-07-01
Three novel classes of exact solutions of the generalized Grad--Shafranov equation for helically symmetric magnetohydrodynamic (MHD) equilibria are presented. The first two classes may be applied to helical MHD equilibria for plasma confined between two coaxial cylinders, while the third one to the modeling of helicoidal magnetic fields and flows in several recently observed astrophysical jets. The same solutions can be also used for the testing of sophisticated numerical codes. It is also shown that all helically symmetric MHD equilibria can be treated by the same general method which is employed to generate exact MHD solutions for systems possessing an ignorable coordinate in a system of three orthogonal basis vectors, although in the case of helical symmetry an [ital orthogonal] ignorable coordinate does not exist, contrary to what happens in the well-known cases of axial and translational symmetries.
Exact geodesic distances in FLRW spacetimes
Cunningham, William J.; Rideout, David; Halverson, James; Krioukov, Dmitri
2017-11-01
Geodesics are used in a wide array of applications in cosmology and astrophysics. However, it is not a trivial task to efficiently calculate exact geodesic distances in an arbitrary spacetime. We show that in spatially flat (3 +1 )-dimensional Friedmann-Lemaître-Robertson-Walker (FLRW) spacetimes, it is possible to integrate the second-order geodesic differential equations, and derive a general method for finding both timelike and spacelike distances given initial-value or boundary-value constraints. In flat spacetimes with either dark energy or matter, whether dust, radiation, or a stiff fluid, we find an exact closed-form solution for geodesic distances. In spacetimes with a mixture of dark energy and matter, including spacetimes used to model our physical universe, there exists no closed-form solution, but we provide a fast numerical method to compute geodesics. A general method is also described for determining the geodesic connectedness of an FLRW manifold, provided only its scale factor.
Introduction to Hubbard model and exact diagonalization
Directory of Open Access Journals (Sweden)
S. Akbar Jafari
2008-06-01
Full Text Available Hubbard model is an important model in the theory of strongly correlated electron systems. In this contribution we introduce this model and the concepts of electron correlation by building on a tight binding model. After enumerating various methods of tackling the Hubbard model, we introduce the numerical method of exact diagonalization in detail. The book keeping and practical implementation aspects are illustrated with analytically solvable example of two-site Hubbard model.
Introduction to Hubbard model and exact diagonalization
S. Akbar Jafari
2008-01-01
Hubbard model is an important model in the theory of strongly correlated electron systems. In this contribution we introduce this model and the concepts of electron correlation by building on a tight binding model. After enumerating various methods of tackling the Hubbard model, we introduce the numerical method of exact diagonalization in detail. The book keeping and practical implementation aspects are illustrated with analytically solvable example of two-site Hubbard model.
Exact BPS bound for noncommutative baby Skyrmions
Energy Technology Data Exchange (ETDEWEB)
Domrin, Andrei, E-mail: domrin@mi.ras.ru [Department of Mathematics and Mechanics, Moscow State University, Leninskie gory, 119992, GSP-2, Moscow (Russian Federation); Lechtenfeld, Olaf, E-mail: lechtenf@itp.uni-hannover.de [Institut für Theoretische Physik and Riemann Center for Geometry and Physics, Leibniz Universität Hannover, Appelstraße 2, 30167 Hannover (Germany); Linares, Román, E-mail: lirr@xanum.uam.mx [Departamento de Física, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco 186, C.P. 09340, México D.F. (Mexico); Maceda, Marco, E-mail: mmac@xanum.uam.mx [Departamento de Física, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco 186, C.P. 09340, México D.F. (Mexico)
2013-11-25
The noncommutative baby Skyrme model is a Moyal deformation of the two-dimensional sigma model plus a Skyrme term, with a group-valued or Grassmannian target. Exact abelian solitonic solutions have been identified analytically in this model, with a singular commutative limit. Inside any given Grassmannian, we establish a BPS bound for the energy functional, which is saturated by these baby Skyrmions. This asserts their stability for unit charge, as we also test in second-order perturbation theory.
Vaidya-like exact solutions with torsion
Blagojević, M
2015-01-01
Starting from the Oliva-Tempo-Troncoso black hole, a solution of the Bergshoeff-Hohm-Townsend massive gravity, a new class of the Vaidya-like exact solutions with torsion is constructed in the three-dimensional Poincar\\'e gauge theory. A particular subclass of these solutions is shown to possess the asymptotic conformal symmetry. The related canonical energy contains a contribution stemming from torsion.
New exact cosmologies on the brane
Astashenok, Artyom V.; Yurov, Artyom V.; Chervon, Sergey V.; Shabanov, Evgeniy V.; Sami, Mohammad
2014-10-01
We develop a method for constructing exact cosmological solutions in brane world cosmology. New classes of cosmological solutions on Randall-Sandrum brane are obtained. The superpotential and Hubble parameter are represented in quadratures. These solutions have inflationary phases under general assumptions and also describe an exit from the inflationary phase without a fine tuning of the parameters. Another class solutions can describe the current phase of accelerated expansion with or without possible exit from it.
Exact tests for Hardy-Weinberg proportions.
Engels, William R
2009-12-01
Exact conditional tests are often required to evaluate statistically whether a sample of diploids comes from a population with Hardy-Weinberg proportions or to confirm the accuracy of genotype assignments. This requirement is especially common when the sample includes multiple alleles and sparse data, thus rendering asymptotic methods, such as the common chi(2)-test, unreliable. Such an exact test can be performed using the likelihood ratio as its test statistic rather than the more commonly used probability test. Conceptual advantages in using the likelihood ratio are discussed. A substantially improved algorithm is described to permit the performance of a full-enumeration exact test on sample sizes that are too large for previous methods. An improved Monte Carlo algorithm is also proposed for samples that preclude full enumeration. These algorithms are about two orders of magnitude faster than those currently in use. Finally, methods are derived to compute the number of possible samples with a given set of allele counts, a useful quantity for evaluating the feasibility of the full enumeration procedure. Software implementing these methods, ExactoHW, is provided.
Exact Eigenfunctions of a Chaotic System
Ausländer, O M
1997-01-01
The interest in the properties of quantum systems, whose classical dynamics are chaotic, derives from their abundance in nature. The spectrum of such systems can be related, in the semiclassical approximation (SCA), to the unstable classical periodic orbits, through Gutzwiller's trace formula. The class of systems studied in this work, tiling billiards on the pseudo-sphere, is special in this correspondence being exact, via Selberg's trace formula. In this work, an exact expression for Green's function (GF) and the eigenfunctions (EF) of tiling billiards on the pseudo-sphere, whose classical dynamics are chaotic, is derived. GF is shown to be equal to the quotient of two infinite sums over periodic orbits, where the denominator is the spectral determinant. Such a result is known to be true for typical chaotic systems, in the leading SCA. From the exact expression for GF, individual EF can be identified. In order to obtain a SCA by finite series for the infinite sums encountered, resummation by analytic contin...
On the exactness of soft theorems
Guerrieri, Andrea L.; Huang, Yu-tin; Li, Zhizhong; Wen, Congkao
2017-12-01
Soft behaviours of S-matrix for massless theories reflect the underlying symmetry principle that enforces its masslessness. As an expansion in soft momenta, sub-leading soft theorems can arise either due to (I) unique structure of the fundamental vertex or (II) presence of enhanced broken-symmetries. While the former is expected to be modified by infrared or ultraviolet divergences, the latter should remain exact to all orders in perturbation theory. Using current algebra, we clarify such distinction for spontaneously broken (super) Poincaré and (super) conformal symmetry. We compute the UV divergences of DBI, conformal DBI, and A-V theory to verify the exactness of type (II) soft theorems, while type (I) are shown to be broken and the soft-modifying higher-dimensional operators are identified. As further evidence for the exactness of type (II) soft theorems, we consider the α' expansion of both super and bosonic open strings amplitudes, and verify the validity of the translation symmetry breaking soft-theorems up to O({α}^' 6}) . Thus the massless S-matrix of string theory "knows" about the presence of D-branes.
Fundamentals of the exact renormalization group
Rosten, Oliver J.
2012-02-01
Various aspects of the Exact Renormalization Group (ERG) are explored, starting with a review of the concepts underpinning the framework and the circumstances under which it is expected to be useful. A particular emphasis is placed on the intuitive picture provided for both renormalization in quantum field theory and universality associated with second order phase transitions. A qualitative discussion of triviality, asymptotic freedom and asymptotic safety is presented. Focusing on scalar field theory, the construction of assorted flow equations is considered using a general approach, whereby different ERGs follow from field redefinitions. It is recalled that Polchinski’s equation can be cast as a heat equation, which provides intuition and computational techniques for what follows. The analysis of properties of exact solutions to flow equations includes a proof that the spectrum of the anomalous dimension at critical fixed-points is quantized. Two alternative methods for computing the β-function in λϕ4 theory are considered. For one of these it is found that all explicit dependence on the non-universal differences between a family of ERGs cancels out, exactly. The Wilson-Fisher fixed-point is rediscovered in a rather novel way. The discussion of nonperturbative approximation schemes focuses on the derivative expansion, and includes a refinement of the arguments that, at the lowest order in this approximation, a function can be constructed which decreases monotonically along the flow. A new perspective is provided on the relationship between the renormalizability of the Wilsonian effective action and of correlation functions, following which the construction of manifestly gauge invariant ERGs is sketched, and some new insights are given. Drawing these strands together suggests a new approach to quantum field theory.
Supersymmetric QCD: exact results and strong coupling
Dine, Michael; Festuccia, Guido; Pack, Lawrence; Park, Chang-Soon; Ubaldi, Lorenzo; Wu, Weitao
2011-05-01
We revisit two longstanding puzzles in supersymmetric gauge theories. The first concerns the question of the holomorphy of the coupling, and related to this the possible definition of an exact (NSVZ) beta function. The second concerns instantons in pure gluodynamics, which appear to give sensible, exact results for certain correlation functions, which nonetheless differ from those obtained using systematic weak coupling expansions. For the first question, we extend an earlier proposal of Arkani-Hamed and Murayama, showing that if their regulated action is written suitably, the holomorphy of the couplings is manifest, and it is easy to determine the renormalization scheme for which the NSVZ formula holds. This scheme, however, is seen to be one of an infinite class of schemes, each leading to an exact beta function; the NSVZ scheme, while simple, is not selected by any compelling physical consideration. For the second question, we explain why the instanton computation in the pure supersymmetric gauge theory is not reliable, even at short distances. The semiclassical expansion about the instanton is purely formal; if infrared divergences appear, they spoil arguments based on holomorphy. We demonstrate that infrared divergences do not occur in the perturbation expansion about the instanton, but explain that there is no reason to think this captures all contributions from the sector with unit topological charge. That one expects additional contributions is illustrated by dilute gas corrections. These are infrared divergent, and so difficult to define, but if non-zero give order one, holomorphic, corrections to the leading result. Exploiting an earlier analysis of Davies et al, we demonstrate that in the theory compactified on a circle of radius β, due to infrared effects, finite contributions indeed arise which are not visible in the formal β → ∞ limit.
Exact formation of hairy planar black holes
Fan, Zhong-Ying; Chen, Bin
2015-01-01
We consider Einstein gravity minimally coupled to a scalar field with a given potential in general dimensions. We obtain large classes of static hairy planar black holes which are asymptotic to AdS space-times. In particular, for a special case $\\mu=(n-2)/2$, we obtain new classes of exact dynamical solutions describing black holes formation. We find there are two classes of collapse solutions. The first class solutions describe the evolution start from AdS space-time with a naked singularity...
Compiling Relational Bayesian Networks for Exact Inference
DEFF Research Database (Denmark)
Jaeger, Manfred; Darwiche, Adnan; Chavira, Mark
2006-01-01
We describe in this paper a system for exact inference with relational Bayesian networks as defined in the publicly available PRIMULA tool. The system is based on compiling propositional instances of relational Bayesian networks into arithmetic circuits and then performing online inference...... by evaluating and differentiating these circuits in time linear in their size. We report on experimental results showing successful compilation and efficient inference on relational Bayesian networks, whose PRIMULA--generated propositional instances have thousands of variables, and whose jointrees have clusters...
Entanglement and relaxation in exactly solvable models
Lychkovskiy, O.
2011-11-01
A system put in contact with a large heat bath normally thermalizes. This means that the state of the system ρℐ( t) approaches an equilibrium state ρ{eq/ℐ}, the latter depending only on macroscopic characteristics of the bath (e.g. temperature), but not on the initial state of the system. The above statement is the cornerstone of the equilibrium statistical mechanics; its validity and its domain of applicability are central questions in the studies of the foundations of statistical mechanics. In the present contribution we discuss the recently proven general theorems about thermalization and demonstrate how they work in exactly solvable models. In particular, we review a necessary condition for the system initial state independence (ISI) of ρ{eq/ℐ}, which was proven in our previous work, and apply it for two exactly solvable models, the XX spin chain and a central spin model with a special interaction with the environment. In the latter case we are able to prove the absence of the system ISI. Also the Eigenstate Thermalization Hypothesis is discussed. It is pointed out that although it is supposed to be generically true in essentially not-integrable ( chaotic) quantum systems, it is how-ever also valid in the integrable XX model.
Exact Solution for a Gravitational Wave Detector
Rabounski, Dmitri; Borissova, Larissa
2008-04-01
The experimental statement on gravitational waves proceeds from the equation for deviating geodesic lines and the equation for deviating non-geodesics. Weber's result was not based upon an exact solution to the equations, but on an approximate analysis of what could be expected: he expected that a plane weak wave of the space metric may displace two resting particles with respect to each other. In this work, exact solutions are presented for the deviation equation of both free and spring-connected particles. The solutions show that a gravitational wave may displace particles in a two-particle system only if they are in motion with respect to each other or the local space (there is no effect if they are at rest). Thus, gravitational waves produce a parametric effect on a two-particle system. According to the solutions, an altered detector construction can be proposed such that it might interact with gravitational waves: 1) a horizontally suspended cylindrical pig, whose butt-ends have basic relative oscillations induced by a laboratory source; 2) a free-mass detector where suspended mirrors have laboratory induced basic oscillations relative to each other.
Bringing RNA into View: RNA and Its Roles in Biology.
Atkins, John F.; Ellington, Andrew; Friedman, B. Ellen; Gesteland, Raymond F.; Noller, Harry F.; Pasquale, Stephen M.; Storey, Richard D.; Uhlenbeck, Olke C.; Weiner, Alan M.
This guide presents a module for college students on ribonucleic acid (RNA) and its role in biology. The module aims to integrate the latest research and its findings into college-level biology and provide an opportunity for students to understand biological processes. Four activities are presented: (1) "RNA Structure: Tapes to Shapes"; (2) "RNA…
Exact renormalization group study of fermionic theories
Comellas, Jordi; Kubyshin, Yuri; Moreno, Enrique
1997-02-01
The exact renormalization group approach (ERG) is developed for the case of pure fermionic theories by deriving a Grassmann version of the ERG equation and applying it to the study of fixed point solutions and critical exponents of the two-dimensional chiral Gross-Neveu model. An approximation based on the derivative expansion and a further truncation in the number of fields is used. Two solutions are obtained analytically in the limit N → ∞, with N being the number of fermionic species. For finite N some fixed point solutions, with their anomalous dimensions and critical exponents, are computed numerically. The issue of separation of physical results from the numerous spurious ones is discussed. We argue that one of the solutions we find can be identified with that of Dashen and Frishman, whereas the others seem to be new ones.
On truncations of the exact renormalization group
Morris, T R
1994-01-01
We investigate the Exact Renormalization Group (ERG) description of (Z_2 invariant) one-component scalar field theory, in the approximation in which all momentum dependence is discarded in the effective vertices. In this context we show how one can perform a systematic search for non-perturbative continuum limits without making any assumption about the form of the lagrangian. Concentrating on the non-perturbative three dimensional Wilson fixed point, we then show that the sequence of truncations n=2,3,\\dots, obtained by expanding about the field \\varphi=0 and discarding all powers \\varphi^{2n+2} and higher, yields solutions that at first converge to the answer obtained without truncation, but then cease to further converge beyond a certain point. No completely reliable method exists to reject the many spurious solutions that are also found. These properties are explained in terms of the analytic behaviour of the untruncated solutions -- which we describe in some detail.
Interference-exact radiative transfer equation
DEFF Research Database (Denmark)
Partanen, Mikko; Haÿrynen, Teppo; Oksanen, Jani
2017-01-01
Maxwell's equations with stochastic or quantum optical source terms accounting for the quantum nature of light. We show that both the nonlocal wave and local particle features associated with interference and emission of propagating fields in stratified geometries can be fully captured by local damping...... equation (RTE) as a physically transparent interference-exact model that extends the useful range of computationally efficient and quantum optically accurate interference-aware optical models from simple structures to full optical devices.......The Purcell effect, i.e., the modification of the spontaneous emission rate by optical interference, profoundly affects the light-matter coupling in optical resonators. Fully describing the optical absorption, emission, and interference of light hence conventionally requires combining the full...
An exactly solvable system from quantum optics
Energy Technology Data Exchange (ETDEWEB)
Maciejewski, Andrzej J., E-mail: maciejka@astro.ia.uz.zgora.pl [J. Kepler Institute of Astronomy, University of Zielona Góra, Licealna 9, PL-65-417 Zielona Góra (Poland); Przybylska, Maria, E-mail: M.Przybylska@if.uz.zgora.pl [Institute of Physics, University of Zielona Góra, Licealna 9, 65-417 Zielona Góra (Poland); Stachowiak, Tomasz, E-mail: stachowiak@cft.edu.pl [Center for Theoretical Physics PAS, Al. Lotników 32/46, 02-668 Warsaw (Poland)
2015-07-31
We investigate a generalisation of the Rabi system in the Bargmann–Fock representation. In this representation the eigenproblem of the considered quantum model is described by a system of two linear differential equations with one independent variable. The system has only one irregular singular point at infinity. We show how the quantisation of the model is related to asymptotic behaviour of solutions in a vicinity of this point. The explicit formulae for the spectrum and eigenfunctions of the model follow from an analysis of the Stokes phenomenon. An interpretation of the obtained results in terms of differential Galois group of the system is also given. - Highlights: • New exactly solvable system from quantum optics is found. • Normalisation condition for system in Bargmann representation is used. • Formulae for spectrum and eigenfunctions from analysis of Stokes phenomenon are given.
Exact eigenfunctions and the open topological string
Mariño, Marcos; Zakany, Szabolcs
2017-08-01
Mirror curves to toric Calabi-Yau threefolds can be quantized and lead to trace class operators on the real line. The eigenvalues of these operators are encoded in the BPS invariants of the underlying threefold, but much less is known about their eigenfunctions. In this paper, we first develop methods in spectral theory to compute these eigenfunctions. We also provide an integral matrix representation which allows them to be studied in a ’t Hooft limit, where they are described by standard topological open string amplitudes. Based on these results, we propose a conjecture for the exact eigenfunctions, which involves both the WKB wavefunction and the standard topological string wavefunction. This conjecture can be made completely explicit in the maximally supersymmetric, or self-dual case, which we work out in detail for local \
Exact and Efficient Sampling of Conditioned Walks
Adorisio, Matteo; Pezzotta, Alberto; de Mulatier, Clélia; Micheletti, Cristian; Celani, Antonio
2017-11-01
A computationally challenging and open problem is how to efficiently generate equilibrated samples of conditioned walks. We present here a general stochastic approach that allows one to produce these samples with their correct statistical weight and without rejections. The method is illustrated for a jump process conditioned to evolve within a cylindrical channel and forced to reach one of its ends. We obtain analytically the exact probability density function of the jumps and offer a direct method for gathering equilibrated samples of a random walk conditioned to stay in a channel with suitable boundary conditions. Unbiased walks of arbitrary length can thus be generated with linear computational complexity—even when the channel width is much smaller than the typical bond length of the unconditioned walk. By profiling the metric properties of the generated walks for various bond lengths we characterize the crossover between weak and strong confinement regimes with great detail.
A Regulatory RNA Inducing Transgenerationally Inherited Phenotypes
DEFF Research Database (Denmark)
Jensen, Lea Møller
. The variation in Arabidopsis enables different regulatory networks and mechanisms to shape the phenotypic characteristics. The thesis describes the identification of regulatory RNA encoded by an enzyme encoding gene. The RNA regulates by inducing transgenerationally inherited phenotypes. The function of the RNA...... is dependent on the genetic background illustrating that polymorphisms are found in either interactors or target genes of the RNA. Furthermore, the RNA provides a mechanistic link between accumulation of glucosinolate and onset of flowering....
RNA Accessibility in cubic time
Directory of Open Access Journals (Sweden)
Hofacker Ivo L
2011-03-01
Full Text Available Abstract Background The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility of the Shine-Dalgarno sequence is essential for translation to start in prokaryotes. Furthermore, many classes of RNA binding proteins require the binding site to be single-stranded. Results We introduce a way to compute the accessibility of all intervals within an RNA sequence in (n3 time. This improves on previous implementations where only intervals of one defined length were computed in the same time. While the algorithm is in the same efficiency class as sampling approaches, the results, especially if the probabilities get small, are much more exact. Conclusions Our algorithm significantly speeds up methods for the prediction of RNA-RNA interactions and other applications that require the accessibility of RNA molecules. The algorithm is already available in the program RNAplfold of the ViennaRNA package.
An Exact Renormalization Group analysis of 3-d Well Developed turbulence
Tomassini, P
1997-01-01
We take advantage of peculiar properties of three dimensional incompressible turbulence to introduce a nonstandard Exact Renormalization Group method. A Galilean invariance preserving regularizing procedure is utilized and a field truncation is adopted to test the method. Results are encouraging: the energy spectrum E(k) in the inertial range scales with exponent -1.666+/- 0.001 and the Kolmogorov constant C_K, computed for several (realistic) shapes of the stirring force correlator, agrees with experimental data.
FLAG: Exact Fourier-Laguerre transform on the ball
Leistedt, Boris; McEwen, Jason
2017-10-01
FLAG is a fast implementation of the Fourier-Laguerre Transform, a novel 3D transform exploiting an exact quadrature rule of the ball to construct an exact harmonic transform in 3D spherical coordinates. The angular part of the Fourier-Laguerre transform uses the MW sampling theorem and the exact spherical harmonic transform implemented in the SSHT code. The radial sampling scheme arises from an exact quadrature of the radial half-line using damped Laguerre polynomials. The radial transform can in fact be used to compute the spherical Bessel transform exactly, and the Fourier-Laguerre transform is thus closely related to the Fourier-Bessel transform.
On truncations of the exact renormalization group
Morris, Tim R.
1994-08-01
We investigate the Exact Renormalization Group (ERG) description of ( Z2 invariant) one-component scalar field theory, in the approximation in which all momentum dependence is discarded in the effective vertices. In this context we show how one can perform a systematic search for non-perturbative continuum limits without making any assumption about the form of the lagrangian. The approximation is seen to be a good one, both qualitatively and quantitatively. We then consider the further approximation of truncating the lagrangian to polynomial in the field dependence. Concentrating on the non-perturbative three dimensional Wilson fixed point, we show that the sequence of truncations n = 2,3,…, obtained by expanding about the field ϕ = 0 and discarding all powers ϕ2 n+2 and higher, yields solutions that at first converge to the answer obtained without truncation, but then cease to further converge beyond a certain point. Within the sequence of truncations, no completely reliable method exists to reject the many spurious solutions that are also generated. These properties are explained in terms of the analytic behaviour of the untruncated solutions - which we describe in some detail.
Exact Fit of Simple Finite Mixture Models
Directory of Open Access Journals (Sweden)
Dirk Tasche
2014-11-01
Full Text Available How to forecast next year’s portfolio-wide credit default rate based on last year’s default observations and the current score distribution? A classical approach to this problem consists of fitting a mixture of the conditional score distributions observed last year to the current score distribution. This is a special (simple case of a finite mixture model where the mixture components are fixed and only the weights of the components are estimated. The optimum weights provide a forecast of next year’s portfolio-wide default rate. We point out that the maximum-likelihood (ML approach to fitting the mixture distribution not only gives an optimum but even an exact fit if we allow the mixture components to vary but keep their density ratio fixed. From this observation we can conclude that the standard default rate forecast based on last year’s conditional default rates will always be located between last year’s portfolio-wide default rate and the ML forecast for next year. As an application example, cost quantification is then discussed. We also discuss how the mixture model based estimation methods can be used to forecast total loss. This involves the reinterpretation of an individual classification problem as a collective quantification problem.
STELLAR: fast and exact local alignments
Directory of Open Access Journals (Sweden)
Weese David
2011-10-01
Full Text Available Abstract Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de.
Exact Hypothesis Tests for Log-linear Models with exactLoglinTest
Directory of Open Access Journals (Sweden)
Brian Caffo
2006-11-01
Full Text Available This manuscript overviews exact testing of goodness of fit for log-linear models using the R package exactLoglinTest. This package evaluates model fit for Poisson log-linear models by conditioning on minimal sufficient statistics to remove nuisance parameters. A Monte Carlo algorithm is proposed to estimate P values from the resulting conditional distribution. In particular, this package implements a sequentially rounded normal approximation and importance sampling to approximate probabilities from the conditional distribution. Usually, this results in a high percentage of valid samples. However, in instances where this is not the case, a Metropolis Hastings algorithm can be implemented that makes more localized jumps within the reference set. The manuscript details how some conditional tests for binomial logit models can also be viewed as conditional Poisson log-linear models and hence can be performed via exactLoglinTest. A diverse battery of examples is considered to highlight use, features and extensions of the software. Notably, potential extensions to evaluating disclosure risk are also considered.
Koenderink, J J; van Doorn, A J
1986-01-01
Many useful notions of partial order and/or similarity and relatedness of different geometrical features of smooth shapes that occur in psychologically valid descriptions of shape have no equivalents in the usual geometrical shape theories. This is especially true where similarities are noted between objects of different connectivity: in almost all of the present theories the topological type generates the primary categorization. It is argued that such relations find a logical place only in shape theories that involve morphogenesis. Any object can be embedded uniquely in a morphogenetic sequence if one takes resolution as the parameter of the sequence. A theory of measurement is presented that allows one to define surfaces and (boundary-) curves on multiple levels of resolution. The embedding is essentially unique and is generated via a partial differential equation that governs the evolution. A canonical projection connects any high resolution specimen to lower resolution versions. The bifurcation set of the projection generates natural part boundaries. Singularities of the evolution are completely characterized as emergence, accretion and versification processes (involving topological change) and singularities by which inflections (inflection points for curves, parabolic curves for surfaces) are generated. The latter singularities involve a single process for the generation of inflections and three other processes by which the existing inflection structure may be changed. Relations with existing theories in vogue in robotics and AI, as well as in psychophysics are discussed.
Exact sampling hardness of Ising spin models
Fefferman, B.; Foss-Feig, M.; Gorshkov, A. V.
2017-09-01
We study the complexity of classically sampling from the output distribution of an Ising spin model, which can be implemented naturally in a variety of atomic, molecular, and optical systems. In particular, we construct a specific example of an Ising Hamiltonian that, after time evolution starting from a trivial initial state, produces a particular output configuration with probability very nearly proportional to the square of the permanent of a matrix with arbitrary integer entries. In a similar spirit to boson sampling, the ability to sample classically from the probability distribution induced by time evolution under this Hamiltonian would imply unlikely complexity theoretic consequences, suggesting that the dynamics of such a spin model cannot be efficiently simulated with a classical computer. Physical Ising spin systems capable of achieving problem-size instances (i.e., qubit numbers) large enough so that classical sampling of the output distribution is classically difficult in practice may be achievable in the near future. Unlike boson sampling, our current results only imply hardness of exact classical sampling, leaving open the important question of whether a much stronger approximate-sampling hardness result holds in this context. The latter is most likely necessary to enable a convincing experimental demonstration of quantum supremacy. As referenced in a recent paper [A. Bouland, L. Mancinska, and X. Zhang, in Proceedings of the 31st Conference on Computational Complexity (CCC 2016), Leibniz International Proceedings in Informatics (Schloss Dagstuhl-Leibniz-Zentrum für Informatik, Dagstuhl, 2016)], our result completes the sampling hardness classification of two-qubit commuting Hamiltonians.
Energy Technology Data Exchange (ETDEWEB)
Domingo, E. (Instituto de Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Madrid, Canto Blanco, Madrid (ES)); Holland, J.J. (California Univ., San Diego, La Jolla, CA (USA). Dept. of Biology); Ahlquist, P. (Wisconsin Univ., Madison, WI (USA). Dept. of Plant Pathology)
1988-01-01
This book contains the proceedings on RNA gentics: Variability of RNA genomes, Volume III. Topics covered include: High error rate, population equilibrium, and evolution of RNA replication systems; Influenza viruses; High rate of nutation and evolution; and Sequence space and quasi species distribution.
Pendar, Hodjat; Platini, Thierry; Kulkarni, Rahul V
2013-04-01
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations; hence, there is considerable interest in quantifying noise in gene expression using stochastic models. However, obtaining exact analytical results for protein distributions has been an intractable task for all but the simplest models. Here, we invoke the partitioning property of Poisson processes to develop a mapping that significantly simplifies the analysis of stochastic models of gene expression. The mapping leads to exact protein distributions using results for mRNA distributions in models with promoter-based regulation. Using this approach, we derive exact analytical results for steady-state and time-dependent distributions for the basic two-stage model of gene expression. Furthermore, we show how the mapping leads to exact protein distributions for extensions of the basic model that include the effects of posttranscriptional and posttranslational regulation. The approach developed in this work is widely applicable and can contribute to a quantitative understanding of stochasticity in gene expression and its regulation.
Upper bounds on minimum cardinality of exact and approximate reducts
Chikalov, Igor
2010-01-01
In the paper, we consider the notions of exact and approximate decision reducts for binary decision tables. We present upper bounds on minimum cardinality of exact and approximate reducts depending on the number of rows (objects) in the decision table. We show that the bound for exact reducts is unimprovable in the general case, and the bound for approximate reducts is almost unimprovable in the general case. © 2010 Springer-Verlag Berlin Heidelberg.
Quasitraces on exact C*-algebras are traces
DEFF Research Database (Denmark)
Haagerup, Uffe
2014-01-01
It is shown that all 2-quasitraces on a unital exact C ∗ -algebra are traces. As consequences one gets: (1) Every stably finite exact unital C ∗ -algebra has a tracial state, and (2) if an AW ∗ -factor of type II 1 is generated (as an AW ∗ -algebra) by an exact C ∗ -subalgebra, then i...
New exact travelling wave solutions of some complex nonlinear equations
Bekir, Ahmet
2009-04-01
In this paper, we establish exact solutions for complex nonlinear equations. The tanh-coth and the sine-cosine methods are used to construct exact periodic and soliton solutions of these equations. Many new families of exact travelling wave solutions of the coupled Higgs and Maccari equations are successfully obtained. These solutions may be important of significance for the explanation of some practical physical problems.
The 5'-3' Distance of RNA Secondary Structures
DEFF Research Database (Denmark)
Han, Hillary S W; Reidys, Christian
2012-01-01
Abstract Recently, Yoffe and colleagues observed that the average distances between 5'-3' ends of RNA molecules are very small and largely independent of sequence length. This observation is based on numerical computations as well as theoretical arguments maximizing certain entropy functionals....... In this article, we compute the exact distribution of 5'-3' distances of RNA secondary structures for any finite n. Furthermore, we compute the limit distribution and show that for n = 30 the exact distribution and the limit distribution are very close. Our results show that the distances of random RNA secondary...... structures are distinctively lower than those of minimum free energy structures of random RNA sequences....
incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
Drory Retwitzer, Matan; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny
2016-07-08
In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
Exact solutions to the supply chain equations for arbitrary, time-dependent demands
DEFF Research Database (Denmark)
Warburton, Roger D.H.; Hodgson, J.P.E.; Nielsen, Erland Hejn
2014-01-01
, so users can determine the inventory behavior to any desired precision. To illustrate, we solve the equations for a non-linear, quadratic time-dependence in the demand. For practical use, only a few terms in the series are required, a proposition illustrated by the For All Practical Purposes (FAPP......We study the impact on inventory of an unexpected, non-linear, time-dependent demand and present the exact solutions over time to the supply chain equations without requiring any approximations. We begin by imposing a boundary condition of stability at infinity, from which we derive expressions...... for the estimated demand and the target work in progress when the demand is time-dependent. The resulting inventory equation is solved in terms of the Lambert modes with all of the demand non-linearities confined to the pre-shape function. The series solution is exact, and all terms are reasonably easy to calculate...
Exact Algorithms for the Clustered Vehicle Routing Problem
Battarra, M.; Erdogan, G.; Vigo, D.
2014-01-01
This study presents new exact algorithms for the clustered vehicle routing problem (CluVRP). The CluVRP is a generalization of the capacitated vehicle routing problem (CVRP), in which the customers are grouped into clusters. As in the CVRP, all the customers must be visited exactly once, but a
Classical charged fluids at equilibrium near an interface: Exact ...
Indian Academy of Sciences (India)
Home; Journals; Pramana – Journal of Physics; Volume 64; Issue 5. Classical charged fluids at equilibrium near an interface: Exact analytical density profiles and surface tension. Françoise Cornu. Invited Talks:- Topic 1. Rigorous results and exact solutions; general aspects of statistical physics; thermodynamics Volume 64 ...
Exact solutions of some nonlinear partial differential equations using ...
Indian Academy of Sciences (India)
Research Articles Volume 81 Issue 2 August 2013 pp 225-236 ... Abstract. The functional variable method is a powerful solution method for obtaining exact solutions of some nonlinear partial differential equations. In this paper ... By using this useful method, we found some exact solutions of the above-mentioned equations.
New exact solutions of the generalized Zakharov–Kuznetsov ...
Indian Academy of Sciences (India)
In §2, an extended trial equation method is described for finding exact travelling wave solutions of nonlinear evolution equations with higher-order nonlinearity. In §3, as an application, some exact solutions to nonlinear partial differential equation such as the generalized Zakharov–Kuznetsov modified equal-width equation ...
New exact travelling wave solutions of bidirectional wave equations
Indian Academy of Sciences (India)
where , , and d are real constants. In general, the exact travelling wave solutions will be helpful in the theoretical and numerical study of the nonlinear evolution systems. In this paper, we obtain exact travelling wave solutions of system (1) using the modiﬁed tanh–coth function method with computerized symbolic ...
Prüstel, Thorsten; Meier-Schellersheim, Martin
2012-01-01
We derive an exact Green's function of the diffusion equation for a pair of disk-shaped interacting particles in two dimensions subject to a backreaction boundary condition. Furthermore, we use the obtained function to calculate exact expressions for the survival probability and the time-dependent rate coefficient for the initially unbound pair and the survival probability of the bound state. The derived expressions will be of particular utility for the description of reversible membrane-bound reactions in cell biology. PMID:22894329
DEFF Research Database (Denmark)
Kjaer, L. K.; Cejvanovic, V.; Henriken, T.
2015-01-01
RNA modification has attracted increasing interest as it is realized that epitranscriptomics is important in disease development. In type 2 diabetes we have suggested that high urinary excretion of 8-oxo-2'-Guanosine (8oxoGuo), as a measure of global RNA oxidation, is associated with poor survival.......9 significant hazard ratio for death compared with the quartile with the lowest 8oxoGuo excretion when adjusted for age, sex, BMI, smoker status, s-HbA1c, urine protein excretion and s-cholesterol. We conclude that it is now established that RNA oxidation is an independent risk factor for death in type 2...... diabetes. In agreement with our previous finding, DNA oxidation did not show any prognostic value. RNA oxidation represents oxidative stress intracellularly, presumably predominantly in the cytosol. The mechanism of RNA oxidation is not clear, but hypothesized to result from mitochondrial dysfunction...
Dissociation between exact and approximate addition in developmental dyslexia.
Yang, Xiujie; Meng, Xiangzhi
2016-09-01
Previous research has suggested that number sense and language are involved in number representation and calculation, in which number sense supports approximate arithmetic, and language permits exact enumeration and calculation. Meanwhile, individuals with dyslexia have a core deficit in phonological processing. Based on these findings, we thus hypothesized that children with dyslexia may exhibit exact calculation impairment while doing mental arithmetic. The reaction time and accuracy while doing exact and approximate addition with symbolic Arabic digits and non-symbolic visual arrays of dots were compared between typically developing children and children with dyslexia. Reaction time analyses did not reveal any differences across two groups of children, the accuracies, interestingly, revealed a distinction of approximation and exact addition across two groups of children. Specifically, two groups of children had no differences in approximation. Children with dyslexia, however, had significantly lower accuracy in exact addition in both symbolic and non-symbolic tasks than that of typically developing children. Moreover, linguistic performances were selectively associated with exact calculation across individuals. These results suggested that children with dyslexia have a mental arithmetic deficit specifically in the realm of exact calculation, while their approximation ability is relatively intact. Copyright © 2016 Elsevier Ltd. All rights reserved.
Isogeometric Analysis and Shape Optimisation
DEFF Research Database (Denmark)
Gravesen, Jens; Evgrafov, Anton; Gersborg, Allan Roulund
One of the attractive features of isogeometric analysis is the exact representation of the geometry. The geometry is furthermore given by a relative low number of control points and this makes isogeometric analysis an ideal basis for shape optimisation. I will describe some of the results we have...... obtained and also some of the problems we have encountered. One of these problems is that the geometry of the shape is given by the boundary alone. And, it is the parametrisation of the boundary which is changed by the optimisation procedure. But isogeometric analysis requires a parametrisation...... of the whole domain. So in every optimisation cycle we need to extend a parametrisation of the boundary of a domain to the whole domain. It has to be fast in order not to slow the optimisation down but it also has to be robust and give a parametrisation of high quality. These are conflicting requirements so we...
Exact Cover Problem in Milton Babbitt's All-partition Array
DEFF Research Database (Denmark)
Bemman, Brian; Meredith, David
2015-01-01
One aspect of analyzing Milton Babbitt’s (1916–2011) all- partition arrays requires finding a sequence of distinct, non-overlapping aggregate regions that completely and exactly covers an irregular matrix of pitch class integers. This is an example of the so-called exact cover problem. Given a set......, A, and a collection of distinct subsets of this set, S, then a subset of S is an exact cover of A if it exhaustively and exclu- sively partitions A. We provide a backtracking algorithm for solving this problem in an all-partition array and compare the output of this algorithm with an analysis...
Exact and approximate computations of watersheds on triangulated terrains
DEFF Research Database (Denmark)
Tsirogiannis, Konstantinos; de Berg, Mark
2011-01-01
The natural way of modeling water flow on a triangulated terrain is to make the fundamental assumption that water follows the direction of steepest descent (dsd). However, computing watersheds and other flow-related structures according to the dsd model in an exact manner is difficult: the dsd...... implementation that computes watersheds on triangulated terrains following strictly the dsd model and using exact arithmetic, and we experimentally investigate its computational cost. Our experiments show that the algorithm cannot handle large data sets effectively, due to the bit-sizes needed in the exact...
How hairpin vortices emerge from exact invariant solutions
Schneider, Tobias M.; Farano, Mirko; de Palma, Pietro; Robinet, Jean-Christoph; Cherubini, Stefania
2017-11-01
Hairpin vortices are among the most commonly observed flow structures in wall-bounded shear flows. However, within the dynamical system approach to turbulence, those structures have not yet been described. They are not captured by known exact invariant solutions of the Navier-Stokes equations nor have other state-space structures supporting hairpins been identified. We show that hairpin structures are observed along an optimally growing trajectory leaving a well known exact traveling wave solution of plane Poiseuille flow. The perturbation triggering hairpins does not correspond to an unstable mode of the exact traveling wave but lies in the stable manifold where non-normality causes strong transient amplification.
Rat1p maintains RNA polymerase II CTD phosphorylation balance
DEFF Research Database (Denmark)
Jimeno-González, Silvia; Schmid, Manfred; Malagon, Francisco
2014-01-01
In S. cerevisiae, the 5'-3' exonuclease Rat1p partakes in transcription termination. Although Rat1p-mediated RNA degradation has been suggested to play a role for this activity, the exact mechanisms by which Rat1p helps release RNA polymerase II (RNAPII) from the DNA template are poorly understoo...
Massive Axial Gauge in the Exact Renormalization Group Approach
Panza, P.; Soldati, R.
The Exact Renormalization Group (ERG) approach to massive gauge theories in the axial gauge is studied and the smoothness of the massless limit is analysed for a formally gauge invariant quantity such as the Euclidean Wilson loop.
Exactly solvable models for multiatomic molecular Bose-Einstein condensates
Energy Technology Data Exchange (ETDEWEB)
Santos, G, E-mail: gfilho@if.ufrgs.br, E-mail: gfilho@cbpf.br [Instituto de Fisica da UFRGS, Av. Bento Goncalves, 9500, Agronomia, Porto Alegre, RS (Brazil)
2011-08-26
I introduce two families of exactly solvable models for multiatomic hetero-nuclear and homo-nuclear molecular Bose-Einstein condensates through the algebraic Bethe ansatz method. The conserved quantities of the respective models are also shown. (paper)
An exact test of the Hardy-Weinberg law.
Chapco, W
1976-03-01
An exact distribution of a finite sample drawn from an infinite population in Hardy-Weinberg Equilibrium is described for k-alleles. Accordingly, an exact test of the law is presented and compared with two x2-tests for two and three alleles. For two alleles, it is shown that the "classical" c2-test is very adequate for sample sizes as small as ten. For three alleles, it is shown that a simpler formulation based on Leven's distribution approximates the exact test of this paper rather closely. However, it is recommended that researchers continue to employ the standard x2-test for all sample sizes and abide by it if the corresponding probability value is not "too close" to the critical level; otherwise, an exact test should be used.
Exact complex integrals in two dimensions for shifted harmonic ...
Indian Academy of Sciences (India)
symmetric. Hamiltonians appear to be special cases of such transformations. In the present work we carry out the ECPS approach to obtain exact complex integrals of a two-dimensional classical dynamical system [14,15]. Rationalization method ...
Exact solutions for the differential equations in fractal heat transfer
Directory of Open Access Journals (Sweden)
Yang Chun-Yu
2016-01-01
Full Text Available In this article we consider the boundary value problems for differential equations in fractal heat transfer. The exact solutions of non-differentiable type are obtained by using the local fractional differential transform method.
Exact and approximate expressions for the period of anharmonic oscillators
Energy Technology Data Exchange (ETDEWEB)
Amore, Paolo [Facultad de Ciencias, Universidad de Colima, Bernal DIaz del Castillo 340, Colima (Mexico); Fernandez, Francisco M [INIFTA (Conicet, UNLP), Blvd. 113 y 64 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)
2005-07-01
In this paper, we present a straightforward systematic method for the exact and approximate calculation of integrals that appear in formulae for the period of anharmonic oscillators and other problems of interest in classical mechanics.
Exact solutions and spacetime singularities in nonlocal gravity
National Research Council Canada - National Science Library
Li, Yao-Dong; Modesto, Leonardo; Rachwał, Lesław
2015-01-01
.... We prove that maximally symmetric spacetimes are exact solutions in both classes, while in dimension higher than four we can also have Anti-de Sitter solutions in the presence of positive cosmological constant...
DEFF Research Database (Denmark)
Nørrelykke, Simon F; Flyvbjerg, Henrik
2011-01-01
-lapse recordings. Three applications are discussed: (i) The effects of finite sampling rate and time, described exactly here, are similar for other stochastic dynamical systems-e.g., motile microorganisms and their time-lapse-recorded trajectories. (ii) The same statistics is satisfied by any experimental system......The stochastic dynamics of the damped harmonic oscillator in a heat bath is simulated with an algorithm that is exact for time steps of arbitrary size. Exact analytical results are given for correlation functions and power spectra in the form they acquire when computed from experimental time...... of finite sampling rate and sampling time for these models as well....
Corollary from the Exact Expression for Enthalpy of Vaporization
Directory of Open Access Journals (Sweden)
A. A. Sobko
2011-01-01
Full Text Available A problem on determining effective volumes for atoms and molecules becomes actual due to rapidly developing nanotechnologies. In the present study an exact expression for enthalpy of vaporization is obtained, from which an exact expression is derived for effective volumes of atoms and molecules, and under certain assumptions on the form of an atom (molecule it is possible to find their linear dimensions. The accuracy is only determined by the accuracy of measurements of thermodynamic parameters at the critical point.
Exact Mean Computation in Dynamic Time Warping Spaces
Brill, Markus; Fluschnik, Till; Froese, Vincent; Jain, Brijnesh; Niedermeier, Rolf; Schultz, David
2017-01-01
Dynamic time warping constitutes a major tool for analyzing time series. In particular, computing a mean series of a given sample of series in dynamic time warping spaces (by minimizing the Fr\\'echet function) is a challenging computational problem, so far solved by several heuristic, inexact strategies. We spot several inaccuracies in the literature on exact mean computation in dynamic time warping spaces. Our contributions comprise an exact dynamic program computing a mean (useful for bench...
DEFF Research Database (Denmark)
Sparvath, Steffen Lynge
for biosensorer, der kan spore enten microRNA’er eller små molekyler, eksemplificeret ved S-adenosylmethionin (SAM). Slutteligt indikerer foreløbige resultater, at apta-FRET SAM sensoren kan udtrykkes i Escherichia coli-celler, hvilket viser, at RNA-origami arkitekturen muliggør cotransskriptionel foldning af...... fra en enkelt RNA-streng, og udfører en lang række komplekse cellulære funktioner. Mange af funktionerne er blevet udnyttet til at skabe funktionelle RNA-baserede nanoapparater, men den nuværende litteratur giver kun få eksempler på cotranskriptionel produktion af RNA-nanostrukturer. I 2014...... introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...
Exact holography of the mass-deformed M2-brane theory
Energy Technology Data Exchange (ETDEWEB)
Jang, Dongmin; Kim, Yoonbai; Kwon, O. Kab [Sungkyunkwan University, Department of Physics, BK21 Physics Research Division, Institute of Basic Science, Suwon (Korea, Republic of); Tolla, D.D. [Sungkyunkwan University, Department of Physics, BK21 Physics Research Division, Institute of Basic Science, Suwon (Korea, Republic of); Sungkyunkwan University, University College, Suwon (Korea, Republic of)
2017-05-15
We test the holographic relation between the vacuum expectation values of gauge invariant operators in N = 6 U{sub k}(N) x U{sub -k}(N) mass-deformed ABJM theory and the LLM geometries with Z{sub k} orbifold in 11-dimensional supergravity. To do so, we apply the Kaluza-Klein reduction to construct a 4-dimensional gravity theory and implement the holographic renormalization procedure. We obtain an exact holographic relation for the vacuum expectation values of the chiral primary operator with conformal dimension Δ = 1, which is given by left angle O{sup (Δ=1)} right angle = N{sup (3)/(2)} f{sub (Δ=1)}, for large N and k = 1. Here the factor f{sub (Δ)} is independent of N. Our results involve an infinite number of exact dual relations for all possible supersymmetric Higgs vacua and so provide a non-trivial test of gauge/gravity duality away from the conformal fixed point. We extend our results to the case of k ≠ 1 for LLM geometries represented by rectangular-shaped Young diagrams. We also discuss the exact mapping of the gauge/gravity at finite N for classical supersymmetric vacuum solutions in field theory side and corresponding classical solutions in gravity side. (orig.)
Persson, Anna S K; Odén, Agneta; Andersson, Matts; Sandborgh-Englund, Gunilla
2009-07-01
To compare the exactness of simulated clinical impressions and stone replicas of crown preparations, using digitization and virtual three-dimensional analysis. Three master dies (mandibular incisor, canine and molar) were prepared for full crowns, mounted in full dental arches in a plane line articulator. Eight impressions were taken using an experimental monophase vinyl polysiloxane-based material. Stone replicas were poured in type IV stone (Vel-Mix Stone; Kerr). The master dies and the stone replicas were digitized in a touch-probe scanner (Procera) Forte; Nobel Biocare AB) and the impressions in a laser scanner (D250, 3Shape A/S), to create virtual models. The resulting point-clouds from the digitization of the master dies were used as CAD-Reference-Models (CRM). Discrepancies between the points in the pointclouds and the corresponding CRM were measured by a matching-software (CopyCAD 6.504 SP2; Delcam Plc). The distribution of the discrepancies was analyzed and depicted on color-difference maps. The discrepancies of the digitized impressions and the stone replicas compared to the CRM were of similar size with a mean+/-SD within 40microm, with the exception of two of the digitized molar impressions. The precision of the digitized impressions and stone replicas did not differ significantly (F=4.2; p=0.053). However, the shape affected the digitization (F=5.4; p=0.013) and the interaction effect of shape and digitization source (impression or stone replica) was pronounced (F=28; pdigitization methods, evaluated by repeated digitizations. The exactness of the digitized impressions varied with shape. Both impressions and stone replicas can be digitized repeatedly with a high reliability.
On the shape of giant soap bubbles.
Cohen, Caroline; Darbois Texier, Baptiste; Reyssat, Etienne; Snoeijer, Jacco H; Quéré, David; Clanet, Christophe
2017-03-07
We study the effect of gravity on giant soap bubbles and show that it becomes dominant above the critical size [Formula: see text], where [Formula: see text] is the mean thickness of the soap film and [Formula: see text] is the capillary length ([Formula: see text] stands for vapor-liquid surface tension, and [Formula: see text] stands for the liquid density). We first show experimentally that large soap bubbles do not retain a spherical shape but flatten when increasing their size. A theoretical model is then developed to account for this effect, predicting the shape based on mechanical equilibrium. In stark contrast to liquid drops, we show that there is no mechanical limit of the height of giant bubble shapes. In practice, the physicochemical constraints imposed by surfactant molecules limit the access to this large asymptotic domain. However, by an exact analogy, it is shown how the giant bubble shapes can be realized by large inflatable structures.
Exact multilocal renormalization group and applications to disordered problems
Chauve, Pascal; Le Doussal, Pierre
2001-11-01
We develop a method, the exact multilocal renormalization group (EMRG) which applies to a broad set of theories. It is based on the systematic multilocal expansion of the Polchinski-Wilson exact renormalization group (ERG) equation together with a scheme to compute correlation functions. Integrating out explicitly the nonlocal interactions, we reduce the ERG equation obeyed by the full interaction functional to a flow equation for a function, its local part. This is done perturbatively around fixed points, but exactly to any given order in the local part. It is thus controlled, at variance with projection methods, e.g., derivative expansions or local potential approximations. Our EMRG method is well-suited to problems such as the pinning of disordered elastic systems, previously described via functional renormalization group (FRG) approach based on a hard cutoff scheme. Since it involves arbitrary cutoff functions, we explicitly verify universality to O(ɛ=4-D), both of the T=0 FRG equation and of correlations. Extension to finite temperature T yields the finite size (L) susceptibility fluctuations characterizing mesoscopic behavior (Δχ)2¯~Lθ/T, where θ is the energy exponent. Finally, we obtain the universal scaling function to O(ɛ1/3) which describes the ground state of a domain wall in a random field confined by a field gradient, compare with exact results and variational method. Explicit two loop exact RG equations are derived and the application to the FRG problem is sketched.
On field redefinitions and exact solutions in string theory
Tseytlin, Arkady A
1993-01-01
String backgrounds associated with gauged $G/H$ WZNW models in general depend non-trivially on $\\alpha'$. We note, however, that there exists a local covariant $\\a'$-dependent field redefinition that relates the exact metric-dilaton background corresponding to the $SL(2,R)/U(1)$ model to its leading-order form ($D=2$ black hole). As a consequence, there exists a `scheme' in which the string effective equations have the latter as an exact solution. However, the corresponding equation for the tachyon (which, like other Weyl anomaly coefficients, has scheme-dependent form) still contains corrections of all orders in $\\alpha'$. As a result, the `probes' (the tachyons) still feel the $\\alpha'$-corrected background. The field redefinitions we discuss contain the dilaton terms in the metric transformation law. We comment on exact forms of the duality transformation in different `schemes'.
Exact renormalization flow and domain walls from holography
Ketov, Sergei V.
2001-03-01
The holographic correspondence between 2d, N=2 quantum field theories and classical 4d, N=2 supergravity coupled to hypermultiplet matter is proposed. The geometrical constraints on the target space of the 4d, N=2 non-linear sigma-models in N=2 supergravity background are interpreted as the exact renormalization group flow equations in two dimensions. Our geometrical description of the renormalization flow is manifestly covariant under general reparametrization of the 2d coupling constants. An explicit exact solution to the 2d renormalization flow, based on its dual holographic description in terms of the Zamolodchikov metric, is considered in the particular case of the four-dimensional NLSM target space described by the SU(2)-invariant (Weyl) anti-self-dual Einstein metrics. The exact regular (Tod-Hitchin) solutions to these metrics are governed by the Painlevé VI equation, and describe domain walls.
Exact semiclassical expansions for one-dimensional quantum oscillators
Energy Technology Data Exchange (ETDEWEB)
Delabaere, E. [UMR CNRS J. A. Dieudonne No. 6621, University of Nice, 06108 Nice Cedex 2 (France); Dillinger, H.; Pham, F. [University of Nice, Department of Maths, UMR CNRS J.A. Dieudonne No. 6621, 06108 Nice Cedex 2 (France)
1997-12-01
A set of rules is given for dealing with WKB expansions in the one-dimensional analytic case, whereby such expansions are not considered as approximations but as exact encodings of wave functions, thus allowing for analytic continuation with respect to whichever parameters the potential function depends on, with an exact control of small exponential effects. These rules, which include also the case when there are double turning points, are illustrated on various examples, and applied to the study of bound state or resonance spectra. In the case of simple oscillators, it is thus shown that the Rayleigh{endash}Schr{umlt o}dinger series is Borel resummable, yielding the exact energy levels. In the case of the symmetrical anharmonic oscillator, one gets a simple and rigorous justification of the Zinn-Justin quantization condition, and of its solution in terms of {open_quotes}multi-instanton expansions.{close_quotes} {copyright} {ital 1997 American Institute of Physics.}
Fuzziness and Foundations of Exact and Inexact Sciences
Dompere, Kofi Kissi
2013-01-01
The monograph is an examination of the fuzzy rational foundations of the structure of exact and inexact sciences over the epistemological space which is distinguished from the ontological space. It is thus concerned with the demarcation problem. It examines exact science and its critique of inexact science. The role of fuzzy rationality in these examinations is presented. The driving force of the discussions is the nature of the information that connects the cognitive relational structure of the epistemological space to the ontological space for knowing. The knowing action is undertaken by decision-choice agents who must process information to derive exact-inexact or true-false conclusions. The information processing is done with a paradigm and laws of thought that constitute the input-output machine. The nature of the paradigm selected depends on the nature of the information structure that is taken as input of the thought processing. Generally, the information structure received from the ontological space i...
Exact solution of the two-axis countertwisting Hamiltonian
Pan, Feng; Zhang, Yao-Zhong; Draayer, Jerry P.
2017-01-01
It is shown that the two-axis countertwisting Hamiltonian is exactly solvable when the quantum number of the total angular momentum of the system is an integer after the Jordan-Schwinger (differential) boson realization of the SU(2) algebra. Algebraic Bethe ansatz is used to get the exact solution with the help of the SU(1,1) algebraic structure, from which a set of Bethe ansatz equations of the problem is derived. It is shown that solutions of the Bethe ansatz equations can be obtained as zeros of the Heine-Stieltjes polynomials. The total number of the four sets of the zeros equals exactly 2 J + 1 for a given integer angular momentum quantum number J, which proves the completeness of the solutions. It is also shown that double degeneracy in level energies may also occur in the J → ∞ limit for integer J case except a unique non-degenerate level with zero excitation energy.
Exact deconstruction of the 6D (2,0) theory
Hayling, J.; Papageorgakis, C.; Pomoni, E.; Rodríguez-Gómez, D.
2017-06-01
The dimensional-deconstruction prescription of Arkani-Hamed, Cohen, Kaplan, Karch and Motl provides a mechanism for recovering the A-type (2,0) theories on T 2, starting from a four-dimensional N=2 circular-quiver theory. We put this conjecture to the test using two exact-counting arguments: in the decompactification limit, we compare the Higgs-branch Hilbert series of the 4D N=2 quiver to the "half-BPS" limit of the (2,0) superconformal index. We also compare the full partition function for the 4D quiver on S 4 to the (2,0) partition function on S 4 × T 2. In both cases we find exact agreement. The partition function calculation sets up a dictionary between exact results in 4D and 6D.
The Problem of Understanding of Nature in Exact Science
Directory of Open Access Journals (Sweden)
Leo Näpinen
2014-10-01
Full Text Available In this short inquiry I would like to defend the statement that exact science deals with the explanation of models, but not with the understanding (comprehending of nature. By the word ‘nature’ I mean nature as physis (as a self-moving and self-developing living organism to which humans also belong, not nature as natura naturata (as a nonevolving creature created by someone or something. The Estonian philosopher of science Rein Vihalemm (2008 has shown with his conception of phi-science (φ-science that exact science is itself an idealized model or theoretical object derived from Galilean mathematical physics.
Exact Solutions for Nonlinear Differential Difference Equations in Mathematical Physics
Directory of Open Access Journals (Sweden)
Khaled A. Gepreel
2013-01-01
Full Text Available We modified the truncated expansion method to construct the exact solutions for some nonlinear differential difference equations in mathematical physics via the general lattice equation, the discrete nonlinear Schrodinger with a saturable nonlinearity, the quintic discrete nonlinear Schrodinger equation, and the relativistic Toda lattice system. Also, we put a rational solitary wave function method to find the rational solitary wave solutions for some nonlinear differential difference equations. The proposed methods are more effective and powerful to obtain the exact solutions for nonlinear difference differential equations.
Exact asymmetric Skyrmion in anisotropic ferromagnet and its helimagnetic application
Directory of Open Access Journals (Sweden)
Anjan Kundu
2016-08-01
Full Text Available Topological Skyrmions as intricate spin textures were observed experimentally in helimagnets on 2d plane. Theoretical foundation of such solitonic states to appear in pure ferromagnetic model, as exact solutions expressed through any analytic function, was made long ago by Belavin and Polyakov (BP. We propose an innovative generalization of the BP solution for an anisotropic ferromagnet, based on a physically motivated geometric (in-equality, which takes the exact Skyrmion to a new class of functions beyond analyticity. The possibility of stabilizing such metastable states in helimagnets is discussed with the construction of individual Skyrmion, Skyrmion crystal and lattice with asymmetry, likely to be detected in precision experiments.
Exact asymmetric Skyrmion in anisotropic ferromagnet and its helimagnetic application
Energy Technology Data Exchange (ETDEWEB)
Kundu, Anjan, E-mail: anjan.kundu@saha.ac.in
2016-08-15
Topological Skyrmions as intricate spin textures were observed experimentally in helimagnets on 2d plane. Theoretical foundation of such solitonic states to appear in pure ferromagnetic model, as exact solutions expressed through any analytic function, was made long ago by Belavin and Polyakov (BP). We propose an innovative generalization of the BP solution for an anisotropic ferromagnet, based on a physically motivated geometric (in-)equality, which takes the exact Skyrmion to a new class of functions beyond analyticity. The possibility of stabilizing such metastable states in helimagnets is discussed with the construction of individual Skyrmion, Skyrmion crystal and lattice with asymmetry, likely to be detected in precision experiments.
Quantifying risks with exact analytical solutions of derivative pricing distribution
Zhang, Kun; Liu, Jing; Wang, Erkang; Wang, Jin
2017-04-01
Derivative (i.e. option) pricing is essential for modern financial instrumentations. Despite of the previous efforts, the exact analytical forms of the derivative pricing distributions are still challenging to obtain. In this study, we established a quantitative framework using path integrals to obtain the exact analytical solutions of the statistical distribution for bond and bond option pricing for the Vasicek model. We discuss the importance of statistical fluctuations away from the expected option pricing characterized by the distribution tail and their associations to value at risk (VaR). The framework established here is general and can be applied to other financial derivatives for quantifying the underlying statistical distributions.
Clock Math — a System for Solving SLEs Exactly
Directory of Open Access Journals (Sweden)
Jakub Hladík
2013-01-01
Full Text Available In this paper, we present a GPU-accelerated hybrid system that solves ill-conditioned systems of linear equations exactly. Exactly means without rounding errors due to using integer arithmetics. First, we scale floating-point numbers up to integers, then we solve dozens of SLEs within different modular arithmetics and then we assemble sub-solutions back using the Chinese remainder theorem. This approach effectively bypasses current CPU floating-point limitations. The system is capable of solving Hilbert’s matrix without losing a single bit of precision, and with a significant speedup compared to existing CPU solvers.
Exact Solution of the Three-Body Santilli-Shillady Model of the Hydrogen Molecule
Directory of Open Access Journals (Sweden)
Pérez-Enríquez R.
2007-04-01
Full Text Available The conventional representation of the H 2 molecule characterizes a 4-body system due to the independence of the orbitals of the two valence electrons as requested by quantum chemistry, under which conditions no exact solution is possible. To overcome this problem, Santilli and Shillady introduced in 1999 a new model of the H 2 -molecu- le in which the two valence electrons are deeply bounded-correlated into a single quasi-particle they called isoelectronium that is permitted by the covering hadronic chemistry. They pointed out that their new H 2 -model is a restricted 3-body system that, as such, is expected to admit an exact solution and suggested independent studies for its identification due to its relevance, e.g., for other molecules. In 2000, Aringazin and Kucherenko did study the Santilli-Shillady restricted 3-body model of the H 2 molecules, but they presented a variational solution that, as such, is not exact. In any case, the latter approach produced significant deviations from experimental data, such as a 19.6% inter-nuclear distance greater than the experimental value. In this paper we present, apparently for the first time, an exact solution of the Santilli-Shillady restricted 3-body model of the Hydrogen molecule along the lines of its originators and show that it does indeed represent correctly all basic data. Intriguingly, our solution confirms that the orbital of the isoelectronium (referred to as its charge distribution around the nuclei must be concentrated in a limited region of space given by the Santilli-Shillady oo-shaped orbits. Our exact solution is constructed by following the Ley-Koo solution to the Schr ̈ odinger equation for a confined hydrogen molecular ion, H + 2 . We show that a confined model to the 3-body molecule reproduces the ground state curve as calculated by Kolos, Szalewics and Monkhorst with a precision up to the 4-th digit and a precision in the representation of the binding energy up to the 5-th digit.
Exact equivalent straight waveguide model for bent and twisted waveguides
DEFF Research Database (Denmark)
Shyroki, Dzmitry
2008-01-01
Exact equivalent straight waveguide representation is given for a waveguide of arbitrary curvature and torsion. No assumptions regarding refractive index contrast, isotropy of materials, or particular morphology in the waveguide cross section are made. This enables rigorous full-vector modeling o...
Thermodynamics of Rh nuclear spins calculated by exact diagonalization
DEFF Research Database (Denmark)
Lefmann, K.; Ipsen, J.; Rasmussen, F.B.
2000-01-01
We have employed the method of exact diagonalization to obtain the full-energy spectrum of a cluster of 16 Rh nuclear spins, having dipolar and RK interactions between first and second nearest neighbours only. We have used this to calculate the nuclear spin entropy, and our results at both positi...
Exact solution for a one-dimensional model for reptation.
Drzewiński, Andrzej; van Leeuwen, J M J
2006-05-01
We discuss the exact solution for the properties of the recently introduced "necklace" model for reptation. The solution gives the drift velocity, diffusion constant, and renewal time for asymptotically long chains. Its properties are also related to a special case of the Rubinstein-Duke model in one dimension.
The functional variable method for finding exact solutions of some ...
Indian Academy of Sciences (India)
and KEWANG CHEN. College of Mathematics and Statistics, Nanjing University of Information Science and Technology, ... Introduction. The effort in finding exact solutions of nonlinear equations is very important for understanding most nonlinear physical phenomena. For instance, the nonlinear wave phenomena observed ...
Exact overflow asymptotics for queues with many Gaussian inputs
Debicki, Krzysztof; Mandjes, M.R.H.
2003-01-01
In this paper we consider a queue fed by a large number of independent continuous-time Gaussian processes with stationary increments. After scaling the buffer exceedance threshold and the (constant) service capacity by the number of sources, we present asymptotically exact results for the
Dynamic Programming Approach for Exact Decision Rule Optimization
Amin, Talha
2013-01-01
This chapter is devoted to the study of an extension of dynamic programming approach that allows sequential optimization of exact decision rules relative to the length and coverage. It contains also results of experiments with decision tables from UCI Machine Learning Repository. © Springer-Verlag Berlin Heidelberg 2013.
More exact tunneling solutions in scalar field theory
Energy Technology Data Exchange (ETDEWEB)
Dutta, Koushik; Hector, Cecelie; Vaudrevange, Pascal M.; Westphal, Alexander
2011-11-15
We present exact bounce solutions and amplitudes for tunneling in (i) a piecewise linear-quartic potential and (ii) a piecewise quartic-quartic potential. We cross check their correctness by comparing with results obtained through the thin-wall approximation and with a piecewise linear-linear potential. We briefly comment on applications in cosmology. (orig.)
Exact solutions for nonlinear variants of Kadomtsev–Petviashvili (n ...
Indian Academy of Sciences (India)
Exact solutions for nonlinear variants of Kadomtsev–Petviashvili (, ) equation using functional variable method. M Mirzazadeh M Eslami. Volume 81 Issue ... The functional variable method is used to establish compactons, solitons, solitary patterns and periodic solutions for these variants. This method is a powerful tool for ...
Timed Fast Exact Euclidean Distance (tFEED) maps
Kehtarnavaz, Nasser; Schouten, Theo E.; Laplante, Philip A.; Kuppens, Harco; van den Broek, Egon
2005-01-01
In image and video analysis, distance maps are frequently used. They provide the (Euclidean) distance (ED) of background pixels to the nearest object pixel. In a naive implementation, each object pixel feeds its (exact) ED to each background pixel; then the minimum of these values denotes the ED to
Exact travelling wave solutions for some important nonlinear ...
Indian Academy of Sciences (India)
problems. More precisely, there is no unified method that can be used to handle all types of nonlinear problems. A powerful and effective method for finding exact ... Explicit solutions to nonlinear problems are of fundamental importance. ... fluid dynamics, fluid flow, quantum field theory, electromagnetic waves and so on [7].
Exact rational expectations, cointegration, and reduced rank regression
DEFF Research Database (Denmark)
Johansen, Søren; Swensen, Anders Rygh
We interpret the linear relations from exact rational expectations models as restrictions on the parameters of the statistical model called the cointegrated vector autoregressive model for non-stationary variables. We then show how reduced rank regression, Anderson (1951), plays an important role...
Exact rational expectations, cointegration, and reduced rank regression
DEFF Research Database (Denmark)
Johansen, Søren; Swensen, Anders Rygh
2008-01-01
We interpret the linear relations from exact rational expectations models as restrictions on the parameters of the statistical model called the cointegrated vector autoregressive model for non-stationary variables. We then show how reduced rank regression, Anderson (1951), plays an important role...
Exact Rational Expectations, Cointegration, and Reduced Rank Regression
DEFF Research Database (Denmark)
Johansen, Søren; Swensen, Anders Rygh
We interpret the linear relations from exact rational expectations models as restrictions on the parameters of the statistical model called the cointegrated vector autoregressive model for non-stationary variables. We then show how reduced rank regression, Anderson (1951), plays an important role...
An Exactly Solvable Model for the Spread of Disease
Mickens, Ronald E.
2012-01-01
We present a new SIR epidemiological model whose exact analytical solution can be calculated. In this model, unlike previous models, the infective population becomes zero at a finite time. Remarkably, these results can be derived from only an elementary knowledge of differential equations.
The Alleged Crisis and the Illusion of Exact Replication
Stroebe, Wolfgang; Strack, Fritz
There has been increasing criticism of the way psychologists conduct and analyze studies. These critiques as well as failures to replicate several high-profile studies have been used as justification to proclaim a replication crisis in psychology. Psychologists are encouraged to conduct more exact
A SAS/IML algorithm for an exact permutation test
Directory of Open Access Journals (Sweden)
Neuhäuser, Markus
2009-03-01
Full Text Available An algorithm written in SAS/IML is presented that can perform an exact permutation test for a two-sample comparison. All possible permutations are considered. The Baumgartner-Weiß-Schindler statistic is exemplarily used as the test statistic for the permutation test.
Exact angular momentum projection based on cranked HFB solution
Energy Technology Data Exchange (ETDEWEB)
Enami, Kenichi; Tanabe, Kosai; Yosinaga, Naotaka [Saitama Univ., Urawa (Japan). Dept. of Physics
1998-03-01
Exact angular momentum projection of cranked HFB solutions is carried out. It is reconfirmed from this calculation that cranked HFB solutions reproduce the intrinsic structure of deformed nucleus. The result also indicates that the energy correction from projection is important for further investigation of nuclear structure. (author)
Exact Solution of a Generalized Nonlinear Schrodinger Equation Dimer
DEFF Research Database (Denmark)
Christiansen, Peter Leth; Maniadis, P.; Tsironis, G.P.
1998-01-01
We present exact solutions for a nonlinear dimer system defined throught a discrete nonlinear Schrodinger equation that contains also an integrable Ablowitz-Ladik term. The solutions are obtained throught a transformation that maps the dimer into a double Sine-Gordon like ordinary nonlinear...
Exact solution for the interior of a black hole
Nieuwenhuizen, T.M.
2008-01-01
Within the Relativistic Theory of Gravitation it is shown that the equation of state p = rho holds near the center of a black hole. For the stiff equation of state p = rho - rho(c) the interior metric is solved exactly. It is matched with the Schwarzschild metric, which is deformed in a narrow range
Exact travelling wave solutions for some important nonlinear ...
Indian Academy of Sciences (India)
The two-dimensional nonlinear physical models and coupled nonlinear systems such as Maccari equations, Higgs equations and Schrödinger–KdV equations have been widely applied in many branches of physics. So, finding exact travelling wave solutions of such equations are very helpful in the theories and numerical ...
Construction of an exact solution of time-dependent Ginzburg ...
Indian Academy of Sciences (India)
A new approach is taken to calculate the speed of front propagation at which the interface moves from a superconducting to a normal region in a superconducting sample. Using time-dependent Ginzburg–Landau (TDGL) equations we have calculated the speed by constructing a new exact solution. This approach is based ...
Electromagnetic shock wave in nonlinear vacuum: exact solution.
Kovachev, Lubomir M; Georgieva, Daniela A; Kovachev, Kamen L
2012-10-01
An analytical approach to the theory of electromagnetic waves in nonlinear vacuum is developed. The evolution of the pulse is governed by a system of nonlinear wave vector equations. An exact solution with its own angular momentum in the form of a shock wave is obtained.
Adaptive filtering for stochastic volatility by using exact sampling
Aihara, ShinIchi; Bagchi, Arunabha; Saha, S.
2013-01-01
We study the sequential identification problem for Bates stochastic volatility model, which is widely used as the model of a stock in finance. By using the exact simulation method, a particle filter for estimating stochastic volatility is constructed. The systems parameters are sequentially
Exact boundary controllability of nodal profile for quasilinear hyperbolic systems
Li, Tatsien; Gu, Qilong
2016-01-01
This book provides a comprehensive overview of the exact boundary controllability of nodal profile, a new kind of exact boundary controllability stimulated by some practical applications. This kind of controllability is useful in practice as it does not require any precisely given final state to be attained at a suitable time t=T by means of boundary controls, instead it requires the state to exactly fit any given demand (profile) on one or more nodes after a suitable time t=T by means of boundary controls. In this book we present a general discussion of this kind of controllability for general 1-D first order quasilinear hyperbolic systems and for general 1-D quasilinear wave equations on an interval as well as on a tree-like network using a modular-structure construtive method, suggested in LI Tatsien's monograph "Controllability and Observability for Quasilinear Hyperbolic Systems"(2010), and we establish a complete theory on the local exact boundary controllability of nodal profile for 1-D quasilinear hyp...
Construction of an exact solution of time-dependent Ginzburg ...
Indian Academy of Sciences (India)
Abstract. A new approach is taken to calculate the speed of front propagation at which the interface moves from a superconducting to a normal region in a superconducting sample. Using time-dependent Ginzburg–Landau (TDGL) equations we have calculated the speed by constructing a new exact solution. This approach ...
New exact solutions of the generalized Zakharov–Kuznetsov ...
Indian Academy of Sciences (India)
In this paper, new exact solutions, including soliton, rational and elliptic integral function solutions, for the generalized Zakharov–Kuznetsov modified equal-width equation are obtained using a new approach called the extended trial equation method. In this discussion, a new version of the trial equation method for the ...
Exact solutions, energy, and charge of stable Q-balls
Energy Technology Data Exchange (ETDEWEB)
Bazeia, D.; Marques, M.A. [Universidade Federal da Paraiba, Departamento de Fisica, Joao Pessoa, PB (Brazil); Menezes, R. [Universidade Federal da Paraiba, Departamento de Ciencias Exatas, Rio Tinto, PB (Brazil); Universidade Federal de Campina Grande, Departamento de Fisica, Campina Grande, PB (Brazil)
2016-05-15
In this work we deal with nontopological solutions of the Q-ball type in two spacetime dimensions. We study models of current interest, described by a Higgs-like and other, similar potentials which unveil the presence of exact solutions. We use the analytic results to investigate how to control the energy and charge to make the Q-balls stable. (orig.)
The exact solutions of differential equation with delay
Hasebe, K; Sugiyama, Y
1998-01-01
The exact solutions of the first order differential equation with delay are derived. The equation has been introduced as a model of traffic flow. The solution describes the traveling cluster of jam, which is characterized by Jacobi's elliptic function. We also obtain the family of solutions of such type of equations.
Exact results on the steady state of a hopping model
Zhang, M. Q.
1987-03-01
A hopping model described by Katz, Lebowitz, and Spohn [J. Stat. Phys. 34, 497 (1983)] and by Valles and Marro [J. Stat. Phys. 43, 441 (1986)] is studied analytically for small lattice systems. The dependence of the nonequilibrium steady state on various parameters and transition rate functions is obtained exactly. The results are compared with simulations on large systems.
Exact solution of the neutron transport equation in spherical geometry
Energy Technology Data Exchange (ETDEWEB)
Anli, Fikret; Akkurt, Abdullah; Yildirim, Hueseyin; Ates, Kemal [Kahramanmaras Suetcue Imam Univ. (Turkey). Faculty of Sciences and Letters
2017-03-15
Solution of the neutron transport equation in one dimensional slab geometry construct a basis for the solution of neutron transport equation in a curvilinear geometry. Therefore, in this work, we attempt to derive an exact analytical benchmark solution for both neutron transport equations in slab and spherical medium by using P{sub N} approximation which is widely used in neutron transport theory.
Exact boundary controllability for a series of membranes elastically connected
Directory of Open Access Journals (Sweden)
Waldemar D. Bastos
2017-01-01
Full Text Available In this article we study the exact controllability with Neumann boundary controls for a system of linear wave equations coupled in parallel by lower order terms on piecewise smooth domains of the plane. We obtain square integrable controls for initial state with finite energy and time of controllability near the optimal value.
Method for generating exact Bianchi type II cosmological models
Energy Technology Data Exchange (ETDEWEB)
Hajj-Boutros, J.
1986-06-01
A method for generating exact Bianchi type II cosmological models with a perfect fluid distribution of matter is presented. Two new classes of Bianchi type II solutions have been generated from Lorenz's solution (D. Lorenz, Phys. Lett. A 79, 19 (1980)). A detailed study of physical and kinematic properties of one of them has been carried out.
A procedure to construct exact solutions of nonlinear evolution ...
Indian Academy of Sciences (India)
physics pp. 337–344. A procedure to construct exact solutions of nonlinear evolution equations. ADEM CENGIZ ÇEVIKEL1,∗, AHMET BEKIR2, MUTLU AKAR3 and. SAIT SAN2. 1Yildiz Technical University, Faculty of Education, Department of Mathematics Education,. Davutpasa Campus, 34210, Esenler, Istanbul, Turkey.
Small catalytic RNA: Structure, function and application
Energy Technology Data Exchange (ETDEWEB)
Monforte, Joseph Albert [Univ. of California, Berkeley, CA (United States)
1991-04-01
We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the ``paperclip`` and ``hammerhead`` RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a ``hammerhead,`` to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 121±s are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus_minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.
Self-regulatory gene: An exact solution for the gene gate model
Vandecan, Yves; Blossey, Ralf
2013-04-01
The stochastic dynamics of gene expression is often described by highly abstract models involving only the key molecular actors DNA, RNA, and protein, neglecting all further details of the transcription and translation processes. One example of such models is the “gene gate model,” which contains a minimal set of actors and kinetic parameters, which allows us to describe the regulation of a gene by both repression and activation. Based on this approach, we formulate a master equation for the case of a single gene regulated by its own product—a transcription factor—and solve it exactly. The obtained gene product distributions display features of mono- and bimodality, depending on the choice of parameters. We discuss our model in the perspective of other models in the literature.
Exact Partition Functions of Interacting Self-Avoiding Walks on Lattices
Directory of Open Access Journals (Sweden)
Hsieh Yu-Hsin
2016-01-01
Full Text Available Ideas and methods of statistical physics have been shown to be useful for understanding some interesting problems in physical systems, e.g. universality and scaling in critical systems. The interacting self-avoiding walk (ISAW on a lattice is the simplest model for homopolymers and serves as the framework of simple models for biopolymers, such as DNA, RNA, and protein, which are important components in complex systems in biology. In this paper, we briefly review our recent work on exact partition functions of ISAW. Based on zeros of these exact partition functions, we have developed a novel method in which both loci of zeros and thermodynamic functions associated with them are considered. With this method, the first zeros can be identified clearly without ambiguity. The critical point of a small system can then be defined as the peak position of the heat capacity component associated with the first zeros. For the system with two phase transitions, two pairs of first zeros corresponding to two phase transitions can be identified and overlapping Cυ can be well separated. ISAW on the simple cubic lattice is such a system where in addition to a standard collapse transition, there is another freezing transition occurring at a lower temperature. Our approach can give a clear scenario for the collapse and the freezing transitions.
Investigation of ALEGRA shock hydrocode algorithms using an exact free surface jet flow solution.
Energy Technology Data Exchange (ETDEWEB)
Hanks, Bradley Wright.; Robinson, Allen C
2014-01-01
Computational testing of the arbitrary Lagrangian-Eulerian shock physics code, ALEGRA, is presented using an exact solution that is very similar to a shaped charge jet flow. The solution is a steady, isentropic, subsonic free surface flow with significant compression and release and is provided as a steady state initial condition. There should be no shocks and no entropy production throughout the problem. The purpose of this test problem is to present a detailed and challenging computation in order to provide evidence for algorithmic strengths and weaknesses in ALEGRA which should be examined further. The results of this work are intended to be used to guide future algorithmic improvements in the spirit of test-driven development processes.
Exact Hamiltonians with Rashba and cubic Dresselhaus spin-orbit couplings on a curved surface
Chang, Jian-Yuan; Wu, Jhih-Sheng; Chang, Ching-Ray
2013-05-01
The exact Hamiltonians for Rashba and cubic Dresselhaus spin-orbit couplings on a curved surface with an arbitrary shape are rigorously derived. Two orthogonal principal curvatures dominate the electronic spin transport, and the asymptotic behavior of the normal confined potential on a curved surface is insignificant. For a curved surface with a large curvature, the higher order momentum terms play an important role in controlling spin transport. The Rashba spin-orbit coupling on a curved surface only induces the extra pseudopotential term, and the cubic Dresselhaus spin-orbit coupling on a curved surface can induce the extra pseudokinetic and pseudomomentum terms. Because of the extra curvature-induced terms and the associated pseudomagnetic fields, spin transport on a curved surface is very different from that on a flat surface. The Hamiltonians on both cylindrical and spherical surfaces are explicitly derived here, and the associated physical properties of electrons are studied in detail.
Exact self-duality in a modified Skyrme model
Ferreira, L. A.
2017-07-01
We propose a modification of the Skyrme model that supports a self-dual sector possessing exact non-trivial finite energy solutions. The action of such a theory possesses the usual quadratic and quartic terms in field derivatives, but the couplings of the components of the Maurer-Cartan form of the Skyrme model is made by a non-constant symmetric matrix, instead of the usual Killing form of the SU(2) Lie algebra. The introduction of such a matrix make the self-duality equations conformally invariant in three space dimensions, even though it may break the global internal symmetries of the original Skyrme model. For the case where that matrix is proportional to the identity we show that the theory possesses exact self-dual Skyrmions of unity topological charges.
Exact results for Wilson loops in arbitrary representations
Energy Technology Data Exchange (ETDEWEB)
Fiol, Bartomeu; Torrents, Genís [Departament de Física Fonamental i Institut de Ciències del Cosmos, Universitat de Barcelona,Martí i Franquès 1, 08028 Barcelona, Catalonia (Spain)
2014-01-08
We compute the exact vacuum expectation value of 1/2 BPS circular Wilson loops of N=4 U(N) super Yang-Mills in arbitrary irreducible representations. By localization arguments, the computation reduces to evaluating certain integrals in a Gaussian matrix model, which we do using the method of orthogonal polynomials. Our results are particularly simple for Wilson loops in antisymmetric representations; in this case, we observe that the final answers admit an expansion where the coefficients are positive integers, and can be written in terms of sums over skew Young diagrams. As an application of our results, we use them to discuss the exact Bremsstrahlung functions associated to the corresponding heavy probes.
arXiv Integrable flows between exact CFTs
Georgiou, George
2017-11-14
We explicitly construct families of integrable σ-model actions smoothly inter-polating between exact CFTs. In the ultraviolet the theory is the direct product of two current algebras at levels k$_{1}$ and k$_{2}$. In the infrared and for the case of two deformation matrices the CFT involves a coset CFT, whereas for a single matrix deformation it is given by the ultraviolet direct product theories but at levels k$_{1}$ and k$_{2}$ − k$_{1}$. For isotropic deformations we demonstrate integrability. In this case we also compute the exact beta-function for the deformation parameters using gravitational methods. This is shown to coincide with previous results obtained using perturbation theory and non-perturbative symmetries.
Exact Interior Reconstruction with Cone-Beam CT
Directory of Open Access Journals (Sweden)
Yangbo Ye
2007-01-01
Full Text Available Using the backprojection filtration (BPF and filtered backprojection (FBP approaches, respectively, we prove that with cone-beam CT the interior problem can be exactly solved by analytic continuation. The prior knowledge we assume is that a volume of interest (VOI in an object to be reconstructed is known in a subregion of the VOI. Our derivations are based on the so-called generalized PI-segment (chord. The available projection onto convex set (POCS algorithm and singular value decomposition (SVD method can be applied to perform the exact interior reconstruction. These results have many implications in the CT field and can be extended to other tomographic modalities, such as SPECT/PET, MRI.
Exact nuclear data uncertainty propagation for fusion neutronics calculations
Energy Technology Data Exchange (ETDEWEB)
Rochman, D., E-mail: rochman@nrg.e [Nuclear Research and Consultancy Group NRG, P.O. Box 25, 1755 ZG Petten (Netherlands); Koning, A.J.; Marck, S.C. van der [Nuclear Research and Consultancy Group NRG, P.O. Box 25, 1755 ZG Petten (Netherlands)
2010-08-15
Recently, we have presented an exact method (now called 'Total Monte Carlo') to propagate uncertainties of fundamental nuclear physics experiments, models and parameters to different types of criticality-safety benchmarks. We now show that such exact uncertainty calculations are directly relevant to the optimal and safe design of fusion reactors by applying this methodology to a series of fusion shielding benchmarks, namely those connected to the Oktavian, Fusion Neutronics Source and LLNL Pulsed Sphere experiments. Uncertainties on neutron and gamma leakage fluxes for 13 shielding benchmarks are obtained, in the mass range from {sup nat}Mg to {sup nat}W. Uncertainties for cross-sections, angular distributions, single- and double-differential emission spectra, and gamma-ray production cross-sections are considered in this uncertainty propagation scheme.
On the Exact Solution of Wave Equations on Cantor Sets
Directory of Open Access Journals (Sweden)
Dumitru Baleanu
2015-09-01
Full Text Available The transfer of heat due to the emission of electromagnetic waves is called thermal radiations. In local fractional calculus, there are numerous contributions of scientists, like Mandelbrot, who described fractal geometry and its wide range of applications in many scientific fields. Christianto and Rahul gave the derivation of Proca equations on Cantor sets. Hao et al. investigated the Helmholtz and diffusion equations in Cantorian and Cantor-Type Cylindrical Coordinates. Carpinteri and Sapora studied diffusion problems in fractal media in Cantor sets. Zhang et al. studied local fractional wave equations under fixed entropy. In this paper, we are concerned with the exact solutions of wave equations by the help of local fractional Laplace variation iteration method (LFLVIM. We develop an iterative scheme for the exact solutions of local fractional wave equations (LFWEs. The efficiency of the scheme is examined by two illustrative examples.
Exactly solvable models in many-body theory
March, N H
2016-01-01
The book reviews several theoretical, mostly exactly solvable, models for selected systems in condensed states of matter, including the solid, liquid, and disordered states, and for systems of few or many bodies, both with boson, fermion, or anyon statistics. Some attention is devoted to models for quantum liquids, including superconductors and superfluids. Open problems in relativistic fields and quantum gravity are also briefly reviewed.The book ranges almost comprehensively, but concisely, across several fields of theoretical physics of matter at various degrees of correlation and at different energy scales, with relevance to molecular, solid-state, and liquid-state physics, as well as to phase transitions, particularly for quantum liquids. Mostly exactly solvable models are presented, with attention also to their numerical approximation and, of course, to their relevance for experiments.
Exact performance analysis of decode-and-forward opportunistic relaying
Tourki, Kamel
2010-06-01
In this paper, we investigate a dual-hop decode-and-forward opportunistic relaying scheme where the source may or may not be able to communicate directly with the destination. In our study, we consider a regenerative relaying scheme in which the decision to cooperate takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We derive an exact closed-form expression for the end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation based on the exact statistics of each hop. Unlike existing works where the analysis focused on high signal-to-noise ratio (SNR) regime, such results are important to enable the designers to take decisions regarding practical systems that operate at low SNR regime. We show that performance simulation results coincide with our analytical results.
A 4PN-exact approximation to General Relativity
Brizuela, David
2010-01-01
An approximation to General Relativity is presented which agrees with the Einstein field equations up to and including the fourth post-Newtonian (PN) order. This approximation is formulated in a fully constrained scheme: all involved equations are explicitly elliptic except the wave equation that describes the two independent degrees of freedom of the gravitational field. The formalism covers naturally the conformal-flat-condition (CFC) approach by Isenberg, Wilson, and Mathews and the improved second PN-order exact approach CFC+. For stationary configurations, like Kerr black holes, agreement with General Relativity is achieved even through 5PN order. In addition, we analyze in detail a particularly interesting 2PN-exact waveless approximation which results from imposing more restrictive conditions. The proposed scheme can be considered as a further development on the waveless approach suggested by Schaefer and Gopakumar [Phys. Rev. D {\\bf 69}, 021501 (2004)].
Retrieving the exact Green's function by wavefield crosscorrelation.
Zheng, Yingcai
2010-03-01
Recent development on the Green's function retrieval by wavefield crosscorrelation has substantially advanced the physical research in a multidisciplinary and unprecedented fashion. However, the underlying assumption of the theory that the sources are in the far-field limits the technology to extracting only the high-frequency part of the Green's function in an open system. This critical approximation can be eliminated using the exact boundary integral equation method. A scheme involving the crosscorrelation kernel is proposed to recover the exact Green's function including all-frequency content. Symmetric difference kernels are analytically constructed for sources on a plane or on a circle and can be reduced to the known Dirac delta kernel under the far-field approximation.
Exact traveling wave solutions of some nonlinear evolution equations
Kumar, Hitender; Chand, Fakir
2014-02-01
Using a traveling wave reduction technique, we have shown that Maccari equation, (2+1)-dimensional nonlinear Schrödinger equation, medium equal width equation, (3+1)-dimensional modified KdV-Zakharov-Kuznetsev equation, (2+1)-dimensional long wave-short wave resonance interaction equation, perturbed nonlinear Schrödinger equation can be reduced to the same family of auxiliary elliptic-like equations. Then using extended F-expansion and projective Riccati equation methods, many types of exact traveling wave solutions are obtained. With the aid of solutions of the elliptic-like equation, more explicit traveling wave solutions expressed by the hyperbolic functions, trigonometric functions and rational functions are found out. It is shown that these methods provide a powerful mathematical tool for solving nonlinear evolution equations in mathematical physics. A variety of structures of the exact solutions of the elliptic-like equation are illustrated.
INTERNAL EXACT OBSERVABILITY OF A PERTURBED EULER-BERNOULLI EQUATION
Directory of Open Access Journals (Sweden)
Nicolae Cîndea
2011-01-01
Full Text Available In this work we prove that the exact internal observability for theEuler-Bernoulli equation is robust with respect to a class of linear perturbations. Our results yield,in particular,that for rectangular domains we have the exact observability in an arbitrarily small time and with an arbitrarily small observation region. The usual method of tackling lower order terms,using Carleman estimates, cannot be applied in this context. More precisely, it is not known if Carleman estimates hold for the evolution Euler-Bernoulli equation with arbitrarily small observation region. Therefore we use a method combining frequency domain techniques,a compactness-uniqueness argument and a Carleman estimate for elliptic problems.
Wilson, Thomas S.; Bearinger, Jane P.
2015-06-09
New shape memory polymer compositions, methods for synthesizing new shape memory polymers, and apparatus comprising an actuator and a shape memory polymer wherein the shape memory polymer comprises at least a portion of the actuator. A shape memory polymer comprising a polymer composition which physically forms a network structure wherein the polymer composition has shape-memory behavior and can be formed into a permanent primary shape, re-formed into a stable secondary shape, and controllably actuated to recover the permanent primary shape. Polymers have optimal aliphatic network structures due to minimization of dangling chains by using monomers that are symmetrical and that have matching amine and hydroxyl groups providing polymers and polymer foams with clarity, tight (narrow temperature range) single transitions, and high shape recovery and recovery force that are especially useful for implanting in the human body.
Energy Technology Data Exchange (ETDEWEB)
Wilson, Thomas S.; Bearinger, Jane P.
2017-08-29
New shape memory polymer compositions, methods for synthesizing new shape memory polymers, and apparatus comprising an actuator and a shape memory polymer wherein the shape memory polymer comprises at least a portion of the actuator. A shape memory polymer comprising a polymer composition which physically forms a network structure wherein the polymer composition has shape-memory behavior and can be formed into a permanent primary shape, re-formed into a stable secondary shape, and controllably actuated to recover the permanent primary shape. Polymers have optimal aliphatic network structures due to minimization of dangling chains by using monomers that are symmetrical and that have matching amine and hydroxl groups providing polymers and polymer foams with clarity, tight (narrow temperature range) single transitions, and high shape recovery and recovery force that are especially useful for implanting in the human body.
Parametrices and exact paralinearization of semi-linear boundary problems
DEFF Research Database (Denmark)
Johnsen, Jon
2008-01-01
The subject is parametrices for semi-linear problems, based on parametrices for linear boundary problems and on non-linearities that decompose into solution-dependent linear operators acting on the solutions. Non-linearities of product type are shown to admit this via exact paralinearization. The...... of homogeneous distributions, tensor products and halfspace extensions have been revised. Examples include the von Karman equation....
A Finite Exact Representation of Register Automata Configurations
Directory of Open Access Journals (Sweden)
Yu-Fang Chen
2014-02-01
Full Text Available A register automaton is a finite automaton with finitely many registers ranging from an infinite alphabet. Since the valuations of registers are infinite, there are infinitely many configurations. We describe a technique to classify infinite register automata configurations into finitely many exact representative configurations. Using the finitary representation, we give an algorithm solving the reachability problem for register automata. We moreover define a computation tree logic for register automata and solve its model checking problem.
Exact Regenerating Codes for Byzantine Fault Tolerance in Distributed Storage
Han, Yunghsiang S.; Zheng, Rong; Mow, Wai Ho
2011-01-01
Due to the use of commodity software and hardware, crash-stop and Byzantine failures are likely to be more prevalent in today's large-scale distributed storage systems. Regenerating codes have been shown to be a more efficient way to disperse information across multiple nodes and recover crash-stop failures in the literature. In this paper, we present the design of regeneration codes in conjunction with integrity check that allows exact regeneration of failed nodes and data reconstruction in ...
Exactly averaged equations for flow and transport in random media
Energy Technology Data Exchange (ETDEWEB)
Shvidler, Mark; Karasaki, Kenzi [Lawrence Berkeley National Lab., Earth Sciences Division, Berkeley, CA (United States)
2001-07-01
It is well known that exact averaging of the equations of flow and transport in random porous media can be realized only for a small number of special, occasionally exotic, fields. On the other hand, the properties of approximate averaging methods are not yet fully understood. For example, the convergence behavior and the accuracy of truncated perturbation series. Furthermore, the calculation of the high-order perturbations is very complicated. These problems for a long time have stimulated attempts to find the answer for the question: Are there in existence some exact general and sufficiently universal forms of averaged equations? If the answer is positive, there arises the problem of the construction of these equations and analyzing them. There exist many publications related to these problems and oriented on different applications: hydrodynamics, flow and transport in porous media, theory of elasticity, acoustic and electromagnetic waves in random fields, etc. We present a method of finding the general form of exactly averaged equations for flow and transport in random fields by using (1) an assumption of the existence of Green's functions for appropriate stochastic problems, (2) some general properties of the Green's functions, and (3) the some basic information about the random fields of the conductivity, porosity and flow velocity. We present a general form of the exactly averaged non-local equations for the following cases. 1. Steady-state flow with sources in porous media with random conductivity. 2. Transient flow with sources in compressible media with random conductivity and porosity. 3. Non-reactive solute transport in random porous media. We discuss the problem of uniqueness and the properties of the non-local averaged equations, for the cases with some types of symmetry (isotropic, transversal isotropic, orthotropic) and we analyze the hypothesis of the structure non-local equations in general case of stochastically homogeneous fields
Exactly Embedded Wavefunction Methods for Characterizing Nitrogen Reduction Catalysis
2015-01-15
SUBTITLE Exactly Embedded Wavefunction Methods for Characterizing Nitrogen Reduction Catalysis 5a. CONTRACT NUMBER N/A 5b. GRANT NUMBER FA9550... catalysis , such as hydrogen and nitrogen reduction. In a significant methodological advance from the past year, we developed an accurate and...1-0288), the Miller group developed new electronic structure embedding methods for the investigation of small- molecular activation catalysis , such as
A Visual Basic Software for Computing Fisher's Exact Probability
Haseeb Ahmad Khan
2003-01-01
Fisher's exact test (FET) is an important statistical method for testing association between two groups. However, the computations involved in FET are extremely tedious and time consuming due to multi-step factorial calculations after the construction of numerous 2x2 tables depending on the smallest cell value. A Visual-Basic computer program, CalcFisher, has been developed to handle the complexities of FET resorting the techniques of looping subroutines and logarithmic conversions. The softw...
Exact Steady Azimuthal Edge Waves in Rotating Fluids
Ionescu-Kruse, Delia
2017-09-01
The full problem of water waves travelling along a constant sloping beach with the shoreline parallel to the Equator, written in a moving frame with the origin at a point on the rotating Earth is introduced. An exact steady solution of this problem moving only in the azimuthal direction, with no variations in this direction, is obtained. The solution is discussed in turn in spherical coordinates, in cylindrical coordinates and in the tangent-plan approximations.
Nucleon-nucleon resonance behavior in an exactly soluble model
Kloet, W. M.; Tjon, J. A.
1983-01-01
The resonance-like structure in 1D 2 and 3F 3 nucleon-nucleon phase parameters at medium energy can be understood from the simple dynamics of coupling to the inelastic NNπ channel. In an exactly soluble coupled channel model the analytic structure of the scattering amplitude is studied in detail. The role of the NΔ branch cut and the presence and origin of dynamical poles is discussed.
Nucleon-nucleon resonance behavior in an exactly soluble model
Energy Technology Data Exchange (ETDEWEB)
Kloet, W.M.; Tjon, J.A. (Rijksuniversiteit Utrecht (Netherlands). Inst. voor Theoretische Fysica)
1983-01-17
The resonance-like structure in /sup 1/D/sub 2/ and /sup 3/F/sub 3/ nucleon-nucleon phase parameters at medium energy can be understood from the simple dynamics of coupling to the inelastic NNsub(..pi..) channel. In an exactly soluble coupled channel model the analytic structure of the scattering amplitude is studied in detail. The role of the N..delta.. branch cut and the presence and origin of dynamical poles is discussed.
Exactly solvable chaos and addition theorems of elliptic functions
Umeno, K
1997-01-01
We review recent developments about a systematic method of constructing of rational mappings as ergordic transformations with non-uniform invariant measures on the unit interval [0,1]. All rational ergordic mappings of [0,1] with explicit non-uniform densities can be characterized by addition theorems of elliptic functions. We call this special class of chaotic mappings exactly solvable chaos and we can classify them by the associated elliptic modular functions.
Unitary-matrix models as exactly solvable string theories
Periwal, Vipul; Shevitz, Danny
1990-01-01
Exact differential equations are presently found for the scaling functions of models of unitary matrices which are solved in a double-scaling limit, using orthogonal polynomials on a circle. For the case of the simplest, k = 1 model, the Painleve II equation with constant 0 is obtained; possible nonperturbative phase transitions exist for these models. Equations are presented for k = 2 and 3, and discussed with a view to asymptotic behavior.
An Exact Method for the Double TSP with Multiple Stacks
DEFF Research Database (Denmark)
Larsen, Jesper; Lusby, Richard Martin; Ehrgott, Matthias
that minimizes the total transportation cost (ignoring the cost of transporting the container between the depots of the two trips) given that the container cannot be repacked at any stage. In this paper we present an exact solution method based on matching k-best TSP solutions for each of the separate pickup...... and delivery TSP problems and show that previously unsolved instances can be solved within seconds using this approach....
An Exact Method for the Double TSP with Multiple Stacks
DEFF Research Database (Denmark)
Lusby, Richard Martin; Larsen, Jesper; Ehrgott, Matthias
2010-01-01
that minimizes the total transportation cost (ignoring the cost of transporting the container between the depots of the two trips) given that the container cannot be repacked at any stage. In this paper we present an exact solution method based on matching k-best TSP solutions for each of the separate pickup...... and delivery TSP problems and show that previously unsolved instances can be solved within seconds using this approach....
Exactly solvable models for atom-molecule Hamiltonians.
Dukelsky, J; Dussel, G G; Esebbag, C; Pittel, S
2004-07-30
We present a family of exactly solvable generalizations of the Jaynes-Cummings model involving the interaction of an ensemble of SU(2) or SU(1,1) quasispins with a single boson field. They are obtained from the trigonometric Richardson-Gaudin models by replacing one of the SU(2) or SU(1,1) degrees of freedom by an ideal boson. The application to a system of bosonic atoms and molecules is reported.
An asymptotically exact theory of functionally graded piezoelectric shells
Le, Khanh Chau
2016-01-01
An asymptotically exact two-dimensional theory of functionally graded piezoelectric shells is derived by the variational-asymptotic method. The error estimation of the constructed theory is given in the energetic norm. As an application, analytical solution to the problem of forced vibration of a functionally graded piezoceramic cylindrical shell with thickness polarization fully covered by electrodes and excited by a harmonic voltage is found.
A fast exact sequential algorithm for the partial digest problem.
Abbas, Mostafa M; Bahig, Hazem M
2016-12-22
Restriction site analysis involves determining the locations of restriction sites after the process of digestion by reconstructing their positions based on the lengths of the cut DNA. Using different reaction times with a single enzyme to cut DNA is a technique known as a partial digestion. Determining the exact locations of restriction sites following a partial digestion is challenging due to the computational time required even with the best known practical algorithm. In this paper, we introduce an efficient algorithm to find the exact solution for the partial digest problem. The algorithm is able to find all possible solutions for the input and works by traversing the solution tree with a breadth-first search in two stages and deleting all repeated subproblems. Two types of simulated data, random and Zhang, are used to measure the efficiency of the algorithm. We also apply the algorithm to real data for the Luciferase gene and the E. coli K12 genome. Our algorithm is a fast tool to find the exact solution for the partial digest problem. The percentage of improvement is more than 75% over the best known practical algorithm for the worst case. For large numbers of inputs, our algorithm is able to solve the problem in a suitable time, while the best known practical algorithm is unable.
Exact and Optimal Quantum Mechanics/Molecular Mechanics Boundaries.
Sun, Qiming; Chan, Garnet Kin-Lic
2014-09-09
Motivated by recent work in density matrix embedding theory, we define exact link orbitals that capture all quantum mechanical (QM) effects across arbitrary quantum mechanics/molecular mechanics (QM/MM) boundaries. Exact link orbitals are rigorously defined from the full QM solution, and their number is equal to the number of orbitals in the primary QM region. Truncating the exact set yields a smaller set of link orbitals optimal with respect to reproducing the primary region density matrix. We use the optimal link orbitals to obtain insight into the limits of QM/MM boundary treatments. We further analyze the popular general hybrid orbital (GHO) QM/MM boundary across a test suite of molecules. We find that GHOs are often good proxies for the most important optimal link orbital, although there is little detailed correlation between the detailed GHO composition and optimal link orbital valence weights. The optimal theory shows that anions and cations cannot be described by a single link orbital. However, expanding to include the second most important optimal link orbital in the boundary recovers an accurate description. The second optimal link orbital takes the chemically intuitive form of a donor or acceptor orbital for charge redistribution, suggesting that optimal link orbitals can be used as interpretative tools for electron transfer. We further find that two optimal link orbitals are also sufficient for boundaries that cut across double bonds. Finally, we suggest how to construct "approximately" optimal link orbitals for practical QM/MM calculations.
Implementation of geometrically exact beam element for nonlinear dynamics modeling
Energy Technology Data Exchange (ETDEWEB)
Wang, Jielong, E-mail: jelon.wang@gmail.com [Commercial Aircraft Corporation of China, Ltd., Beijing Aeronautical Science & Technology Research Institute (China)
2015-12-15
The paper develops a new type of geometrically exact beam element featuring large displacements and rotations together with small warping. The dimension reduction approach based on variational asymptotic method has been explored, and a linear two-dimensional finite element procedure has been implemented to predict the cross-sectional stiffness and recover the cross-sectional strain fields of the beam. The total and incremental variables mixed formula of governing equations of motion is presented, in which the Wiener–Milenković parameters are selected to vectorize the finite rotation. The dynamic problem of geometrically exact beam has been solved by the implicit Radau IIA algorithms, the time histories of large translations and rotations with small three-dimensional warping have been integrated. Numerical simulations have been performed and the results have been compared to those of commercial software LS-DYNA. It can be concluded that the current modeling approach features high accuracy and that the new geometrically exact beam with warping is robust enough to predict large deformations with small strain.
Exact EGB models for spherical static perfect fluids
Energy Technology Data Exchange (ETDEWEB)
Hansraj, Sudan; Chilambwe, Brian; Maharaj, Sunil D. [University of KwaZulu-Natal, Astrophysics and Cosmology Research Unit, School of Mathematics, Statistics and Computer Science, Private Bag 54001, Durban (South Africa)
2015-06-15
We obtain a new exact solution to the field equations for a 5-dimensional spherically symmetric static distribution in the Einstein-Gauss-Bonnet modified theory of gravity. By using a transformation, the study is reduced to the analysis of a single second order nonlinear differential equation. In general the condition of pressure isotropy produces a first order differential equation which is an Abel equation of the second kind. An exact solution is found. The solution is examined for physical admissibility. In particular a set of constants is found which ensures that a pressure-free hypersurface exists which defines the boundary of the distribution. Additionally the isotropic pressure and the energy density are shown to be positive within the radius of the sphere. The adiabatic sound-speed criterion is also satisfied within the fluid ensuring a subluminal sound speed. Furthermore, the weak, strong and dominant conditions hold throughout the distribution. On setting the Gauss-Bonnet coupling to zero, an exact solution for 5-dimensional perfect fluids in the standard Einstein theory is obtained. Plots of the dynamical quantities for the Gauss-Bonnet and the Einstein case reveal that the pressure is unaffected, while the energy density increases under the influence of the Gauss-Bonnet term. (orig.)
Functional determinants, index theorems, and exact quantum black hole entropy
Murthy, Sameer; Reys, Valentin
2015-12-01
The exact quantum entropy of BPS black holes can be evaluated using localization in supergravity. An important ingredient in this program, that has been lacking so far, is the one-loop effect arising from the quadratic fluctuations of the exact deformation (the QV operator). We compute the fluctuation determinant for vector multiplets and hyper multiplets around Q-invariant off-shell configurations in four-dimensional N=2 supergravity with AdS 2 × S 2 boundary conditions, using the Atiyah-Bott fixed-point index theorem and a subsequent zeta function regularization. Our results extend the large-charge on-shell entropy computations in the literature to a regime of finite charges. Based on our results, we present an exact formula for the quantum entropy of BPS black holes in N=2 supergravity. We explain cancellations concerning 1/8 -BPS black holes in N=8 supergravity that were observed in arXiv:1111.1161. We also make comments about the interpretation of a logarithmic term in the topological string partition function in the low energy supergravity theory.
Determining the Exact Mass of Neutrino through Logical Mass Analysis
Angus, Andrew
2003-03-01
The primary purpose of this paper is to demonstrate that a neutrino has a definite mass. Secondly, the purpose of this paper is to show through reaction equation the genesis of neutrino from nuclear reactions induced by electricity. The author used a method called logical mass analysis to determine the exact mass of neutrino which eluded scientists since 1930. The author determined the exact mass of three types of neutrinos as follows: a. neutrino-p has rest mass of 0.2395 MeV, b. neutrino-d has a rest mass of 0.059 MeV, c. the neutrino-t has a rest mass of 0.444 MeV. The author formally defines a neutrino as a leptonic particle with a mass ranging from 1/10 to 9/10 of an electron mass. The importance of this paper lies in the fact that exact mass of neutrinos have eluded scientists for more than 60 years since its postulated existence in 1930 as a massless particle. This paper is also important because this paper will give experimental scientists a basis of identifying different types of neutrinos and its definite masses during experimentation.
Exact Outage Probability of Dual-Hop CSI-Assisted AF Relaying Over Nakagami-m Fading Channels
Xia, Minghua
2012-10-01
In this correspondence, considering dual-hop channel state information (CSI)-assisted amplify-and-forward (AF) relaying over Nakagami- m fading channels, the cumulative distribution function (CDF) of the end-to-end signal-to-noise ratio (SNR) is derived. In particular, when the fading shape factors m1 and m2 at consecutive hops take non-integer values, the bivariate H-function and G -function are exploited to obtain an exact analytical expression for the CDF. The obtained CDF is then applied to evaluate the outage performance of the system under study. The analytical results of outage probability coincide exactly with Monte-Carlo simulation results and outperform the previously reported upper bounds in the low and medium SNR regions.
Characterization of RNA interference in rat PC12 cells
DEFF Research Database (Denmark)
Thonberg, Håkan; Schéele, Camilla C; Dahlgren, Cecilia
2004-01-01
Double-stranded RNA can initiate post transcriptional gene silencing in mammalian cell cultures via a mechanism known as RNA interference (RNAi). The sequence-specific degradation of homologous mRNA is triggered by 21-nucleotide RNA-duplexes termed short interfering RNA (siRNA). The homologous...... strand of the siRNA guides a multi-protein complex, RNA-induced silencing complex (RISC), to cleave target mRNA. Although the exact function and composition of RISC is still unclear, it has been shown to include several proteins of the Argonaute protein family. Here we report of a robust system...... to achieve RNAi in a cultured rat neuronal cell line, PC12. Targeting of neuropeptide Y mRNA by synthetic siRNA results in knock down of the mRNA levels with an IC50 of approximately 0.1 nM. The mRNA knockdown lasts for at least 96 h and is not dependent on protein synthesis. Further, PC12 cells were ablated...
Discriminative Shape Alignment
DEFF Research Database (Denmark)
Loog, M.; de Bruijne, M.
2009-01-01
The alignment of shape data to a common mean before its subsequent processing is an ubiquitous step within the area shape analysis. Current approaches to shape analysis or, as more specifically considered in this work, shape classification perform the alignment in a fully unsupervised way......, not taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two...
RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction.
Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong
2014-07-01
Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA-RNA interactions and 1619 RNA-protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA-RNA/RNA-protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA-RNA/RNA-protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. © 2014 Zhang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Triggering of RNA interference with RNA-RNA, RNA-DNA, and DNA-RNA nanoparticles.
Afonin, Kirill A; Viard, Mathias; Kagiampakis, Ioannis; Case, Christopher L; Dobrovolskaia, Marina A; Hofmann, Jen; Vrzak, Ashlee; Kireeva, Maria; Kasprzak, Wojciech K; KewalRamani, Vineet N; Shapiro, Bruce A
2015-01-27
Control over cellular delivery of different functionalities and their synchronized activation is a challenging task. We report several RNA and RNA/DNA-based nanoparticles designed to conditionally activate the RNA interference in various human cells. These nanoparticles allow precise control over their formulation, stability in blood serum, and activation of multiple functionalities. Importantly, interferon and pro-inflammatory cytokine activation assays indicate the significantly lower responses for DNA nanoparticles compared to the RNA counterparts, suggesting greater potential of these molecules for therapeutic use.
Quantifying circular RNA expression from RNA-seq data using model-based framework.
Li, Musheng; Xie, Xueying; Zhou, Jing; Sheng, Mengying; Yin, Xiaofeng; Ko, Eun-A; Zhou, Tong; Gu, Wanjun
2017-07-15
Circular RNAs (circRNAs) are a class of non-coding RNAs that are widely expressed in various cell lines and tissues of many organisms. Although the exact function of many circRNAs is largely unknown, the cell type-and tissue-specific circRNA expression has implicated their crucial functions in many biological processes. Hence, the quantification of circRNA expression from high-throughput RNA-seq data is becoming important to ascertain. Although many model-based methods have been developed to quantify linear RNA expression from RNA-seq data, these methods are not applicable to circRNA quantification. Here, we proposed a novel strategy that transforms circular transcripts to pseudo-linear transcripts and estimates the expression values of both circular and linear transcripts using an existing model-based algorithm, Sailfish. The new strategy can accurately estimate transcript expression of both linear and circular transcripts from RNA-seq data. Several factors, such as gene length, amount of expression and the ratio of circular to linear transcripts, had impacts on quantification performance of circular transcripts. In comparison to count-based tools, the new computational framework had superior performance in estimating the amount of circRNA expression from both simulated and real ribosomal RNA-depleted (rRNA-depleted) RNA-seq datasets. On the other hand, the consideration of circular transcripts in expression quantification from rRNA-depleted RNA-seq data showed substantial increased accuracy of linear transcript expression. Our proposed strategy was implemented in a program named Sailfish-cir. Sailfish-cir is freely available at https://github.com/zerodel/Sailfish-cir . tongz@medicine.nevada.edu or wanjun.gu@gmail.com. Supplementary data are available at Bioinformatics online.
Frames for exact inversion of the rank order coder.
Masmoudi, Khaled; Antonini, Marc; Kornprobst, Pierre
2012-02-01
Our goal is to revisit rank order coding by proposing an original exact decoding procedure for it. Rank order coding was proposed by Thorpe et al. who stated that the order in which the retina cells are activated encodes for the visual stimulus. Based on this idea, the authors proposed in [1] a rank order coder/decoder associated to a retinal model. Though, it appeared that the decoding procedure employed yields reconstruction errors that limit the model bit-cost/quality performances when used as an image codec. The attempts made in the literature to overcome this issue are time consuming and alter the coding procedure, or are lacking mathematical support and feasibility for standard size images. Here we solve this problem in an original fashion by using the frames theory, where a frame of a vector space designates an extension for the notion of basis. Our contribution is twofold. First, we prove that the analyzing filter bank considered is a frame, and then we define the corresponding dual frame that is necessary for the exact image reconstruction. Second, to deal with the problem of memory overhead, we design a recursive out-of-core blockwise algorithm for the computation of this dual frame. Our work provides a mathematical formalism for the retinal model under study and defines a simple and exact reverse transform for it with over than 265 dB of increase in the peak signal-to-noise ratio quality compared to [1]. Furthermore, the framework presented here can be extended to several models of the visual cortical areas using redundant representations.
Path Following in the Exact Penalty Method of Convex Programming.
Zhou, Hua; Lange, Kenneth
2015-07-01
Classical penalty methods solve a sequence of unconstrained problems that put greater and greater stress on meeting the constraints. In the limit as the penalty constant tends to ∞, one recovers the constrained solution. In the exact penalty method, squared penalties are replaced by absolute value penalties, and the solution is recovered for a finite value of the penalty constant. In practice, the kinks in the penalty and the unknown magnitude of the penalty constant prevent wide application of the exact penalty method in nonlinear programming. In this article, we examine a strategy of path following consistent with the exact penalty method. Instead of performing optimization at a single penalty constant, we trace the solution as a continuous function of the penalty constant. Thus, path following starts at the unconstrained solution and follows the solution path as the penalty constant increases. In the process, the solution path hits, slides along, and exits from the various constraints. For quadratic programming, the solution path is piecewise linear and takes large jumps from constraint to constraint. For a general convex program, the solution path is piecewise smooth, and path following operates by numerically solving an ordinary differential equation segment by segment. Our diverse applications to a) projection onto a convex set, b) nonnegative least squares, c) quadratically constrained quadratic programming, d) geometric programming, and e) semidefinite programming illustrate the mechanics and potential of path following. The final detour to image denoising demonstrates the relevance of path following to regularized estimation in inverse problems. In regularized estimation, one follows the solution path as the penalty constant decreases from a large value.
Path Following in the Exact Penalty Method of Convex Programming
Zhou, Hua; Lange, Kenneth
2015-01-01
Classical penalty methods solve a sequence of unconstrained problems that put greater and greater stress on meeting the constraints. In the limit as the penalty constant tends to ∞, one recovers the constrained solution. In the exact penalty method, squared penalties are replaced by absolute value penalties, and the solution is recovered for a finite value of the penalty constant. In practice, the kinks in the penalty and the unknown magnitude of the penalty constant prevent wide application of the exact penalty method in nonlinear programming. In this article, we examine a strategy of path following consistent with the exact penalty method. Instead of performing optimization at a single penalty constant, we trace the solution as a continuous function of the penalty constant. Thus, path following starts at the unconstrained solution and follows the solution path as the penalty constant increases. In the process, the solution path hits, slides along, and exits from the various constraints. For quadratic programming, the solution path is piecewise linear and takes large jumps from constraint to constraint. For a general convex program, the solution path is piecewise smooth, and path following operates by numerically solving an ordinary differential equation segment by segment. Our diverse applications to a) projection onto a convex set, b) nonnegative least squares, c) quadratically constrained quadratic programming, d) geometric programming, and e) semidefinite programming illustrate the mechanics and potential of path following. The final detour to image denoising demonstrates the relevance of path following to regularized estimation in inverse problems. In regularized estimation, one follows the solution path as the penalty constant decreases from a large value. PMID:26366044
Thermodynamics of Rh nuclear spins calculated by exact diagonalization
DEFF Research Database (Denmark)
Lefmann, K.; Ipsen, J.; Rasmussen, F.B.
2000-01-01
We have employed the method of exact diagonalization to obtain the full-energy spectrum of a cluster of 16 Rh nuclear spins, having dipolar and RK interactions between first and second nearest neighbours only. We have used this to calculate the nuclear spin entropy, and our results at both positive...... and negative temperatures follow the second-order high-temperature series expansions for |T| > 3 nK. Our findings do not agree with the measurements of the former Rh experiment in Helsinki, where a deviation is seen at much higher temperatures....
Exact solution of large asymmetric traveling salesman problems.
Miller, D L; Pekny, J F
1991-02-15
The traveling salesman problem is one of a class of difficult problems in combinatorial optimization that is representative of a large number of important scientific and engineering problems. A survey is given of recent applications and methods for solving large problems. In addition, an algorithm for the exact solution of the asymmetric traveling salesman problem is presented along with computational results for several classes of problems. The results show that the algorithm performs remarkably well for some classes of problems, determining an optimal solution even for problems with large numbers of cities, yet for other classes, even small problems thwart determination of a provably optimal solution.
Exact elegant Laguerre-Gaussian vector wave packets.
Nasalski, W
2013-03-15
An exact closed-form representation is derived of a vector elegant Laguerre-Gaussian wave packet. Its space-time representation consists of three mutually orthogonal field components--of a common azimuthal index and different radial indices--uniquely distinguished by first three powers of the paraxial parameter. The transverse components are of tm-radial and te-azimuthal polarization and appear, under their normal incidence, to be eigenmodes of any horizontally planar, homogeneous and isotropic structure, with eigenvalues given by the reflection and transmission coefficients. In this context, the interrelations between the cross-polarization symmetries of wave packets in free space and at medium planar interfaces are discussed.
A static axisymmetric exact solution of f(R)-gravity
Energy Technology Data Exchange (ETDEWEB)
Gutierrez-Pineres, Antonio C., E-mail: acgutierrez@correo.nucleares.unam.mx [Facultad de Ciencias Basicas, Universidad Tecnologica de Bolivar, CO 131001 Cartagena de Indias (Colombia); Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, A.P. 70-543, 04510 Mexico D.F. (Mexico); Lopez-Monsalvo, Cesar S., E-mail: cesar.slm@correo.nucleares.unam.mx [Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, A.P. 70-543, 04510 Mexico D.F. (Mexico)
2013-01-29
We present an exact, axially symmetric, static, vacuum solution for f(R)-gravity in Weyl's canonical coordinates. We obtain a general explicit expression for the dependence of df(R)/dR upon the r and z coordinates and then the corresponding explicit form of f(R), which must be consistent with the field equations. We analyze in detail the modified Schwarzschild solution in prolate spheroidal coordinates. Finally, we study the curvature invariants and show that, in the case of f(R){ne}R, this solution corresponds to a naked singularity.
The Problem of Understanding of Nature in Exact Science
Leo Näpinen
2014-01-01
In this short inquiry I would like to defend the statement that exact science deals with the explanation of models, but not with the understanding (comprehending) of nature. By the word ‘nature’ I mean nature as physis (as a self-moving and self-developing living organism to which humans also belong), not nature as natura naturata (as a nonevolving creature created by someone or something). The Estonian philosopher of science Rein Vihalemm (2008) has shown with his conception of phi-scienc...
A class of exact classical solutions to string theory.
Coley, A A
2002-12-31
We show that the recently obtained class of spacetimes for which all of the scalar curvature invariants vanish (which can be regarded as generalizations of pp-wave spacetimes) are exact solutions in string theory to all perturbative orders in the string tension scale. As a result the spectrum of the theory can be explicitly obtained, and these spacetimes are expected to provide some hints for the study of superstrings on more general backgrounds. Since these Lorentzian spacetimes suffer no quantum corrections to all loop orders they may also offer insights into quantum gravity.
Exact solutions for the spin tune for model storage rings
Mane, S R
2002-01-01
We present exact analytical expressions for the spin tune for arbitrary values of the orbital action for several storage ring models. The models we treat contain Siberian Snakes, the use of which is essential to preserve the polarization of beams in high-energy proton storage rings. Our solutions contain some novel features. We also prove a previously conjectured claim about the behavior of spin tuneshifts in rings with multiple Snakes. The conjecture is based on numerical simulations, but our proof is analytical, and also nonperturbative.
Towards the exact Bremsstrahlung function of ABJM theory
Bianchi, Marco S.; Griguolo, Luca; Mauri, Andrea; Penati, Silvia; Preti, Michelangelo; Seminara, Domenico
2017-08-01
We present the three-loop calculation of the Bremsstrahlung function associated to the 1/2-BPS cusp in ABJM theory, including color subleading corrections. Using the BPS condition we reduce the computation to that of a cusp with vanishing angle. We work within the framework of heavy quark effective theory (HQET) that further simplifies the analytic evaluation of the relevant cusp anomalous dimension in the near-BPS limit. The result passes nontrivial tests, such as exponentiation, and is in agreement with the conjecture made in [1] for the exact expression of the Bremsstrahlung function, based on the relation with fermionic latitude Wilson loops.
Exact Regenerating Codes for Byzantine Fault Tolerance in Distributed Storage
Han, Yunghsiang S; Mow, Wai Ho
2011-01-01
Due to the use of commodity software and hardware, crash-stop and Byzantine failures are likely to be more prevalent in today's large-scale distributed storage systems. Regenerating codes have been shown to be a more efficient way to disperse information across multiple nodes and recover crash-stop failures in the literature. In this paper, we present the design of regeneration codes in conjunction with integrity check that allows exact regeneration of failed nodes and data reconstruction in presence of Byzantine failures. A progressive decoding mechanism is incorporated in both procedures to leverage computation performed thus far. The fault-tolerance and security properties of the schemes are also analyzed.
Instantaneous Bethe-Salpeter equation with exact propagators
Energy Technology Data Exchange (ETDEWEB)
Lucha, Wolfgang [Institut fuer Hochenergiephysik, Oesterreichische Akademie der Wissenschaften, Nikolsdorfergasse 18, A-1050 Vienna (Austria); Schoeberl, Franz F [Institut fuer Theoretische Physik, Universitaet Wien, Boltzmanngasse 5, A-1090 Vienna (Austria)
2005-11-01
Consequent application of the instantaneous approximation to both the interaction and all propagators of the bound-state constituents allows us to forge, within the framework of the Bethe-Salpeter formalism for the description of bound states, an instantaneous form of the Bethe-Salpeter equation with exact (i.e., full) propagators of the bound-state constituents. This instantaneous equation generalizes the well-known Salpeter equation, the derivation of which needs the additional assumption of free propagation of the bound-state constituents.
Towards an exact factorization of the molecular wave function
Parashar, Shubham; Sajeev, Y.; Ghosh, Swapan K.
2015-10-01
An exact single-product factorisation of the molecular wave function for the timedependent Schrödinger equation is investigated by using an ansatz involving a phase factor. By using the Frenkel variational method, we obtain the Schrödinger equations for the electronic and nuclear wave functions. The concept of a potential energy surface (PES) is retained by introducing a modified Hamiltonian as suggested earlier by Cederbaum. The parameter ω in the phase factor is chosen such that the equations of motion retain the physically appealing Born- Oppenheimer-like form, and is therefore unique.
Approximating the exact value of an American option
Directory of Open Access Journals (Sweden)
Stefano Herzel
2007-10-01
Full Text Available An American option is a derivative security that can be exercised at any time before expiration. Under standard hypotheses it can be shown that its arbitrage-free price is the solution of an optimal stopping problem. Usually, if the underlying asset follows a diffusion, the stopping time problem does not have a closed form solution. Therefore, discrete time models have been proposed to determine an approximated solution. I formulate some conditions on the discrete process to insure convergence of the approximations to the exact value. I also show how to apply such conditions to check the correctness of some of the most popular discretization schemes.
Exact partition functions for gauge theories on Rλ3
Directory of Open Access Journals (Sweden)
Jean-Christophe Wallet
2016-11-01
Full Text Available The noncommutative space Rλ3, a deformation of R3, supports a 3-parameter family of gauge theory models with gauge-invariant harmonic term, stable vacuum and which are perturbatively finite to all orders. Properties of this family are discussed. The partition function factorizes as an infinite product of reduced partition functions, each one corresponding to the reduced gauge theory on one of the fuzzy spheres entering the decomposition of Rλ3. For a particular sub-family of gauge theories, each reduced partition function is exactly expressible as a ratio of determinants. A relation with integrable 2-D Toda lattice hierarchy is indicated.
Exact solutions to relativistic singular fractional power potentials
Agboola, Davids; Zhang, Yao-Zhong
2013-12-01
We present (exact) solutions of the Dirac equation with equally mixed interactions for a single fermion bounded by the family of fractional power singular potentials. Closed-form expressions as well as numerical values for the energies were obtained. The wave functions and the allowed values of the potential parameters for the first two members of the family are obtained in terms of a set of algebraic equations. The non-relativistic limit is also discussed and using the Hellmann-Feynmann theorem, some useful expectation values are obtained.
Mass Deformed Exact S-parameter in Conformal Theories
DEFF Research Database (Denmark)
Sannino, Francesco
2010-01-01
the existence of a universal lower bound on the opportunely normalized S parameter and explore its theoretical and phenomenological implications. Our exact results constitute an ideal framework to correctly interpret the lattice studies of the conformal window of strongly interacting theories....... leads to drastically different limiting values of S. Our results apply to any fermion matter representation and can be used as benchmark for the determination of certain relevant properties of the conformal window of any generic vector like gauge theory with fermionic matter. We finally suggest...
Exact Modeling of Cardiovascular System Using Lumped Method
Ghasemalizadeh, Omid; Firoozabadi, Bahar; Hassani, Kamran
2014-01-01
Electrical analogy (Lumped method) is an easy way to model human cardiovascular system. In this paper Lumped method is used for simulating a complete model. It describes a 36-vessel model and cardiac system of human body with details that could show hydrodynamic parameters of cardiovascular system. Also this paper includes modeling of pulmonary, atrium, left and right ventricles with their equivalent circuits. Exact modeling of right and left ventricles pressure increases the accuracy of our simulation. In this paper we show that a calculated pressure for aorta from our complex circuit is near to measured pressure by using advanced medical instruments.
Energy Technology Data Exchange (ETDEWEB)
Reading, Matthew W.
2017-07-04
Technologies for making self-erecting structures are described herein. An exemplary self-erecting structure comprises a plurality of shape-memory members that connect two or more hub components. When forces are applied to the self-erecting structure, the shape-memory members can deform, and when the forces are removed the shape-memory members can return to their original pre-deformation shape, allowing the self-erecting structure to return to its own original shape under its own power. A shape of the self-erecting structure depends on a spatial orientation of the hub components, and a relative orientation of the shape-memory members, which in turn depends on an orientation of joining of the shape-memory members with the hub components.
Shyam, Vikram (Inventor); Poinsatte, Philip (Inventor); Thurman, Douglas (Inventor)
2017-01-01
One or more embodiments of techniques or systems for shaped recess flow control are provided herein. A shaped recess or cavity can be formed on a surface associated with fluid flow. The shaped recess can be configured to create or induce fluid effects, temperature effects, or shedding effects that interact with a free stream or other structures. The shaped recess can be formed at an angle to a free stream flow and may be substantially "V" shaped. The shaped recess can be coupled with a cooling channel, for example. The shaped recess can be upstream or downstream from a cooling channel and aligned in a variety of manners. Due to the fluid effects, shedding effects, and temperature effects created by a shaped recess, lift-off or separation of cooling jets of cooling channels can be mitigated, thereby enhancing film cooling effectiveness.
The use of artificial microRNA technology to control gene expression in Arabidopsis thaliana.
Eamens, Andrew L; McHale, Marcus; Waterhouse, Peter M
2014-01-01
In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like (DCL) endonucleases, are essential in controlling gene expression. One such sRNA class, the microRNAs (miRNAs) control the expression of closely related genes to regulate all aspects of plant development, including the determination of leaf shape, leaf polarity, flowering time, and floral identity. A single miRNA sRNA silencing signal is processed from a long precursor transcript of nonprotein-coding RNA, termed the primary miRNA (pri-miRNA). A region of the pri-miRNA is partially self-complementary allowing the transcript to fold back onto itself to form a stem-loop structure of imperfectly dsRNA. Artificial miRNA (amiRNA) technology uses endogenous pri-miRNAs, in which the miRNA and miRNA* (passenger strand of the miRNA duplex) sequences have been replaced with corresponding amiRNA/amiRNA* sequences that direct highly efficient RNA silencing of the targeted gene. Here, we describe the rules for amiRNA design, as well as outline the PCR and bacterial cloning procedures involved in the construction of an amiRNA plant expression vector to control target gene expression in Arabidopsis thaliana.
Albertazzi, Liliana; Da Pos, Osvaldo; Canal, Luisa; Micciolo, Rocco; Malfatti, Michela; Vescovi, Massimo
2013-01-01
This article presents an experimental study on the naturally biased association between shape and color. For each basic geometric shape studied, participants were asked to indicate the color perceived as most closely related to it, choosing from the Natural Color System Hue Circle. Results show that the choices of color for each shape were not…
Mooney, Carla
2014-01-01
There are shapes everywhere you look. You can put shapes together or build with them. What can you build with three circles? In this title, students will explore and understand that certain attributes define what a shape is called. This title will allow students to identify the main purpose of a text, including what the author wants to answer, explain, or describe.
Exact coherent structures: from fluid turbulence to cardiac arrhythmias
Grigoriev, Roman; Marcotte, Christopher; Byrne, Gregory
2014-03-01
Ventricular fibrillation, a life threatening cardiac arrhythmia, is an example of spatiotemporally chaotic state dominated by multiple interacting spiral waves. Recent studies of weak fluid turbulence suggest that spatiotemporal chaos in general can be understood as a walk among exact unstable regular solutions (exact coherent states, ECS) of nonlinear evolution equations. Several classes of ECS are believed to play a dominant role; most typically these are equilibria and periodic orbits or relative equilibria and relative periodic orbits for systems with global continuous symmetries. Numerical methods originally developed in the context of fluid turbulence can also be applied to models of cardiac dynamics which possess translational and rotational symmetries and, indeed, allowed us to identify relative equilibria and periodic orbits describing isolated spirals with, respectively, fixed and drifting cores. In order to find regular solutions featuring multiple interacting spirals a new approach is required that takes into consideration the dynamics of slowly drifting cores associated with local, rather than global, symmetries. We describe how local symmetries can be reduced and more general types of ECS computed that dominate spiral wave chaos in models of cardiac tissue.
Exactly Energy Conserving Implicit Moment Particle in Cell Formulation
Lapenta, Giovanni
2016-01-01
We report a new particle in cell (PIC) method based on the implicit moment method (IMM). The novelty of the new method is that unlike any of its predecessors at the same time retains the explicit computational cycle and conserves energy exactly. Recent research has presented fully implicit methods where energy conservation is obtained as part of a non linear iteration procedure. The new method, referred to as Energy Conserving Implicit Moment Method (ECIMM), does not require any non linear iteration and its computational cycle is similar to that of explicit PIC. The properties of then new method are: i) it conserves energy exactly to round-off for any time step or grid spacing; ii) it is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency and allowing the user to select any desired time step; iii) it eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length. T...
Exactly solvable PT-symmetric Hamiltonian having no Hermitian counterpart
Bender, Carl M.; Mannheim, Philip D.
2008-07-01
In a recent paper Bender and Mannheim showed that the unequal-frequency fourth-order derivative Pais-Uhlenbeck oscillator model has a realization in which the energy eigenvalues are real and bounded below, the Hilbert-space inner product is positive definite, and time evolution is unitary. Central to that analysis was the recognition that the Hamiltonian HPU of the model is PT symmetric. This Hamiltonian was mapped to a conventional Dirac-Hermitian Hamiltonian via a similarity transformation whose form was found exactly. The present paper explores the equal-frequency limit of the same model. It is shown that in this limit the similarity transform that was used for the unequal-frequency case becomes singular and that HPU becomes a Jordan-block operator, which is nondiagonalizable and has fewer energy eigenstates than eigenvalues. Such a Hamiltonian has no Hermitian counterpart. Thus, the equal-frequency PT theory emerges as a distinct realization of quantum mechanics. The quantum mechanics associated with this Jordan-block Hamiltonian can be treated exactly. It is shown that the Hilbert space is complete with a set of nonstationary solutions to the Schrödinger equation replacing the missing stationary ones. These nonstationary states are needed to establish that the Jordan-block Hamiltonian of the equal-frequency Pais-Uhlenbeck model generates unitary time evolution.
On spherical dust fluctuations: the exact vs. the perturbative approach
Sussman, Roberto A; Dunsby, Peter K S; German, Gabriel
2014-01-01
We examine the relation between the dynamics of Lema\\^{\\i}tre-Tolman-Bondi (LTB) dust models (with and without $\\Lambda$) and the dynamics of dust perturbations in two of the more familiar formalisms used in cosmology: the metric based Cosmological Perturbation Theory (CPT) and the Covariant Gauge Invariant (GIC) perturbations. For this purpose we recast the evolution of LTB models in terms of a covariant and gauge invariant formalism of local and non-local "exact fluctuations " on a Friedmann-Lema\\^{\\i}tre-Robertson-Walker (FLRW) background defined by suitable averages of covariant scalars. We examine the properties of these fluctuations, which can be defined for a confined comoving domain or for an asymptotic domain extending to whole time slices. In particular, the non-local density fluctuation provides a covariant and precise definition for the notion of the "density contrast ". We show that in their linear regime these LTB exact fluctuations (local and non-local) are fully equivalent to the conventional ...
Visualizing Exact and Approximated 3D Empirical Attainment Functions
Directory of Open Access Journals (Sweden)
Tea Tušar
2014-01-01
Full Text Available Most real-world engineering optimization problems are inherently multiobjective, for example, searching for trade-off solutions of high quality and low cost. As no single optimal solution exists for such problems, multiobjective optimizers provide sets of optimal (or near-optimal trade-off solutions to choose from. The empirical attainment function (EAF is a powerful tool that can be used to analyze and compare the performance of these optimizers. While the visualization of EAFs is rather straightforward in two objectives, the three-objective case presents a great challenge as we need to visualize a large number of 3D cuboids. This paper addresses the visualization of exact as well as approximated 3D EAF values and differences in these values provided by two competing multiobjective optimizers. We show that the exact EAFs can be visualized using slicing and maximum intensity projection (MIP, while the approximated EAFs can be visualized using slicing, MIP, and direct volume rendering. In addition, the paper demonstrates the use of the proposed visualization techniques on a steel casting optimization problem.
Exact complexity: The spectral decomposition of intrinsic computation
Energy Technology Data Exchange (ETDEWEB)
Crutchfield, James P., E-mail: chaos@ucdavis.edu [Complexity Sciences Center and Department of Physics, University of California at Davis, One Shields Avenue, Davis, CA 95616 (United States); Ellison, Christopher J., E-mail: cellison@wisc.edu [Center for Complexity and Collective Computation, University of Wisconsin-Madison, Madison, WI 53706 (United States); Riechers, Paul M., E-mail: pmriechers@ucdavis.edu [Complexity Sciences Center and Department of Physics, University of California at Davis, One Shields Avenue, Davis, CA 95616 (United States)
2016-03-06
We give exact formulae for a wide family of complexity measures that capture the organization of hidden nonlinear processes. The spectral decomposition of operator-valued functions leads to closed-form expressions involving the full eigenvalue spectrum of the mixed-state presentation of a process's ϵ-machine causal-state dynamic. Measures include correlation functions, power spectra, past-future mutual information, transient and synchronization informations, and many others. As a result, a direct and complete analysis of intrinsic computation is now available for the temporal organization of finitary hidden Markov models and nonlinear dynamical systems with generating partitions and for the spatial organization in one-dimensional systems, including spin systems, cellular automata, and complex materials via chaotic crystallography. - Highlights: • We provide exact, closed-form expressions for a hidden stationary process' intrinsic computation. • These include information measures such as the excess entropy, transient information, and synchronization information and the entropy-rate finite-length approximations. • The method uses an epsilon-machine's mixed-state presentation. • The spectral decomposition of the mixed-state presentation relies on the recent development of meromorphic functional calculus for nondiagonalizable operators.
Some exact BPS solutions for exotic vortices and monopoles
Directory of Open Access Journals (Sweden)
Handhika S. Ramadhan
2016-07-01
Full Text Available We present several analytical solutions of BPS vortices and monopoles in the generalized Abelian Maxwell–Higgs and Yang–Mills–Higgs theories, respectively. These models have recently been extensively studied and several exact solutions have already been obtained in [1,2]. In each theory, the dynamics is controlled by the additional two positive scalar-field-dependent functions, f(|ϕ| and w(|ϕ|. For the case of vortices, we work in the ordinary symmetry-breaking Higgs potential, while for the case of monopoles we have the ordinary condition of the Prasad–Sommerfield limit. Our results generalize the exact solutions found previously. We also present solutions for BPS vortices with higher winding number. These solutions suffer from the condition that w(|ϕ| has negative value at some finite range of r, but we argue that since it satisfies the weaker positive-value conditions then the corresponding energy density is still positive-definite and, thus, they are acceptable BPS solutions.
Semiclassical versus exact quantization of the Sinh-Gordon model
Energy Technology Data Exchange (ETDEWEB)
Grossehelweg, Juliane
2009-12-15
In this work we investigate the semiclassics of the Sinh-Gordon model. The Sinh-Gordon model is integrable, its explicit solutions of the classical and the quantum model are well known. This allows for a comprehensive investigation of the semiclassical quantization of the classical model as well as of the semiclassical limit of the exact quantum solution. Semiclassical means in this case that the key objects of quantum theory are constructed as formal power series. A quantity playing an important role in the quantum theory is the Q-function. The purpose of this work is to investigate to what extend the classical integrability of the model admits of a construction of the semiclassical expansion of the Q-function. Therefore we used two conceptual independent approaches. In the one approach we start from the exact nonperturbative solution of the quantum model and calculate the semiclassical limit up to the next to leading order. Thereby we found the spectral curve, as well as the semiclassical expansion of the Q-function and of the eigenvalue of the monodromy matrix. In the other approach we constructed the first two orders of the semiclassical expansion of the Q-function, starting from the classical solution theory. The results of both approaches coincide. (orig.)
Exact and approximate solutions for transient squeezing flow
Lang, Ji; Santhanam, Sridhar; Wu, Qianhong
2017-10-01
In this paper, we report two novel theoretical approaches to examine a fast-developing flow in a thin fluid gap, which is widely observed in industrial applications and biological systems. The problem is featured by a very small Reynolds number and Strouhal number, making the fluid convective acceleration negligible, while its local acceleration is not. We have developed an exact solution for this problem which shows that the flow starts with an inviscid limit when the viscous effect has no time to appear and is followed by a subsequent developing flow, in which the viscous effect continues to penetrate into the entire fluid gap. An approximate solution is also developed using a boundary layer integral method. This solution precisely captures the general behavior of the transient fluid flow process and agrees very well with the exact solution. We also performed numerical simulation using Ansys-CFX. Excellent agreement between the analytical and the numerical solutions is obtained, indicating the validity of the analytical approaches. The study presented herein fills the gap in the literature and will have a broad impact on industrial and biomedical applications.
Reduced description of exact coherent states in parallel shear flows.
Beaume, Cédric; Chini, Gregory P; Julien, Keith; Knobloch, Edgar
2015-04-01
A reduced description of exact coherent structures in the transition regime of plane parallel shear flows is developed, based on the Reynolds number scaling of streamwise-averaged (mean) and streamwise-varying (fluctuation) velocities observed in numerical simulations. The resulting system is characterized by an effective unit Reynolds number mean equation coupled to linear equations for the fluctuations, regularized by formally higher-order diffusion. Stationary coherent states are computed by solving the resulting equations simultaneously using a robust numerical algorithm developed for this purpose. The algorithm determines self-consistently the amplitude of the fluctuations for which the associated mean flow is just such that the fluctuations neither grow nor decay. The procedure is used to compute exact coherent states of a flow introduced by Drazin and Reid [Hydrodynamic Stability (Cambridge University Press, Cambridge, UK, 1981)] and studied by Waleffe [Phys. Fluids 9, 883 (1997)]: a linearly stable, plane parallel shear flow confined between stationary stress-free walls and driven by a sinusoidal body force. Numerical continuation of the lower-branch states to lower Reynolds numbers reveals the presence of a saddle node; the saddle node allows access to upper-branch states that are, like the lower-branch states, self-consistently described by the reduced equations. Both lower- and upper-branch states are characterized in detail.
DEFF Research Database (Denmark)
Winter, Pawel; Sterner, Henrik; Sterner, Peter
2009-01-01
We provide a unified description of (weighted) alpha shapes, beta shapes and the corresponding simplicialcomplexes. We discuss their applicability to various protein-related problems. We also discuss filtrations of alpha shapes and touch upon related persistence issues.We claim that the full...... potential of alpha-shapes and related geometrical constructs in protein-related problems yet remains to be realized and verified. We suggest parallel algorithms for (weighted) alpha shapes, and we argue that future use of filtrations and kinetic variants for larger proteins will need such implementation....
DEFF Research Database (Denmark)
Prats, Miquel; Lim, Sungwoo; Jowers, Iestyn
2009-01-01
This paper is concerned with how design shapes are generated and explored by means of sketching. It presents research into the way designers transform shapes from one state to another using sketch representations. An experimental investigation of the sketching processes of designers is presented....... Connections between sketches are defined in terms of shape transformations and described according to shape rules. These rules provide a formal description of the shape exploration process and develop understanding of the mechanics of sketching in design. The paper concludes by discussing the important...
Extracellular RNA Communication (ExRNA)
Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...
Exactly energy conserving semi-implicit particle in cell formulation
Energy Technology Data Exchange (ETDEWEB)
Lapenta, Giovanni, E-mail: giovanni.lapenta@kuleuven.be
2017-04-01
We report a new particle in cell (PIC) method based on the semi-implicit approach. The novelty of the new method is that unlike any of its semi-implicit predecessors at the same time it retains the explicit computational cycle and conserves energy exactly. Recent research has presented fully implicit methods where energy conservation is obtained as part of a non-linear iteration procedure. The new method (referred to as Energy Conserving Semi-Implicit Method, ECSIM), instead, does not require any non-linear iteration and its computational cycle is similar to that of explicit PIC. The properties of the new method are: i) it conserves energy exactly to round-off for any time step or grid spacing; ii) it is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency and allowing the user to select any desired time step; iii) it eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length; iv) the particle mover has a computational complexity identical to that of the explicit PIC, only the field solver has an increased computational cost. The new ECSIM is tested in a number of benchmarks where accuracy and computational performance are tested. - Highlights: • We present a new fully energy conserving semi-implicit particle in cell (PIC) method based on the implicit moment method (IMM). The new method is called Energy Conserving Implicit Moment Method (ECIMM). • The novelty of the new method is that unlike any of its predecessors at the same time it retains the explicit computational cycle and conserves energy exactly. • The new method is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency. • The new method eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length. • These
Conformal invariance and new exact solutions of the elastostatics equations
Chirkunov, Yu. A.
2017-03-01
We fulfilled a group foliation of the system of n-dimensional (n ≥ 2) Lame equations of the classical static theory of elasticity with respect to the infinite subgroup contained in normal subgroup of main group of this system. It permitted us to move from the Lame equations to the equivalent unification of two first-order systems: automorphic and resolving. We obtained a general solution of the automorphic system. This solution is an n-dimensional analogue of the Kolosov-Muskhelishvili formula. We found the main Lie group of transformations of the resolving system of this group foliation. It turned out that in the two-dimensional and three-dimensional cases, which have a physical meaning, this system is conformally invariant, while the Lame equations admit only a group of similarities of the Euclidean space. This is a big success, since in the method of group foliation, resolving equations usually inherit Lie symmetries subgroup of the full symmetry group that was not used for the foliation. In the three-dimensional case for the solutions of the resolving system, we found the general form of the transformations similar to the Kelvin transformation. These transformations are the consequence of the conformal invariance of the resolving system. In the three-dimensional case with a help of the complex dependent and independent variables, the resolving system is written as a simple complex system. This allowed us to find non-trivial exact solutions of the Lame equations, which direct for the Lame equations practically impossible to obtain. For this complex system, all the essentially distinct invariant solutions of the maximal rank we have found in explicit form, or we reduced the finding of those solutions to the solving of the classical one-dimensional equations of the mathematical physics: the heat equation, the telegraph equation, the Tricomi equation, the generalized Darboux equation, and other equations. For the resolving system, we obtained double wave of a
Isogeometric analysis and shape optimization in electromagnetism
DEFF Research Database (Denmark)
Nguyen, Dang Manh
In this thesis a recently proposed numerical method for solving partial differential equations, isogeometric analysis (IGA), is utilized for the purpose of shape optimization, with a particular emphasis on applications to two-dimensional design problems arising in electromagnetic applications...... parametrization are combined into an iterative algorithm for shape optimization of two dimensional electromagnetic problems. The algorithm may also be relevant for problems in other engineering disciplines. Using the methods developed in this thesis, remarkably we have obtained antennas that perform one million....... The study is motivated by the fact that in contrast with most commonly utilized finite element approximations, IGA allows one to exactly represent geometries arising in computer aided design applications with relatively few variables using splines. The following problems coming from theoretical...
Free quantum motion exactly equals sub-quantum ballistic diffusion
Groessing, Gerhard; Pascasio, Johannes Mesa; Schwabl, Herbert
2010-01-01
By modelling quantum systems with the aid of (classical) non-equilibrium thermodynamics, the quantum mechanical "decay of the wave packet" is shown to simply result from sub-quantum diffusion with a specific diffusion coefficient varying in time due to a particle's changing thermal environment. It is thereby proven that free quantum motion strictly equals ballistic diffusion on the sub-quantum level. The exact quantum mechanical trajectory distributions and the velocity field of the Gaussian wave packet are thus derived solely from classical physics. Moreover, also quantum motion in a linear (e.g., gravitational) potential is shown to equal said sub-quantum ballistic diffusion. Quantitative statements on the trajectories' characteristic behaviour are obtained which cannot be formulated in any other existing model for quantum systems.
Benchmarking GW against exact diagonalization for semiempirical models
DEFF Research Database (Denmark)
Kaasbjerg, Kristen; Thygesen, Kristian Sommer
2010-01-01
captures around 65% of the ground-state correlation energy. The lowest lying excitations are overscreened by GW leading to an underestimation of electron affinities and ionization potentials by 0.15 eV on average corresponding to ∼3%. One-shot G0W0 calculations starting from Hartree-Fock reduce...... the screening and improve the low-lying excitation energies. The effect of the GW self-energy on the molecular excitation energies is shown to be similar to the inclusion of final-state relaxations in Hartree-Fock theory. We discuss the breakdown of the GW approximation in systems with short-range interactions...... (Hubbard models) where correlation effects dominate over screening/relaxation effects. Finally we illustrate the important role of the derivative discontinuity of the true exchange-correlation functional by computing the exact Kohn-Sham levels of benzene....
Mathematics of epidemics on networks from exact to approximate models
Kiss, István Z; Simon, Péter L
2017-01-01
This textbook provides an exciting new addition to the area of network science featuring a stronger and more methodical link of models to their mathematical origin and explains how these relate to each other with special focus on epidemic spread on networks. The content of the book is at the interface of graph theory, stochastic processes and dynamical systems. The authors set out to make a significant contribution to closing the gap between model development and the supporting mathematics. This is done by: Summarising and presenting the state-of-the-art in modeling epidemics on networks with results and readily usable models signposted throughout the book; Presenting different mathematical approaches to formulate exact and solvable models; Identifying the concrete links between approximate models and their rigorous mathematical representation; Presenting a model hierarchy and clearly highlighting the links between model assumptions and model complexity; Providing a reference source for advanced undergraduate...
Off-diagonal Bethe ansatz for exactly solvable models
Wang, Yupeng; Cao, Junpeng; Shi, Kangjie
2015-01-01
This book serves as an introduction of the off-diagonal Bethe Ansatz method, an analytic theory for the eigenvalue problem of quantum integrable models. It also presents some fundamental knowledge about quantum integrability and the algebraic Bethe Ansatz method. Based on the intrinsic properties of R-matrix and K-matrices, the book introduces a systematic method to construct operator identities of transfer matrix. These identities allow one to establish the inhomogeneous T-Q relation formalism to obtain Bethe Ansatz equations and to retrieve corresponding eigenstates. Several longstanding models can thus be solved via this method since the lack of obvious reference states is made up. Both the exact results and the off-diagonal Bethe Ansatz method itself may have important applications in the fields of quantum field theory, low-dimensional condensed matter physics, statistical physics and cold atom systems.
An exact "Tour de France" passes through CERN
CERN Bulletin
2011-01-01
In August 2011, the renowned French mountaineer Lionel Daudet set off from Mont Blanc on a "Tour de la France exacte", strictly following the 5,000 km of land borders and coastline without using a single motorised vehicle. And about a week into his expedition, the French border led him… to CERN of course… where he described his experience as out of the ordinary. Lionel Daudet at one of the posts marking the French border in Meyrin (next to the Linac 4 building). The words "out of the ordinary" are not used lightly by a man who has scaled France's highest peaks in extreme conditions and conquered the world's greatest climbs (mainly solo), from Alaska to Patagonia. "I had never visited a physics lab before today," confesses Lionel Daudet, sitting at a table in the CERN cafeteria. "You get the feeling that knowledge is being built here. When I crossed this particular border...
Chiral Exact Relations for Helicities in Hall Magnetohydrodynamic Turbulence
Banerjee, Supratik
2016-01-01
Besides total energy, three-dimensional incompressible Hall magnetohydrodynamics (MHD) possesses two inviscid invariants which are the magnetic helicity and the generalized helicity. New exact relations are derived for homogeneous (non-isotropic) stationary Hall MHD turbulence (and also for its inertialess electron MHD limit) with non-zero helicities and in the asymptotic limit of large Reynolds numbers. The universal laws are written only in terms of mixed second-order structure functions, i.e. the scalar product of two different increments. It provides, therefore, a direct measurement of the dissipation rates for the corresponding invariant flux. This study shows that the generalized helicity cascade is strongly linked to the left polarized fluctuations while the magnetic helicity cascade is linked to the right polarized fluctuations.
Analyse pire cas exact du réseau AFDX
Adnan, Muhammad
2013-01-01
L'objectif principal de cette thèse est de proposer les méthodes permettant d'obtenir le délai de transmission de bout en bout pire cas exact d'un réseau AFDX. Actuellement, seules des bornes supérieures pessimistes peuvent être calculées en utilisant les approches de type Calcul Réseau ou par Trajectoires. Pour cet objectif, différentes approches et outils existent et ont été analysées dans le contexte de cette thèse. Cette analyse a mis en évidence le besoin de nouvelles approches. Dans un ...
Precise orbit computation for the Geosat Exact Repeat Mission
Haines, Bruce J.; Born, George H.; Rosborough, George W.; Marsh, James G.; Williamson, Ronald G.
1990-03-01
Results are reported from an extensive investigation of orbit-determination strategies for the Geosat Exact Repeat Mission (ERM). The goal is to establish optimum geodetic parameters and procedures for the computation of the most accurate Geosat orbits possible and to apply these procedures for routine computation during the ERM for the following purposes: (1) to enhance the value of the Geosat oceanographic investigations by providing the user community with improved ephemerides, (2) to develop orbit determination techniques for the upcoming altimetric mission Topex/Poseidon, and (3) to assess the radial orbit accuracy obtainable with recently developed gravity models. To this end, ephemerides for the entire first year of the ERM have been computed using the GEODYN II orbit program on the Cyber 205 supercomputer system at the NASA Goddard.
Exact Score Distribution Computation for Similarity Searches in Ontologies
Schulz, Marcel H.; Köhler, Sebastian; Bauer, Sebastian; Vingron, Martin; Robinson, Peter N.
Semantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., protein function prediction with the Gene Ontology. In this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a P-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik’s definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the Human Phenotype Ontology.
Exact analytical thermodynamic expressions for a Brownian heat engine.
Taye, Mesfin Asfaw
2015-09-01
The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time t. Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed form expressions for the free energy, the rate of entropy production, and the rate of entropy flow from the system to the outside. We show that when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In the long time limit, the rate of entropy production balances the rate of entropy extraction, and at equilibrium both entropy production and extraction rates become zero. Furthermore, via the present model, many thermodynamic theories can be checked.
Exact confidence intervals for channelized Hotelling observer performance
Wunderlich, Adam; Noo, Frederic; Heilbrun, Marta
2013-03-01
Task-based assessments of image quality constitute a rigorous, principled approach to the evaluation of imaging system performance. To conduct such assessments, it has been recognized that mathematical model observers are very useful, particularly for purposes of imaging system development and optimization. One type of model observer that has been widely applied in the medical imaging community is the channelized Hotelling observer (CHO). In the present work, we address the need for reliable confidence interval estimators of CHO performance. Specifically, we observe that a procedure proposed by Reiser for interval estimation of the Mahalanobis distance can be applied to obtain confidence intervals for CHO performance. In addition, we find that these intervals are well-defined with theoretically-exact coverage probabilities, which is a new result not proved by Reiser. The confidence intervals are tested with Monte Carlo simulation and demonstrated with an example comparing x-ray CT reconstruction strategies.
Efficient Exact Inference With Loss Augmented Objective in Structured Learning.
Bauer, Alexander; Nakajima, Shinichi; Muller, Klaus-Robert
2016-08-19
Structural support vector machine (SVM) is an elegant approach for building complex and accurate models with structured outputs. However, its applicability relies on the availability of efficient inference algorithms--the state-of-the-art training algorithms repeatedly perform inference to compute a subgradient or to find the most violating configuration. In this paper, we propose an exact inference algorithm for maximizing nondecomposable objectives due to special type of a high-order potential having a decomposable internal structure. As an important application, our method covers the loss augmented inference, which enables the slack and margin scaling formulations of structural SVM with a variety of dissimilarity measures, e.g., Hamming loss, precision and recall, Fβ-loss, intersection over union, and many other functions that can be efficiently computed from the contingency table. We demonstrate the advantages of our approach in natural language parsing and sequence segmentation applications.
Exact traveling wave solutions for system of nonlinear evolution equations.
Khan, Kamruzzaman; Akbar, M Ali; Arnous, Ahmed H
2016-01-01
In this work, recently deduced generalized Kudryashov method is applied to the variant Boussinesq equations, and the (2 + 1)-dimensional breaking soliton equations. As a result a range of qualitative explicit exact traveling wave solutions are deduced for these equations, which motivates us to develop, in the near future, a new approach to obtain unsteady solutions of autonomous nonlinear evolution equations those arise in mathematical physics and engineering fields. It is uncomplicated to extend this method to higher-order nonlinear evolution equations in mathematical physics. And it should be possible to apply the same method to nonlinear evolution equations having more general forms of nonlinearities by utilizing the traveling wave hypothesis.
Exact supersymmetric string solutions in curved gravitational backgrounds
Antoniadis, Ignatios; Kounnas, Costas
1994-01-01
We construct a new class of exact and stable superstring solutions based on $N=4$ superconformal world-sheet symmetry. In a subclass of these, the full spectrum of string excitations is derived in a modular-invariant way. In the weak curvature limit, our solutions describe a target space with non-trivial metric and topology, and generalize the previously known (semi) wormhole. The effective field theory limit is identified in certain cases, with solutions of the $N=4$ and $N=8$ extended gauged supergravities, in which the number of space-time supersymmetries is reduced by a factor of 2 because of the presence of non-trivial dilaton, gravitational and/or gauge backgrounds. In the context of string theory, our solutions correspond to stable non-critical superstrings in the strong coupling region; the super-Liouville field couples to a unitary matter system with central charge $5\\le{\\hat c}_M\\le 9$.
Branes for Higgs phases and exact conformal field theories
Sfetsos, K
1999-01-01
We consider multicenter supergravity solutions corresponding to Higgs phases of supersymmetric Yang-Mills theories with Z_N symmetric vacuua. In certain energy regimes, we find a description in terms of a generalized wormhole solution that corresponds to the SL(2,R)/U(1) \\times SU(2)/U(1) exact conformal field theory. We show that U-dualities map these backgrounds to purely gravitational ones and comment on the relation to the black holes arising from intersecting D1 and D5 branes. We also discuss supersymmetric properties of the various solutions and the relation to 2-dim solitons, on flat space, of the reduced axion-dilaton-gravity equations. Finally, we address the problem of understanding other supergravity solutions from the multicenter ones. As prototype examples we use rotating D3 branes and NS5 and D5 branes associated to non-Abelian duals of 4-dim hyper-Kahler metrics with SO(3) isometry.
Exactness of the Bogoliubov approximation in random external potentials
Jaeck, Thomas; Zagrebnov, Valentin A.
2010-12-01
We investigate the validity of the Bogoliubov c-number approximation in the case of interacting Bose-gas in a homogeneous random media. To take into account the possible occurence of type III generalized Bose-Einstein condensation (i.e., the occurrence of condensation in an infinitesimal band of low kinetic energy modes without macroscopic occupation of any of them) we generalize the c-number substitution procedure to this band of modes with low momentum. We show that, as in the case of the one-mode condensation for translation-invariant interacting systems, this procedure has no effect on the exact value of the pressure in the thermodynamic limit, assuming that the c-numbers are chosen according to a suitable variational principle. We then discuss the relation between these c-numbers and the (total) density of the condensate.
Kinematics of roller chain drives - Exact and approximate analysis
DEFF Research Database (Denmark)
Fuglede, Niels; Thomsen, Jon Juel
2016-01-01
An exact and approximate kinematic analysis of a roller chain drive modeled as a four-bar mechanism is presented. The span connects the sprockets such that they rotate in the same direction, and the sprocket size, number of teeth, and shaft center distance can be arbitrary. The driven sprocket...... angular position, velocity and acceleration, as well as span length, are calculated and their (discontinuous) variation with driver angular position and main design parameters is illustrated. Kinematic predictions for the chain span motion are compared to results of multibody simulation, and there is seen...... to be very good agreement. All together this gives new insights into the characteristics of chain drive kinematics and the influence of main design parameters....
Thim's Experiment and Exact Rotational Space-Time Transformations
Hsu, Leonardo
2014-01-01
Thim measured the transverse Doppler shift using a system consisting of a stationary antenna and pickup, in addition to a number of intermediate antennas mounted on the rim of a rotating disk. No such shift was detected, although the experiment should have had enough sensitivity to measure it, as predicted by the Lorentz transformations. However, using the Lorentz transformations to analyze the results of experiments involving circular motion, while commonly done, is inappropriate because such an analysis involves non-inertial frames, which are outside the range of validity of special relativity. In this paper, we re-analyze Thim's experiment using exact rotational space-time transformations, finding that his null result is consistent with theoretical predictions.
Exact complexity: The spectral decomposition of intrinsic computation
Crutchfield, James P.; Ellison, Christopher J.; Riechers, Paul M.
2016-03-01
We give exact formulae for a wide family of complexity measures that capture the organization of hidden nonlinear processes. The spectral decomposition of operator-valued functions leads to closed-form expressions involving the full eigenvalue spectrum of the mixed-state presentation of a process's ɛ-machine causal-state dynamic. Measures include correlation functions, power spectra, past-future mutual information, transient and synchronization informations, and many others. As a result, a direct and complete analysis of intrinsic computation is now available for the temporal organization of finitary hidden Markov models and nonlinear dynamical systems with generating partitions and for the spatial organization in one-dimensional systems, including spin systems, cellular automata, and complex materials via chaotic crystallography.
Exact Constraint Design and its potential for Robust Embodiment
DEFF Research Database (Denmark)
Eifler, Tobias; Howard, Thomas J.
2017-01-01
The design of exact, also referred to as minimal, constraints means applying just enough constraints between the various components of a mechanical assembly, in order to unambiguously define their positions in six degrees of freedom (3 translations, 3 rotations), their desired motions respectively....... To ensure a predictable and reliable product performance, a systematic design of the corresponding elementary mechanical interfaces between components is of utmost importance. Over constraints, i. e. part-to-part connections with redundant interfaces which constrain one single degree of freedom, are largely...... Constraint Design. Examples are the calculation of a mechanisms’ mobility using the Grübler-Kutzbach criterion, the analysis of statically determinate assemblies by means of the screw theory or so called Schlussartenmatrizen, as well as the analysis of engaging surfaces in terms of location schemes...
Exactly solvable models for symmetry-enriched topological phases
Cheng, Meng; Gu, Zheng-Cheng; Jiang, Shenghan; Qi, Yang
2017-09-01
We construct fixed-point wave functions and exactly solvable commuting-projector Hamiltonians for a large class of bosonic symmetry-enriched topological (SET) phases, based on the concept of equivalent classes of symmetric local unitary transformations. We argue that for onsite unitary symmetries, our construction realizes all SETs free of anomaly, as long as the underlying topological order itself can be realized with a commuting-projector Hamiltonian. We further extend the construction to antiunitary symmetries (e.g., time-reversal symmetry), mirror-reflection symmetries, and to anomalous SETs on the surface of three-dimensional symmetry-protected topological phases. Mathematically, our construction naturally leads to a generalization of group extensions of unitary fusion categories to antiunitary symmetries.
Kitaev honeycomb tensor networks: Exact unitary circuits and applications
Schmoll, Philipp; Orús, Román
2017-01-01
The Kitaev honeycomb model is a paradigm of exactly solvable models, showing nontrivial physical properties such as topological quantum order, Abelian and non-Abelian anyons, and chirality. Its solution is one of the most beautiful examples of the interplay of different mathematical techniques in condensed matter physics. In this paper, we show how to derive a tensor network (TN) description of the eigenstates of this spin-1/2 model in the thermodynamic limit, and in particular for its ground state. In our setting, eigenstates are naturally encoded by an exact 3d TN structure made of fermionic unitary operators, corresponding to the unitary quantum circuit building up the many-body quantum state. In our derivation we review how the different "solution ingredients" of the Kitaev honeycomb model can be accounted for in the TN language, namely, Jordan-Wigner transformation, braidings of Majorana modes, fermionic Fourier transformation, and Bogoliubov transformation. The TN built in this way allows for a clear understanding of several properties of the model. In particular, we show how the fidelity diagram is straightforward both at zero temperature and at finite temperature in the vortex-free sector. We also show how the properties of two-point correlation functions follow easily. Finally, we also discuss the pros and cons of contracting of our 3d TN down to a 2d projected entangled pair state (PEPS) with finite bond dimension. The results in this paper can be extended to generalizations of the Kitaev model, e.g., to other lattices, spins, and dimensions.
Directory of Open Access Journals (Sweden)
Lorenz Ronny
2011-11-01
Full Text Available Abstract Background Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties. Results The ViennaRNA Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying RNAlib and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions. Conclusions The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from http://www.tbi.univie.ac.at/RNA.
Adenosine-to-Inosine RNA Editing in Health and Disease.
Gatsiou, Aikaterini; Vlachogiannis, Nikolaos; Lunella, Federica Francesca; Sachse, Marco; Stellos, Konstantinos
2017-09-26
Adenosine deamination in transcriptome results in the formation of inosine, a process that is called A-to-I RNA editing. Adenosine deamination is one of the more than 140 described RNA modifications. A-to-I RNA editing is catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes and is essential for life. Recent Advances: Accumulating evidence supports a critical role of RNA editing in all aspects of RNA metabolism, including mRNA stability, splicing, nuclear export, and localization, as well as in recoding of proteins. These advances have significantly enhanced the understanding of mechanisms involved in development and in homeostasis. Furthermore, recent studies have indicated that RNA editing may be critically involved in cancer, aging, neurological, autoimmune, or cardiovascular diseases. This review summarizes recent and significant achievements in the field of A-to-I RNA editing and discusses the importance and translational value of this RNA modification for gene expression, cellular, and organ function, as well as for disease development. Elucidation of the exact RNA editing-dependent mechanisms in a single-nucleotide level may pave the path toward the development of novel therapeutic strategies focusing on modulation of ADAR function in the disease context. Antioxid. Redox Signal. 00, 000-000.
Bioinformatics Analysis of Small RNA Transcriptomes: The Detailed Workflow.
Ilnytskyy, Slava; Bilichak, Andriy
2017-01-01
Next-generation sequencing became a method of choice for the investigation of small RNA transcriptomes in plants and animals. Although a technical side of sequencing itself is becoming routine, and experimental costs are affordable, data analysis still remains a challenge, especially for researchers with limited computational experience. Here, we present a detailed description of a computational workflow designed to take raw sequencing reads as input, to obtain small RNA predictions, and to detect the differentially expressed microRNAs as a result. The exact commands and pieces of code are provided and hopefully can be adapted and used by other researchers to facilitate the study of small RNA regulation.
Perspectives in shape analysis
Bruckstein, Alfred; Maragos, Petros; Wuhrer, Stefanie
2016-01-01
This book presents recent advances in the field of shape analysis. Written by experts in the fields of continuous-scale shape analysis, discrete shape analysis and sparsity, and numerical computing who hail from different communities, it provides a unique view of the topic from a broad range of perspectives. Over the last decade, it has become increasingly affordable to digitize shape information at high resolution. Yet analyzing and processing this data remains challenging because of the large amount of data involved, and because modern applications such as human-computer interaction require real-time processing. Meeting these challenges requires interdisciplinary approaches that combine concepts from a variety of research areas, including numerical computing, differential geometry, deformable shape modeling, sparse data representation, and machine learning. On the algorithmic side, many shape analysis tasks are modeled using partial differential equations, which can be solved using tools from the field of n...
Fifty Years of the Exact Solution of the Two-Dimensional Ising Model by Onsager
Bhattacharjee, Somendra M.; Khare, Avinash
1995-01-01
The exact solution of the two-dimensional Ising model by Onsager in 1944 represents one of the landmarks in theoretical physics. On the occassion of the fifty years of the exact solution, we give a historical review of this model. After briefly discussing the exact solution by Onsager, we point out some of the recent developments in this field. The exact solution by Onsager has inspired several developments in various other fields. Some of these are also briefly mentioned.
RNA Sequencing Analysis of Salivary Extracellular RNA.
Majem, Blanca; Li, Feng; Sun, Jie; Wong, David T W
2017-01-01
Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA sequencing. Therefore, the chapter is divided into two main sections regarding the type of the library constructed (small and long ncRNA libraries), from saliva collection, RNA extraction and quantification to cDNA library generation and corresponding QCs. Using these invaluable technical tools, one can identify thousands of ncRNA species in saliva. These methods indicate that salivary exRNA provides an efficient medium for biomarker discovery of oral and systemic diseases.
Small catalytic RNA: Structure, function and application
Energy Technology Data Exchange (ETDEWEB)
Monforte, J.A.
1991-04-01
We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the paperclip'' and hammerhead'' RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a hammerhead,'' to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.
Directory of Open Access Journals (Sweden)
Zofia Szweykowska-Kulińska
2014-12-01
Full Text Available Among the numerous hypotheses offering a scenario for the origin of life on Earth, the one called “The RNA World” has gained the most attention. According to this hypothesis RNA acted as a genetic information storage material, as a catalyst of all metabolic reactions, and as a regulator of all processes in the primordial world. Various experiments show that RNA molecules could have been synthesized abiotically, with the potential to mediate a whole repertoire of metabolic reactions. Ribozymes carrying out aminoacyl-tRNA reactions have been found in SELEX (systematic evolution of ligands by exponential enrichment approaches and the development of a ribosome from a RNA-built protoribosome is easy to imagine. Transfer RNA aminoacylation, protoribosome origin, and the availability of amino acids on early Earth allowed the genetic code to evolve. Encoded proteins most likely stabilized RNA molecules and were able to create channels across membranes. In the modern cell, DNA replaced RNA as the main depositor of genetic information and proteins carry out almost all metabolic reactions. However, RNA is still playing versatile, crucial roles in the cell. Apart from its classical functions in the cell, a huge small RNA world is controlling gene expression, chromatin condensation, response to environmental cues, and protecting the cell against the invasion of various nucleic acids forms. Long non-coding RNAs act as crucial gene expression regulators. Riboswitches act at the level of transcription, splicing or translation and mediate feedback regulation on biosynthesis and transport of the ligand they sense. Alternative splicing generates genetic variability and increases the protein repertoire in response to developmental or environmental changes. All these regulatory functions are essential in shaping cell plasticity in the changing milieu. Recent discoveries of new, unexpected and important functions of RNA molecules support the hypothesis that we
Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure.
Takeuchi, Yosuke; Endo, Masayuki; Suzuki, Yuki; Hidaka, Kumi; Durand, Guillaume; Dausse, Eric; Toulmé, Jean-Jacques; Sugiyama, Hiroshi
2016-01-01
RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.
Energy Technology Data Exchange (ETDEWEB)
Xie, M. [Lawrence Berkeley Lab., CA (United States)
1995-12-31
I present an exact calculation of free-electron-laser (FEL) eigenmodes (fundamental as well as higher order modes) in the exponential-gain regime. These eigenmodes specify transverse profiles and exponential growth rates of the laser field, and they are self-consistent solutions of the coupled Maxwell-Vlasov equations describing the FEL interaction taking into account the effects due to energy spread, emittance and betatron oscillations of the electron beam, and diffraction and guiding of the laser field. The unperturbed electron distribution is assumed to be of Gaussian shape in four dimensional transverse phase space and in the energy variable, but uniform in longitudinal coordinate. The focusing of the electron beam is assumed to be matched to the natural wiggler focusing in both transverse planes. With these assumptions the eigenvalue problem can be reduced to a numerically manageable integral equation and solved exactly with a kernel iteration method. An approximate, but more efficient solution of the integral equation is also obtained for the fundamental mode by a variational technique, which is shown to agree well with the exact results. Furthermore, I present a handy formula, obtained from interpolating the numerical results, for a quick calculation of FEL exponential growth rate. Comparisons with simulation code TDA will also be presented. Application of these solutions to the design and multi-dimensional parameter space optimization for an X-ray free electron laser driven by SLAC linac will be demonstrated. In addition, a rigorous analysis of transverse mode degeneracy and hence the transverse coherence of the X-ray FEL will be presented based on the exact solutions of the higher order guided modes.
Tat RNA silencing suppressor activity contributes to perturbation of lymphocyte miRNA by HIV-1
Directory of Open Access Journals (Sweden)
Yu Lianbo
2011-05-01
lymphocytes as a tractable model to investigate interplay between HIV-1 and host RNA silencing. The subset of miRNA determined to be perturbed by Tat RSS in HIV-1 infection provides a focal point to define the gene networks that shape the cellular environment for HIV-1 replication.
Approaching the RNA ligand for RIG-I?
Schlee, Martin; Hartmann, Evelyn; Coch, Christoph; Wimmenauer, Vera; Janke, Markus; Barchet, Winfried; Hartmann, Gunther
2009-01-01
Innate and antigen-specific antiviral immunity are triggered by immunorecognition of viral nucleic acids. The helicase retinoic acid-inducible gene I (RIG-I) (also known as DDX58) is the key sensor of negative strand RNA viruses in the cytosol of cells. RNA containing a triphosphate at the 5'-end was shown to activate RIG-I, but the exact structure of RNA supporting 5'-triphosphate recognition, the requirement of a 5'-triphosphate group, as well as the existence of RNA structures detected by RIG-I in the absence of 5'-triphosphate remain controversial. Here, we revisit the literature on RIG-I and RIG-I ligands. The literature proposes at least six different RIG-I ligands: (i) single strand with a 5'-triphosphate, (ii) double-stranded RNA with a 5'-triphosphate, (iii) 5'-triphosphate single-stranded RNA with A- and U-rich 3'-sequences, (iv) double-stranded RNA of intermediate length (>300 and <2000 bp) without 5'-triphosphate, (v) blunt-end short double-stranded RNA (23-30 bp) without 5'-triphosphate, and (vi) short double-stranded RNA (23-30 bp) with 5'-monophosphate. RIG-I thus seems promiscuous for a variety of different RNA molecules, very similar to the Toll-like receptors, of which 10 family members are sufficient for the safe detection of the microbial cosmos. In the light of these outstanding publications, it seems an unlikely possibility that there is a fundamental shortcoming in the design of all studies. Looking closely, the only issue that comes to mind is the in vitro transcription technique used by all investigators without confirming the identity of RNA products. This technique, together with the different biological systems used, the lack of dose responses and of proper comparison of different published ligands and controls leave us with more questions than answers as to what the exact RIG-I ligand is, if in fact it exists.
Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification
DEFF Research Database (Denmark)
Mullari, Meeli; Lyon, David; Jensen, Lars Juhl
2017-01-01
RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, and aberrations in RBP functions have been linked to many diseases, including neurological disorders and cancer. Human cells encode thousands of RNA-binding proteins...... with unique RNA-binding properties. These properties are regulated through modularity of a large variety of RNA-binding domains, rendering RNA-protein interactions difficult to study. Recently, the introduction of proteomics methods has provided novel insights into RNA-binding proteins at a systems level....... However, determining the exact protein sequence regions that interact with RNA remains challenging and laborious, especially considering that many RBPs lack canonical RNA-binding domains. Here we describe a streamlined proteomic workflow called peptide cross-linking and affinity purification (p...
Exact results and open questions in first principle functional RG
Le Doussal, Pierre
2010-01-01
Some aspects of the functional RG (FRG) approach to pinned elastic manifolds (of internal dimension d) at finite temperature T > 0 are reviewed and reexamined in this much expanded version of Le Doussal (2006) [67]. The particle limit d = 0 provides a test for the theory: there the FRG is equivalent to the decaying Burgers equation, with viscosity ν ˜ T-both being formally irrelevant. An outstanding question in FRG, i.e. how temperature regularizes the otherwise singular flow of T = 0 FRG, maps to the viscous layer regularization of inertial range Burgers turbulence (i.e. to the construction of the inviscid limit). Analogy between Kolmogorov scaling and FRG cumulant scaling is discussed. First, multi-loop FRG corrections are examined and the direct loop expansion at T > 0 is shown to fail already in d = 0, a hierarchy of ERG equations being then required (introduced in Balents and Le Doussal (2005) [36]). Next we prove that the FRG function R( u) and higher cumulants defined from the field theory can be obtained for any d from moments of a renormalized potential defined in an sliding harmonic well. This allows to measure the fixed point function R( u) in numerics and experiments. In d = 0 the beta function (of the inviscid limit) is obtained from first principles to four loop. For Sinai model (uncorrelated Burgers initial velocities) the ERG hierarchy can be solved and the exact function R( u) is obtained. Connections to exact solutions for the statistics of shocks in Burgers and to ballistic aggregation are detailed. A relation is established between the size distribution of shocks and the one for droplets. A droplet solution to the ERG functional hierarchy is found for any d, and the form of R( u) in the thermal boundary layer is related to droplet probabilities. These being known for the d = 0 Sinai model the function R( u) is obtained there at any T. Consistency of the ɛ=4-d expansion in one and two loop FRG is studied from first principles, and connected to
Miao, Zhichao; Adamiak, Ryszard W; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M; Chen, Shi-Jie; Cheng, Clarence; Chojnowski, Grzegorz; Chou, Fang-Chieh; Cordero, Pablo; Cruz, José Almeida; Ferré-D'Amaré, Adrian R; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V; Dunin-Horkawicz, Stanislaw; Kladwang, Wipapat; Krokhotin, Andrey; Lach, Grzegorz; Magnus, Marcin; Major, François; Mann, Thomas H; Masquida, Benoît; Matelska, Dorota; Meyer, Mélanie; Peselis, Alla; Popenda, Mariusz; Purzycka, Katarzyna J; Serganov, Alexander; Stasiewicz, Juliusz; Szachniuk, Marta; Tandon, Arpit; Tian, Siqi; Wang, Jian; Xiao, Yi; Xu, Xiaojun; Zhang, Jinwei; Zhao, Peinan; Zok, Tomasz; Westhof, Eric
2015-06-01
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5-3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson-Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/. © 2015 Miao et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Kappers, A.M.L.; Bergmann Tiest, W.M.
2014-01-01
The shape of objects cannot only be recognized by vision, but also by touch. Vision has the advantage that shapes can be seen at a distance, but touch has the advantage that during exploration many additional object properties become available, such as temperature (Jones, 2009), texture (Bensmaia,
Exact Ramsey Theory: Green-Tao numbers and SAT
Kullmann, Oliver
2010-01-01
We consider the links between Ramsey theory in the integers, based on van der Waerden's theorem, and (boolean, CNF) SAT solving. We aim at using the problems from exact Ramsey theory, concerned with computing Ramsey-type numbers, as a rich source of test problems, where especially methods for solving hard problems can be developed. In order to control the growth of the problem instances, we introduce "transversal extensions" as a natural way of constructing mixed parameter tuples (k_1, ..., k_m) for van-der-Waerden-like numbers N(k_1, ..., k_m), such that the growth of these numbers is guaranteed to be linear. Based on Green-Tao's theorem we introduce the "Green-Tao numbers" grt(k_1, ..., k_m), which in a sense combine the strict structure of van der Waerden problems with the (pseudo-)randomness of the distribution of prime numbers. Using standard SAT solvers (look-ahead, conflict-driven, and local search) we determine the basic values. It turns out that already for this single form of Ramsey-type problems, w...
Strong interactions and exact solutions in nonlinear massive gravity
Koyama, Kazuya; Niz, Gustavo; Tasinato, Gianmassimo
2011-09-01
We investigate strong coupling effects in a covariant massive gravity model, which is a candidate for a ghost-free nonlinear completion of Fierz-Pauli. We analyze the conditions to recover general relativity via the Vainshtein mechanism in the weak field limit, and find three main cases depending on the choice of parameters. In the first case, the potential is such that all nonlinearities disappear and the vDVZ discontinuity cannot be avoided. In the second case, the Vainshtein mechanism allows to recover general relativity within a macroscopic radius from a source. In the last case, the strong coupling of the scalar graviton completely shields the massless graviton, and weakens gravity when approaching the source. In the second part of the paper, we explore new exact vacuum solutions, that asymptote to de Sitter or anti de Sitter space depending on the choice of parameters. The curvature of the space is proportional to the mass of the graviton, thus providing a cosmological background which may explain the present-day acceleration in terms of the graviton mass. Moreover, by expressing the potential for nonlinear massive gravity in a convenient form, we also suggest possible connections with a higher-dimensional framework.
An exactly solvable, spatial model of mutation accumulation in cancer
Paterson, Chay; Nowak, Martin A.; Waclaw, Bartlomiej
2016-12-01
One of the hallmarks of cancer is the accumulation of driver mutations which increase the net reproductive rate of cancer cells and allow them to spread. This process has been studied in mathematical models of well mixed populations, and in computer simulations of three-dimensional spatial models. But the computational complexity of these more realistic, spatial models makes it difficult to simulate realistically large and clinically detectable solid tumours. Here we describe an exactly solvable mathematical model of a tumour featuring replication, mutation and local migration of cancer cells. The model predicts a quasi-exponential growth of large tumours, even if different fragments of the tumour grow sub-exponentially due to nutrient and space limitations. The model reproduces clinically observed tumour growth times using biologically plausible rates for cell birth, death, and migration rates. We also show that the expected number of accumulated driver mutations increases exponentially in time if the average fitness gain per driver is constant, and that it reaches a plateau if the gains decrease over time. We discuss the realism of the underlying assumptions and possible extensions of the model.
X(3872) in lattice QCD with exact chiral symmetry
Energy Technology Data Exchange (ETDEWEB)
Chiu, T.-W. [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China)]. E-mail: twchiu@phys.ntu.edu.tw; Hsieh, T.-H. [Physics Section, Commission of General Education, National United University, Miao-Li 36003, Taiwan (China)
2007-03-08
We investigate the mass spectrum of 1{sup ++} exotic mesons with quark content (cqc-barq-bar), using molecular and diquark-antidiquark operators, in quenched lattice QCD with exact chiral symmetry. For the molecular operator {l_brace}(q-bar{gamma}{sub i}c)(c-bar{gamma}{sub 5}q)-(c-bar{gamma}{sub i}q)(q-bar{gamma}{sub 5}c){r_brace} and the diquark-antidiquark operator {l_brace}(q{sup T}C{gamma}{sub i}c)(q-barC{gamma}{sub 5}c-bar{sup T})-(q-barC{gamma}{sub i}{sup T}c-bar{sup T})(q{sup T}C= {gamma}{sub 5}c){r_brace}, both detect a resonance with mass around 3890+/-30 MeV in the limit m{sub q}->m{sub u}, which is naturally identified with X(3872). Further, heavier exotic meson resonances with J{sup PC}=1{sup ++} are also detected, with quark content (csc-bar s-bar) around 4100+/-50 MeV.
Tracking the exact vertical movement of freestanding graphene
Ghosh, Pijush; Thompson, Josh; Thibado, Paul; Neek-Amal, Mehdi; Peeters, Francois
2015-03-01
Intrinsic ripples in freestanding graphene have, unsurprisingly, been exceedingly difficult to study with common experimental methods. In notable breakthroughs, individual ripple geometry was recently imaged using transmission electron microscopy as well as scanning tunneling microscopy, but these measurements are thus far limited to static graphene configurations. Thermally-activated flexural phonon modes could generate dynamic changes in curvature which would be of great interest to observe. Here, we present how to track the exact vertical movement of a one-square-angstrom region of freestanding graphene using scanning tunneling microscopy. This allows a direct measurement of the out-of-plane time trajectory and fluctuations at one point in space over long periods of time. Based on these data, we also present a model from elasticity theory to explain the unusual very-low frequency oscillations that are observed. Unexpectedly, we sometimes detect a sudden colossal jump, which we interpret as due to mirror buckling. This innovative technique provides a much needed atomic-scale probe for the time-dependent behaviors of intrinsic ripples in freestanding graphene. Financial support was provided, in part, by the Office of Naval Research under Grant N00014-10-1-0181, the National Science Foundation under Grant DMR-0855358.
Unitary networks from the exact renormalization of wave functionals
Fliss, Jackson R.; Leigh, Robert G.; Parrikar, Onkar
2017-06-01
The exact renormalization group (ERG) for O (N ) vector models (at large N ) on flat Euclidean space can be interpreted as the bulk dynamics corresponding to a holographically dual higher spin gauge theory on AdSd +1. This was established in the sense that at large N the generating functional of correlation functions of single-trace operators is reproduced by the on-shell action of the bulk higher spin theory, which is most simply presented in a first-order (phase space) formalism. In this paper, we extend the ERG formalism to the wave functionals of arbitrary states of the O (N ) vector model at the free fixed point. We find that the ERG flow of the ground state and a specific class of excited states is implemented by the action of unitary operators which can be chosen to be local. Consequently, the ERG equations provide a continuum notion of a tensor network. We compare this tensor network with the entanglement renormalization networks, MERA, and its continuum version, cMERA, which have appeared recently in holographic contexts. In particular, the ERG tensor network appears to share the general structure of cMERA but differs in important ways. We comment on possible holographic implications.
Entanglement, decoherence and thermal relaxation in exactly solvable models
Lychkovskiy, Oleg
2011-07-01
Exactly solvable models provide an opportunity to study different aspects of reduced quantum dynamics in detail. We consider the reduced dynamics of a single spin in finite XX and XY spin 1/2 chains. First we introduce a general expression describing the evolution of the reduced density matrix. This expression proves to be tractable when the combined closed system (i.e. open system plus environment) is integrable. Then we focus on comparing decoherence and thermalization timescales in the XX chain. We find that for a single spin these timescales are comparable, in contrast to what should be expected for a macroscopic body. This indicates that the process of quantum relaxation of a system with few accessible states can not be separated in two distinct stages - decoherence and thermalization. Finally, we turn to finite-size effects in the time evolution of a single spin in the XY chain. We observe three consecutive stages of the evolution: regular evolution, partial revivals, irregular (apparently chaotic) evolution. The duration of the regular stage is proportional to the number of spins in the chain. We observe a "quiet and cold period" in the end of the regular stage, which breaks up abruptly at some threshold time.
Transient transport in amorphous solids: An exact calculation
Khantha, M.; Balakrishnan, V.
1985-08-01
An exact analytic result that is valid at all times is obtained for the decay of the transient photocurrent in amorphous materials. The motion of the charge carriers across the sample is modeled by a biased continuous-time random walk, and the current is calculated for an arbitrary event-time distribution. This is a generalization of the earlier results of Shlesinger and of Scher and Montroll wherein the short- and long-time features in the decay of the photocurrent were obtained for long-tailed event-time distributions using certain approximate solutions and periodic boundary conditions. We impose physical boundary conditions, and our solution may be used with any type of event-time distribution modeling the carrier transport. We discuss in detail the transition from the short-time to the long-time form of the power-law decay for a temporally fractal event-time distribution. The main advantage in using this form is that it enables us to vary the power-law index continuously. It also serves to highlight the dependence of the magnitude of the transition time on the details of the clustering of event times.
Propagation of nuclear data uncertainty: Exact or with covariances
Directory of Open Access Journals (Sweden)
van Veen D.
2010-10-01
Full Text Available Two distinct methods of propagation for basic nuclear data uncertainties to large scale systems will be presented and compared. The “Total Monte Carlo” method is using a statistical ensemble of nuclear data libraries randomly generated by means of a Monte Carlo approach with the TALYS system. These libraries are then directly used in a large number of reactor calculations (for instance with MCNP after which the exact probability distribution for the reactor parameter is obtained. The second method makes use of available covariance files and can be done in a single reactor calculation (by using the perturbation method. In this exercise, both methods are using consistent sets of data files, which implies that covariance files used in the second method are directly obtained from the randomly generated nuclear data libraries from the first method. This is a unique and straightforward comparison allowing to directly apprehend advantages and drawbacks of each method. Comparisons for different reactions and criticality-safety benchmarks from 19F to actinides will be presented. We can thus conclude whether current methods for using covariance data are good enough or not.
Exact numerical calculation of fixation probability and time on graphs.
Hindersin, Laura; Möller, Marius; Traulsen, Arne; Bauer, Benedikt
2016-12-01
The Moran process on graphs is a popular model to study the dynamics of evolution in a spatially structured population. Exact analytical solutions for the fixation probability and time of a new mutant have been found for only a few classes of graphs so far. Simulations are time-expensive and many realizations are necessary, as the variance of the fixation times is high. We present an algorithm that numerically computes these quantities for arbitrary small graphs by an approach based on the transition matrix. The advantage over simulations is that the calculation has to be executed only once. Building the transition matrix is automated by our algorithm. This enables a fast and interactive study of different graph structures and their effect on fixation probability and time. We provide a fast implementation in C with this note (Hindersin et al., 2016). Our code is very flexible, as it can handle two different update mechanisms (Birth-death or death-Birth), as well as arbitrary directed or undirected graphs. Copyright Â© 2016 Elsevier Ireland Ltd. All rights reserved.
Exact rebinning methods for three-dimensional PET.
Liu, X; Defrise, M; Michel, C; Sibomana, M; Comtat, C; Kinahan, P; Townsend, D
1999-08-01
The high computational cost of data processing in volume PET imaging is still hindering the routine application of this successful technique, especially in the case of dynamic studies. This paper describes two new algorithms based on an exact rebinning equation, which can be applied to accelerate the processing of three-dimensional (3-D) PET data. The first algorithm, FOREPROJ, is a fast-forward projection algorithm that allows calculation of the 3-D attenuation correction factors (ACF's) directly from a two-dimensional (2-D) transmission scan, without first reconstructing the attenuation map and then performing a 3-D forward projection. The use of FOREPROJ speeds up the estimation of the 3-D ACF's by more than a factor five. The second algorithm, FOREX, is a rebinning algorithm that is also more than five times faster, compared to the standard reprojection algorithm (3DRP) and does not suffer from the image distortions generated by the even faster approximate Fourier rebinning (FORE) method at large axial apertures. However, FOREX is probably not required by most existing scanners, as the axial apertures are not large enough to show improvements over FORE with clinical data. Both algorithms have been implemented and applied to data simulated for a scanner with a large axial aperture (30 degrees), and also to data acquired with the ECAT HR and the ECAT HR+ scanners. Results demonstrate the excellent accuracy achieved by these algorithms and the important speedup when the sinogram sizes are powers of two.
Parametrices and exact paralinearisation of semi-linear boundary problems
DEFF Research Database (Denmark)
Johnsen, Jon
The subject is to establish solution formulae for elliptic (and parabolic) semi-linear boundary problems. The result should be new in at least two respects: the desired formulae result from a parametrix construction for semi-linear problems, using only parametrices from the linear theory and the ......The subject is to establish solution formulae for elliptic (and parabolic) semi-linear boundary problems. The result should be new in at least two respects: the desired formulae result from a parametrix construction for semi-linear problems, using only parametrices from the linear theory...... and the mild assumption that the non-linearity may be decomposed into a suitable solution-dependent linear operator acting on the solution itself. Secondly non-linearities of so-called product type are shown to admit such decompositions via exact paralinearisation. The parametrices give regularity properties...... under rather weak conditions, with examples of properties that are unobtainable by boot-strap methods. Regularity improvements in submanifolds are deduced from the auxiliary result that operators of type 1,1 are pseudo-local on large parts of their domains. The framework is flexible, encompassing...
Exact tensor network ansatz for strongly interacting systems
Zaletel, Michael P.
It appears that the tensor network ansatz, while not quite complete, is an efficient coordinate system for the tiny subset of a many-body Hilbert space which can be realized as a low energy state of a local Hamiltonian. However, we don't fully understand precisely which phases are captured by the tensor network ansatz, how to compute their physical observables (even numerically), or how to compute a tensor network representation for a ground state given a microscopic Hamiltonian. These questions are algorithmic in nature, but their resolution is intimately related to understanding the nature of quantum entanglement in many-body systems. For this reason it is useful to compute the tensor network representation of various `model' wavefunctions representative of different phases of matter; this allows us to understand how the entanglement properties of each phase are expressed in the tensor network ansatz, and can serve as test cases for algorithm development. Condensed matter physics has many illuminating model wavefunctions, such as Laughlin's celebrated wave function for the fractional quantum Hall effect, the Bardeen-Cooper-Schrieffer wave function for superconductivity, and Anderson's resonating valence bond ansatz for spin liquids. This thesis presents some results on exact tensor network representations of these model wavefunctions. In addition, a tensor network representation is given for the time evolution operator of a long-range one-dimensional Hamiltonian, which allows one to numerically simulate the time evolution of power-law interacting spin chains as well as two-dimensional strips and cylinders.
Symmetry reductions and exact solutions of Shallow water wave equations
Clarkson, P A
1994-01-01
In this paper we study symmetry reductions and exact solutions of the shallow water wave (SWW) equation u_{xxxt} + \\alpha u_x u_{xt} + \\beta u_t u_{xx} - u_{xt} - u_{xx} = 0,\\eqno(1) where \\alpha and \\beta are arbitrary, nonzero, constants, which is derivable using the so-called Boussinesq approximation. Two special cases of this equation, or the equivalent nonlocal equation obtained by setting u_x=U, have been discussed in the literature. The case \\alpha=2\\beta was discussed by Ablowitz, Kaup, Newell and Segur [{\\it Stud.\\ Appl.\\ Math.}, {\\bf53} (1974) 249], who showed that this case was solvable by inverse scattering through a second order linear problem. This case and the case \\alpha=\\beta were studied by Hirota and Satsuma [{\\it J.\\ Phys.\\ Soc.\\ Japan}, {\\bf40} (1976) 611] using Hirota's bi-linear technique. Further the case \\alpha=\\beta is solvable by inverse scattering through a third order linear problem. In this paper a catalogue of symmetry reductions is obtained using the classical Lie method and th...
Any Two Learning Algorithms Are (Almost) Exactly Identical
Wolpert, David H.
2000-01-01
This paper shows that if one is provided with a loss function, it can be used in a natural way to specify a distance measure quantifying the similarity of any two supervised learning algorithms, even non-parametric algorithms. Intuitively, this measure gives the fraction of targets and training sets for which the expected performance of the two algorithms differs significantly. Bounds on the value of this distance are calculated for the case of binary outputs and 0-1 loss, indicating that any two learning algorithms are almost exactly identical for such scenarios. As an example, for any two algorithms A and B, even for small input spaces and training sets, for less than 2e(-50) of all targets will the difference between A's and B's generalization performance of exceed 1%. In particular, this is true if B is bagging applied to A, or boosting applied to A. These bounds can be viewed alternatively as telling us, for example, that the simple English phrase 'I expect that algorithm A will generalize from the training set with an accuracy of at least 75% on the rest of the target' conveys 20,000 bytes of information concerning the target. The paper ends by discussing some of the subtleties of extending the distance measure to give a full (non-parametric) differential geometry of the manifold of learning algorithms.
Pressure in an exactly solvable model of active fluid
Marini Bettolo Marconi, Umberto; Maggi, Claudio; Paoluzzi, Matteo
2017-07-01
We consider the pressure in the steady-state regime of three stochastic models characterized by self-propulsion and persistent motion and widely employed to describe the behavior of active particles, namely, the Active Brownian particle (ABP) model, the Gaussian colored noise (GCN) model, and the unified colored noise approximation (UCNA) model. Whereas in the limit of short but finite persistence time, the pressure in the UCNA model can be obtained by different methods which have an analog in equilibrium systems, in the remaining two models only the virial route is, in general, possible. According to this method, notwithstanding each model obeys its own specific microscopic law of evolution, the pressure displays a certain universal behavior. For generic interparticle and confining potentials, we derive a formula which establishes a correspondence between the GCN and the UCNA pressures. In order to provide explicit formulas and examples, we specialize the discussion to the case of an assembly of elastic dumbbells confined to a parabolic well. By employing the UCNA we find that, for this model, the pressure determined by the thermodynamic method coincides with the pressures obtained by the virial and mechanical methods. The three methods when applied to the GCN give a pressure identical to that obtained via the UCNA. Finally, we find that the ABP virial pressure exactly agrees with the UCNA and GCN results.
Exact solutions in a model of vertical gas migration
Energy Technology Data Exchange (ETDEWEB)
Silin, Dmitriy B.; Patzek, Tad W.; Benson, Sally M.
2006-06-27
This work is motivated by the growing interest in injectingcarbon dioxide into deep geological formations as a means of avoidingatmospheric emissions of carbon dioxide and consequent global warming.One of the key questions regarding the feasibility of this technology isthe potential rate of leakage out of the primary storage formation. Weseek exact solutions in a model of gas flow driven by a combination ofbuoyancy, viscous and capillary forces. Different combinations of theseforces and characteristic length scales of the processes lead todifferent time scaling and different types of solutions. In the case of athin, tight seal, where the impact of gravity is negligible relative tocapillary and viscous forces, a Ryzhik-type solution implies square-rootof time scaling of plume propagation velocity. In the general case, a gasplume has two stable zones, which can be described by travelling-wavesolutions. The theoretical maximum of the velocity of plume migrationprovides a conservative estimate for the time of vertical migration.Although the top of the plume has low gas saturation, it propagates witha velocity close to the theoretical maximum. The bottom of the plumeflows significantly more slowly at a higher gas saturation. Due to localheterogeneities, the plume can break into parts. Individual plumes alsocan coalesce and from larger plumes. The analytical results are appliedto studying carbon dioxide flow caused by leaks from deep geologicalformations used for CO2 storage. The results are also applicable formodeling flow of natural gas leaking from seasonal gas storage, or formodeling of secondary hydrocarbon migration.
Exact coherent structures and chaotic dynamics in a model of cardiac tissue
Energy Technology Data Exchange (ETDEWEB)
Byrne, Greg; Marcotte, Christopher D.; Grigoriev, Roman O., E-mail: roman.grigoriev@physics.gatech.edu [School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332-0430 (United States)
2015-03-15
Unstable nonchaotic solutions embedded in the chaotic attractor can provide significant new insight into chaotic dynamics of both low- and high-dimensional systems. In particular, in turbulent fluid flows, such unstable solutions are referred to as exact coherent structures (ECS) and play an important role in both initiating and sustaining turbulence. The nature of ECS and their role in organizing spatiotemporally chaotic dynamics, however, is reasonably well understood only for systems on relatively small spatial domains lacking continuous Euclidean symmetries. Construction of ECS on large domains and in the presence of continuous translational and/or rotational symmetries remains a challenge. This is especially true for models of excitable media which display spiral turbulence and for which the standard approach to computing ECS completely breaks down. This paper uses the Karma model of cardiac tissue to illustrate a potential approach that could allow computing a new class of ECS on large domains of arbitrary shape by decomposing them into a patchwork of solutions on smaller domains, or tiles, which retain Euclidean symmetries locally.
Exact Scale Invariance in Mixing of Binary Candidates in Voting Model
Mori, Shintaro; Hisakado, Masato
2010-03-01
We introduce a voting model and discuss the scale invariance in the mixing of candidates. The Candidates are classified into two categories μ\\in \\{0,1\\} and are called as “binary” candidates. There are in total N=N0+N1 candidates, and voters vote for them one by one. The probability that a candidate gets a vote is proportional to the number of votes. The initial number of votes (“seed”) of a candidate μ is set to be sμ. After infinite counts of voting, the probability function of the share of votes of the candidate μ obeys gamma distributions with the shape exponent sμ in the thermodynamic limit Z0=N1s1+N0s0\\to ∞. Between the cumulative functions \\{xμ\\} of binary candidates, the power-law relation 1-x1 ˜ (1-x0)α with the critical exponent α=s1/s0 holds in the region 1-x0,1-x1≪ 1. In the double scaling limit (s1,s0)\\to (0,0) and Z0 \\to ∞ with s1/s0=α fixed, the relation 1-x1=(1-x0)α holds exactly over the entire range 0≤ x0,x1 ≤ 1. We study the data on horse races obtained from the Japan Racing Association for the period 1986 to 2006 and confirm scale invariance.
14N overtone NMR spectra under magic angle spinning: Experiments and numerically exact simulations
O'Dell, Luke A.; Brinkmann, Andreas
2013-02-01
It was recently shown that high resolution 14N overtone NMR spectra can be obtained directly under magic angle spinning (MAS) conditions [L. A. O'Dell and C. I. Ratcliffe, Chem. Phys. Lett. 514, 168 (2011)], 10.1016/j.cplett.2011.08.030. Preliminary experimental results showed narrowed powder pattern widths, a frequency shift that is dependent on the MAS rate, and an apparent absence of spinning sidebands, observations which appeared to be inconsistent with previous theoretical treatments. Herein, we reproduce these effects using numerically exact simulations that take into account the full nuclear spin Hamiltonian. Under sample spinning, the 14N overtone signal is split into five (0, ±1, ±2) overtone sidebands separated by the spinning frequency. For a powder sample spinning at the magic angle, the +2ωr sideband is dominant while the others show significantly lower signal intensities. The resultant MAS powder patterns show characteristic quadrupolar lineshapes from which the 14N quadrupolar parameters and isotropic chemical shift can be determined. Spinning the sample at other angles is shown to alter both the shapes and relative intensities of the five overtone sidebands, with MAS providing the benefit of averaging dipolar couplings and shielding anisotropy. To demonstrate the advantages of this experimental approach, we present the 14N overtone MAS spectrum obtained from L-histidine, in which powder patterns from all three nitrogen sites are clearly resolved.
Exact solution of corner-modified banded block-Toeplitz eigensystems
Cobanera, Emilio; Alase, Abhijeet; Ortiz, Gerardo; Viola, Lorenza
2017-05-01
Motivated by the challenge of seeking a rigorous foundation for the bulk-boundary correspondence for free fermions, we introduce an algorithm for determining exactly the spectrum and a generalized-eigenvector basis of a class of banded block quasi-Toeplitz matrices that we call corner-modified. Corner modifications of otherwise arbitrary banded block-Toeplitz matrices capture the effect of boundary conditions and the associated breakdown of translational invariance. Our algorithm leverages the interplay between a non-standard, projector-based method of kernel determination (physically, a bulk-boundary separation) and families of linear representations of the algebra of matrix Laurent polynomials. Thanks to the fact that these representations act on infinite-dimensional carrier spaces in which translation symmetry is restored, it becomes possible to determine the eigensystem of an auxiliary projected block-Laurent matrix. This results in an analytic eigenvector Ansatz, independent of the system size, which we prove is guaranteed to contain the full solution of the original finite-dimensional problem. The actual solution is then obtained by imposing compatibility with a boundary matrix, whose shape is also independent of system size. As an application, we show analytically that eigenvectors of short-ranged fermionic tight-binding models may display power-law corrections to exponential behavior, and demonstrate the phenomenon for the paradigmatic Majorana chain of Kitaev.
Berrada, K.; Eleuch, H.
2017-09-01
Various schemes have been proposed to improve the parameter-estimation precision. In the present work, we suggest an alternative method to preserve the estimation precision by considering a model that closely describes a realistic experimental scenario. We explore this active way to control and enhance the measurements precision for a two-level quantum system interacting with classical electromagnetic field using ultra-short strong pulses with an exact analytical solution, i.e. beyond the rotating wave approximation. In particular, we investigate the variation of the precision with a few cycles pulse and a smooth phase jump over a finite time interval. We show that by acting on the shape of the phase transient and other parameters of the considered system, the amount of information may be increased and has smaller decay rate in the long time. These features make two-level systems incorporated in ultra-short, of-resonant and gradually changing phase good candidates for implementation of schemes for the quantum computation and the coherent information processing.
Combinatorics of RNA-RNA interaction
DEFF Research Database (Denmark)
Li, Thomas J X; Reidys, Christian
2012-01-01
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...
Directory of Open Access Journals (Sweden)
Kaba Dramane
2010-10-01
Full Text Available Abstract Background Landmark based geometric morphometrics (GM allows the quantitative comparison of organismal shapes. When applied to systematics, it is able to score shape changes which often are undetectable by traditional morphological studies and even by classical morphometric approaches. It has thus become a fast and low cost candidate to identify cryptic species. Due to inherent mathematical properties, shape variables derived from one set of coordinates cannot be compared with shape variables derived from another set. Raw coordinates which produce these shape variables could be used for data exchange, however they contain measurement error. The latter may represent a significant obstacle when the objective is to distinguish very similar species. Results We show here that a single user derived dataset produces much less classification error than a multiple one. The question then becomes how to circumvent the lack of exchangeability of shape variables while preserving a single user dataset. A solution to this question could lead to the creation of a relatively fast and inexpensive systematic tool adapted for the recognition of cryptic species. Conclusions To preserve both exchangeability of shape and a single user derived dataset, our suggestion is to create a free access bank of reference images from which one can produce raw coordinates and use them for comparison with external specimens. Thus, we propose an alternative geometric descriptive system that separates 2-D data gathering and analyzes.
Evolution of regular geometrical shapes in fiber lumens
Le, Ngoc Lieu
2017-08-17
The geometry of polymeric hollow fibers for hemodialysis or desalination is a key factor determining their performance. Deformations are frequently observed, but they are rather random. Here we were able to exactly control the shape evolution of the internal channels or lumens of polymeric hollow fibers, leading to polygonal geometries with increasing number of sides. The elasticity of the incipient channel skin and instabilities during fiber formation are affected by the internal coagulant fluid composition and flow rate; and highly influence the polygonal shape. We propose a holistic explanation by analyzing the thermodynamic, kinetic and rheological aspects involved in the skin formation and their synergy.
Santo, Loredana
2016-02-01
Recent advances in shape memory polymer (SMP) foam research are reviewed. The SMPs belong to a new class of smart polymers which can have interesting applications in microelectromechanical systems, actuators and biomedical devices. They can respond to specific external stimulus changing their configuration and then remember the original shape. In the form of foams, the shape memory behaviour can be enhanced because they generally have higher compressibility. Considering also the low weight, and recovery force, the SMP foams are expected to have great potential applications primarily in aerospace. This review highlights the recent progress in characterization, evaluation, and proposed applications of SMP foams mainly for aerospace applications.
Segmentation of Overlapping Shapes using Test Ray Intersections
DEFF Research Database (Denmark)
Rasmusson, Allan
into the correct shapes in a postprocessing step. The postprocessing step is unfortunately often both difficult and computationally expensive. Another approach is to incorporate descriptions of the overlapping shapes into a segmentation algorithm which normally only segments the union of all particle profiles...... provide exact information about shape contours which can be exploited for the separation of overlapping shapes. The resulting procedure may be performed either as a separate postprocessing step after a single contour of all particles is segmented or it may be performed in combination with an existing......As the use of digital images have become standard in everyday bioimaging, people are naturally trying to utilize computer algorithms for automating laborious and repetetive image analysis tasks. A preliminary task is the segmentation of structures of interest from digital images. This may in itself...
What exactly is Universal Grammar, and has anyone seen it?
Dąbrowska, Ewa
2015-01-01
Universal Grammar (UG) is a suspect concept. There is little agreement on what exactly is in it; and the empirical evidence for it is very weak. This paper critically examines a variety of arguments that have been put forward as evidence for UG, focussing on the three most powerful ones: universality (all human languages share a number of properties), convergence (all language learners converge on the same grammar in spite of the fact that they are exposed to different input), and poverty of the stimulus (children know things about language which they could not have learned from the input available to them). I argue that these arguments are based on premises which are either false or unsubstantiated. Languages differ from each other in profound ways, and there are very few true universals, so the fundamental crosslinguistic fact that needs explaining is diversity, not universality. A number of recent studies have demonstrated the existence of considerable differences in adult native speakers' knowledge of the grammar of their language, including aspects of inflectional morphology, passives, quantifiers, and a variety of more complex constructions, so learners do not in fact converge on the same grammar. Finally, the poverty of the stimulus argument presupposes that children acquire linguistic representations of the kind postulated by generative grammarians; constructionist grammars such as those proposed by Tomasello, Goldberg and others can be learned from the input. We are the only species that has language, so there must be something unique about humans that makes language learning possible. The extent of crosslinguistic diversity and the considerable individual differences in the rate, style and outcome of acquisition suggest that it is more promising to think in terms of a language-making capacity, i.e., a set of domain-general abilities, rather than an innate body of knowledge about the structural properties of the target system.
What exactly is Universal Grammar, and has anyone seen it?
Directory of Open Access Journals (Sweden)
Ewa eDabrowska
2015-06-01
Full Text Available Universal Grammar (UG is a suspect concept. There is little agreement on what exactly is in it; and the empirical evidence for it is very weak. This paper critically examines a variety of arguments that have been put forward as evidence for UG, focussing on the three most powerful ones: universality (all human languages share a number of properties, convergence (all language learners converge on the same grammar in spite of the fact that they are exposed to different input, and poverty of the stimulus (children know things about language which they could not have learned from the input available to them. I argue that these arguments are based on premises which are either false or unsubstantiated. Languages differ from each other in profound ways, and there are very few true universals, so the fundamental crosslinguistic fact that needs explaining is diversity, not universality. A number of recent studies have demonstrated the existence of considerable differences in adult native speakers’ knowledge of the grammar of their language, including aspects of inflectional morphology, passives, quantifiers, and a variety of more complex constructions, so learners do not in fact converge on the same grammar. Finally, the poverty of the stimulus argument presupposes that children acquire linguistic representations of the kind postulated by generative grammarians; constructionist grammars such as those proposed by Tomasello, Goldberg and others can be learned from the input. We are the only species that has language, so there must be something unique about humans that makes language learning possible. The extent of crosslinguistic diversity and the considerable individual differences in the rate, style and outcome of acquisition suggest that it is more promising to think in terms of a language-making capacity, i.e. a set of domain-general abilities, rather than an innate body of knowledge about the structural properties of the target system.
Exact simulation of conditioned Wright-Fisher models.
Zhao, Lei; Lascoux, Martin; Waxman, David
2014-12-21
Forward and backward simulations play an increasing role in population genetics, in particular when inferring the relative importance of evolutionary forces. It is therefore important to develop fast and accurate simulation methods for general population genetics models. Here we present an exact simulation method that generates trajectories of an allele׳s frequency in a finite population, as described by a general Wright-Fisher model. The method generates conditioned trajectories that start from a known frequency at a known time, and which achieve a specific final frequency at a known final time. The simulation method applies irrespective of the smallness of the probability of the transition between the initial and final states, because it is not based on rejection of trajectories. We illustrate the method on several different populations where a Wright-Fisher model (or related) applies, namely (i) a locus with 2 alleles, that is subject to selection and mutation; (ii) a locus with 3 alleles, that is subject to selection; (iii) a locus in a metapopulation consisting of two subpopulations of finite size, that are subject to selection and migration. The simulation method allows the generation of conditioned trajectories that can be used for the purposes of visualisation, the estimation of summary statistics, and the development/testing of new inferential methods. The simulated trajectories provide a very simple approach to estimating quantities that cannot easily be expressed in terms of the transition matrix, and can be applied to finite Markov chains other than the Wright-Fisher model. Copyright © 2014 Elsevier Ltd. All rights reserved.
Miao, Zhichao; Adamiak, Ryszard W.; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M.; Chen, Shi-Jie; Cheng, Clarence; Chojnowski, Grzegorz; Chou, Fang-Chieh; Cordero, Pablo; Cruz, José Almeida; Ferré-D'Amaré, Adrian R.; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V.; Dunin-Horkawicz, Stanislaw; Kladwang, Wipapat; Krokhotin, Andrey; Lach, Grzegorz; Magnus, Marcin; Major, François; Mann, Thomas H.; Masquida, Benoît; Matelska, Dorota; Meyer, Mélanie; Peselis, Alla; Popenda, Mariusz; Purzycka, Katarzyna J.; Serganov, Alexander; Stasiewicz, Juliusz; Szachniuk, Marta; Tandon, Arpit; Tian, Siqi; Wang, Jian; Xiao, Yi; Xu, Xiaojun; Zhang, Jinwei; Zhao, Peinan; Zok, Tomasz; Westhof, Eric
2015-01-01
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5–3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson–Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/. PMID:25883046
RNA structures regulating nidovirus RNA synthesis
Born, Erwin van den
2006-01-01
Viruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus-stranded RNA viruses, like nidoviruses, the RNA genome is directly involved in translation (resulting in the
DEFF Research Database (Denmark)
Nielsen, Henrik
2011-01-01
Working with RNA is not a special discipline in molecular biology. However, RNA is chemically and structurally different from DNA and a few simple work rules have to be implemented to maintain the integrity of the RNA. Alkaline pH, high temperatures, and heavy metal ions should be avoided when...... possible and ribonucleases kept in check. The chapter outlines the specific precautions recommended for work with RNA and describes some of the modifications to standard protocols in molecular biology that are relevant to RNA work. The methods are applicable to all types of RNA and require a minimum...
Shape memory polyurethane foams
Directory of Open Access Journals (Sweden)
B. K. Kim
2012-01-01
Full Text Available Molded flexible polyurethane (PU foams have been synthesized from polypropylene glycol (PPG with different molecular weights (Mw and functionalities (f, and 2,4/2,6-toluene diisocyanate (TDI-80 with water as blowing agent. It was found that the glassy state properties of the foam mainly depended on the urethane group content while the rubbery state properties on the crosslink density. That is, PPG of low MW and low f (more urethane groups provided superior glass state modulus, strength, density, shape fixity and glass transition temperature (Tg, while that of high Mw and high f (higher crosslink density showed high rubbery modulus and shape recovery. Consequently shape fixity of low Mw PPG decreased from 85 to 72% while shape recovery increased from 52 to 63% as the content of high Mw PPG increased from 0 to 40%.
Reinforced Airfoil Shaped Body
DEFF Research Database (Denmark)
2011-01-01
The present invention relates to an airfoil shaped body with a leading edge and a trailing edge extending along the longitudinal extension of the body and defining a profile chord, the airfoil shaped body comprising an airfoil shaped facing that forms the outer surface of the airfoil shaped body...... and surrounds an internal volume of the body, a distance member that is connected to the facing inside the body and extends from the facing and into the internal volume of the body, and at least one reinforcing member that operates in tension for reinforcing the facing against inward deflections...... and that is connected to the facing inside the internal volume of the body at the same side of the profile chord as the connection of the distance member to the facing and to the distance member at a distance from the facing....
Shaft mode shape demonstration
Grissom, R.
1985-01-01
The dynamic response of a rotating machine is directly influenced by its geometric configuration and all aspects of the rotor construction. These determine two significant parameters, mass distribution and stiffness, which yield a spectrum of natural frequencies and mode shapes. The mode shapes can be presented as snapshots of the characteristic amplitude/phase reponse patterns of the shaft, due to the major forcing function of unbalance, at different rotative speeds. To demonstrate the three shaft mode shapes of the rotor rig using the Shaft Mode Demonstrator and oscilloscopes. The synchronous (1X) amplitude and phase of the rotor vibration in the vertical direction from several points along the shaft is displayed on corresponding points of the demonstrator. Unfiltered vibration from vertical and horizontal probe pairs is displayed on the oscilloscopes in orbit format for a dynamic presentation of the mode shape.
An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression.
Corley, Meredith; Solem, Amanda; Phillips, Gabriela; Lackey, Lela; Ziehr, Benjamin; Vincent, Heather A; Mustoe, Anthony M; Ramos, Silvia B V; Weeks, Kevin M; Moorman, Nathaniel J; Laederach, Alain
2017-11-21
Chronic obstructive pulmonary disease (COPD) affects over 65 million individuals worldwide, where α-1-antitrypsin deficiency is a major genetic cause of the disease. The α-1-antitrypsin gene, SERPINA1, expresses an exceptional number of mRNA isoforms generated entirely by alternative splicing in the 5'-untranslated region (5'-UTR). Although all SERPINA1 mRNAs encode exactly the same protein, expression levels of the individual mRNAs vary substantially in different human tissues. We hypothesize that these transcripts behave unequally due to a posttranscriptional regulatory program governed by their distinct 5'-UTRs and that this regulation ultimately determines α-1-antitrypsin expression. Using whole-transcript selective 2'-hydroxyl acylation by primer extension (SHAPE) chemical probing, we show that splicing yields distinct local 5'-UTR secondary structures in SERPINA1 transcripts. Splicing in the 5'-UTR also changes the inclusion of long upstream ORFs (uORFs). We demonstrate that disrupting the uORFs results in markedly increased translation efficiencies in luciferase reporter assays. These uORF-dependent changes suggest that α-1-antitrypsin protein expression levels are controlled at the posttranscriptional level. A leaky-scanning model of translation based on Kozak translation initiation sequences alone does not adequately explain our quantitative expression data. However, when we incorporate the experimentally derived RNA structure data, the model accurately predicts translation efficiencies in reporter assays and improves α-1-antitrypsin expression prediction in primary human tissues. Our results reveal that RNA structure governs a complex posttranscriptional regulatory program of α-1-antitrypsin expression. Crucially, these findings describe a mechanism by which genetic alterations in noncoding gene regions may result in α-1-antitrypsin deficiency. Copyright © 2017 the Author(s). Published by PNAS.
Shape memory polyurethane nanocomposites
Cao, Feina
Shape memory polymers are smart materials which can remember their original shapes. However, the low recovery stress and low mechanical strength limit the commercial applications of shape memory polymers. In this study, nanoclays were introduced to shape memory polyurethanes (SMPU) to augment these properties by enhance the network of SMPU. Several factors which influence the shape recovery stress were evaluated, including the nature of polymer chain by using different monomers, type of clay particles, extent of filler dispersion, clay content and deformation conditions. It was found that only reactive clay particles were well dispersed into polyurethane matrix by the tethering between --CH2CH 2OH functional groups in clay surfactants and polyurethane chains. Two different shape memory polyurethanes (Systems I & II) prepared by bulk polymerization were compared. The shape memory effect of System I was triggered by melting of the soft segment crystals, while that of System II was by glass transition of the soft segments. It was seen that the reactive clay particles dispersed well in both polyurethane matrices and augmented the recovery stress, e.g., 20% increase with 1 wt % nanoclay in System I and 40% increase with 5 wt % nanoclay in System II were observed. In System I, clay particles interfered with soft segment crystallization, and promoted phase mixing between the hard and soft segments, thus affecting the fixity and recovery ratio. Nevertheless, the soft segment crystallinity was still enough and in some cases increased due to stretching to exhibit excellent shape fixity and shape recovery ratio. The higher loading of clay particles accelerated the stress relaxation, resulting in reduction of recovery stress. In System II, no significant effect of clay particles in phase separation was observed, so there was no influence of clay on shape fixity and recovery ratio. The recovery stress increased with reactive nanoclay content. It was also found that the recovery
Shaping the Global Environment
2002-04-09
SHAPING THE GLOBAL ENVIRONMENT BY LIEUTENANT COLONEL MICHAEL D. ELLERBE United States Army DISTRIBUTION STATEMENT A: Approved for public release...THE GLOBAL ENVIRONMENT by Lieutenant Colonel Michael D. Ellerbe United States Army Colonel Jef Troxel Project Advisor The views expressed in this...Distribution is unlimited. ii ABSTRACT AUTHOR: Michael D. Ellerbe TITLE: SHAPING THE GLOBAL ENVIRONMENT FORMAT: Strategy Research Project DATE: 09 April
On Characterizing Particle Shape
Ennis, Bryan J.; Rickman, Douglas; Rollins, A. Brent; Ennis, Brandon
2014-01-01
It is well known that particle shape affects flow characteristics of granular materials, as well as a variety of other solids processing issues such as compaction, rheology, filtration and other two-phase flow problems. The impact of shape crosses many diverse and commercially important applications, including pharmaceuticals, civil engineering, metallurgy, health, and food processing. Two applications studied here include the dry solids flow of lunar simulants (e.g. JSC-1, NU-LHT-2M, OB-1), and the flow properties of wet concrete, including final compressive strength. A multi-dimensional generalized, engineering method to quantitatively characterize particle shapes has been developed, applicable to both single particle orientation and multi-particle assemblies. The two-dimension, three dimension inversion problem is also treated, and the application of these methods to DEM model particles will be discussed. In the case of lunar simulants, flow properties of six lunar simulants have been measured, and the impact of particle shape on flowability - as characterized by the shape method developed here -- is discussed, especially in the context of three simulants of similar size range. In the context of concrete processing, concrete construction is a major contributor to greenhouse gas production, of which the major contributor is cement binding loading. Any optimization in concrete rheology and packing that can reduce cement loading and improve strength loading can also reduce currently required construction safety factors. The characterization approach here is also demonstrated for the impact of rock aggregate shape on concrete slump rheology and dry compressive strength.
Exact Simulation of Polarized Light Reflectance by Particle Deposits
Ramezan Pour, B.
2016-12-01
The research examines two methods for prediction of polarized bidirectional reflectance and transmittance from plane parallel layers of randomly distributed, wavelength—sized particles. The first method is based on an exact superposition solution to Maxwell's time harmonic wave equations for a deposit of spherical particles that are exposed to a plane incident wave. We use a FORTRAN-90 implementation of this solution (the Multiple Sphere T Matrix (MSTM) code), coupled with parallel computational platforms, to directly simulate the reflection from particle layers via a configurational averaging strategy. In this approach, a target, in the form of a cylindrical volume with radius well in excess of thickness and containing a collection of monodisperse, non-overlapping spheres, is created using Monte Carlo sampling methods. The polarimetric scattering properties of the target, for plane wave incidence, are then computed using MSTM. This process is repeated over multiple sampled targets to calculate the random—medium reflectance and transmittance properties of the particles, as a function of sphere size parameter, refractive index, and sphere volume fraction. The second method examined is based upon the vector radiative transport equation (RTE). Mie theory is used in our RTE model to predict the extinction coefficient, albedo, and scattering phase function of the particles, and the solution of the RTE is obtained from adding—doubling method applied to a plane—parallel configuration. For sphere size parameters of order unity, the results indicate that the MSTM and RTE predictions, for the most part, converge when the particle volume fraction decreases below five percent. With regard to the MSTM method, a considerable number of target samples can be required to generate averaged scattering matrices that display the expected polarimetric features of reflection from a randomly inhomogenous plane parallel layer. The MSTM results do, however, reveal characteristics
Exact positioning of the robotic arm end effector
Korepanov, Valery; Dudkin, Fedir
2016-07-01
substantiation of the possibility of exact positioning of the robotic arm end effector and algorithm of its operation are reported.
Visualization of RNA structure models within the Integrative Genomics Viewer.
Busan, Steven; Weeks, Kevin M
2017-07-01
Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
RNA modifications by oxidation
DEFF Research Database (Denmark)
Poulsen, Henrik E; Specht, Elisabeth; Broedbaek, Kasper
2012-01-01
The past decade has provided exciting insights into a novel class of central (small) RNA molecules intimately involved in gene regulation. Only a small percentage of our DNA is translated into proteins by mRNA, yet 80% or more of the DNA is transcribed into RNA, and this RNA has been found...... to encompass various classes of novel regulatory RNAs, including, e.g., microRNAs. It is well known that DNA is constantly oxidized and repaired by complex genome maintenance mechanisms. Analogously, RNA also undergoes significant oxidation, and there are now convincing data suggesting that oxidation......, and the consequent loss of integrity of RNA, is a mechanism for disease development. Oxidized RNA is found in a large variety of diseases, and interest has been especially devoted to degenerative brain diseases such as Alzheimer disease, in which up to 50-70% of specific mRNA molecules are reported oxidized, whereas...
Advancement of the Emerging Field of RNA Nanotechnology.
Jasinski, Daniel; Haque, Farzin; Binzel, Daniel W; Guo, Peixuan
2017-02-28
The field of RNA nanotechnology has advanced rapidly during the past decade. A variety of programmable RNA nanoparticles with defined shape, size, and stoichiometry have been developed for diverse applications in nanobiotechnology. The rising popularity of RNA nanoparticles is due to a number of factors: (1) removing the concern of RNA degradation in vitro and in vivo by introducing chemical modification into nucleotides without significant alteration of the RNA property in folding and self-assembly; (2) confirming the concept that RNA displays very high thermodynamic stability and is suitable for in vivo trafficking and other applications; (3) obtaining the knowledge to tune the immunogenic properties of synthetic RNA constructs for in vivo applications; (4) increased understanding of the 4D structure and intermolecular interaction of RNA molecules; (5) developing methods to control shape, size, and stoichiometry of RNA nanoparticles; (6) increasing knowledge of regulation and processing functions of RNA in cells; (7) decreasing cost of RNA production by biological and chemical synthesis; and (8) proving the concept that RNA is a safe and specific therapeutic modality for cancer and other diseases with little or no accumulation in vital organs. Other applications of RNA nanotechnology, such as adapting them to construct 2D, 3D, and 4D structures for use in tissue engineering, biosensing, resistive biomemory, and potential computer logic gate modules, have stimulated the interest of the scientific community. This review aims to outline the current state of the art of RNA nanoparticles as programmable smart complexes and offers perspectives on the promising avenues of research in this fast-growing field.
Study of coupled nonlinear partial differential equations for finding exact analytical solutions.
Khan, Kamruzzaman; Akbar, M Ali; Koppelaar, H
2015-07-01
Exact solutions of nonlinear partial differential equations (NPDEs) are obtained via the enhanced (G'/G)-expansion method. The method is subsequently applied to find exact solutions of the Drinfel'd-Sokolov-Wilson (DSW) equation and the (2+1)-dimensional Painlevé integrable Burgers (PIB) equation. The efficiency of this method for finding these exact solutions is demonstrated. The method is effective and applicable for many other NPDEs in mathematical physics.
Exact Traveling Wave Solutions for Wick-Type Stochastic Schamel KdV Equation
Directory of Open Access Journals (Sweden)
Hossam A. Ghany
2014-01-01
Full Text Available F-expansion method is proposed to seek exact solutions of nonlinear partial differential equations. By means of Hermite transform, inverse Hermite transform, and white noise analysis, the variable coefficients and Wick-type stochastic Schamel KdV equations are completely described. Abundant exact traveling wave solutions for variable coefficients Schamel KdV equations are given. These solutions include exact stochastic Jacobi elliptic functions, trigonometric functions, and hyperbolic functions solutions.
RNA Nanostructures – Methods and Protocols | Center for Cancer Research
RNA nanotechnology is a young field with many potential applications. The goal is to utilize designed RNA strands, such that the obtained constructs have specific properties in terms of shape and functionality. RNA has potential functionalities that are comparable to that of proteins, but possesses (compared to proteins) simpler design principles akin to DNA. The promise is that designed RNA complexes may make possible novel types of molecular assemblies with applications in medicine (as therapeutics or diagnostics), material science, imaging, structural biology, and basic research.
Indian Academy of Sciences (India)
First page Back Continue Last page Overview Graphics. Antisense RNA Approach. Antisense RNA approach is already well documented and well established in therapeutic research. Our system can also be subjected to such an approach. Which gene to target? Our objective would be to target the leader RNA as is thought ...
Dan Cullen
2004-01-01
In contrast to DNA, messenger RNA (mRNA) in complex substrata is rarely analyzed, in large part because labile RNA molecules are difficult to purify. Nucleic acid extractions from fungi that colonize soil are particularly difficult and plagued by humic substances that interfere with Taq polymerase (Tebbe and Vahjen 1993 and references therein). Magnetic capture...
RNA self-assembly and RNA nanotechnology.
Grabow, Wade W; Jaeger, Luc
2014-06-17
CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such
Fast Prediction of RNA-RNA Interaction
Salari, Raheleh; Backofen, Rolf; Sahinalp, S. Cenk
Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.
Centerline Longitudinal Shunt Slot Excitation by Elliptic shaped single Ridge Waveguide
Directory of Open Access Journals (Sweden)
Mehdi Moradian
2011-07-01
Full Text Available The Application of elliptic shaped ridge waveguide is presented for excitation of a centreline longitudinal shunt slot antenna. The proposed method is realized by adding elliptic shaped to the ridge of the single ridge waveguide. The elliptic shaped ridge is placed exactly under the longitudinal slot and the slot placed along centreline of the waveguide. It is shown that for a typical slot, the slot normalized conductance can be increased by increasing the elliptic shaped depth. The simulation results show that the proposed structure can be considered as a proper candidate for replacing the conventional longitudinal shunt slot.
Gomes, Henrique
2011-01-01
This thesis consists of two parts, connected by one central theme: the dynamics of the "shape of space". The first part of the thesis concerns the construction of a theory of gravity dynamically equivalent to general relativity (GR) in 3+1 form (ADM). What is special about this theory is that it does not possess foliation invariance, as does ADM. It replaces that "symmetry" by another: local conformal invariance. In so doing it more accurately reflects a theory of the "shape of space", giving us reason to call it \\emph{shape dynamics} (SD). In the first part we will try to present some of the highlights of results so far, and indicate what we can and cannot do with shape dynamics. Because this is a young, rapidly moving field, we have necessarily left out some interesting new results which are not yet in print and were developed alongside the writing of the thesis. The second part of the thesis will develop a gauge theory for "shape of space"--theories. To be more precise, if one admits that the physically re...
Energy Technology Data Exchange (ETDEWEB)
Pȩkalski, J.; Ciach, A. [Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warszawa (Poland); Almarza, N. G. [Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid (Spain)
2015-01-07
The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk. Exact and asymptotic expressions for the local density and for the effective potential between the confining surfaces are obtained for a one-dimensional lattice model introduced by J. Pȩkalski et al. [J. Chem. Phys. 138, 144903 (2013)]. The simple asymptotic formulas are shown to be in good quantitative agreement with exact results for slits containing at least 5 layers. We observe that the incommensurability of the system size and the average distance between the clusters or layers in the bulk leads to structural deformations that are different for different values of the chemical potential μ. The change of the type of defects is reflected in the dependence of density on μ that has a shape characteristic for phase transitions. Our results may help to avoid misinterpretation of the change of the type of defects as a phase transition in simulations of inhomogeneous systems. Finally, we show that a system confined by soft elastic walls may exhibit bistability such that two system sizes that differ approximately by the average distance between the clusters or layers are almost equally probable. This may happen when the equilibrium separation between the soft boundaries of an empty slit corresponds to the largest stress in the confined self-assembling system.
DEFF Research Database (Denmark)
Nysteen, Anders; Kristensen, Philip Trøst; McCutcheon, Dara
2015-01-01
We develop a wavefunction approach to describe the scattering of two photons on a quantum emitter embedded in a one-dimensional waveguide. Our method allows us to calculate the exact dynamics of the complete system at all times, as well as the transmission properties of the emitter. We show...... that the nonlinearity of the emitter with respect to incoming photons depends strongly on the emitter excitation and the spectral shape of the incoming pulses, resulting in transmission of the photons which depends crucially on their separation and width. In addition, for counter-propagating pulses, we analyze...... the induced level of quantum correlations in the scattered state, and we show that the emitter behaves as a nonlinear beam-splitter when the spectral width of the photon pulses is similar to the emitter decay rate....
Shape memory polymer medical device
Maitland, Duncan [Pleasant Hill, CA; Benett, William J [Livermore, CA; Bearinger, Jane P [Livermore, CA; Wilson, Thomas S [San Leandro, CA; Small, IV, Ward; Schumann, Daniel L [Concord, CA; Jensen, Wayne A [Livermore, CA; Ortega, Jason M [Pacifica, CA; Marion, III, John E.; Loge, Jeffrey M [Stockton, CA
2010-06-29
A system for removing matter from a conduit. The system includes the steps of passing a transport vehicle and a shape memory polymer material through the conduit, transmitting energy to the shape memory polymer material for moving the shape memory polymer material from a first shape to a second and different shape, and withdrawing the transport vehicle and the shape memory polymer material through the conduit carrying the matter.
Combinatorics of RNA-RNA interaction.
Li, Thomas J X; Reidys, Christian M
2012-02-01
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.
DEFF Research Database (Denmark)
Olivarius, Signe
of the transcriptome, 5’ end capture of RNA is combined with next-generation sequencing for high-throughput quantitative assessment of transcription start sites by two different methods. The methods presented here allow for functional investigation of coding as well as noncoding RNA and contribute to future...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA...
Energy Technology Data Exchange (ETDEWEB)
DICKEY,FRED M.; WEICHMAN,LOUIS S.; SHAGAM,RICHARD N.
2000-03-16
Industrial, military, medical, and research and development applications of lasers frequently require a beam with a specified irradiance distribution in some plane. A common requirement is a laser profile that is uniform over some cross-section. Such applications include laser/material processing, laser material interaction studies, fiber injection systems, optical data image processing, lithography, medical applications, and military applications. Laser beam shaping techniques can be divided into three areas: apertured beams, field mappers, and multi-aperture beam integrators. An uncertainty relation exists for laser beam shaping that puts constraints on system design. In this paper the authors review the basics of laser beam shaping and present applications and limitations of various techniques.
Combinatorics of locally optimal RNA secondary structures.
Fusy, Eric; Clote, Peter
2014-01-01
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles).
Sander, Bjoern; Golas, Monika M; Makarov, Evgeny M; Brahms, Hero; Kastner, Berthold; Lührmann, Reinhard; Stark, Holger
2006-10-20
In eukaryotes, pre-mRNA exons are interrupted by large noncoding introns. Alternative selection of exons and nucleotide-exact removal of introns are performed by the spliceosome, a highly dynamic macromolecular machine. U4/U6.U5 tri-snRNP is the largest and most conserved building block of the spliceosome. By 3D electron cryomicroscopy and labeling, the exon-aligning U5 snRNA loop I is localized at the center of the tetrahedrally shaped tri-snRNP reconstructed to approximately 2.1 nm resolution in vitrified ice. Independent 3D reconstructions of its subunits, U4/U6 and U5 snRNPs, show how U4/U6 and U5 combine to form tri-snRNP and, together with labeling experiments, indicate a close proximity of the spliceosomal core components U5 snRNA loop I and U4/U6 at the center of tri-snRNP. We suggest that this central tri-snRNP region may be the site to which the prespliceosomal U2 snRNA has to approach closely during formation of the catalytic core of the spliceosome.
Lake, Kayll
2010-12-01
The title immediately brings to mind a standard reference of almost the same title [1]. The authors are quick to point out the relationship between these two works: they are complementary. The purpose of this work is to explain what is known about a selection of exact solutions. As the authors state, it is often much easier to find a new solution of Einstein's equations than it is to understand it. Even at first glance it is very clear that great effort went into the production of this reference. The book is replete with beautifully detailed diagrams that reflect deep geometric intuition. In many parts of the text there are detailed calculations that are not readily available elsewhere. The book begins with a review of basic tools that allows the authors to set the notation. Then follows a discussion of Minkowski space with an emphasis on the conformal structure and applications such as simple cosmic strings. The next two chapters give an in-depth review of de Sitter space and then anti-de Sitter space. Both chapters contain a remarkable collection of useful diagrams. The standard model in cosmology these days is the ICDM model and whereas the chapter on the Friedmann-Lemaître-Robertson-Walker space-times contains much useful information, I found the discussion of the currently popular a representation rather too brief. After a brief but interesting excursion into electrovacuum, the authors consider the Schwarzschild space-time. This chapter does mention the Swiss cheese model but the discussion is too brief and certainly dated. Space-times related to Schwarzschild are covered in some detail and include not only the addition of charge and the cosmological constant but also the addition of radiation (the Vaidya solution). Just prior to a discussion of the Kerr space-time, static axially symmetric space-times are reviewed. Here one can find a very interesting discussion of the Curzon-Chazy space-time. The chapter on rotating black holes is rather brief and, for
Targeting MicroRNA Function in Acute Pancreatitis
Directory of Open Access Journals (Sweden)
Hong Xiang
2017-09-01
Full Text Available Acute pancreatitis (AP is a common gastrointestinal disorder that featured by acute inflammatory responses leading to systemic inflammatory response syndrome (SIRS or multiple organ failure. A worldwide increase in annual incidence has been observed during the past decade with high acute hospitalization and mortality. Lack of any specific treatment for AP, even to this day, is a reminder that there is much to be learned about the exact pathogenesis of AP. Fortunately, the discovery of microRNA (miRNA has started an entirely new thought process regarding the molecular mechanism associated with the disease processes. Given the extensive effort made on miRNA research, certain types of miRNA have been identified across a variety of biological processes, including cell differentiation, apoptosis, metabolism, and inflammatory responses. Mutations in miRNA sequences or deregulation of miRNA expression may contribute to the alteration of a pivotal physiological function leading to AP. Designing miRNA-related tools for AP diagnosis and treatment presents a novel and potential research frontier. In this mini-review, we summarize the current knowledge of various miRNAs closely interacting with AP and the possible development of targeted miRNA therapies in this disease, which may benefit the development of potential disease biomarkers and novel treatment targets for future medical implications.
Exact Riemann solver for RMHD in the case of shocks only
D.E.A. van Odyck (Daniel)
2005-01-01
textabstractIn this paper the quasi-1D relativistic magneto-hydrodynamic (RMHD) equations are numerically solved with a Lax-Friedrichs scheme. The RMHD shock relations are studied in detail. An ansatz is made to build an exact Riemann solver for RMHD. The results of the exact Riemann solver are
Directory of Open Access Journals (Sweden)
Juan Carlos Ceballos V.
2005-10-01
Full Text Available The exact boundary controllability of the higher order nonlinear Schrodinger equation with constant coefficients on a bounded domain with various boundary conditions is studied. We derive the exact boundary controllability for this equation for sufficiently small initial and final states.
Exact inference for the linear model with groupwise heteroscedastic spherical disturbances
Bekker, Paul; Leertouwer, Erik
2000-01-01
Exact inference on a single coefficient in a linear regression model, as introduced by Bekker (1997), is elaborated for the case of normally distributed heteroscedastic disturbances. Instead of approximate inference based on feasible generalized least squares, exact confidence sets are formulated
Some comments on developments in exact solutions in statistical mechanics since 1944
Baxter, R. J.
2010-11-01
Onsager and Kaufman calculated the partition function of the Ising model exactly in 1944 and 1949. Since then there have been many developments in the exact solution of similar, but usually more complicated, models. Here I shall mention a few, and show how some of the latest work seems to be returning once again to the properties observed by Onsager and Kaufman.
Shaping Adolescent Gambling Behavior.
Arcuri, Alan F.; And Others
1985-01-01
Surveyed the incidence of casino gambling by adolescents. Results indicated that 64 percent of the students at one Atlantic City high school had gambled at the casinos. The dangers of shaping compulsive gambling behavior through societal acceptance of legalized gambling are discussed. (Author/BL)
DEFF Research Database (Denmark)
Simovska, Venka; Jensen, Bjarne Bruun
"Shape Up: a School Community Approach to Influencing the Determinants of Childhood Overweight and Obesity, Lessons Learnt" is a report that aims to provide a synthesis of the project overall evaluation documentation, with a view to systematically review and discuss lessons learnt, and to suggest...... recommendations concerning future practice and policy in the area of preventing childhood overweight and obesity....
Aerodynamically shaped vortex generators
DEFF Research Database (Denmark)
Hansen, Martin Otto Laver; Velte, Clara Marika; Øye, Stig
2016-01-01
An aerodynamically shaped vortex generator has been proposed, manufactured and tested in a wind tunnel. The effect on the overall performance when applied on a thick airfoil is an increased lift to drag ratio compared with standard vortex generators. Copyright © 2015 John Wiley & Sons, Ltd....
OECD Publishing (NJ3), 2010
2010-01-01
"Trends Shaping Education 2010" brings together evidence showing the effects on education of globalisation, social challenges, changes in the workplace, the transformation of childhood, and ICT. To make the content accessible, each trend is presented on a double page, containing an introduction, two charts with brief descriptive text and a set of…
Gross, Michael
2015-10-05
Earth is much more complex than all the other solar system objects that we know. Thanks to its rich and diverse geology, our planet can offer habitats to a wide range of living species. Emerging insights suggest that this is not just a happy coincidence, but that life itself has in many ways helped to shape the planet.
Shaping Faster Question Answering.
Brooks, Lloyd O.
To test a hypothesis that question answering speed and accuracy can be increased by an automated shaping procedure, a film, "The Analysis of Behavior," was presented individually by a teaching machine during twice-per-week sessions to one high school student and 12 junior college students. Six of the students were informed of monetary rewards for…
Martínez, Sol Sáez; de la Rosa, Félix Martínez; Rojas, Sergio
2017-01-01
In Advanced Calculus, our students wonder if it is possible to graphically represent a tornado by means of a three-dimensional curve. In this paper, we show it is possible by providing the parametric equations of such tornado-shaped curves.
Indian Academy of Sciences (India)
The line shape is also simulated by the Monte–Carlo method, the molecular dissociation contributes to 57% neutral atoms and 53% emission intensity in front of the limiter, and 85% neutral atoms and 82% emission intensity in front of the wall. The processes of atoms and molecules influence on the energy balance is ...
2002-01-01
A Japanese team has found a way to bend and shape silicon substrates by growing a thin layer of diamond on top. The technique has been proposed as an alternative to mechanical bending, which is currently used to make reflective lenses for X-ray systems and particle physics systems (2 paragraphs).
Ferromagnetic shape memory alloys
Indian Academy of Sciences (India)
ugc
(sensor), magnetocaloric (refrigeration), and shape memory effect. (actuation) may be important for their future application. Magnetoresistance (8%). Giant magnetocaloric ..... Experimental studies on Ga. 2. MnNi: SEM, EDAX, DSC. T. M. = 780 K. Homogeneous, composition Ga. 1.9. Mn. 0.8. Ni. 1.02. Secondary electron ...
Shaping of a scroll wave filament by cardiac fibers
Energy Technology Data Exchange (ETDEWEB)
Berenfeld, Omer; Wellner, Marcel; Jalife, Jose; Pertsov, Arkady M.
2001-06-01
Scroll waves of electrical excitation in heart tissue are implicated in the development of lethal cardiac arrhythmias. Here we study the relation between the geometry of myocardial fibers and the equilibrium shape of a scroll wave filament. Our theory accommodates a wide class of myocardial models with spatially varying diffusivity tensor, adjusted to fit fiber geometry. We analytically predict the exact equilibrium shapes of the filaments. The major conclusion is that the filament shape is a compromise between a straight line and full alignment with the fibers. The degree of alignment increases with the anisotropy ratio. The results, being purely geometrical, are independent of details of ionic membrane mechanisms. Our theoretical predictions have been verified to excellent accuracy by numerically simulating the stable equilibration of a scroll filament in a model of the FitzHugh-Nagumo type.
Duality based contact shape optimization
DEFF Research Database (Denmark)
Vondrák, Vít; Dostal, Zdenek; Rasmussen, John
2001-01-01
An implementation of semi-analytic method for the sensitivity analysis in contact shape optimization without friction is described. This method is then applied to the contact shape optimization.......An implementation of semi-analytic method for the sensitivity analysis in contact shape optimization without friction is described. This method is then applied to the contact shape optimization....
Improving small-angle X-ray scattering data for structural analyses of the RNA world.
Rambo, Robert P; Tainer, John A
2010-03-01
Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through investigations on the SAM-I riboswitch, the Group I intron P4-P6 domain, 30S ribosomal subunit from Sulfolobus solfataricus (30S), brome mosaic virus tRNA-like structure (BMV TLS), Thermotoga maritima asd lysine riboswitch, the recombinant tRNA(val), and yeast tRNA(phe) that many problems with SAXS experiments on RNA samples derive from heterogeneity of the folded RNA. Furthermore, we propose and test a general approach to reducing these sample limitations for accurate SAXS analyses of RNA. Together our method and results show that SAXS with synchrotron radiation has great potential to provide accurate RNA shapes, conformations, and assembly states in solution that inform RNA biological functions in fundamental ways.
Evolutionary triplet models of structured RNA.
Directory of Open Access Journals (Sweden)
Robert K Bradley
2009-08-01
Full Text Available The reconstruction and synthesis of ancestral RNAs is a feasible goal for paleogenetics. This will require new bioinformatics methods, including a robust statistical framework for reconstructing histories of substitutions, indels and structural changes. We describe a "transducer composition" algorithm for extending pairwise probabilistic models of RNA structural evolution to models of multiple sequences related by a phylogenetic tree. This algorithm draws on formal models of computational linguistics as well as the 1985 protosequence algorithm of David Sankoff. The output of the composition algorithm is a multiple-sequence stochastic context-free grammar. We describe dynamic programming algorithms, which are robust to null cycles and empty bifurcations, for parsing this grammar. Example applications include structural alignment of non-coding RNAs, propagation of structural information from an experimentally-characterized sequence to its homologs, and inference of the ancestral structure of a set of diverged RNAs. We implemented the above algorithms for a simple model of pairwise RNA structural evolution; in particular, the algorithms for maximum likelihood (ML alignment of three known RNA structures and a known phylogeny and inference of the common ancestral structure. We compared this ML algorithm to a variety of related, but simpler, techniques, including ML alignment algorithms for simpler models that omitted various aspects of the full model and also a posterior-decoding alignment algorithm for one of the simpler models. In our tests, incorporation of basepair structure was the most important factor for accurate alignment inference; appropriate use of posterior-decoding was next; and fine details of the model were least important. Posterior-decoding heuristics can be substantially faster than exact phylogenetic inference, so this motivates the use of sum-over-pairs heuristics where possible (and approximate sum-over-pairs. For more exact
Effects of particle shape on volume and mass estimates of interstellar grains
Greenberg, J. M.; Hong, S. S.
1975-01-01
Mass estimates of interstellar grain materials based on visual extinction characteristics are shown to be insensitive to shape and, so long as the wavelength dependence of extinction is defined well into the infrared, they are also insensitive to size distribution. Spheroidal particles are treated by an approximate analytical method. Spheres and cylinders (core mantle as well as homogeneous) are treated by exact methods.
Mycoviruses, RNA silencing, and viral RNA recombination.
Nuss, Donald L
2011-01-01
In contrast to viruses of plants and animals, viruses of fungi, mycoviruses, uniformly lack an extracellular phase to their replication cycle. The persistent, intracellular nature of the mycovirus life cycle presents technical challenges to experimental design. However, these properties, coupled with the relative simplicity and evolutionary position of the fungal host, also provide opportunities for examining fundamental aspects of virus-host interactions from a perspective that is quite different from that pertaining for most plant and animal virus infections. This chapter presents support for this view by describing recent advances in the understanding of antiviral defense responses against one group of mycoviruses for which many of the technical experimental challenges have been overcome, the hypoviruses responsible for hypovirulence of the chestnut blight fungus Cryphonectria parasitica. The findings reveal new insights into the induction and suppression of RNA silencing as an antiviral defense response and an unexpected role for RNA silencing in viral RNA recombination. Copyright © 2011 Elsevier Inc. All rights reserved.
Jacobson, Alec
2015-01-01
Shape articulation transforms a lifeless geometric object into a vibrant character. Computers enrich artists' toolsets dramatically. They not only endow artists with the power to manipulate virtual 2D and 3D scenes, but they also eliminate tedium and expedite prototyping, freeing artists to focus on creative aspects. With such power comes a temptation to lean entirely on the computer. Computationally intensive animation systems sacrifice real-time feedback for physical accuracy. How can we leverage modern computational power to create the best possible shape deformations while maintaining real-time performance as a mandatory invariant? This article summarizes efforts to answer this, culminating in a deformation system with the quality of slow, nonlinear optimization, but at lightning speed.
DEFF Research Database (Denmark)
Andersen, Susan; Tolstrup, Janne Schurmann; Rod, Morten Hulvej
2015-01-01
BACKGROUND: The social environment at schools is an important setting to promote educational attainment, and health and well-being of young people. However, within upper secondary education there is a need for evidence-based school intervention programmes. The Shaping the Social intervention...... is a comprehensive programme integrating social and educational activities to promote student well-being and reduce smoking and dropout in upper secondary vocational education. The evaluation design is reported here. METHODS/DESIGN: The evaluation employed a non-randomised cluster controlled design, and schools were...... national education registers through a 2-year follow-up period. DISCUSSION: Shaping the Social was designed to address that students at Danish vocational schools constitute a high risk population concerning health behaviour as well as school dropout by modifying the school environment, alongside developing...
Ott, Eric A.
2005-01-01
Scoping of shape changing airfoil concepts including both aerodynamic analysis and materials-related technology assessment effort was performed. Three general categories of potential components were considered-fan blades, booster and compressor blades, and stator airfoils. Based on perceived contributions to improving engine efficiency, the fan blade was chosen as the primary application for a more detailed assessment. A high-level aerodynamic assessment using a GE90-90B Block 4 engine cycle and fan blade geometry indicates that blade camber changes of approximately +/-4deg would be sufficient to result in fan efficiency improvements nearing 1 percent. Constraints related to flight safety and failed mode operation suggest that use of the baseline blade shape with actuation to the optimum cruise condition during a portion of the cycle would be likely required. Application of these conditions to the QAT fan blade and engine cycle was estimated to result in an overall fan efficiency gain of 0.4 percent.
DEFF Research Database (Denmark)
Andersen, Susan; Tolstrup, Janne Schurmann; Rod, Morten Hulvej
2015-01-01
is a comprehensive programme integrating social and educational activities to promote student well-being and reduce smoking and dropout in upper secondary vocational education. The evaluation design is reported here. METHODS/DESIGN: The evaluation employed a non-randomised cluster controlled design, and schools were......BACKGROUND: The social environment at schools is an important setting to promote educational attainment, and health and well-being of young people. However, within upper secondary education there is a need for evidence-based school intervention programmes. The Shaping the Social intervention...... national education registers through a 2-year follow-up period. DISCUSSION: Shaping the Social was designed to address that students at Danish vocational schools constitute a high risk population concerning health behaviour as well as school dropout by modifying the school environment, alongside developing...
DEFF Research Database (Denmark)
Buur, Jacob; Mack, Alexandra
- in particular in a large corporation? This workshop explores how innovation is socially shaped in organizations. Based on our experiences with practices around innovation and collaboration, we start from three proposition about the social shaping of innovation: • Ideas don't thrive as text (i.e. we need......Why is it that some business proposals – no matter how well researched with users and business developed – don’t seem to make it through the organizational jungle to become a real product, while others do? How shall we understand the innovative practices that we engage with our ethnographic work...... to consider other media) • Ideas need socialization (ideas are linked to people, we need to be careful about how we support the social innovation context) • Ideas are local (ideas spring out of a local contingency, we need to take care in how we like them to travel)....
Biomedical Shape Memory Polymers
Directory of Open Access Journals (Sweden)
SHEN Xue-lin
2017-07-01
Full Text Available Shape memory polymers(SMPs are a class of functional "smart" materials that have shown bright prospects in the area of biomedical applications. The novel smart materials with multifunction of biodegradability and biocompatibility can be designed based on their general principle, composition and structure. In this review, the latest process of three typical biodegradable SMPs(poly(lactide acide, poly(ε-caprolactone, polyurethane was summarized. These three SMPs were classified in different structures and discussed, and shape-memory mechanism, recovery rate and fixed rate, response speed was analysed in detail, also, some biomedical applications were presented. Finally, the future development and applications of SMPs are prospected: two-way SMPs and body temperature induced SMPs will be the focus attension by researchers.
Topology of RNA-RNA interaction structures
DEFF Research Database (Denmark)
Andersen, Jørgen Ellegaard; Huang, Fenix Wenda; Penner, Robert
2012-01-01
Abstract The topological filtration of interacting RNA complexes is studied, and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that, for two interacting RNAs, called interaction structures, there exis...... complexity, this grammar for genus zero interaction structures provides not only minimum free energy solutions but also the complete partition function and base pairing probabilities.......Abstract The topological filtration of interacting RNA complexes is studied, and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that, for two interacting RNAs, called interaction structures, there exist...
RNA decay by messenger RNA interferases
DEFF Research Database (Denmark)
Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo
2008-01-01
Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs....
Audiometric shape and presbycusis.
Demeester, Kelly; van Wieringen, Astrid; Hendrickx, Jan-jaap; Topsakal, Vedat; Fransen, Erik; van Laer, Lut; Van Camp, Guy; Van de Heyning, Paul
2009-04-01
The aim of this study was to describe the prevalence of specific audiogram configurations in a healthy, otologically screened population between 55 and 65 years old. The audiograms of 1147 subjects (549 males and 598 females between 55 and 65 years old) were collected through population registries and classified according to the configuration of hearing loss. Gender and noise/solvent-exposure effects on the prevalence of the different audiogram shapes were determined statistically. In our population 'Flat' audiograms were most dominantly represented (37%) followed by 'High frequency Gently sloping' audiograms (35%) and 'High frequency Steeply sloping' audiograms (27%). 'Low frequency Ascending' audiograms, 'Mid frequency U-shape' audiograms and 'Mid frequency Reverse U-shape' audiograms were very rare (together less than 1%). The 'Flat'-configuration was significantly more common in females, whereas the 'High frequency Steeply sloping'-configuration was more common in males. Exposure to noise and/or solvents did not change this finding. In addition, females with a 'Flat' audiogram had a significantly larger amount of overall hearing loss compared to males. Furthermore, our data reveal a significant association between the prevalence of 'High frequency Steeply sloping' audiograms and the degree of noise/solvent exposure, despite a relatively high proportion of non-exposed subjects showing a 'High frequency Steeply sloping' audiogram as well.
Towards robust and effective shape modeling: sparse shape composition.
Zhang, Shaoting; Zhan, Yiqiang; Dewan, Maneesh; Huang, Junzhou; Metaxas, Dimitris N; Zhou, Xiang Sean
2012-01-01
Organ shape plays an important role in various clinical practices, e.g., diagnosis, surgical planning and treatment evaluation. It is usually derived from low level appearance cues in medical images. However, due to diseases and imaging artifacts, low level appearance cues might be weak or misleading. In this situation, shape priors become critical to infer and refine the shape derived by image appearances. Effective modeling of shape priors is challenging because: (1) shape variation is complex and cannot always be modeled by a parametric probability distribution; (2) a shape instance derived from image appearance cues (input shape) may have gross errors; and (3) local details of the input shape are difficult to preserve if they are not statistically significant in the training data. In this paper we propose a novel Sparse Shape Composition model (SSC) to deal with these three challenges in a unified framework. In our method, a sparse set of shapes in the shape repository is selected and composed together to infer/refine an input shape. The a priori information is thus implicitly incorporated on-the-fly. Our model leverages two sparsity observations of the input shape instance: (1) the input shape can be approximately represented by a sparse linear combination of shapes in the shape repository; (2) parts of the input shape may contain gross errors but such errors are sparse. Our model is formulated as a sparse learning problem. Using L1 norm relaxation, it can be solved by an efficient expectation-maximization (EM) type of framework. Our method is extensively validated on two medical applications, 2D lung localization in X-ray images and 3D liver segmentation in low-dose CT scans. Compared to state-of-the-art methods, our model exhibits better performance in both studies. Copyright © 2011 Elsevier B.V. All rights reserved.
Roles of Fission Yeast Grc3 Protein in Ribosomal RNA Processing and Heterochromatic Gene Silencing*
Kitano, Erina; Hayashi, Aki; Kanai, Daigo; Shinmyozu, Kaori; Nakayama, Jun-ichi
2011-01-01
Grc3 is an evolutionarily conserved protein. Genome-wide budding yeast studies suggest that Grc3 is involved in rRNA processing. In the fission yeast Schizosaccharomyces pombe, Grc3 was identified as a factor exhibiting distinct nuclear dot localization, yet its exact physiological function remains unknown. Here, we show that S. pombe Grc3 is required for both rRNA processing and heterochromatic gene silencing. Cytological analysis revealed that Grc3 nuclear dots correspond to heterochromatic...
An Exact Hot-Tube Solution For Thin Tape Helix Traveling-Wave Tube
Wong, Patrick; Lau, Y. Y.; Gilgenbach, Ronald; Chernin, David; Hoff, Brad
2017-10-01
The exact hot-tube dispersion relation for a thin tape helix traveling-wave tube (TWT) is derived for the first time, based on its exact cold-tube solution. This is an attempt to provide a reliable determination of the Pierce parameters, in particular the ``AC space-charge'' parameter QC, for a realistic TWT. The determination of QC remains an outstanding issue. The numerical results from the exact formulation will be compared with other approximate models of TWT that were commonly used in the literature for QC. This work was supported by AFOSR Grant No. FA9550-15-1-0097.
Exact beta function from the holographic loop equation of large-N QCD4
Bochicchio, Marco
2007-09-01
We construct and study a quantum holographic effective action, Γq, whose critical equation implies the holographic loop equation of large-N QCD4 for planar self-avoiding loops in a certain regularization scheme. We extract from Γq the exact beta function in the given scheme. For the Wilsonean coupling constant the beta function is exactly one loop and the first coefficient, β0, agrees with its value in perturbation theory. For the canonical coupling constant the exact beta function has a NSV Z form and the first two coefficients in powers of the coupling, β0 and β1, agree with their value in perturbation theory.
Exact Travelling Wave Solutions of two Important Nonlinear Partial Differential Equations
Kim, Hyunsoo; Bae, Jae-Hyeong; Sakthivel, Rathinasamy
2014-04-01
Coupled nonlinear partial differential equations describing the spatio-temporal dynamics of predator-prey systems and nonlinear telegraph equations have been widely applied in many real world problems. So, finding exact solutions of such equations is very helpful in the theories and numerical studies. In this paper, the Kudryashov method is implemented to obtain exact travelling wave solutions of such physical models. Further, graphic illustrations in two and three dimensional plots of some of the obtained solutions are also given to predict their behaviour. The results reveal that the Kudryashov method is very simple, reliable, and effective, and can be used for finding exact solution of many other nonlinear evolution equations.
An exact limit of the Aharony-Bergman-Jafferis-Maldacena theory
Bianchi, Marco S.; Leoni, Matias
2016-08-01
We study planar Aharony-Bergman-Jafferis-Maldacena (ABJM) theory in a limit where one coupling is negligible compared to the other. We provide a recipe for exactly solving the expectation value of bosonic Bogomol'nyi-Prasad-Sommerfield (BPS) Wilson loops on arbitrary smooth contours, or the leading divergence for cusped ones, using results from localization. As an application, we compute the exact (generalized) cusp anomalous dimension and Bremsstrahlung function and use it to determine the interpolating h -function. We finally prove a conjecture on the exact form of the dilatation operator in a closed sector, hinting at the integrability of this limit.
Formulations and exact algorithms for the vehicle routing problem with time windows
DEFF Research Database (Denmark)
Kallehauge, Brian
2008-01-01
In this paper we review the exact algorithms proposed in the last three decades for the solution of the vehicle routing problem with time windows (VRPTW). The exact algorithms for the VRPTW are in many aspects inherited from work on the traveling salesman problem (TSP). In recognition of this fact...... this paper is structured relative to four seminal papers concerning the formulation and exact solution of the TSP, i.e. the arc formulation, the arc-node formulation, the spanning tree formulation, and the path formulation. We give a detailed analysis of the formulations of the VRPTW and a review...
RNA Localization in Astrocytes
DEFF Research Database (Denmark)
Thomsen, Rune
2012-01-01
Messenger RNA (mRNA) localization is a mechanism by which polarized cells can regulate protein synthesis to specific subcellular compartments in a spatial and temporal manner, and plays a pivotal role in multiple physiological processes from embryonic development to cell differentiation......, regulation of the blood brain barrier and glial scar tissue formation. Despite the involvement in various CNS functions only a limited number of studies have addressed mRNA localization in astrocytes. This PhD project was initially focused on developing and implementing methods that could be used to asses mRNA...... localization in astrocyte protrusions, and following look into the subcellular localization pattern of specific mRNA species of both primary astrocytes isolated from cortical hemispheres of newborn mice, and the mouse astrocyte cell line, C8S. The Boyden chamber cell fractionation assay was optimized, in a way...
Dynamics of miRNA driven feed-forward loop depends upon miRNA action mechanisms.
Duk, Maria A; Samsonova, Maria G; Samsonov, Alexander M
2014-01-01
We perform the theoretical analysis of a gene network sub-system, composed of a feed-forward loop, in which the upstream transcription factor regulates the target gene via two parallel pathways: directly, and via interaction with miRNA. As the molecular mechanisms of miRNA action are not clear so far, we elaborate three mathematical models, in which miRNA either represses translation of its target or promotes target mRNA degradation, or is not re-used, but degrades along with target mRNA. We examine the feed-forward loop dynamics quantitatively at the whole time interval of cell cycle. We rigorously proof the uniqueness of solutions to the models and obtain the exact solutions in one of them analytically. We have shown that different mechanisms of miRNA action lead to a variety of types of dynamical behavior of feed-forward loops. In particular, we found that the ability of feed-forward loop to dampen fluctuations introduced by transcription factor is the model and parameter dependent feature. We also discuss how our results could help a biologist to infer the mechanism of miRNA action.
Hearon, Keith; Singhal, Pooja; Horn, John; Small, Ward; Olsovsky, Cory; Maitland, Kristen C.; Wilson, Thomas S.; Maitland, Duncan J.
2013-01-01
Porous shape memory polymers (SMPs) include foams, scaffolds, meshes, and other polymeric substrates that possess porous three-dimensional macrostructures. Porous SMPs exhibit active structural and volumetric transformations and have driven investigations in fields ranging from biomedical engineering to aerospace engineering to the clothing industry. The present review article examines recent developments in porous SMPs, with focus given to structural and chemical classification, methods of characterization, and applications. We conclude that the current body of literature presents porous SMPs as highly interesting smart materials with potential for industrial use. PMID:23646038
Liu, Jiamin; Udupa, Jayaram K
2009-04-01
Active shape models (ASM) are widely employed for recognizing anatomic structures and for delineating them in medical images. In this paper, a novel strategy called oriented active shape models (OASM) is presented in an attempt to overcome the following five limitations of ASM: 1) lower delineation accuracy, 2) the requirement of a large number of landmarks, 3) sensitivity to search range, 4) sensitivity to initialization, and 5) inability to fully exploit the specific information present in the given image to be segmented. OASM effectively combines the rich statistical shape information embodied in ASM with the boundary orientedness property and the globally optimal delineation capability of the live wire methodology of boundary segmentation. The latter characteristics allow live wire to effectively separate an object boundary from other nonobject boundaries with similar properties especially when they come very close in the image domain. The approach leads to a two-level dynamic programming method, wherein the first level corresponds to boundary recognition and the second level corresponds to boundary delineation, and to an effective automatic initialization method. The method outputs a globally optimal boundary that agrees with the shape model if the recognition step is successful in bringing the model close to the boundary in the image. Extensive evaluation experiments have been conducted by utilizing 40 image (magnetic resonance and computed tomography) data sets in each of five different application areas for segmenting breast, liver, bones of the foot, and cervical vertebrae of the spine. Comparisons are made between OASM and ASM based on precision, accuracy, and efficiency of segmentation. Accuracy is assessed using both region-based false positive and false negative measures and boundary-based distance measures. The results indicate the following: 1) The accuracy of segmentation via OASM is considerably better than that of ASM; 2) The number of landmarks
A Comparison of Exact Versus Perturbed Pole Locations of Dielectric Objects in Dielectric Medium
National Research Council Canada - National Science Library
Worthy, Mark
1997-01-01
The dielectric properties of soils and plastic targets are given. The approach for finding exact pole locations from a dielectric infinite slab, a dielectric sphere, and a dielectric infinite cylinder is presented (and applied...
Exact results in a lattice model of a binary reactant mixture
Energy Technology Data Exchange (ETDEWEB)
Thomas, P.B. [Department of Physics, Brookhaven National Laboratory, Upton, New York 11973 (United States)
1995-04-01
We study phase separation in a binary mixture of two particles, which can react with each other and form a third compound. We determine the exact phase boundaries for a restricted range of the interaction parameters.
On a revisit to the Painlevé test for integrability and exact solutions ...
Indian Academy of Sciences (India)
-dual equations for (2) gauge fields. Susanto Chakraborty Pranab Krishna Chanda. Research Articles Volume 66 ... Keywords. Painlevé analysis; integrability; auto-Backlund transformation; exact solutions; (2) gauge field; self-duality ...
Exact unsteady solutions to the Navier-Stokes and viscous MHD equations
Energy Technology Data Exchange (ETDEWEB)
Bogoyavlenskij, Oleg I
2003-02-10
Infinite-dimensional families of exact solutions that depend on all four variables t,x,y,z are derived for the Navier-Stokes equations and for viscous magnetohydrodynamics equations. Soliton-like solutions--viscons--are introduced.
Exact solutions of time-fractional heat conduction equation by the fractional complex transform
Directory of Open Access Journals (Sweden)
Li Zheng-Biao
2012-01-01
Full Text Available The Fractional Complex Transform is extended to solve exactly time-fractional differential equations with the modified Riemann-Liouville derivative. How to incorporate suitable boundary/initial conditions is also discussed.
Exact Solutions for Some Fractional Partial Differential Equations by the Method
Directory of Open Access Journals (Sweden)
Bin Zheng
2013-01-01
derivative. Based on a certain variable transformation, these fractional partial differential equations are transformed into ordinary differential equations of integer order. With the aid of mathematical software, a variety of exact solutions for them are obtained.
Exact simulation of Brown-Resnick random fields at a finite number of locations
DEFF Research Database (Denmark)
Dieker, Ton; Mikosch, Thomas Valentin
2015-01-01
We propose an exact simulation method for Brown-Resnick random fields, building on new representations for these stationary max-stable fields. The main idea is to apply suitable changes of measure....
Exact inference for the linear model with groupwise heteroscedastic spherical disturbances
Bekker, P.A.
2002-01-01
Exact nonparametric inference on a single coefficient in a linear regression model, as considered by Bekker (Working Paper, Department of Economics, University of Groningen, 1997), is elaborated for the case of spherically distributed heteroscedastic disturbances. Instead of approximate inference
An Exact Model-Based Method for Near-Field Sources Localization with Bistatic MIMO System.
Singh, Parth Raj; Wang, Yide; Chargé, Pascal
2017-03-30
In this paper, we propose an exact model-based method for near-field sources localization with a bistatic multiple input, multiple output (MIMO) radar system, and compare it with an approximated model-based method. The aim of this paper is to propose an efficient way to use the exact model of the received signals of near-field sources in order to eliminate the systematic error introduced by the use of approximated model in most existing near-field sources localization techniques. The proposed method uses parallel factor (PARAFAC) decomposition to deal with the exact model. Thanks to the exact model, the proposed method has better precision and resolution than the compared approximated model-based method. The simulation results show the performance of the proposed method.
Flatland Position-Dependent-Mass: Polar Coordinates, Separability and Exact Solvability
Mazharimousavi, S. Habib; Mustafa, Omar
2010-10-01
The kinetic energy operator with position-dependent-mass in plane polar coordinates is obtained. The separability of the corresponding Schrödinger equation is discussed. A hypothetical toy model is reported and two exactly solvable examples are studied.
Exact Kolmogorov and total variation distances between some familiar discrete distributions
Directory of Open Access Journals (Sweden)
Adell José A
2006-01-01
Full Text Available We give exact closed-form expressions for the Kolmogorov and the total variation distances between Poisson, binomial, and negative binomial distributions with different parameters. In the Poisson case, such expressions are related with the Lambert function.
Geosat Exact Repeat Mission Waveform Data Records (WDR) (NODC Accession 0061150)
National Oceanic and Atmospheric Administration, Department of Commerce — This accession contains waveform data records (WDRs) from the US Navy Geodetic Satellite (GEOSAT) Exact Repeat Mission (ERM) for the time period of November 08, 1986...
Energy Technology Data Exchange (ETDEWEB)
Barut, A.O. (Colorado Univ., Boulder (USA). Dept. of Physics); Oezaltin, O.; Uenal, N. (Dicle Univ., Diyarbakir (Turkey). Dept. of Physics)
1985-01-01
The Heisenberg equations for the Dirac electron in an external electromagnetic plane wave have been solved exactly in terms of incomplete ..gamma..-functions. As a special case the solution for a crossed constant electric and magnetic field is given.
Three classes of exact solutions to Klein-Gordon-Schrodinger equation
National Research Council Canada - National Science Library
Xia, Hongming; He, Wansheng; Hu, Linxia; Gao, Zhongshe
2013-01-01
Basing on the priori assumption principle, the main goal of this paper is to propose the rational expansion method that can be used to handle the exact solution of the nonlinear partial differential equation...
On a stochastic gene expression with pre-mRNA, mRNA and protein contribution.
Rudnicki, Ryszard; Tomski, Andrzej
2015-12-21
In this paper we develop a model of stochastic gene expression, which is an extension of the model investigated in the paper [T. Lipniacki, P. Paszek, A. Marciniak-Czochra, A.R. Brasier, M. Kimmel, Transcriptional stochasticity in gene expression, J. Theor. Biol. 238 (2006) 348-367]. In our model, stochastic effects still originate from random fluctuations in gene activity status, but we precede mRNA production by the formation of pre-mRNA, which enriches classical transcription phase. We obtain a stochastically regulated system of ordinary differential equations (ODEs) describing evolution of pre-mRNA, mRNA and protein levels. We perform mathematical analysis of a long-time behavior of this stochastic process, identified as a piece-wise deterministic Markov process (PDMP). We check exact results using numerical simulations for the distributions of all three types of particles. Moreover, we investigate the deterministic (adiabatic) limit state of the process, when depending on parameters it can exhibit two specific types of behavior: bistability and the existence of the limit cycle. The latter one is not present when only two kinds of gene expression products are considered. Copyright © 2015 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Tao, Jianmin [Los Alamos National Laboratory; Perdew, John P [TULANE UNIV; Staroverov, Viktor N [UNIV OF WESTERN ONTARIO; Scuseria, Gustavo E [RICE UNIV
2008-01-01
We construct a nonlocal density functional approximation with full exact exchange, while preserving the constraint-satisfaction approach and justified error cancellations of simpler semilocal functionals. This is achieved by interpolating between different approximations suitable for two extreme regions of the electron density. In a 'normal' region, the exact exchange-correlation hole density around an electron is semilocal because its spatial range is reduced by correlation and because it integrates over a narrow range to -1. These regions are well described by popular semilocal approximations (many of which have been constructed nonempirically), because of proper accuracy for a slowly-varying density or because of error cancellation between exchange and correlation. 'Abnormal' regions, where non locality is unveiled, include those in which exchange can dominate correlation (one-electron, nonuniform high-density, and rapidly-varying limits), and those open subsystems of fluctuating electron number over which the exact exchange-correlation hole integrates to a value greater than -1. Regions between these extremes are described by a hybrid functional mixing exact and semi local exchange energy densities locally (i.e., with a mixing fraction that is a function of position r and a functional of the density). Because our mixing fraction tends to 1 in the high-density limit, we employ full exact exchange according to the rigorous definition of the exchange component of any exchange-correlation energy functional. Use of full exact exchange permits the satisfaction of many exact constraints, but the nonlocality of exchange also requires balanced nonlocality of correlation. We find that this nonlocality can demand at least five empirical parameters (corresponding roughly to the four kinds of abnormal regions). Our local hybrid functional is perhaps the first accurate size-consistent density functional with full exact exchange. It satisfies other known
Exact Solution of Mutator Model with Linear Fitness and Finite Genome Length
Saakian, David B.
2017-08-01
We considered the infinite population version of the mutator phenomenon in evolutionary dynamics, looking at the uni-directional mutations in the mutator-specific genes and linear selection. We solved exactly the model for the finite genome length case, looking at the quasispecies version of the phenomenon. We calculated the mutator probability both in the statics and dynamics. The exact solution is important for us because the mutator probability depends on the genome length in a highly non-trivial way.
Eisinga, Rob; Heskes, Tom; Pelzer, Ben; Te Grotenhuis, Manfred
2017-01-25
The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is typically of interest to conduct pairwise comparison tests. Current approaches to such tests rely on large-sample approximations, due to the numerical complexity of computing the exact distribution. These approximate methods lead to inaccurate estimates in the tail of the distribution, which is most relevant for p-value calculation. We propose an efficient, combinatorial exact approach for calculating the probability mass distribution of the rank sum difference statistic for pairwise comparison of Friedman rank sums, and compare exact results with recommended asymptotic approximations. Whereas the chi-squared approximation performs inferiorly to exact computation overall, others, particularly the normal, perform well, except for the extreme tail. Hence exact calculation offers an improvement when small p-values occur following multiple testing correction. Exact inference also enhances the identification of significant differences whenever the observed values are close to the approximate critical value. We illustrate the proposed method in the context of biological machine learning, were Friedman rank sum difference tests are commonly used for the comparison of classifiers over multiple datasets. We provide a computationally fast method to determine the exact p-value of the absolute rank sum difference of a pair of Friedman rank sums, making asymptotic tests obsolete. Calculation of exact p-values is easy to implement in statistical software and the implementation in R is provided in one of the Additional files and is also available at http://www.ru.nl/publish/pages/726696/friedmanrsd.zip .
Conservation laws and exact solutions for nonlinear diffusion in anisotropic media
Avdonina, Elena D.; Ibragimov, Nail H.
2013-10-01
Conservation laws and exact solutions of nonlinear differential equations describing diffusion phenomena in anisotropic media with external sources are constructed. The construction is based on the method of nonlinear self-adjointness. Numerous exact solutions are obtained by using the recent method of conservation laws. These solutions are different from group invariant solutions and can be useful for investigating diffusion phenomena in complex media, e.g. in oil industry.
TVT-Exact and midurethral sling (SLING-IUFT) operative procedures: a randomized study.
Aniuliene, Rosita; Aniulis, Povilas; Skaudickas, Darijus
2015-01-01
The aim of the study is to compare results, effectiveness and complications of TVT exact and midurethral sling (SLING-IUFT) operations in the treatment of female stress urinary incontinence (SUI). A single center nonblind, randomized study of women with SUI who were randomized to TVT-Exact and SLING-IUFT was performed by one surgeon from April 2009 to April 2011. SUI was diagnosed on coughing and Valsalva test and urodynamics (cystometry and uroflowmetry) were assessed before operation and 1 year after surgery. This was a prospective randomized study. The follow up period was 12 months. 76 patients were operated using the TVT-Exact operation and 78 patients - using the SLING-IUFT operation. There was no statistically significant differences between groups for BMI, parity, menopausal status and prolapsed stage (no patients had cystocele greater than stage II). Mean operative time was significantly shorter in the SLING-IUFT group (19 ± 5.6 min.) compared with the TVT-Exact group (27 ± 7.1 min.). There were statistically significant differences in the effectiveness of both procedures: TVT-Exact - at 94.5% and SLING-IUFT - at 61.2% after one year. Hospital stay was statistically significantly shorter in the SLING-IUFT group (1. 2 ± 0.5 days) compared with the TVT-Exact group (3.5 ± 1.5 days). Statistically significantly fewer complications occurred in the SLING-IUFT group. the TVT-Exact and SLING-IUFT operations are both effective for surgical treatment of female stress urinary incontinence. The SLING-IUFT involved a shorter operation time and lower complications rate., the TVT-Exact procedure had statistically significantly more complications than the SLING-IUFT operation, but a higher effectiveness.
On exact traveling-wave solutions for local fractional Korteweg-de Vries equation
Yang, Xiao-Jun; Tenreiro Machado, J. A.; Baleanu, Dumitru; Cattani, Carlo
2016-08-01
This paper investigates the Korteweg-de Vries equation within the scope of the local fractional derivative formulation. The exact traveling wave solutions of non-differentiable type with the generalized functions defined on Cantor sets are analyzed. The results for the non-differentiable solutions when fractal dimension is 1 are also discussed. It is shown that the exact solutions for the local fractional Korteweg-de Vries equation characterize the fractal wave on shallow water surfaces.
The Exact Root Algorithm for Computing the Real Roots of an Nth Degree Polynomial
E. A. Adebile; V. I. Idoko
2010-01-01
Problem statement: The need to find an efficient and reliable algorithm for computing the exact real roots of the steady-state polynomial encountered in the investigation of temperature profiles in biological tissues during Microwave heating and other similar cases as found in the literature gave rise to this study. Approach: The algorithm (simply called ERA-Exact Root Algorithm) adopted polynomial deflation technique and uses Newton-Raphson iterative procedure though with a modified terminat...
On exact traveling-wave solutions for local fractional Korteweg-de Vries equation.
Yang, Xiao-Jun; Tenreiro Machado, J A; Baleanu, Dumitru; Cattani, Carlo
2016-08-01
This paper investigates the Korteweg-de Vries equation within the scope of the local fractional derivative formulation. The exact traveling wave solutions of non-differentiable type with the generalized functions defined on Cantor sets are analyzed. The results for the non-differentiable solutions when fractal dimension is 1 are also discussed. It is shown that the exact solutions for the local fractional Korteweg-de Vries equation characterize the fractal wave on shallow water surfaces.
Separation of Variables and Exactly Soluble Time-Dependent Potentials in Quantum Mechanics
Efthimiou, Costas John; Spector, Donald
1993-01-01
We use separation of variables as a tool to identify and to analyze exactly soluble time-dependent quantum mechanical potentials. By considering the most general possible time-dependent re-definition of the spatial coordinate, as well as general transformations on the wavefunctions, we show that separation of variables applies and exact solubility occurs only in a very restricted class of time-dependent models. We consider the formal structure underlying our findings, and the relationship bet...
Computing Symmetric Boolean Functions by Circuits with Few Exact Threshold Gates
DEFF Research Database (Denmark)
Hansen, Kristoffer Arnsfelt
2007-01-01
We consider constant depth circuits augmented with few exact threshold gates with arbitrary weights. We prove strong (up to exponential) size lower bounds for such circuits computing symmetric Boolean functions. Our lower bound is expressed in terms of a natural parameter, the balance, of symmetric...... functions. Furthermore, in the quasi-polynomial size setting our results provides an exact characterization of the class of symmetric functions in terms of their balance....
Exact solution for spin precession in the radiationless relativistic Kepler problem
Energy Technology Data Exchange (ETDEWEB)
Mane, S.R., E-mail: srmane001@gmail.com
2014-11-11
There is interest in circulating beams of polarized particles in all-electric storage rings to search for nonzero permanent electric dipole moments of subatomic particles. To this end, it is helpful to derive exact analytical solutions of the spin precession in idealized models, both for pedagogical reasons and to serve as benchmark tests for analysis and design of experiments. This paper derives exact solutions for the spin precession in the relativistic Kepler problem. Some counterintuitive properties of the solutions are pointed out.
Exact solution for spin precession in the radiationless relativistic Kepler problem
Mane, S. R.
2014-11-01
There is interest in circulating beams of polarized particles in all-electric storage rings to search for nonzero permanent electric dipole moments of subatomic particles. To this end, it is helpful to derive exact analytical solutions of the spin precession in idealized models, both for pedagogical reasons and to serve as benchmark tests for analysis and design of experiments. This paper derives exact solutions for the spin precession in the relativistic Kepler problem. Some counterintuitive properties of the solutions are pointed out.
Pairwise harmonics for shape analysis
Zheng, Youyi
2013-07-01
This paper introduces a simple yet effective shape analysis mechanism for geometry processing. Unlike traditional shape analysis techniques which compute descriptors per surface point up to certain neighborhoods, we introduce a shape analysis framework in which the descriptors are based on pairs of surface points. Such a pairwise analysis approach leads to a new class of shape descriptors that are more global, discriminative, and can effectively capture the variations in the underlying geometry. Specifically, we introduce new shape descriptors based on the isocurves of harmonic functions whose global maximum and minimum occur at the point pair. We show that these shape descriptors can infer shape structures and consistently lead to simpler and more efficient algorithms than the state-of-the-art methods for three applications: intrinsic reflectional symmetry axis computation, matching shape extremities, and simultaneous surface segmentation and skeletonization. © 2012 IEEE.
Mast Wake Reduction by Shaping
National Research Council Canada - National Science Library
Beauchamp, Charles H
2005-01-01
The present invention relates to various mast shapes, in which the mast shapes minimize the production of visible, electro-optic, infrared and radar cross section wake signatures produced by water surface piercing masts...
Energy Technology Data Exchange (ETDEWEB)
Dubrovsky, V. G.; Topovsky, A. V. [Novosibirsk State Technical University, Karl Marx prosp. 20, Novosibirsk 630092 (Russian Federation)
2013-03-15
New exact solutions, nonstationary and stationary, of Veselov-Novikov (VN) equation in the forms of simple nonlinear and linear superpositions of arbitrary number N of exact special solutions u{sup (n)}, n= 1, Horizontal-Ellipsis , N are constructed via Zakharov and Manakov {partial_derivative}-dressing method. Simple nonlinear superpositions are represented up to a constant by the sums of solutions u{sup (n)} and calculated by {partial_derivative}-dressing on nonzero energy level of the first auxiliary linear problem, i.e., 2D stationary Schroedinger equation. It is remarkable that in the zero energy limit simple nonlinear superpositions convert to linear ones in the form of the sums of special solutions u{sup (n)}. It is shown that the sums u=u{sup (k{sub 1})}+...+u{sup (k{sub m})}, 1 Less-Than-Or-Slanted-Equal-To k{sub 1} < k{sub 2} < Horizontal-Ellipsis < k{sub m} Less-Than-Or-Slanted-Equal-To N of arbitrary subsets of these solutions are also exact solutions of VN equation. The presented exact solutions include as superpositions of special line solitons and also superpositions of plane wave type singular periodic solutions. By construction these exact solutions represent also new exact transparent potentials of 2D stationary Schroedinger equation and can serve as model potentials for electrons in planar structures of modern electronics.
Hasegawa, Hideo
2009-07-01
Generalized Bose-Einstein and Fermi-Dirac distributions in nonextensive quantum statistics have been discussed by the maximum-entropy method (MEM) with the optimum Lagrange multiplier based on the exact integral representation [A. K. Rajagopal, R. S. Mendes, and E. K. Lenzi, Phys. Rev. Lett. 80, 3907 (1998)]. It has been shown that the (q-1) expansion in the exact approach agrees with the result obtained by the asymptotic approach valid for O(q-1). Model calculations have been made with a uniform density of states for electrons and with the Debye model for phonons. Based on the result of the exact approach, we have proposed the interpolation approximation to the generalized distributions, which yields results in agreement with the exact approach within O(q-1) and in high- and low-temperature limits. By using the four methods of the exact, interpolation, factorization, and superstatistical approaches, we have calculated coefficients in the generalized Sommerfeld expansion and electronic and phonon specific heats at low temperatures. A comparison among the four methods has shown that the interpolation approximation is potentially useful in the nonextensive quantum statistics. Supplementary discussions have been made on the (q-1) expansion of the generalized distributions based on the exact approach with the use of the un-normalized MEM, whose results also agree with those of the asymptotic approach.
Issues in Biological Shape Modelling
DEFF Research Database (Denmark)
Hilger, Klaus Baggesen
This talk reflects parts of the current research at informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations, modifications, and applications of the elements of constructing models of shape or appear......This talk reflects parts of the current research at informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations, modifications, and applications of the elements of constructing models of shape...
Ratkanthwar, Kedar
2013-01-01
An exact comb polyisoprene (PI) with three branches, with the middle branch having twice the molecular weight of the two other identical external branches, was synthesized by using anionic polymerization high vacuum techniques and appropriate chlorosilane chemistry. The synthetic approach involves (a) the selective replacement of the two chlorines of 4-(dichloromethylsilyl) diphenylethylene (DCMSDPE, key molecule) with identical PI chains by titration with PILi, (b) the addition of sec-BuLi to the double bond of DPE followed by the polymerization of isoprene from the newly created anionic site to form a 3-arm living star PI, (c) the selective replacement of the two chlorines of trichloromethylsilane with 3-arm star PI to form an H-shape intermediate, and (d) the replacement of the remaining chlorine of trichloromethylsilane by linear PI chains with double the molecular weight. All intermediate and final products were characterized via size exclusion chromatography, temperature gradient interaction chromatography and 1H-NMR spectroscopy. As expected, due to the inability to control the exact stoichiometry of the linking reactants, the main product (exact comb PI) is contaminated by a few by-products, despite the fact that anionic polymerization is the most efficient way to produce well-defined polymers. © 2013 The Royal Society of Chemistry.
Preparation of Small RNAs Using Rolling Circle Transcription and Site-Specific RNA Disconnection
Directory of Open Access Journals (Sweden)
Xingyu Wang
2015-01-01
Full Text Available A facile and robust RNA preparation protocol was developed by combining rolling circle transcription (RCT with RNA cleavage by RNase H. Circular DNA with a complementary sequence was used as the template for promoter-free transcription. With the aid of a 2′-O-methylated DNA, the RCT-generated tandem repeats of the desired RNA sequence were disconnected at the exact end-to-end position to harvest the desired RNA oligomers. Compared with the template DNA, more than 4 × 103 times the amount of small RNA products were obtained when modest cleavage was carried out during transcription. Large amounts of RNA oligomers could easily be obtained by simply increasing the reaction volume.
RNAthermsw: direct temperature simulations for predicting the location of RNA thermometers.
Directory of Open Access Journals (Sweden)
Alexander Churkin
Full Text Available The mechanism of RNA thermometers is a subject of growing interest. Also known as RNA thermosensors, these temperature-sensitive segments of the mRNA regulate gene expression by changing their secondary structure in response to temperature fluctuations. The detection of RNA thermometers in various genes of interest is valuable as it could lead to the discovery of new thermometers participating in fundamental processes such as preferential translation during heat-shock. RNAthermsw is a user-friendly webserver for predicting the location of RNA thermometers using direct temperature simulations. It operates by analyzing dotted figures generated as a result of a moving window that performs successive energy minimization folding predictions. Inputs include the RNA sequence, window size, and desired temperature change. RNAthermsw can be freely accessed at http://www.cs.bgu.ac.il/~rnathemsw/RNAthemsw/ (with the slash sign at the end. The website contains a help page with explanations regarding the exact usage.
Shape feature extraction and pattern recognition of sand particles and their impact
Shrestha, Bim P.; Suman, Sandip K.
2005-11-01
Sand deposition is the major problem of Nepalese rivers and it causes substantial impact to different sectors including hydropower generation, natural resource management, and many others. Due to the typical nature of soil and sand of Nepalese mountains it has almost become impossible to predict and manage the upcoming natural disasters and hazards. Sand deposition in rivers affect landslides, aquatic life of rives, environmental disorders and many others. Sedimentation causes not only disasters but also reduces the overall efficiency of hydropower generation units as well. A systematic approach to the problem has been identified in this work. Sand particles are collected from the erosion sensitive power plants and its digital images have been acquired. Software has been developed on MATLAB 6.5 platform to extract the exact shape of sand particles collected. These shapes have further been analyzed by artificial neural network. This network has been first trained for the known input and known output. After that it is trained for unknown input and known output. Finally these networks can recognize any shape given to it and gives the shape which is nearest to the seven predefined shape. The software is trained for seven types of shapes with shape number 1 to 7 in increasing number of sharp edges. The shape with shape number seven is having large number of sharp edges and considered as most erosive where as shape with shape number one is having round edges and considered as least erosive.
Engineering cooperative tecto-RNA complexes having programmable stoichiometries.
Novikova, Irina V; Hassan, Bachar H; Mirzoyan, Marina G; Leontis, Neocles B
2011-04-01
High affinity and specificity RNA-RNA binding interfaces can be constructed by combining pairs of GNRA loop/loop-receptor interaction motifs. These interactions can be fused using flexible four-way junction motifs to create divalent, self-assembling scaffolding units ('tecto-RNA') that have favorable properties for nanomedicine and other applications. We describe the design and directed assembly of tecto-RNA units ranging from closed, cooperatively assembling ring-shaped complexes of programmable stoichiometries (dimers, trimers and tetramers) to open multimeric structures. The novelty of this work is that tuning of the stoichiometries of self-assembled complexes is achieved by precise positioning of the interaction motifs in the monomer units rather than changing their binding specificities. Structure-probing and transmission electron microscopy studies as well as thermodynamic analysis support formation of closed cooperative complexes that are highly resistant to nuclease digestion. The present designs provide two helical arms per RNA monomer for further functionalization aims.
Shu, Dan; Li, Hui; Shu, Yi; Xiong, Gaofeng; Carson, William E; Haque, Farzin; Xu, Ren; Guo, Peixuan
2015-10-27
MicroRNAs play important roles in regulating the gene expression and life cycle of cancer cells. In particular, miR-21, an oncogenic miRNA is a major player involved in tumor initiation, progression, invasion and metastasis in several cancers, including triple negative breast cancer (TNBC). However, delivery of therapeutic miRNA or anti-miRNA specifically into cancer cells in vivo without collateral damage to healthy cells remains challenging. We report here the application of RNA nanotechnology for specific and efficient delivery of anti-miR-21 to block the growth of TNBC in orthotopic mouse models. The 15 nm therapeutic RNA nanoparticles contains the 58-nucleotide (nt) phi29 pRNA-3WJ as a core, a 8-nt sequence complementary to the seed region of miR-21, and a 39-nt epidermal growth factor receptor (EGFR) targeting aptamer for internalizing RNA nanoparticles into cancer cells via receptor mediated endocytosis. The RNase resistant and thermodynamically stable RNA nanoparticles remained intact after systemic injection into mice and strongly bound to tumors with little or no accumulation in healthy organs 8 h postinjection, and subsequently repressed tumor growth at low doses. The observed specific cancer targeting and tumor regression is a result of several key attributes of RNA nanoparticles: anionic charge which disallows nonspecific passage across negatively charged cell membrane; "active" targeting using RNA aptamers which increases the homing of RNA nanoparticles to cancer cells; nanoscale size and shape which avoids rapid renal clearance and engulfment by lung macrophages and liver Kupffer cells; favorable biodistribution profiles with little accumulation in healthy organs, which minimizes nonspecific side effects; and favorable pharmacokinetic profiles with extended in vivo half-life. The results demonstrate the clinical potentials of RNA nanotechnology based platform to deliver miRNA based therapeutics for cancer treatment.
Zeptosecond precision pulse shaping.
Köhler, Jens; Wollenhaupt, Matthias; Bayer, Tim; Sarpe, Cristian; Baumert, Thomas
2011-06-06
We investigate the temporal precision in the generation of ultrashort laser pulse pairs by pulse shaping techniques. To this end, we combine a femtosecond polarization pulse shaper with a polarizer and employ two linear spectral phase masks to mimic an ultrastable common-path interferometer. In an all-optical experiment we study the interference signal resulting from two temporally delayed pulses. Our results show a 2σ-precision of 300 zs = 300 × 10(-21) s in pulse-to-pulse delay. The standard deviation of the mean is 11 zs. The obtained precision corresponds to a variation of the arm's length in conventional delay stage based interferometers of 0.45 Å. We apply these precisely generated pulse pairs to a strong-field quantum control experiment. Coherent control of ultrafast electron dynamics via photon locking by temporal phase discontinuities on a few attosecond timescale is demonstrated.
DEFF Research Database (Denmark)
Stenholt, Rasmus; Madsen, Claus B.
2011-01-01
Enabling users to shape 3-D boxes in immersive virtual environments is a non-trivial problem. In this paper, a new family of techniques for creating rectangular boxes of arbitrary position, orientation, and size is presented and evaluated. These new techniques are based solely on position data......F) docking experiment against an existing technique, which requires the user to perform the rotation and scaling of the box explicitly. The precision of the users' box construction is evaluated by a novel error metric measuring the difference between two boxes. The results of the experiment strongly indicate...... that for precision docking of 9 DoF boxes, some of the proposed techniques are significantly better than ones with explicit rotation and scaling. Another interesting result is that the number of DoF simultaneously controlled by the user significantly influences the precision of the docking....
Magnetic Shape Memory Microactuators
Directory of Open Access Journals (Sweden)
Manfred Kohl
2014-11-01
Full Text Available By introducing smart materials in micro systems technologies, novel smart microactuators and sensors are currently being developed, e.g., for mobile, wearable, and implantable MEMS (Micro-electro-mechanical-system devices. Magnetic shape memory alloys (MSMAs are a promising material system as they show multiple coupling effects as well as large, abrupt changes in their physical properties, e.g., of strain and magnetization, due to a first order phase transformation. For the development of MSMA microactuators, considerable efforts are undertaken to fabricate MSMA foils and films showing similar and just as strong effects compared to their bulk counterparts. Novel MEMS-compatible technologies are being developed to enable their micromachining and integration. This review gives an overview of material properties, engineering issues and fabrication technologies. Selected demonstrators are presented illustrating the wide application potential.
Plant RNA binding proteins for control of RNA virus infection
Directory of Open Access Journals (Sweden)
Sung Un eHuh
2013-12-01
Full Text Available Plant RNA viruses have effective strategies to infect host plants through either direct or indirect interactions with various host proteins, thus suppressing the host immune system. When plant RNA viruses enter host cells exposed RNAs of viruses are recognized by the host immune system through processes such as siRNA-dependent silencing. Interestingly, some host RNA binding proteins have been involved in the inhibition of RNA virus replication, movement, and translation through RNA-specific binding. Host plants intensively use RNA binding proteins for defense against viral infections in nature. In this mini review, we will summarize the function of some host RNA binding proteins which act in a sequence-specific binding manner to the infecting virus RNA. It is important to understand how plants effectively suppresses RNA virus infections via RNA binding proteins, and this defense system can be potentially developed as a synthetic virus defense strategy for use in crop engineering.
Generation of siRNA Nanosheets for Efficient RNA Interference
Kim, Hyejin; Lee, Jae Sung; Lee, Jong Bum
2016-04-01
After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances.
Saha, Shambaditya; Hyman, Anthony A
2017-08-07
Several neurological disorders are linked to tandem nucleotide repeat expansion in the mutated gene. Jain and Vale (2017. Nature. https://doi.org/10.1038/nature22386) show that, above a pathological threshold repeat number, base pairing interactions drive phase separation of RNA into membrane-less gels, suggesting that RNA can scaffold the assembly of phase-separated compartments that sequester proteins/RNAs causing toxicity. © 2017 Saha and Hyman.
Chiba, Yasutaka
2017-09-01
Fisher's exact test is commonly used to compare two groups when the outcome is binary in randomized trials. In the context of causal inference, this test explores the sharp causal null hypothesis (i.e. the causal effect of treatment is the same for all subjects), but not the weak causal null hypothesis (i.e. the causal risks are the same in the two groups). Therefore, in general, rejection of the null hypothesis by Fisher's exact test does not mean that the causal risk difference is not zero. Recently, Chiba (Journal of Biometrics and Biostatistics 2015; 6: 244) developed a new exact test for the weak causal null hypothesis when the outcome is binary in randomized trials; the new test is not based on any large sample theory and does not require any assumption. In this paper, we extend the new test; we create a version of the test applicable to a stratified analysis. The stratified exact test that we propose is general in nature and can be used in several approaches toward the estimation of treatment effects after adjusting for stratification factors. The stratified Fisher's exact test of Jung (Biometrical Journal 2014; 56: 129-140) tests the sharp causal null hypothesis. This test applies a crude estimator of the treatment effect and can be regarded as a special case of our proposed exact test. Our proposed stratified exact test can be straightforwardly extended to analysis of noninferiority trials and to construct the associated confidence interval. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.