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Sample records for base pair step

  1. From one to N Cooper pairs, step by step

    International Nuclear Information System (INIS)

    We suggest a method for the analytical solution of Richardson equations. We reveal a connection between one-pair Cooper problem and BCS superconductivity. The ground state energy is controlled by binding energy of a Cooper pair. The superconducting gap is due to many-body effects induced by Pauli blocking. We extend the one-pair Cooper configuration towards Bardeen-Cooper-Schrieffer (BCS) model of superconductivity by adding one-by-one electron pairs to an energy layer, where a small attraction acts. To do it, we solve Richardson's equations analytically in the dilute limit of pairs on the one-Cooper pair scale. We find, through only keeping the first order term in this expansion, that the N correlated pair energy reads as the energy of N isolated pairs within a N(N-1) correction induced by the Pauli exclusion principle which tends to decrease the average pair binding energy when the pair number increases. Quite remarkably, extension of this first-order result to the dense regime gives the BCS condensation energy exactly. This leads us to suggest a different understanding of the BCS condensation energy with a pair number equal to the number of pairs feeling the potential and an average pair binding energy reduced by Pauli blocking to half the single Cooper pair energy - instead of the more standard but far larger superconducting gap.

  2. Report on Pairing-based Cryptography.

    Science.gov (United States)

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

  3. Arithmetic Operators for Pairing-Based Cryptography

    OpenAIRE

    Beuchat, Jean-Luc; Brisebarre, Nicolas; Detrey, Jérémie; Okamoto, Eiji

    2007-01-01

    Since their introduction in constructive cryptographic applications, pairings over (hyper)elliptic curves are at the heart of an ever increasing number of protocols. Software implementations being rather slow, the study of hardware architectures became an active research area. In this paper, we first study an accelerator for the eta_T pairing over F_3[x]/(x^97 + x^12 + 2). Our architecture is based on a unified arithmetic operator which performs addition, multiplication, and cubing over F_3^9...

  4. PLATYPUS : A STEP-based Integration Framework

    OpenAIRE

    Plantec, Alain; Ribaud, Vincent

    2006-01-01

    STEP is an ISO standard (ISO-10303) for the computer-interpretable representation and exchange of product data. Parts of STEP standardize conceptual structures and usage of information in generic or specific domains. The standardization process of these constructs is an approach which can be applied to a data-based integration. Platypus is a STEP-based meta-environment. From the data integration point of view, the STEP technology is primarily used for management. A key point is the automatic ...

  5. Density functional calculations of planar DNA base-pairs

    CERN Document Server

    Machado, M V T; Artacho, E; Sánchez-Portál, D; Soler, J M; Machado, Maider; Ordejon, Pablo; Artacho, Emilio; Sanchez-Portal, Daniel; Soler, Jose M.

    1999-01-01

    We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT scheme, which is specially suited for systems with large numbers of atoms. As a first step towards the study of large DNA systems, in this work: (i) We establish the reliability of the approximations of our method (including pseudopotentials and basis sets) for the description of the hydrogen-bonded base pairs, by comparing our results with those of former calculations. We show that the interaction energies at Hartree-Fock geometries are in very good agreement with those of second order M{ø}ller-Plesset (MP2) perturbation theory (the most accurate technique that can be applied at present for system of the sizes of the base-pairs). (ii) We perform DFT structural optimizations for the 30 different DNA base-pairs, only three of which had been previously studied with DFT. Our ...

  6. Step Counting Using Smartphone-Based Accelerometer

    Directory of Open Access Journals (Sweden)

    Ms. Najme Zehra Naqvi

    2012-05-01

    Full Text Available This paper presents a method for counting the number of steps taken by a user, while walking at any variable speed, using smartphone-based accelerometer. For this purpose, the steps are detected based on a relation between frequency of step, which varies inversely with speed of motion, and the magnitude of accelerometer signal. The pattern of the forward acceleration was observed to arrive at the final relation.

  7. Control of a Backward-Facing Step flow through vortex pairing and phase locking

    CERN Document Server

    Duriez, Thomas; Wesfreid, Jose Eduardo; Artana, Guillermo

    2014-01-01

    Many experimental and numerical studies report a large reduction of the recirculation bubble in Backward-Facing Step flows or airfoils in stall situation when excited at the natural shedding frequency $f_0$. Through a simple experiment using Dielectric Barrier Discharge actuator, we find a different result. For a given Reynolds number, the frequency of the perturbation is varied for a fixed duty-cycle dc = 27%. Through phase-averaging of Particle Image Velocimetry measurements, we show that the actuation creates a forced vortex which interacts with the natural shedding with a different phase velocity than the unforced one. The largest reduction of the recirculation bubble (-35%) is obtained in a very narrow frequency range around $0.73 f_0$ where early vortex pairing occurs between forced and unforced vortices. Phase averaging shows that in this case, the actuation clearly forces the vortex pairing in the shear layer. On the contrary, when the forcing frequency is higher, the shear layer behaves like an ampli...

  8. Treatment of pairing correlations based on the equations of motion for zero-coupled pair operators

    International Nuclear Information System (INIS)

    The pairing problem is treated by means of the equations of motion for zero-coupled pair operators. Exact equations for the seniority-v states of N particles are derived. These equations can be solved by a step-by-step procedure which consists of progressively adding pairs of particles to a core. The theory can be applied at several levels of approximation depending on the number of core states which are taken into account. Some numerical applications to the treatment of v = 0, v = 1, and v = 2 states in the Ni isotopes are performed. The accuracy of various approximations is tested by comparison with exact results. For the seniority-one and seniority-two problems it turns out that the results obtained from the first-order theory are very accurate, while those of higher order calculations are practically exact. Concerning the seniority-zero problem, a fifth-order calculation reproduces quite well the three lowest states

  9. Treatment of pairing correlations based on the equations of motion for zero-coupled pair operators

    Energy Technology Data Exchange (ETDEWEB)

    Andreozzi, F.; Covello, A.; Gargano, A.; Ye, L.J.; Porrino, A.

    1985-07-01

    The pairing problem is treated by means of the equations of motion for zero-coupled pair operators. Exact equations for the seniority-v states of N particles are derived. These equations can be solved by a step-by-step procedure which consists of progressively adding pairs of particles to a core. The theory can be applied at several levels of approximation depending on the number of core states which are taken into account. Some numerical applications to the treatment of v = 0, v = 1, and v = 2 states in the Ni isotopes are performed. The accuracy of various approximations is tested by comparison with exact results. For the seniority-one and seniority-two problems it turns out that the results obtained from the first-order theory are very accurate, while those of higher order calculations are practically exact. Concerning the seniority-zero problem, a fifth-order calculation reproduces quite well the three lowest states.

  10. An Identity Based Aggregate Signature from Pairings

    Directory of Open Access Journals (Sweden)

    Yike Yu

    2011-04-01

    Full Text Available An aggregate signature is a useful digital signature that supports aggregation: Given n signatures on n distinct messages from n distinct users, aggregate signature scheme is possible to aggregate all these signature into a single short signature. This single signature, along with the n original messages will convince any verifier that the n users did indeed sign the n original messages respectively (i.e., for i=1,...,n user i signed message  mi. In this paper, we propose an identity based aggregate signature scheme which requires constant pairing operations in the verification and the size of aggregate signature is independent of the number of signers. We prove that the proposed signature scheme is secure against existential forgery under adaptively chosen message and identity attack in the random oracle model assuming the intractability of the computational Diffie-Hellman problem.

  11. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies.

    Science.gov (United States)

    Hirao, Ichiro; Kimoto, Michiko; Yamashige, Rie

    2012-12-18

    Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the

  12. Generating photon pairs from a silicon microring resonator using an electronic step recovery diode for pump pulse generation

    CERN Document Server

    Savanier, Marc

    2016-01-01

    Generation of photon pairs from compact, manufacturable and inexpensive silicon (Si) photonic devices at room temperature may help develop practical applications of quantum photonics. An important characteristic of photon-pair generation is the two-photon joint spectral intensity (JSI), which describes the frequency correlations of the photon pair. In particular, heralded single-photon generation requires uncorrelated photons, rather than the highly anti-correlated photons conventionally obtained under continuous-wave (CW) pumping. Recent attempts to achieve such a factorizable JSI have used short optical pulses from mode-locked lasers, which are much more expensive and bigger table-top or rack-sized instruments compared to the Si microchip pair generator, dominate the cost and inhibit the miniaturization of the source. Here, we generate photon pairs from a Si microring resonator by using an electronic step-recovery diode to drive an electro-optic modulator which carves the pump light from a CW optical diode ...

  13. Ab Initio Molecular Dynamics with Explicit Solvent Reveals a Two-Step Pathway in the Frustrated Lewis Pair Reaction.

    Science.gov (United States)

    Pu, Maoping; Privalov, Timofei

    2015-12-01

    The role solvent plays in reactions involving frustrated Lewis pairs (FLPs)-for example, the stoichiometric mixture of a bulky Lewis acid and a bulky Lewis base-still remains largely unexplored at the molecular level. For a reaction of the phosphorus/boron FLP and dissolved CO2 gas, first principles (Born-Oppenheimer) molecular dynamics with explicit solvent reveals a hitherto unknown two-step reaction pathway-one that complements the concerted (one-step) mechanism known from the minimum-energy-path calculations. The rationalization of the discovered reaction pathway-that is, the stepwise formation of PC and OB bonds-is that the environment (typical organic solvents) stabilizes an intermediate which results from nucleophilic attack of the phosphorus Lewis base on CO2 . This finding is significant because presently the concerted reaction-path paradigm predominates in the rationalization of FLP reactivity. Herein we point out how to attain experimental proof of our results. PMID:26524999

  14. An ensemble of SVM classifiers based on gene pairs.

    Science.gov (United States)

    Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

    2013-07-01

    In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. PMID:23668348

  15. Looped out and perpendicular: Deformation of Watson–Crick base pair associated with actinomycin D binding

    OpenAIRE

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-01-01

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5′-GXC/CYG-5′ complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson–Crick X/Y base pairs are looped ou...

  16. Strong enhancement of vibrational relaxation by Watson-Crick base pairing.

    Science.gov (United States)

    Woutersen, Sander; Cristalli, Gloria

    2004-09-15

    We have studied the ultrafast dynamics of NH-stretch vibrational excitations in Watson-Crick base pairs consisting of adenine and uracil derivatives. To estimate the influence of the A:U hydrogen bonding on the vibrational dynamics, we have also studied the uracil derivative in monomeric form. The vibrational relaxation of the NH-stretching mode is found to occur much faster in the Watson-Crick base pair than in monomeric uracil. From the delay dependence of the transient vibrational spectra, it can be concluded that both in base-paired and monomeric uracil, the energy relaxation takes place in two steps, the first step being a rapid transfer of energy from the NH-stretching mode to an accepting mode, the second step the relaxation of this accepting mode. The transient spectra show evidence that in the base pair the hydrogen bond between the nucleobases acts as the accepting mode, and that the hydrogen bonding between the bases is responsible for the extremely fast vibrational relaxation in this system. PMID:15352831

  17. Strong enhancement of vibrational relaxation by Watson-Crick base pairing

    Science.gov (United States)

    Woutersen, Sander; Cristalli, Gloria

    2004-09-01

    We have studied the ultrafast dynamics of NH-stretch vibrational excitations in Watson-Crick base pairs consisting of adenine and uracil derivatives. To estimate the influence of the A:U hydrogen bonding on the vibrational dynamics, we have also studied the uracil derivative in monomeric form. The vibrational relaxation of the NH-stretching mode is found to occur much faster in the Watson-Crick base pair than in monomeric uracil. From the delay dependence of the transient vibrational spectra, it can be concluded that both in base-paired and monomeric uracil, the energy relaxation takes place in two steps, the first step being a rapid transfer of energy from the NH-stretching mode to an accepting mode, the second step the relaxation of this accepting mode. The transient spectra show evidence that in the base pair the hydrogen bond between the nucleobases acts as the accepting mode, and that the hydrogen bonding between the bases is responsible for the extremely fast vibrational relaxation in this system.

  18. DNA pairing is an important step in the process of targeted nucleotide exchange

    OpenAIRE

    Drury, Miya D.; Kmiec, Eric B.

    2003-01-01

    Modified single-stranded DNA oligonucleotides can direct the repair of genetic mutations in yeast, plant and mammalian cells. The mechanism by which these molecules exert their effect is being elucidated, but the first phase is likely to involve the homologous alignment of the single strand with its complementary sequence in the target gene. In this study, we establish the importance of such DNA pairing in facilitating the gene repair event. Oligonucleotide-directed repair occurs at a low fre...

  19. Attribute pair-based visual recognition and memory.

    Directory of Open Access Journals (Sweden)

    Masahiko Morita

    Full Text Available BACKGROUND: In the human visual system, different attributes of an object, such as shape, color, and motion, are processed separately in different areas of the brain. This raises a fundamental question of how are these attributes integrated to produce a unified perception and a specific response. This "binding problem" is computationally difficult because all attributes are assumed to be bound together to form a single object representation. However, there is no firm evidence to confirm that such representations exist for general objects. METHODOLOGY/PRINCIPAL FINDINGS: Here we propose a paired-attribute model in which cognitive processes are based on multiple representations of paired attributes. In line with the model's prediction, we found that multiattribute stimuli can produce an illusory perception of a multiattribute object arising from erroneous integration of attribute pairs, implying that object recognition is based on parallel perception of paired attributes. Moreover, in a change-detection task, a feature change in a single attribute frequently caused an illusory perception of change in another attribute, suggesting that multiple pairs of attributes are stored in memory. CONCLUSIONS/SIGNIFICANCE: The paired-attribute model can account for some novel illusions and controversial findings on binocular rivalry and short-term memory. Our results suggest that many cognitive processes are performed at the level of paired attributes rather than integrated objects, which greatly facilitates the binding problem and provides simpler solutions for it.

  20. ID-Based Signature Scheme with Weil Pairing

    Directory of Open Access Journals (Sweden)

    Neetu Sharma

    2013-09-01

    Full Text Available Digital signature is an essential component in cryptography. Digital signaturesguarantee end-to-end message integrity and authentication information about the origin of a message. In this paper we propose a new identification based digital signature scheme with weil pairing. Also we analyze security and efficiency of our scheme. Security of our scheme is based on expressing the torsion point of curve into linear combination of its basis points; it is more complicated than solving ECDLP(Elliptic Curve Discrete Logarithm Problem. We claim that our new identification based digital signature scheme is more secure and efficient than the existing scheme of Islam et al(S. K. Hafizul Islam, G.P. Biswas, An Efficient and Provably-secure Digital signature Scheme based on Elliptic Curve Bilinear Pairings, Theoretical and Applied Informatics ISSN 18965334 Vol.24, no. 2, 2012, pp. 109 118 based on bilinear pairing.

  1. Calix[4]pyrrole-based ion pair receptors.

    Science.gov (United States)

    Kim, Sung Kuk; Sessler, Jonathan L

    2014-08-19

    Ion pair receptors, which are able to bind concurrently both a cation and an anion, often display higher selectivity and affinity for specific ion pairs than simple ion receptors capable of recognizing primarily either a cation or an anion. This enhancement in recognition function is attributable to direct or indirect cooperative interactions between cobound ions via electrostatic attractions between oppositely charged ions, as well as to positive allosteric effects. In addition, by virtue of binding the counterions of the targeted ion, ion pair receptors can minimize the solvation of the counterions, which can otherwise have a negative effect on the interactions between the receptors and the targeted ions. As a result of their more favorable interactions, ion pair receptors are attractive for use in applications, such as extraction and sensing, where control of the binding interactions is advantageous. In this Account, we illustrate this potential in the context of ion pair receptors based on the calix[4]pyrrole scaffold. Both simple ditopic ion pair receptors, containing sites for the recognition of a single anion and single cation, and so-called multitopic ion pair receptors will be discussed. The latter systems differ from conventional, so-called ditopic ion pair receptors in that they contain more than one binding site for a given targeted ion (e.g., a cation). This permits a level of selectivity and control over binding function not normally seen for simple ion or ion pair receptors containing one or two binding sites, respectively. Calix[4]pyrroles are macrocyclic compounds consisting of four pyrrole units linked via fully substituted sp(3) hybridized meso carbon atoms. They are effective receptors for Lewis basic anions (e.g., halides) in typical organic media and under certain conditions will recognize ion pairs containing charge diffuse cations, such as a small alkylammonium, imidazolium, or cesium cations. The calix[4]pyrrole framework is further

  2. Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries

    Science.gov (United States)

    Vidigal, Joana A.; Ventura, Andrea

    2015-01-01

    The CRISPR-Cas9 system is a powerful tool to edit eukaryotic genomes that has recently been adapted for functional screens. Several of its applications—including the disruption of genes using Cas9-nickase and the generation of large deletions—require co-expression of two distinct guide RNAs (gRNAs). However, the lack of experimental approaches to generate pools of paired gRNA vectors prevents these applications from being scalable. Here we report a simple, inexpensive, one-step method that allows for the rapid and efficient cloning of gRNA pairs into expression vectors. We show that this method can be used to generate pooled libraries and is therefore suitable for in vivo and in vitro functional screens. PMID:26278926

  3. The thermodynamics and kinetics of a nucleotide base pair

    Science.gov (United States)

    Wang, Yujie; Gong, Sha; Wang, Zhen; Zhang, Wenbing

    2016-03-01

    The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.

  4. Ultrafast dynamics in DNA base pairs following ultraviolet excitation.

    Science.gov (United States)

    Orr-Ewing, Andrew

    2015-03-01

    Photo-protective mechanisms in DNA are essential to maintain the integrity of the genetic code by preventing damage from absorption of solar ultraviolet (UV) radiation. We have used time-resolved infra-red (TRIR) spectroscopy to observe the dynamics of Watson-Crick nucleobase pairs following absorption of femtosecond UV laser pulses. The base pairs are prepared as nucleosides in solution, and photo-induced dynamics are probed in the carbonyl and N-H bond stretching regions using broadband IR pulses with picosecond time resolution. Results will be presented for the guanine-cytosine (G-C) base pair, contrasting the rapid recovery of ground-state products (the photo-protection pathway) with formation of other photoproducts which might represent photo-damage mechanisms. This work is a collaboration with the group of Prof F. Temps (Christian-Albrechts-Universitat zu Kiel). This research is supported by ERC Advanced Grant 290966 CAPRI.

  5. Free energy analysis and mechanism of base pair stacking in nicked DNA.

    Science.gov (United States)

    Häse, Florian; Zacharias, Martin

    2016-09-01

    The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner. PMID:27407106

  6. Theoretical analysis of noncanonical base pairing interactions in RNA molecules

    Indian Academy of Sciences (India)

    Dhananjay Bhattacharyya; Siv Chand Koripella; Abhijit Mitra; Vijay Babu Rajendran; Bhabdyuti Sinha

    2007-08-01

    Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their ‘away from equilibrium’ geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H…O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H…O/N and/or one C-H…O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.

  7. Social Networks-Based Adaptive Pairing Strategy for Cooperative Learning

    Science.gov (United States)

    Chuang, Po-Jen; Chiang, Ming-Chao; Yang, Chu-Sing; Tsai, Chun-Wei

    2012-01-01

    In this paper, we propose a grouping strategy to enhance the learning and testing results of students, called Pairing Strategy (PS). The proposed method stems from the need of interactivity and the desire of cooperation in cooperative learning. Based on the social networks of students, PS provides members of the groups to learn from or mimic…

  8. NEW ID-BASED GROUP SIGNATURE FROM PAIRINGS

    Institute of Scientific and Technical Information of China (English)

    Chen Xiaofeng; Zhang Fangguo; Kwangjo Kim

    2006-01-01

    We argue that traditional identity-based systems from pairings seem unsuitable for designing group signature schemes due to the problem of key escrow. In this paper we first propose new ID-based public key systems without trusted PKG (Private Key Generator) from bilinear pairings. In our new ID-based systems, if the dishonest PKG impersonates an honest user to communicate with others, the user can provide a proof of treachery of the PKG afterwards, which is similar to certificate-based systems. Therefore, our systems reach the Girault's trusted level 3. We then propose a group signature scheme under the new ID-based systems, the security and performance of which rely on the new systems. The size of the group public key and the length of the signature are independent on the numbers of the group.

  9. Waveguide-based OPO source of entangled photon pairs

    International Nuclear Information System (INIS)

    In this paper, we present a compact source of narrow-band energy-time-entangled photon pairs in the telecom regime based on a Ti-indiffused periodically poled lithium niobate (PPLN) waveguide resonator, i.e. a waveguide with end-face dielectric multi-layer mirrors. This is a monolithic doubly resonant optical parametric oscillator (OPO) far below threshold, which generates photon pairs by spontaneous parametric down-conversion (SPDC) at around 1560 nm with a 117 MHz (0.91 pm)-bandwidth. A coherence time of 2.7 ns is estimated by a time correlation measurement and a high quality of the entangled states is confirmed by a Bell-type experiment. Since highly coherent energy-time-entangled photon pairs in the telecom regime are suitable for long distance transmission and manipulation, this source is well suited to the requirements of quantum communication.

  10. Partition function and base pairing probabilities of RNA heterodimers

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2006-03-01

    Full Text Available Abstract Background RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. Results We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures. Availability RNAcofold is distributed as part of the Vienna RNA Package, http://www.tbi.univie.ac.at/RNA/. Contact Stephan H. Bernhart – berni@tbi.univie.ac.at

  11. Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

    Czech Academy of Sciences Publication Activity Database

    Dabkowska, I.; Gonzalez, H. V.; Jurečka, Petr; Hobza, Pavel

    2005-01-01

    Roč. 109, - (2005), s. 1131-1136. ISSN 1089-5639 R&D Projects: GA ČR(CZ) GA203/05/0009 Grant ostatní: IVF (XE) S-004-2003; KBN(PL) 4T09A01224 Institutional research plan: CEZ:AV0Z40550506 Keywords : base pairs * complete basis set * DNA Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.898, year: 2005

  12. Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.

    Science.gov (United States)

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-05-14

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition. PMID:12011426

  13. Looped out and perpendicular: Deformation of Watson–Crick base pair associated with actinomycin D binding

    Science.gov (United States)

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-01-01

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5′-GXC/CYG-5′ complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson–Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition. PMID:12011426

  14. Using an Isomorphic Problem Pair to Learn Introductory Physics: Transferring from a Two-step Problem to a Three-step Problem

    CERN Document Server

    Lin, Shih-Yin

    2016-01-01

    In this study, we examine introductory physics students' ability to perform analogical reasoning between two isomorphic problems which employ the same underlying physics principles but have different surface features. Three hundred and eighty two students from a calculus-based and an algebra-based introductory physics course were asked to learn from a solved problem provided and take advantage of what they learned from it to solve another isomorphic problem (which we call the quiz problem). The solved problem provided has two sub-problems while the quiz problem has three sub-problems, which is known to be challenging for introductory students from previous research. In addition to the solved problem, students also received extra scaffolding supports that were intended to help them discern and exploit the underlying similarities of the isomorphic solved and quiz problems. The results suggest that students had great difficulty in transferring what they learned from a 2-step problem to a 3-step problem. Although...

  15. The effect of base pair mismatch on DNA strand displacement

    CERN Document Server

    Broadwater, Bo

    2016-01-01

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single base pair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration, and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term, the concurrent displacement model, and used the first passage t...

  16. Lewis pair polymerization by classical and frustrated Lewis pairs: Acid, base and monomer scope and polymerization mechanism

    KAUST Repository

    Zhang, Yuetao

    2012-01-01

    Classical and frustrated Lewis pairs (LPs) of the strong Lewis acid (LA) Al(C 6F 5) 3 with several Lewis base (LB) classes have been found to exhibit exceptional activity in the Lewis pair polymerization (LPP) of conjugated polar alkenes such as methyl methacrylate (MMA) as well as renewable α-methylene-γ-butyrolactone (MBL) and γ-methyl- α-methylene-γ-butyrolactone (γ-MMBL), leading to high molecular weight polymers, often with narrow molecular weight distributions. This study has investigated a large number of LPs, consisting of 11 LAs as well as 10 achiral and 4 chiral LBs, for LPP of 12 monomers of several different types. Although some more common LAs can also be utilized for LPP, Al(C 6F 5) 3-based LPs are far more active and effective than other LA-based LPs. On the other hand, several classes of LBs, when paired with Al(C 6F 5) 3, can render highly active and effective LPP of MMA and γ-MMBL; such LBs include phosphines (e.g., P tBu 3), chiral chelating diphosphines, N-heterocyclic carbenes (NHCs), and phosphazene superbases (e.g., P 4- tBu). The P 4- tBu/Al(C 6F 5) 3 pair exhibits the highest activity of the LP series, with a remarkably high turn-over frequency of 9.6 × 10 4 h -1 (0.125 mol% catalyst, 100% MMA conversion in 30 s, M n = 2.12 × 10 5 g mol -1, PDI = 1.34). The polymers produced by LPs at RT are typically atactic (P γMMBL with ∼47% mr) or syndio-rich (PMMA with ∼70-75% rr), but highly syndiotactic PMMA with rr ∼91% can be produced by chiral or achiral LPs at -78 °C. Mechanistic studies have identified and structurally characterized zwitterionic phosphonium and imidazolium enolaluminates as the active species of the current LPP system, which are formed by the reaction of the monomer·Al(C 6F 5) 3 adduct with P tBu 3 and NHC bases, respectively. Kinetic studies have revealed that the MMA polymerization by the tBu 3P/ Al(C 6F 5) 3 pair is zero-order in monomer concentration after an initial induction period, and the polymerization

  17. Graphene/Lead (Pb)-based Cooper -pair splitter

    Science.gov (United States)

    Borzenets, Ivan; Shimazaki, Yuya; Jones, Gareth; Russo, Saverio; Yamamoto, Michihisa; Tarucha, Seigo

    2015-03-01

    We have fabricated a Cooper-pair splitter device based on a superconductor- two normal leads, ``Y'' shaped junction with graphene as the base material. (Compared to nanowire-based devices, the two dimensional nature of graphene allows for the normal leads to be placed arbitrarily close together and in a non-parallel arrangement.) The superconducting lead is created by contacting graphene with lead (Pb), thus inducing a supercurrent via the proximity effect. The normal metal leads are patterned into quantum dots by etching nano-constrictions with self-aligned side gates. Quantum dots strongly suppress two electron processes, allowing only one electron to pass at a time. Thus, the Cooper-pair splitting efficiency is enhanced as the split electrons must necessarily tunnel through different quantum dots. Using a DC measurement we have demonstrated enhanced currents though both normal leads when both quantum dots are in resonance and the input lead is in the superconducting regime: demonstrating Cooper-pair splitting. (This is contrary to the classical regime of currents though a three resistor junction.) Shot noise measurements would demonstrate that the split electrons tunnel at the same time. Demonstrating that the split electrons have opposite spin would show that such a device could be used as a source of quantum entangled electrons.

  18. Coherent Pair Production in Deformed Crystals with a Complex Base

    Science.gov (United States)

    Mkrtchyan, A. R.; Saharian, A. A.; Parazian, V. V.

    We investigate the coherent electron-positron pair creation by high-energy photons in a periodically deformed single crystal with a complex base. The formula for the corresponding differential cross-section is derived for an arbitrary deformation field. The conditions are specified under which the influence of the deformation is considerable. The case is considered in detail when the photon enters into the crystal at small angles with respect to a crystallographic axis. The results of the numerical calculations are presented for SiO2 single crystal and Moliere parametrization of the screened atomic potentials in the case of the deformation field generated by the acoustic wave of S type. In dependence of the parameters, the presence of deformation can either enhance or reduce the pair creation cross-section. This can be used to control the parameters of the positron sources for storage rings and colliders.

  19. Coherent pair production in deformed crystals with a complex base

    CERN Document Server

    Mkrtchyan, A R; Saharian, A A

    2006-01-01

    We investigate the coherent electron-positron pair creation by high-energy photons in a periodically deformed single crystal with a complex base. The formula for the corresponding differential cross-section is derived for an arbitrary deformation field. The conditions are specified under which the influence of the deformation is considerable. The case is considered in detail when the photon enters into the crystal at small angles with respect to a crystallographic axis. The results of the numerical calculations are presented for $\\mathrm{SiO}_{2}$ single crystal and Moliere parametrization of the screened atomic potentials in the case of the deformation field generated by the acoustic wave of $S$ type. In dependence of the parameters, the presence of deformation can either enhance or reduce the pair creation cross-section. This can be used to control the parameters of the positron sources for storage rings and colliders.

  20. An ID-based Blind Signature Scheme from Bilinear Pairings

    Directory of Open Access Journals (Sweden)

    B.Umaprasada Rao

    2010-03-01

    Full Text Available Blind signatures, introduced by Chaum, allow a user to obtain a signature on a message without revealing any thing about the message to the signer. Blind signatures play on important role in plenty of applications such as e-voting, e-cash system where anonymity is of great concern. Identity based(ID-based public key cryptography can be a good alternative for certified based public key setting, especially when efficient key management and moderate security are required. In this paper, we propose an ID-based blind signature scheme from bilinear pairings. The proposed scheme is based on the Hess ID- based digital signature scheme. Also we analyze security and efficiency of the proposed scheme.

  1. Physics of base-pairing dynamics in DNA

    Science.gov (United States)

    Manghi, Manoel; Destainville, Nicolas

    2016-05-01

    As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

  2. Single base pair mutation analysis by PNA directed PCR clamping

    DEFF Research Database (Denmark)

    Ørum, H.; Nielsen, P.E.; Egholm, M.; Berg, R.H.; Buchardt, O.; Stanley, C.

    1993-01-01

    A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and bind to their complementary nucleic acid sequences with higher thermal stability and specificity...... than the corresponding deoxyribooligonucleotides and that they cannot function as primers for DNA polymerases. We show that a PNA/DNA complex can effectively block the formation of a PCR product when the PNA is targeted against one of the PCR primer sites. Furthermore, we demonstrate that this blockage...... allows selective amplification/suppression of target sequences that differ by only one base pair. Finally we show that PNAs can be designed in such a way that blockage can be accomplished when the PNA target sequence is located between the PCR primers....

  3. Nonclassically paired photons from sources based on cold atoms

    Science.gov (United States)

    Głódź, Małgorzata; Janowicz, Maciej; Kowalski, Krzysztof; Szonert, Jerzy

    2015-01-01

    In this short review some essentials concerning creation and testing of nonclassically correlated photons (biphotons) are given. In the introduction we remind the role which the experimentally produced entangled states have been playing for the foundations of the quantum physics, by witnessing against the model of local hidden variables. The well established sources of biphotons are based on spontaneous parametric down conversion in nonlinear crystals. A popular source with two BBO crystals is described, which generates pairs of photons nearly maximally entangled in polarization. Crystalbased sources rely on intrinsically broadband transitions, therefore thus produced biphotons are also broadband. Additional efforts (like applying optical cavities) are needed to reach narrowband biphotons which would comply with the requirements of some implementations in the quantum communication science. The topical issue of our article is a review of another, more recent approaches based on narrowband transitions between levels in cold atoms. Such method provides naturally narrowband biphotons. First, the principles are given of an atomic source of nonclassically paired photons, which is operated in a pulsed write-read mode. Such source is based on two separated in time Raman transitions triggered successively in two Λ-schemes. Next, cw-mode sources based (mainly) on spontaneous four wave mixing process (SFWM) are presented in a generic four-level scheme. Some underlying physics is sketched and profiles of biphoton correlation functions in the time domain are explained. Among other presented SFWM sources, one proves in testing high degree entanglement of generated biphotons, both in time-frequency and polarization (hyperentanglement).

  4. Paired structures and other opposite-based models

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco, Camilo; Gómez, Daniel;

    2015-01-01

    In this paper we present a new class of fuzzy sets, paired fuzzy sets, that tries to overcome any conflict between families of fuzzy sets that share a main characteristic: that they are generated from two basic opposite fuzzy sets. Hence, the first issue is to formalize the notion of opposition, ...... viewed as a particular paired structure when the classical fuzzy negation is considered; on the other hand, the relationship of this model with bipolarity is reconsidered from our paired view....

  5. Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies.

    Science.gov (United States)

    Roy, Ashim; Panigrahi, Swati; Bhattacharyya, Malyasri; Bhattacharyya, Dhananjay

    2008-03-27

    The importance of non-Watson-Crick base pairs in the three-dimensional structure of RNA is now well established. The structure and stability of these noncanonical base pairs are, however, poorly understood. We have attempted to understand structural features of 33 frequently occurring base pairs using density functional theory. These are of three types, namely (i) those stabilized by two or more polar hydrogen bonds between the bases, (ii) those having one polar and another C-H...O/N type interactions, and (iii) those having one H-bond between the bases and another involving one of the sugars linked to the bases. We found that the base pairs having two polar H-bonds are very stable as compared to those having one C-H...O/N interaction. Our quantitatively analysis of structures of these optimized base pairs indicates that they possess a different amount of nonplanarity with large propeller or buckle values as also observed in the crystal structures. We further found that geometry optimization does not modify the hydrogen-bonding pattern, as values of shear and open angle of the base pairs remain conserved. The structures of initial crystal geometry and final optimized geometry of some base pairs having only one polar H-bond and a C-H...O/N interaction, however, are significantly different, indicating the weak nature of the nonpolar interaction. The base pair flexibility, as measured from normal-mode analysis, in terms of the intrinsic standard deviations of the base pair structural parameters are in conformity with those calculated from RNA crystal structures. We also noticed that deformation of a base pair along the stretch direction is impossible for all of the base pairs, and movements of the base pairs along shear and open are also quite restricted. The base pair opening mode through alteration of propeller or buckle is considerably less restricted for most of the base pairs. PMID:18318519

  6. Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

    Indian Academy of Sciences (India)

    Purshotam Sharma; Abhijit Mitra; Sitansh Sharma; Harjinder Singh

    2007-09-01

    The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G∗∗ level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.

  7. Step-count promotion through a school-based intervention.

    Science.gov (United States)

    Shore, Stuart M; Sachs, Michael L; DuCette, Joseph P; Libonati, Joseph R

    2014-08-01

    The purpose was to determine the effects of a school-based pedometer intervention (SBPI) on daily accrued steps, academic performance, attendance, tardiness, and fitness performance in middle school students. Students from one, public middle school were assigned to a control (n = 46) or a 6-week SBPI (n = 46). Both groups recorded daily accrued pedometer steps. Grade point average (GPA), tardiness, absenteeism, and physical fitness scores were assessed. While baseline daily accrued step-counts were similar (p = NS), SBPI significantly increased daily accrued step-counts versus control (p academic performance increased in both groups, while SBPI had reduced tardiness (p performance decreased from pre- to postintervention in both groups. These data suggest that SBPI can increase physical activity levels and decrease tardiness in middle school students, without translating into short-term improvements in academic or physical fitness performance. PMID:23606186

  8. Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.

    Science.gov (United States)

    Sponer, Judit E; Spacková, Nad'a; Kulhanek, Petr; Leszczynski, Jerzy; Sponer, Jirí

    2005-03-17

    Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions. PMID:16838999

  9. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general

  10. SWITCHED-CAPACITOR BASED STEP-DOWN RESONANT CONVERTERS

    Institute of Scientific and Technical Information of China (English)

    Y.P.B.Yeung; K.W.E.Cheng; K.K.Law

    2001-01-01

    A family of switched-capacitor based resonant converters is present.All converters are in step-downmode.By adding different number of switched-capacitor cells,different output voltage conversion ratio can beobtained.All switching devices in the converters operate under zero-current switching.Both high frequencyoperations and high efficiency are possible.

  11. Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs

    CERN Document Server

    Wu, Yuan-Yan; Zhang, Xi; Tan, Zhi-Jie

    2015-01-01

    Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5 to 50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ~6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ~29nm to ~45nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ~6 bps at each helix end have...

  12. Raising the barrier for photoinduced DNA charge injection with a cyclohexyl artificial base pair.

    Science.gov (United States)

    Singh, Arunoday P N; Harris, Michelle A; Young, Ryan M; Miller, Stephen A; Wasielewski, Michael R; Lewis, Frederick D

    2015-01-01

    The effects of an artificial cyclohexyl base pair on the quantum yields of fluorescence and dynamics of charge separation and charge recombination have been investigated for several synthetic DNA hairpins. The hairpins possess stilbenedicarboxamide, perylenediimide, or naphthalenediimide linkers and base-paired stems. In the absence of the artificial base pair hole injection into both adenine and guanine purine bases is exergonic and irreversible, except in the case of stilbene with adenine for which it is slightly endergonic and reversible. Insertion of the artificial base pair renders hole injection endergonic or isoergonic except in the case of the powerful naphthalene acceptor for which it remains exergonic. Both hole injection and charge recombination are slower for the naphthalene acceptor in the presence of the artificial base pair than in its absence. The effect of an artificial base pair on charge separation and charge recombination in hairpins possessing stilbene and naphthalene acceptor linkers and a stilbenediether donor capping group has also been investigated. In the case of the stilbene acceptor-stilbene donor capped hairpins photoinduced charge separation across six base pairs is efficient in the absence of the artificial base pair but does not occur in its presence. In the case of the naphthalene acceptor-stilbene donor capped hairpins the artificial base pair slows but does not stop charge separation and charge recombination, leading to the formation of long-lived charge separated states. PMID:26442603

  13. Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

    OpenAIRE

    Hisae Tateishi-Karimata; Miki Nakano; Naoki Sugimoto

    2014-01-01

    The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stabi...

  14. Predicting the Mechanism and Kinetics of the Watson-Crick to Hoogsteen Base Pairing Transition

    NARCIS (Netherlands)

    J. Vreede; P.G. Bolhuis; D.W.H. Swenson

    2016-01-01

    DNA duplexes predominantly contain Watson-Crick (WC) base pairs. Yet, a non-negligible number of base pairs converts to the Hoogsteen (HG) hydrogen bonding pattern, involving a 180° rotation of the purine base relative to Watson-Crick. These WC to HG conversions alter the conformation of DNA, and ma

  15. Roles of ion pairing on electroreduction of carbon dioxide based on imidazolium-based salts

    International Nuclear Information System (INIS)

    Highlights: • The significant electrocatalytic effects of imidazolium salts are due to a strong ion-pairing. • DFT calculation predicts the ion pair [BMIM+][CO2.−] conformation. • The extent of ion-pairing decreases with increasing the size of the alkyl substituent. - Abstract: The roles of ion pairing on CO2 electroreduction involving imidazolium-based salts are explored on an Ag electrode in a DMF solution. The electroreductive behaviours of CO2 and the IR results establish the dominant role of the cation of imidazolium-based salts in CO2 electrocatalytic reduction process. Density functional theory (DFT) calculations predict that the ion pair formation is mainly driven by the attraction of the four nearby and positively charged hydrogen atoms which are at the C2, N1 and N3-positions of an imidazolium cation for the negatively charged oxygen atoms in the CO2.− species. The electrostatic interaction between an imidazolium cation and the CO2.− species decreases with increasing the size of the alkyl substituent at the N1-position of that imidazolium cation

  16. SIMULATION COMPARISON AND STEPS TO DO SIMULATION BY AUTOLISP (AUTOCAD) AND PRO-E FOR GEAR PAIR.

    OpenAIRE

    PRATIK A. SOLANKI; KALPESH P. PATEL; J.R.LIMBACHIYA

    2012-01-01

    This paper gives the basic idea of steps required for doing simulation in AutoCAD with the help of AutoLisp and Pro-Engineering. It includes the comparison between both methods. AutoCAD 2005 and Pro-E wildfireV4.0 used as software to do simulation (Animation).

  17. Tunnel Conductance of Watson-Crick Nucleoside-Base Pairs from Telegraph Noise

    OpenAIRE

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-01-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base-pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive ...

  18. Key technology of ship product data exchange based on STEP

    Institute of Scientific and Technical Information of China (English)

    SHI Dong-yan; YANG Jing-tong; QIU Chang-hua; XUE Kai

    2005-01-01

    In this paper, in order to implement the share and exchange of the ship product data, a new kind of global function model is established. By researching on the development and trend of the application of ship STEP (standard for the exchange of product model data) standards, the AIM (application interpreted model) of AP216 is developed and improved as an example, aiming at the characteristics and practical engineering of ship industry in our country. The data exchange interfaces are formed based on STEP in the CAD/CAM for the ship by all function modules and shared databases under the global function model. The share and exchange of all information and data are solved in the design, manufacture and all life-cycle of ship products among different computer application systems. The research work makes foundation for the ship industry informatization.

  19. Conducting Task-Based Interviews with Pairs of Children: Consensus, Conflict, Knowledge Construction and Turn Taking

    Science.gov (United States)

    Houssart, Jenny; Evens, Hilary

    2011-01-01

    This article explores theoretical and methodological issues associated with task-based interviews conducted with pairs of children. We explore different approaches to interviews from sociological, psychological and subject-based perspectives. Our interviews, concerning mathematical questions and carried out with pairs of 10 and 11-year-olds, are…

  20. A novel pseudo-complementary PNA G-C base pair

    DEFF Research Database (Denmark)

    Olsen, Anne G.; Dahl, Otto; Petersen, Asger Bjørn; Nielsen, John; Nielsen, Peter E.

    2011-01-01

    Pseudo-complementary oligonucleotide analogues and mimics provide novel opportunities for targeting duplex structures in RNA and DNA. Previously, a pseudo-complementary A-T base pair has been introduced. Towards sequence unrestricted targeting, a pseudo-complementary G-C base pair consisting of the...

  1. Development of artificial nucleic acid that recognizes a CG base pair in triplex DNA formation.

    Science.gov (United States)

    Hari, Yoshiyuki

    2013-01-01

    An oligonucleotide that can form a triplex with double-stranded DNA is called a triplex-forming oligonucleotide (TFO). TFOs have gained considerable attention because of their potential as gene targeting tools. However, triplex DNA formation involves inherent problems for practical use. The most important problem is that natural nucleotides in TFO do not have sufficient affinity and base pair-selectivity to pyrimidine-purine base pair, like a CG or TA base pair, within dsDNA. This suggests that dsDNA region including a CG or TA base pair cannot be targeted. Therefore, artificial nucleotides, especially with non-natural nucleobases, capable of direct recognition of a CG or TA base pair via hydrogen bond formation have been developed; however, nucleotides with better selectivity and stronger affinity are necessary for implementing this dsDNA-targeting technology using TFOs. Under such a background, we considered that facile and efficient synthesis of various nucleobase derivatives in TFOs would be useful for finding an ideal nucleobase for recognition of a CG or TA base pair because detailed and rational exploration of nucleobase structures is facilitated. Recently, to develop a nucleobase recognizing a CG base pair, we have used post-elongation modification, i.e., modification after oligonucleotide synthesis, for the facile synthesis of nucleobase derivatives. This review mainly summarizes our recent findings on the development of artificial nucleobases and nucleotides for recognition of a CG base pair in triplexes formed between dsDNA and TFOs. PMID:24189561

  2. The Impact of a Peer-Learning Agent Based on Pair Programming in a Programming Course

    Science.gov (United States)

    Han, Keun-Woo; Lee, EunKyoung; Lee, YoungJun

    2010-01-01

    This paper analyzes the educational effects of a peer-learning agent based on pair programming in programming courses. A peer-learning agent system was developed to facilitate the learning of a programming language through the use of pair programming strategies. This system is based on the role of a peer-learning agent from pedagogical and…

  3. Fingerprint Identification Using SIFT-Based Minutia Descriptors and Improved All Descriptor-Pair Matching

    Directory of Open Access Journals (Sweden)

    Jiuqiang Han

    2013-03-01

    Full Text Available The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1 the similar patterns of parallel ridges; and (2 high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM, is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements.

  4. Theory of tunneling across hydrogen-bonded base pairs for DNA recognition and sequencing

    Science.gov (United States)

    Lee, Myeong H.; Sankey, Otto F.

    2009-05-01

    We present the results of first-principles calculations for the electron tunnel current through hydrogen-bonded DNA base pairs and for (deoxy)nucleoside-nucleobase pairs. Electron current signals either through a base pair or through a deoxynucleoside-nucleobase pair are a potential mechanism for recognition or identification of the DNA base on a single-stranded DNA polymer. Four hydrogen-bonded complexes are considered: guanine-cytosine, diaminoadenine-thymine, adenine-thymine, and guanine-thymine. First, the electron tunneling properties are examined through their complex band structure (CBS) and the metal contact’s Fermi-level alignment. For gold contacts, the metal Fermi level lies near the highest occupied molecular orbital for all DNA base pairs. The decay constant determined by the complex band structure at the gold Fermi level shows that tunnel current decays more slowly for base pairs with three hydrogen bonds (guanine-cytosine and diaminoadenine-thymine) than for base pairs with two hydrogen bonds (adenine-thymine and guanine-thymine). The decay length and its dependence on hydrogen-bond length are examined. Second, the conductance is computed using density functional theory Green’s-function scattering methods and these results agree with estimates made from the tunneling decay constant obtained from the CBS. Changing from a base pair to a deoxynucleoside-nucleobase complex shows a significant decrease in conductance. It also becomes difficult to distinguish the current signal by only the number of hydrogen bonds.

  5. A Project Risk Ranking Approach Based on Set Pair Analysis

    Institute of Scientific and Technical Information of China (English)

    Gao Feng; Chen Yingwu

    2006-01-01

    Set Pair Analysis (SPA) is a new methodology to describe and process system uncertainty. It is different from stochastic or fuzzy methods in reasoning and operation, and it has been applied in many areas recently. In this paper, the application of SPA in risk ranking is presented, which includes review of risk ranking, introduction of Connecting Degree (CD) that is a key role in SPA., Arithmetic and Tendency Grade (TG) of CDs, and a risk ranking approach proposed. Finally a case analysis is presented to illustrate the reasonability of this approach. It is found that this approach is very convenient to operate, while the ranking result is more comprehensible.

  6. Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-08-01

    Full Text Available The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I and 2'-deoxyribo-2,6-diaminopurine (D as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G•C > D•T ≈ I•C > A•T > G•T > I•T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

  7. INSURANCE CONTRACTS BASED ON INDICES, A STEP TOWARDS WEATHER DERIVATIVES

    Directory of Open Access Journals (Sweden)

    Boton#537; Horia-Mircea

    2012-07-01

    Full Text Available The aim of this paper is to analyze the methodology of structuring an index based insurance contract. The weather has always been the biggest risk factor in agriculture, affecting all aspects of the economic sectors. In the developed countries of the world, there is a significant number of rain-dependent farmers. To gain insight into potential growth of weather markets in developed countries, we are going to analyze the case of India. In 2003, Basix microfinance company in Hyderabad and ICICI Lombard insurance company in Mumbai have launched a pilot weather insurance, which had as basic index phenomena for Mahahbubnagar district of Andhra Pradesh. Further detail can be found in the full-paper. In the paper we will enumerate the appropriate steps in the determining the necessity for the use of index based insurances. The appropriate stages are making a comparison between index based insurances and traditional insurances, and optimizing the use of weather indices in insurance contracts. In order for the contracts to be successful , the recommended steps are : developing a product based in an index, and after the we need to plan and implement the contract. In planning the implementation it is needed that we: identify the risks and areas where they manifest, then identify the best distribution channels; after this we can develop a prototype of the contract. The next step would the testing of the negotiability of the contract, then the contract is opened to be finalized. After this the index based insurance contract can be introduced to the market, but the program needs monitoring in order to insure its successfulness. In order for the market and contract to grow the necessary step are: having access to the necessary meteorological data, determine the optimal way of integrating the contract in the existing economical context, technical feasibility, property rights and the legal framework. In the end, the aim is to familiarize the literacy field and

  8. A Step Response Based Mixed-Signal BIST Approach

    Science.gov (United States)

    Walker, Alvernon

    2001-01-01

    A new Mixed-Signal Built-in Self-test approach that is based upon the step response of a reconfigurable (or multifunction) analog block is presented in this paper. The technique requires the overlapping step response of the Circuit Under Test (CUT) for two circuit configurations. Each configuration can be realized by changing the topology of the CUT or by sampling two CUT nodes with differing step responses. The technique can effectively detect both soft and hard faults and does not require an analog-to-digital converter (ADC) and/or digital-to-analog converter( DAC). It also does not require any precision voltage sources or comparators. The approach does not require any additional analog circuits to realize the test signal generator and a two input analog multiplexer for CUT test node sampling. The paper is concluded with the application of the proposed approach to a circuit found in the work of Epstein et a1 and two ITC 97 analog benchmark circuits.

  9. Covering All the Bases in Genetics: Simple Shorthands and Diagrams for Teaching Base Pairing to Biology Undergraduates

    Directory of Open Access Journals (Sweden)

    Sergei Kuchin

    2011-03-01

    Full Text Available Explaining base pairing is an important element in teaching undergraduate genetics. I propose a teaching approach that aims to close the gap between the mantra “A pairs with T, and G pairs with C” and the “intimidating” chemical diagrams. The approach offers a set of simple “shorthands” for the key bases that can be used to quickly deduce all canonical and wobble pairs that the students need to know. The approach can be further developed to analyze mutagenic mismatch pairing.

  10. THE CONSTRUCTIONS OF ALMOST BINARY SEQUENCE PAIRS WITH THREE-LEVEL CORRELATION BASED ON CYCLOTOMY

    Institute of Scientific and Technical Information of China (English)

    Peng Xiuping; Xu Chengqian

    2012-01-01

    In this paper,a new class of almost binary sequence pair with a single zero element is presented.The almost binary sequence pairs with three-level correlation are constructed based on cyclotomic numbers of order 2,4,and 6.Most of them have good correlation and balance property,whose maximum nontrivial correlation magnitudes are 2 and the difference between the numbers of occurrence of +1's and -1's are 0 or 1.In addition,the corresponding binary sequence pairs are investigated as well and we can also get some kinds of binary sequence pairs with optimum balance and good correlation.

  11. Thermodynamics of the formation of Ag(I)-mediated azole base pairs in DNA duplexes.

    Science.gov (United States)

    Schweizer, Kristina; Léon, J Christian; Ravoo, Bart Jan; Müller, Jens

    2016-07-01

    Isothermal titration calorimetry was applied to determine the thermodynamic parameters for the specific binding of Ag(I) ions to a series of DNA duplexes comprising Im:Im or Tr:Tr mispairs to form metal-mediated Im-Ag(I)-Im or Tr-Ag(I)-Tr base pairs (Im=imidazole nucleoside; Tr=1.2,4-triazole nucleoside). A total of seven different duplexes are discussed, incorporating one to three artificial base pairs in neighboring or non-neighboring positions. The association constant related to the formation of Tr-Ag(I)-Tr base pairs is estimated to be <10(3)M(-1). In contrast, Im-Ag(I)-Im base pairs are much more stable. The intrinsic association constant for their formation is in the order of 10(6)M(-1) and is therefore larger than that for the formation of T-Hg(II)-T and C-Ag(I)-C base pairs consisting of natural nucleobases. Two neighboring Im-Ag(I)-Im base pairs form cooperatively, whereas two remotely located Im-Ag(I)-Im base pairs form non-cooperatively. In general, the specific binding of Ag(I) to Im:Im-containing duplexes is enthalpically driven, with a significant additional entropic contribution in most cases. PMID:27032292

  12. A cohesin-based structural platform supporting homologous chromosome pairing in meiosis.

    Science.gov (United States)

    Ding, Da-Qiao; Haraguchi, Tokuko; Hiraoka, Yasushi

    2016-08-01

    The pairing and recombination of homologous chromosomes during the meiotic prophase is necessary for the accurate segregation of chromosomes in meiosis. However, the mechanism by which homologous chromosomes achieve this pairing has remained an open question. Meiotic cohesins have been shown to affect chromatin compaction; however, the impact of meiotic cohesins on homologous pairing and the fine structures of cohesion-based chromatin remain to be determined. A recent report using live-cell imaging and super-resolution microscopy demonstrated that the lack of meiotic cohesins alters the chromosome axis structures and impairs the pairing of homologous chromosomes. These results suggest that meiotic cohesin-based chromosome axis structures are crucial for the pairing of homologous chromosomes. PMID:26856595

  13. Self-organised criticality in base-pair breathing in DNA with a defect

    CERN Document Server

    Duduiala, Ciprian-Ionut; Laughton, Charles A

    2011-01-01

    We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to -1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or 'melting') and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.

  14. A new improved ID-based proxy ring signature scheme from bilinear pairings

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Ring signature and proxy signature are of vital importance to secure electronic commerce. Recently,the bilinear pairing such as Weil pairing or Tate pairing on elliptic curves and hyperelliptic curves is playing an important role in security solutions. Several ID-based signature schemes have been put forward, many of which are based on bilinear pairings. In key management and moderate security demand scenarios, ID-based public key cryptosystem is more preferable than other public key infrastructure based systems. In this paper, an improved ID-based proxy ring signature scheme from bilinear pairings is proposed which combines the advantages of proxy signature and of ring signatures. Our scheme can guarantee the profits of the proxy signer via preventing the original signer form generating the proxy ring signature. Furthermore, bilinear pairings are introduced to minimize the computation overhead and to improve the related performance of our scheme. In contrast with Zhang's scheme, our scheme is a computational efficiency improvement for signature verification because the computational cost of bilinear pairings required is reduced from O(n) to O( 1 ). In addition, the proxy ring signature presented in this paper can perfectly satisfy all the security requirements of proxy ring signature, i.e.signer-ambiguity, non-forgeability, verification, non-deniability and distinguishability.

  15. Metal-semiconductor pair nanoparticles by a physical route based on bipolar mixing

    Science.gov (United States)

    Kala, Shubhra; Theissmann, Ralf; Rouenhoff, Marcel; Kruis, Frank Einar

    2016-03-01

    In this report a methodology is described and demonstrated for preparing Au-Ge pair nanoparticles with known compositions by extending and modifying the basic steps normally used to synthesize nanoparticles in carrier gas. For the formation of pair nanoparticles by bipolar mixing, two oppositely charged aerosols of nanoparticles having the desired size are produced with the help of two differential mobility analyzers. Then both are allowed to pass through a tube, which provides sufficient residence time to result in nanoparticle pair formation due to Brownian collisions influenced by Coulomb forces. The effect of residence time on the formation of nanoparticle pairs as well as the influence of diffusion and discharging is described. Subsequently, necessary modifications to the experimental setup are demonstrated systematically. The kinetics of nanoparticles pair formation in a carrier gas is also calculated and compared with measurements made with the help of an online aerosol size analysis technique. This synthesis of nanoparticle pairs can be seen as a possible route towards Janus-type nanoparticles.

  16. An ID-based Blind Signature Scheme from Bilinear Pairings

    OpenAIRE

    B. Umaprasada Rao; K.A.Ajmath

    2010-01-01

    Blind signatures, introduced by Chaum, allow a user to obtain a signature on a message without revealing any thing about the message to the signer. Blind signatures play on important role in plenty of applications such as e-voting, e-cash system where anonymity is of great concern. Identity based(ID-based) public key cryptography can be a good alternative for certified based public key setting, especially when efficient key management and moderate security are required. In this paper, we prop...

  17. Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints

    OpenAIRE

    Hamada, Michiaki

    2012-01-01

    A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily ...

  18. Theory of nodal s ± -wave pairing symmetry in the Pu-based 115 superconductor family.

    Science.gov (United States)

    Das, Tanmoy; Zhu, Jian-Xin; Graf, Matthias J

    2015-01-01

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s(±) wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface "hot-spots" in the inter-band scattering channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s(±) wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry. PMID:25721375

  19. Flow-based market coupling. Stepping stone towards nodal pricing?

    International Nuclear Information System (INIS)

    For achieving one internal energy market for electricity by 2014, market coupling is deployed to integrate national markets into regional markets and ultimately one European electricity market. The extent to which markets can be coupled depends on the available transmission capacities between countries. Since interconnections are congested from time to time, congestion management methods are deployed to divide the scarce available transmission capacities over market participants. For further optimization of the use of available transmission capacities while maintaining current security of supply levels, flow-based market coupling (FBMC) will be implemented in the CWE region by 2013. Although this is an important step forward, important hurdles for efficient congestion management remain. Hence, flow based market coupling is compared to nodal pricing, which is often considered as the most optimal solution from theoretical perspective. In the context of decarbonised power systems it is concluded that advantages of nodal pricing are likely to exceed its disadvantages, warranting further development of FBMC in the direction of nodal pricing.

  20. Doppler Broadening Analysis of Steel Specimens Using Accelerator Based In Situ Pair Production

    International Nuclear Information System (INIS)

    Positron Annihilation Spectroscopy (PAS) techniques can be utilized as a sensitive probe of defects in materials. Studying these microscopic defects is very important for a number of industries in order to predict material failure or structural integrity. We have been developing gamma-induced pair-production techniques to produce positrons in thick samples (∼4-40 g/cm2, or ∼0.5-5 cm in steel). These techniques are called 'Accelerator-based Gamma-induced Positron Annihilation Spectroscopy'(AG-PAS). We have begun testing the capabilities of this technique for imaging of defect densities in thick structural materials. As a first step, a linear accelerator (LINAC) was employed to produce photon beams by stopping 15 MeV electrons in a 1 mm thick tungsten converter. The accelerator is capable of operating with 30-60 ns pulse width, up to 200 mA peak current at 1 kHz repetition rate. The highly collimated bremsstrahlung beam impinged upon our steel tensile specimens, after traveling through a 1.2 m thick concrete wall. Annihilation radiation was detected by a well-shielded and collimated high-purity germanium detector (HPGe). Conventional Doppler broadening spectrometry (DBS) was performed to determine S, W and T parameters for our samples.

  1. Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise

    International Nuclear Information System (INIS)

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break.

  2. Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise.

    Science.gov (United States)

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-05-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break. PMID:19420603

  3. On the internal d-wave structure of s+/- pairs in Iron-based Superconductors

    Science.gov (United States)

    Ong, Tze Tzen; Coleman, Piers

    2014-03-01

    A key issue in understanding the high temperature iron-based superconductors concerns the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. Whereas electronically paired superconductors generally avoid the Coulomb interaction through the formation of higher angular momentum pairs, iron based superconductors involve s-wave (s+/-) pairs with zero angular momentum. By taking account of the orbital degrees of freedom of the iron atoms, here we show that the s+/- pairs in these materials possess hidden d-wave symmetry, forming orbital triplets in which the the d-wave angular momentum of the pairs is compensated by the internal angular momentum of the orbitals. The recent observation of a gap with octahedral structure in KFe2As2 materials can be understood as a transition to a ``high spin'' configuration of the d-wave orbital triplets, through the alignment of the two angular momentum components of the pair. We acknowledge funding from DOE grant DE-FG02-99ER45790.

  4. Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise

    Science.gov (United States)

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-05-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break.

  5. Entanglement and Sources of Magnetic Anisotropy in Radical Pair-Based Avian Magnetoreceptors

    CERN Document Server

    Hogben, Hannah J; Hore, P J

    2012-01-01

    One of the principal models of magnetic sensing in migratory birds rests on the quantum spin-dynamics of transient radical pairs created photochemically in ocular cryptochrome proteins. We consider here the role of electron spin entanglement and coherence in determining the sensitivity of a radical pair-based geomagnetic compass and the origins of the directional response. It emerges that the anisotropy of radical pairs formed from spin-polarized molecular triplets could form the basis of a more sensitive compass sensor than one founded on the conventional hyper?ne-anisotropy model. This property offers new and more flexible opportunities for the design of biologically inspired magnetic compass sensors.

  6. Distribution of Primes and of Interval Prime Pairs Based on $\\Theta$ Function

    CERN Document Server

    Fan, Yifang

    2010-01-01

    $\\Theta$ function is defined based upon Kronecher symbol. In light of the principle of inclusion-exclusion, $\\Theta$ function of sine function is used to denote the distribution of composites and primes. The structure of Goldbach Conjecture has been analyzed, and $\\Xi$ function is brought forward by the linear diophantine equation; by relating to $\\Theta$ function, the interval distribution of composite pairs and prime pairs (i.e. the Goldbach Conjecture) is thus obtained. In the end, Abel's Theorem (Multiplication of Series) is used to discuss the lower limit of the distribution of the interval prime pairs.

  7. Comparison of Three Cre-LoxP Based Paired-End Library Construction Methods

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Ze; Nath, Nandita; Tritt, Andrew; Liang, Shoudan; Han, James; Pennacchio, Len; Chen, Feng

    2013-03-26

    Paired-end library sequencing has been proven useful in scaffold construction during de novo whole genome shotgun assembly. The ability of generating mate pairs with > 8 Kb insert sizes is especially important for genomes containing long repeats. To make mate paired libraries for next generation sequencing, DNA fragments need to be circularized to bring the ends together. There are several methods that can be used for DNA circulation, namely ligation, hybridization and Cre-LoxP recombination. With higher circularization efficiency with large insert DNA fragments, Cre-LoxP recombination method generally has been used for constructing >8 kb insert size paired-end libraries. Second fragmentation step is also crucial for maintaining high library complexity and uniform genome coverage. Here we will describe the following three fragmentation methods: restriction enzyme digestion, random shearing and nick translation. We will present the comparison results for these three methods. Our data showed that all three methods are able to generate paired-end libraries with greater than 20 kb insert. Advantages and disadvantages of these three methods will be discussed as well.

  8. Rule Based Ensembles Using Pair Wise Neural Network Classifiers

    Directory of Open Access Journals (Sweden)

    Moslem Mohammadi Jenghara

    2015-03-01

    Full Text Available In value estimation, the inexperienced people's estimation average is good approximation to true value, provided that the answer of these individual are independent. Classifier ensemble is the implementation of mentioned principle in classification tasks that are investigated in two aspects. In the first aspect, feature space is divided into several local regions and each region is assigned with a highly competent classifier and in the second, the base classifiers are applied in parallel and equally experienced in some ways to achieve a group consensus. In this paper combination of two methods are used. An important consideration in classifier combination is that much better results can be achieved if diverse classifiers, rather than similar classifiers, are combined. To achieve diversity in classifiers output, the symmetric pairwise weighted feature space is used and the outputs of trained classifiers over the weighted feature space are combined to inference final result. In this paper MLP classifiers are used as the base classifiers. The Experimental results show that the applied method is promising.

  9. A self-adaptive step Cuckoo search algorithm based on dimension by dimension improvement

    OpenAIRE

    Ren, Lu; Li, Haiyang; He, Xingshi

    2015-01-01

    The choice of step length plays an important role in convergence speed and precision of Cuckoo search algorithm. In the paper, a self-adaptive step Cuckoo search algorithm based on dimensional improvement is provided. First, since the step in the original self-adaptive step Cuckoo search algorithm is not updated when the current position of the nest is in the optimal position, simple modification of the step is made for the update. Second, evaluation strategy based on dimension by dimension u...

  10. Multi-hop teleportation based on W state and EPR pairs

    Science.gov (United States)

    Hai-Tao, Zhan; Xu-Tao, Yu; Pei-Ying, Xiong; Zai-Chen, Zhang

    2016-05-01

    Multi-hop teleportation has significant value due to long-distance delivery of quantum information. Many studies about multi-hop teleportation are based on Bell pairs, partially entangled pairs or W state. The possibility of multi-hop teleportation constituted by partially entangled pairs relates to the number of nodes. The possibility of multi-hop teleportation constituted by double W states is after n-hop teleportation. In this paper, a multi-hop teleportation scheme based on W state and EPR pairs is presented and proved. The successful possibility of quantum information transmitted hop by hop through intermediate nodes is deduced. The possibility of successful transmission is after n-hop teleportation. Project supported by the National Natural Science Foundation of China (Grant No. 61571105), the Prospective Future Network Project of Jiangsu Province, China (Grant No. BY2013095-1-18), and the Independent Project of State Key Laboratory of Millimeter Waves, China (Grant No. Z201504).

  11. STEPPING - Smartphone-Based Portable Pedestrian Indoor Navigation

    Science.gov (United States)

    Lukianto, C.; Sternberg, H.

    2011-12-01

    Many current smartphones are fitted with GPS receivers, which, in combination with a map application form a pedestrian navigation system for outdoor purposes. However, once an area with insufficient satellite signal coverage is entered, these navigation systems cease to function. For indoor positioning, there are already several solutions available which are usually based on measured distances to reference points. These solutions can achieve resolutions as low as the sub-millimetre range depending on the complexity of the set-up. STEPPING project, developed at HCU Hamburg Germany aims at designing an indoor navigation system consisting of a small inertial navigation system and a new, robust sensor fusion algorithm running on a current smartphone. As this system is theoretically able to integrate any available positioning method, it is independent of a particular method and can thus be realized on a smartphone without affecting user mobility. Potential applications include --but are not limited to: Large trade fairs, airports, parking decks and shopping malls, as well as ambient assisted living scenarios.

  12. A process definition repository based on step AP 213

    Energy Technology Data Exchange (ETDEWEB)

    Butler, J.W.

    1997-09-01

    Over the years, in the context of numerically controlled machined part manufacturing, the loss, misinterpretation, and redundancy of re-inputting manufacturing instructions and data during the evolution of a product design into the finished product has been a resource depleting and costly endeavor. It is the intent of this project to utilize the emerging standards from the International Standards Organization, ISO 10303 Standard for the Exchange of Product Model Data, commonly referred to as STEP, to store and retrieve process planning information for a set of production work instructions. The project focuses on the utilization of the 1995 version of the Draft International Standard ISO/DIS 10303-213:1995 (E) Application protocol: Numerical control process plans for machined parts (AP213). This project illustrates the methodologies used to build an object-oriented Process Definition Repository (PDR), describes both the benefits and shortcomings experienced in implementing AP213, and recommends enhancements to AP213 for process planning information. The deliverable will be a Part 21 data file, based on the application-interpreted model for AP213 and integrated with product design data.

  13. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

    KAUST Repository

    Chawla, Mohit

    2015-06-27

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.

  14. Distribution of Primes and of Interval Prime Pairs Based on $\\Theta$ Function

    OpenAIRE

    Fan, Yifang; Li, Zhiyu

    2010-01-01

    $\\Theta$ function is defined based upon Kronecher symbol. In light of the principle of inclusion-exclusion, $\\Theta$ function of sine function is used to denote the distribution of composites and primes. The structure of Goldbach Conjecture has been analyzed, and $\\Xi$ function is brought forward by the linear diophantine equation; by relating to $\\Theta$ function, the interval distribution of composite pairs and prime pairs (i.e. the Goldbach Conjecture) is thus obtained. In the end, Abel's ...

  15. Intra-inter band pairing, order parameter symmetry in Fe-based superconductors: A model study

    International Nuclear Information System (INIS)

    Highlights: • MS deals with exciting research fields of condensed matter physics, the Fe-based superconductors. • Fe-based superconductors with multiple gaps, it is important to show why it have a singleTc. • We show the essestial requirement of both the intra and inter-band pairing channels. • Signature of the above shown in characteristic ratio, thermal behaviour of specific heat jump. - Abstract: In the quest of why there should be a single transition temperature in a multi-gapped system like Fe-based materials we use two band model for simplicity. The model comprises of spin density wave (SDW), orbital density wave (ODW) arising due to nested pieces of the electron and hole like Fermi surfaces; together with superconductivity of different pairing symmetries around electron and hole like Fermi surfaces. We show that either only intra or only inter band pairing is insufficient to describe some of the experimental results like large to small gap ratio, thermal behaviour of electronic specific heat jump etc. It is shown that the inter-band pairing is essential in Fe-based materials having multiple gaps to produce a single global Tc. Some of our results in this scenario, matches with the earlier published work (Dolgov et al., 2009), and also have differences. The origin of difference between the two is also discussed. Combined intra–inter band pairing mechanism produces the specific heat jump to superconducting transition temperature ratio proportional to square of the transition temperature, both in the electron and hole doped regime, for sign changing s± wave symmetry which takes the d + s pairing symmetry form. Our work thus demonstrates the importance of combined intra-inter band pairing irrespective of the pairing mechanism

  16. Physical implementation of pair-based spike timing dependent plasticity

    International Nuclear Information System (INIS)

    Full text: Objective Spike-timing-dependent plasticity (STOP) is one of several plasticity rules which leads to learning and memory in the brain. STOP induces synaptic weight changes based on the timing of the pre- and post-synaptic neurons. A neural network which can mimic the adaptive capability of biological brains in the temporal domain, requires the weight of single connections to be altered by spike timing. To physically realise this network into silicon, a large number of interconnected STOP circuits on the same substrate is required. This imposes two significant limitations in terms of power and area. To cover these limitations, very large scale integrated circuit (VLSI) technology provides attractive features in terms of low power and small area requirements. An example is demonstrated by (lndiveli et al. 2006). The objective of this paper is to present a new implementation of the STOP circuit which demonstrates better power and area in comparison to previous implementations. Methods The proposed circuit uses complementary metal oxide semiconductor (CMOS) technology as depicted in Fig. I. The synaptic weight can be stored on a capacitor and charging/discharging current can lead to potentiation and depression. HSpice simulation results demonstrate that the average power, peak power, and area of the proposed circuit have been reduced by 6, 8 and 15%, respectively, in comparison with Indiveri's implementation. These improvements naturally lead to packing more STOP circuits onto the same substrate, when compared to previous proposals. Hence, this new implementation is quite interesting for real-world large neural networks.

  17. Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase iota.

    Science.gov (United States)

    Johnson, Robert E; Prakash, Louise; Prakash, Satya

    2005-07-26

    Because of the near geometric identity of Watson-Crick (W-C) GxC and AxT base pairs, a given DNA polymerase forms the four possible correct base pairs with nearly identical catalytic efficiencies. However, human DNA polymerase iota (Pol iota), a member of the Y family of DNA polymerases, exhibits a marked template specificity, being more efficient at incorporating the correct nucleotide opposite template purines than opposite pyrimidines. By using 7-deazaadenine and 7-deazaguanine as the templating residues, which disrupt Hoogsteen base pair formation, we show that, unlike the other DNA polymerases belonging to the A, B, or Y family, DNA synthesis by Pol iota is severely inhibited by these N7-modified bases. These observations provide biochemical evidence that, during normal DNA synthesis, template purines adopt a syn conformation in the Pol iota active site, enabling the formation of a Hoogsteen base pair with the incoming pyrimidine nucleotide. Additionally, mutational studies with Leu-62, which lies in close proximity to the templating residue in the Pol iota ternary complex, have indicated that both factors, steric constraints within the active site and the stability provided by the hydrogen bonds in the Hoogsteen base pair, contribute to the efficiency of correct nucleotide incorporation opposite template purines by Pol iota. PMID:16014707

  18. A Step-by-Step Design Methodology for a Base Case Vanadium Redox-Flow Battery

    Science.gov (United States)

    Moore, Mark; Counce, Robert M.; Watson, Jack S.; Zawodzinski, Thomas A.; Kamath, Haresh

    2012-01-01

    The purpose of this work is to develop an evolutionary procedure to be used by Chemical Engineering students for the base-case design of a Vanadium Redox-Flow Battery. The design methodology is based on the work of Douglas (1985) and provides a profitability analysis at each decision level so that more profitable alternatives and directions can be…

  19. Practical Biostatistics A Friendly Step-by-Step Approach for Evidence-based Medicine

    CERN Document Server

    Suchmacher, Mendel

    2012-01-01

    Evidence-based medicine aims to apply the best available evidence gained from the scientific method to medical decision making. It is a practice that uses statistical analysis of scientific methods and outcomes to drive further experimentation and diagnosis. The profusion of evidence-based medicine in medical practice and clinical research has produced a need for life scientists and clinical researchers to assimilate biostatistics into their work to meet efficacy and practical standards. Practical Biostatistics provides researchers, medical professionals, and students with a friendly, practica

  20. Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

    Science.gov (United States)

    Vercoutere, Wenonah; DeGuzman, Veronica

    2003-01-01

    The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

  1. A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs

    International Nuclear Information System (INIS)

    Graphical abstract: Reactions of methyldiazonium ion at the different sites of the DNA bases in the Watson-Crick GC and AT base pairs were investigated employing density functional and second order Moller-Plesset (MP2) perturbation theories. Display Omitted Highlights: → Methylation of the DNA bases is important as it can cause mutation and cancer. → Methylation reactions of the GC and AT base pairs with CH3N2+ were not studied earlier theoretically. → Experimental observations have been explained using theoretical methods. - Abstract: Methylation of the DNA bases in the Watson-Crick GC and AT base pairs by the methyldiazonium ion was investigated employing density functional and second order Moller-Plesset (MP2) perturbation theories. Methylation at the N3, N7 and O6 sites of guanine, N1, N3 and N7 sites of adenine, O2 and N3 sites of cytosine and the O2 and O4 sites of thymine were considered. The computed reactivities for methylation follow the order N7(guanine) > N3(adenine) > O6(guanine) which is in agreement with experiment. The base pairing in DNA is found to play a significant role with regard to reactivities of the different sites.

  2. Sub-base-pair resolution during DNA separation in an optofluidic chip

    OpenAIRE

    Pollnau, Markus; Hammer, Manfred; Dongre, Chaitanya; Hoekstra, Hugo J.W.M.

    2014-01-01

    DNA sequencing in a lab-on-a-chip aims at providing cheap, high-speed analysis of low reagent volumes to, e.g., identify genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions or deletions from DNA fragments in the diagnostically relevant range of 150-1000 base-pairs requires a sizing accuracy of S < 10^-3, while only S < 10^-2 were reported. Here we demonstrate a sizing accuracy of S = 4 x 10^-4, thereby paving the way for the envisaged appli...

  3. Solvent effect on the anharmonic vibrational frequencies in guanine-cytosine base pair

    Science.gov (United States)

    Bende, A.; Muntean, C. M.

    2012-02-01

    We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson-Crick and Hoogsteen base pair configurations. The results are obtained by considering the DFT method together with the Polarizable Continuum Model (PCM) using PBE and B3PW91 exchange-correlation functionals and triple-ζ valence basis set. We investigate the importance of anharmonic corrections for the vibrational modes taking into account the solvent effect of the water environment. In particular, the unusual anharmonic effect of the H+ vibration in the case of the Hoogsteen base pair configuration is discussed.

  4. English Writing Strategy —Based on Three Steps

    Institute of Scientific and Technical Information of China (English)

    翁朝袅

    2012-01-01

    Many junior high school students have trouble in writing English composition,and this paper is primarily divided into three steps of pre-writing,while-writing and post-writing to answer the question:How to write a composition.

  5. Resumption-based big-step and small-step interpreters for While with interactive I/O

    CERN Document Server

    Nakata, Keiko

    2011-01-01

    In this tutorial, we program big-step and small-step total interpreters for the While language extended with input and output primitives. While is a simple imperative language consisting of skip, assignment, sequence, conditional and loop. We first develop trace-based interpreters for While. Traces are potentially infinite nonempty sequences of states. The interpreters assign traces to While programs: for us, traces are denotations of While programs. The trace is finite if the program is terminating and infinite if the program is non-terminating. However, we cannot decide (i.e., write a program to determine), for any given program, whether its trace is finite or infinite, which amounts to deciding the halting problem. We then extend While with interactive input/output primitives. Accordingly, we extend the interpreters by generalizing traces to resumptions. The tutorial is based on our previous work with T. Uustalu on reasoning about interactive programs in the setting of constructive type theory.

  6. Efficient replication bypass of size-expanded DNA base pairs in bacterial cells

    OpenAIRE

    Delaney, James C.; GAO, JIANMIN; Liu, Haibo; Shrivastav, Nidhi; Essigmann, John M.; Kool, Eric T.

    2009-01-01

    Supersize me! Size-expanded DNA bases (xDNA) are able to encode natural DNA sequences in replication. In vitro experiments with a DNA polymerase show nucleotide incorporation opposite the xDNA bases with correct pairing. In vivo experiments using E. coli show that two xDNA bases (xA and xC, see picture) encode the correct replication partners.

  7. Live demonstration: Gesture-Based remote control using stereo pair of dynamic vision sensors

    OpenAIRE

    J. Lee; Delbruck, T; Park, P K J; Pfeiffer, M.; Shin, C W; Ryu, H; Kang, B C

    2012-01-01

    This demonstration shows a natural gesture interface for console entertainment devices using as input a stereo pair of dynamic vision sensors. The event-based processing of the sparse sensor output allows fluid interaction at a laptop processor load of less than 3%.

  8. DNA electronic circular dichroism on the inter-base pair scale

    DEFF Research Database (Denmark)

    Di Meo, Florent; Nørby, Morten Steen; Rubio-Magnieto, Jenifer;

    2015-01-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the...

  9. Genome filtering using methylation-sensitive restriction enzymes with six-base pair recognition sites

    Science.gov (United States)

    The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl sensitive restriction enzymes with six base pair recognition sites...

  10. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes

    Science.gov (United States)

    Léon, J. Christian; Sinha, Indranil; Müller, Jens

    2016-01-01

    The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase. PMID:27089326

  11. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

    Science.gov (United States)

    Yang, Bo; Rodgers, M. T.

    2015-08-01

    Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

  12. Student Opinions about the Seven-Step Procedure in Problem-Based Hospitality Management Education

    Science.gov (United States)

    Zwaal, Wichard; Otting, Hans

    2014-01-01

    This study investigates how hospitality management students appreciate the role and application of the seven-step procedure in problem-based learning. A survey was developed containing sections about personal characteristics, recall of the seven steps, overall report marks, and 30 statements about the seven-step procedure. The survey was…

  13. The Sentiment Trend Analysis of Twitter Based on Set Pair Contact Degree

    Directory of Open Access Journals (Sweden)

    Chunying Zhang

    2013-01-01

    Full Text Available Sentiment trend of twitter users have a great influence on their friends and the crowd listened. This paper directs at the user sentiment state of twitter, the unique medium, and applies set pair analysis method for trend analysis. First, we begin with set pair contact degree, then based on set pair affective computing model to make comparison with the size relationship of same degree, difference degree, opposition degree of the emotion, to build the user sentiment trend analysis model; Secondly, we analyze the influence for the user's own sentiment trend when the value changed of difference coefficient ; thirdly, after analyze to obtain one user's sentiment orientation threshold as prerequisite for user behavior prediction. Finally, setting an example to calculate the sentiment trend of one twitter, then to get the conclusion is that the analysis of user emotion from a three-dimensional angle is more realistic than the single angle.

  14. Identification of DNA base-pairing via tunnel-current decay

    OpenAIRE

    He, Jin; Lin, Lisha; Zhang, Peiming; Lindsay, Stuart

    2007-01-01

    We propose a new approach for reading the sequence of a DNA molecule passing between electrodes on a nanopore, using hydrogen-bond mediated tunneling signals. The base-electrode interaction is modeled using a nucleobase functionalized STM probe that is pulled away from a nucleoside monolayer. Watson-Crick recognition results in slow-decay of the tunnel current, uniquely characteristic of the base-pair in over half the reads. Thirteen independent reads would yield the desired 99.99% accuracy.

  15. Acid-Base Pairs in Lewis Acidic Zeolites Promote Direct Aldol Reactions by Soft Enolization.

    Science.gov (United States)

    Lewis, Jennifer D; Van de Vyver, Stijn; Román-Leshkov, Yuriy

    2015-08-17

    Hf-, Sn-, and Zr-Beta zeolites catalyze the cross-aldol condensation of aromatic aldehydes with acetone under mild reaction conditions with near quantitative yields. NMR studies with isotopically labeled molecules confirm that acid-base pairs in the Si-O-M framework ensemble promote soft enolization through α-proton abstraction. The Lewis acidic zeolites maintain activity in the presence of water and, unlike traditional base catalysts, in acidic solutions. PMID:26138135

  16. Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

    Directory of Open Access Journals (Sweden)

    Rie Kawai

    2012-03-01

    Full Text Available Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienylimidazo[4,5-b]pyridine (Ds and pyrrole-2-carbaldehyde (Pa functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.

  17. DNA Aptamer Generation by Genetic Alphabet Expansion SELEX (ExSELEX) Using an Unnatural Base Pair System.

    Science.gov (United States)

    Kimoto, Michiko; Matsunaga, Ken-ichiro; Hirao, Ichiro

    2016-01-01

    Genetic alphabet expansion of DNA using unnatural base pair systems is expected to provide a wide variety of novel tools and methods. Recent rapid progress in this area has enabled the creation of several types of unnatural base pairs that function as a third base pair in polymerase reactions. Presently, a major topic is whether the genetic alphabet expansion system actually increases nucleic acid functionalities. We recently applied our unnatural base pair system to in vitro selection (SELEX), using a DNA library containing four natural bases and an unnatural base, and succeeded in the generation of high-affinity DNA aptamers that specifically bind to target proteins. Only a few hydrophobic unnatural bases greatly augmented the affinity of the aptamers. Here, we describe a new approach (genetic alphabet Expansion SELEX, ExSELEX), using our hydrophobic unnatural base pair system for high affinity DNA aptamer generation. PMID:26552815

  18. Aviram-Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps

    Science.gov (United States)

    Agapito, Luis A.; Gayles, Jacob; Wolowiec, Christian; Kioussis, Nicholas

    2012-04-01

    We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab initio non-equilibrium Green’s function (NEGF) theory to determine the electrical response of graphene—base-pair—graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the cytosine-guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the thymine-adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps.

  19. A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs

    Science.gov (United States)

    Shukla, P. K.; Ganapathy, Vinay; Mishra, P. C.

    2011-09-01

    Methylation of the DNA bases in the Watson-Crick GC and AT base pairs by the methyldiazonium ion was investigated employing density functional and second order Møller-Plesset (MP2) perturbation theories. Methylation at the N3, N7 and O6 sites of guanine, N1, N3 and N7 sites of adenine, O2 and N3 sites of cytosine and the O2 and O4 sites of thymine were considered. The computed reactivities for methylation follow the order N7(guanine) > N3(adenine) > O6(guanine) which is in agreement with experiment. The base pairing in DNA is found to play a significant role with regard to reactivities of the different sites.

  20. Theoretical investigation of the molecular structure of the pi kappa DNA base pair.

    Science.gov (United States)

    Florián, J; Leszczyński, J

    1995-04-01

    The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition pattern. Recently, these bases were proposed as an extension of the genetic alphabet from four to six letters (Piccirilli et al, Nature 343,33 (1990)). By the HF/6-31G* method with full geometry optimization we calculated the 12 degree propeller twist for the minimum energy structure of this complex. The linearity of hydrogen bonds is preserved in the twisted structure by virtue of the pyramidal arrangement of the kappa-base amino groups. The rings of both the pi and kappa molecules remain nearly planar. This nonplanar structure of the pi kappa base pair is only 0.1 kcal/mol more stable than the planar (Cs) conformation. The HF/6-31G* level gas-phase interaction energy of pi kappa (-13.5 kcal/mol) calculated by us turned out to be nearly the same as the interaction energy obtained previously for the adenine-thymine base pair (-13.4 kcal/mol) at the same computational level. The inclusion of p-polarization functions on hydrogens, electron correlation effects (MP2/6-31G** level), and the correction for the basis set superposition error (BSSE) increase this energy to -14.0 kcal/mol. PMID:7626240

  1. Student Opinions about the Seven-step Procedure in Problem-based Hospitality Management Education

    Directory of Open Access Journals (Sweden)

    Hans Otting

    2014-06-01

    Full Text Available This study investigates how hospitality management students appreciate the role and application of the seven-step procedure in problem-based learning. A survey was developed containing sections about personal characteristics, recall of the seven steps, overall report marks, and 30 statements about the seven-step procedure. The survey was administered to a sample of 101 first-, second- and third-year hotel school students. Results show a low recall but positive opinion about the seven-step procedure. Particularly step 4 (conceptualizing, step 6 (self-study between tutorials and step 7 (synthesizing new information need attention. Some suggestions are put forward for strengthening the process of problem-based hospitality education.

  2. DSP-Based Stepping Motor Drivers for the LHC Collimators

    CERN Document Server

    Masi, A; Losito, R; Martino, M

    2008-01-01

    The control electronics of the LHC collimators stepping motors will be located in radiation safe zones up to 800 meters far from the motors. With such cable lengths the standard chopping drivers do not work properly because of the voltage losses on the cable and even more because of the high cable capacitance. The capacitance in fact produces a ringing phenomenon on the driver feedback current that limits the control chopping frequency to the point of being incompatible with the tight EM emissions requirements of the LHC tunnel. In some cases the feedback loop may even become unstable and the driver would fail. The problem was solved by accurately modeling the overall motor-cable system taking into account non-linearities due to hysteresis and eddy currents and by designing an adaptive digital controller, self-tuning to the real cable length. The controller will aim at increasing the chopping frequency to reduce the spectral density of the emissions and at damping the oscillations of the feedback current to a...

  3. A light scattering study of the evolution of pairing in Fe-based superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hackl, Rudi; Kretzschmar, Florian; Muschler, Bernhard; Boehm, Thomas [Walther-Meissner-Institut, DE-85748 Garching (Germany); Wen, Hai-Hu [Nanjing University, Nanjing 210093 (China); Tsurkan, Vladimir [University of Augsburg, DE-86159 Augsburg (Germany); Academy of Sciences of Moldova, MD-2028 Chisinau (Moldova, Republic of); Deisenhofer, Joachim; Loidl, Alois [University of Augsburg, DE-86159 Augsburg (Germany)

    2013-07-01

    The iron-based superconductors are a laboratory for exploring the relevance of electron-electron interactions beyond electron-phonon coupling, being at work in conventional superconductors, since the Fermi surfaces can be varied systematically by atomic substitution. This enables one to systematically study magnetism and superconductivity as a function of the Fermi surface topology. Inelastic light scattering affords a window into the electronic properties of the ordered states. In particular, the evolution of the superconducting pairing upon doping can be probed since light scattering allows access to the anisotropy of the energy gap and, in some cases, of the pairing potential. Ba{sub 1-x}K{sub x}Fe{sub 2}As{sub 2} is one of those cases since the competition between s- and d-wave pairing leads to the appearance of exciton-like modes below the gap edges of the various bands. Along with the results from other materials having different Fermi surface cross-sections the data in Ba{sub 1-x}K{sub x}Fe{sub 2}As{sub 2} support the spin fluctuation scenario driven by interband coupling. The experiments show that there exist alternative routes for the analysis of the pairing interaction in superconductors with unconventional coupling and anisotropic gaps.

  4. Comparison of NIR FRET pairs for quantitative transferrin-based assay

    Science.gov (United States)

    Sinsuebphon, Nattawut; Bevington, Travis; Zhao, Lingling; Ken, Abe; Barroso, Margarida; Intes, Xavier

    2014-02-01

    Transferrin (Tfn) is commonly used as a drug delivery carrier for cancer treatment. Tfn cellular internalization can be observed by Förster resonance energy transfer (FRET), which occurs when two fluorophores - donor and acceptor - are a few nanometers apart. Donor fluorescence lifetime can be used to sense and quantify FRET occurrence. In FRET state, the donor is quenched leading to a significant reduction in its lifetime. In this study, donor and acceptor near-infrared (NIR) fluorophore-labeled Tfn were used to quantify cellular internalization in breast cancer cell line (T47D). Based on donor lifetime, quantum yield and spectral data, seven NIR FRET pairs were chosen for this comparison. Performance of the different NIR FRET pairs was evaluated in vitro in multiwell plate settings and by analyzing the relationship between quenched donor fraction and acceptor:donor ratio. Additionally, we performed brightness comparison between each pairs. Several parameters, such as brightness, lifetime, R0 and FRET donor population values are used to identify the most suitable NIR FRET pair for in vivo studies in preclinical settings.

  5. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water.

    Science.gov (United States)

    Cafferty, Brian J; Fialho, David M; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. PMID:27108699

  6. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

    Science.gov (United States)

    Cafferty, Brian J.; Fialho, David M.; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V.

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. PMID:27108699

  7. XOEM plus OWL-based STEP Product Information Uniform Description and Implementation

    Directory of Open Access Journals (Sweden)

    Chengfeng Jian

    2011-12-01

    Full Text Available Aimed at the current inconsistencies in the OWL-based STEP description, the mapping rules between EXPRESS and OWL are established on the base of uniform semantic model named XOEM+OWL, then the implementation method of STEP-OWL converter is put forward and the corresponding examples are shown.

  8. XOEM plus OWL-based STEP Product Information Uniform Description and Implementation

    OpenAIRE

    Chengfeng Jian; Haizhong Meng

    2011-01-01

    Aimed at the current inconsistencies in the OWL-based STEP description, the mapping rules between EXPRESS and OWL are established on the base of uniform semantic model named XOEM+OWL, then the implementation method of STEP-OWL converter is put forward and the corresponding examples are shown.

  9. Optimization of the pyridyl nucleobase scaffold for polymerase recognition and unnatural base pair replication

    Czech Academy of Sciences Publication Activity Database

    Hari, Y.; Hwang, G. T.; Leconte, A. M.; Joubert, Nicolas; Hocek, Michal; Romesberg, F. E.

    2008-01-01

    Roč. 9, č. 17 (2008), s. 2796-2799. ISSN 1439-4227 R&D Projects: GA MŠk LC512 Grant ostatní: NIH(US) GM60005 Institutional research plan: CEZ:AV0Z40550506 Keywords : pyridines * C-nucleosides * base-pairs * DNA polymerase * replication Subject RIV: CC - Organic Chemistry Impact factor: 3.322, year: 2008

  10. Does base-pairing strength play a role in microRNA repression?

    Science.gov (United States)

    Carmel, Ido; Shomron, Noam; Heifetz, Yael

    2012-11-01

    MicroRNAs (miRNAs) are short, single-stranded RNAs that silence gene expression by either degrading mRNA or repressing translation. Each miRNA regulates a specific set of mRNA "targets" by binding to complementary sequences in their 3' untranslated region. In this study, we examined the importance of the base-pairing strength of the miRNA-target duplex to repression. We hypothesized that if base-pairing strength affects the functionality of miRNA repression, organisms with higher body temperature or that live at higher temperatures will have miRNAs with higher G/C content so that the miRNA-target complex will remain stable. In the nine model organisms examined, we found a significant correlation between the average G/C content of miRNAs and physiological temperature, supporting our hypothesis. Next, for each organism examined, we compared the average G/C content of miRNAs that are conserved among distant organisms and that of miRNAs that are evolutionarily recent. We found that the average G/C content of ancient miRNAs is lower than recent miRNAs in homeotherms, whereas the trend was inversed in poikilotherms, suggesting that G/C content is associated with temperature, thus further supporting our hypothesis. In the organisms examined, the average G/C content of miRNA "seed" sequences was higher than that of mature miRNAs, which was higher than pre-miRNA loops, suggesting an association between the degree of functionality of the sequence and its average G/C content. Our analyses show a possible association between the base-pairing strength of miRNA-targets and the temperature of an organism, suggesting that base-pairing strength plays a role in repression by miRNAs. PMID:23019592

  11. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

    OpenAIRE

    Cafferty, Brian J.; Fialho, David M.; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V.

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ...

  12. Application of Set Pair Analysis-Based Similarity Forecast Model and Wavelet Denoising for Runoff Forecasting

    OpenAIRE

    Chien-Ming Chou

    2014-01-01

    This study presents the application of a set pair analysis-based similarity forecast (SPA-SF) model and wavelet denoising to forecast annual runoff. The SPA-SF model was built from identical, discrepant and contrary viewpoints. The similarity between estimated and historical data can be obtained. The weighted average of the annual runoff values characterized by the highest connection coefficients was regarded as the predicted value of the estimated annual runoff. In addition, runoff time seri...

  13. Chlamydomonas reinhardtii telomere repeats form unstable structures involving guanine-guanine base pairs.

    OpenAIRE

    Petracek, M E; Berman, J.

    1992-01-01

    Unusual DNA structures involving four guanines in a planar formation (guanine tetrads) are formed by guanine-rich (G-rich) telomere DNA and other G-rich sequences (reviewed in (1)) and may be important in the structure and function of telomeres. These structures result from intrastrand and/or interstrand Hoogsteen base pairs between the guanines. We used the telomeric repeat of Chlamydomonas reinhardtii, TTTTAGGG, which contains 3 guanines and has a long interguanine A + T tract, to determine...

  14. Pairing-Free ID-Based Key-Insulated Signature Scheme

    Institute of Scientific and Technical Information of China (English)

    Guo-Bin Zhu; Hu Xiong; Zhi-Guang Qin

    2015-01-01

    Abstract⎯Without the assumption that the private keys are kept secure perfectly, cryptographic primitives cannot be deployed in the insecure environments where the key leakage is inevitable. In order to reduce the damage caused by the key exposure in the identity-based (ID-based) signature scenarios efficiently, we propose an ID-based key-insulated signature scheme in this paper, which eliminates the expensive bilinear pairing operations. Compared with the previous work, our scheme minimizes the computation cost without any extra cost. Under the discrete logarithm (DL) assumption, a security proof of our scheme in the random oracle model has also been given.

  15. Iron-based superconductors: Current status of materials and pairing mechanism

    International Nuclear Information System (INIS)

    Highlight: • An up-to-date review by the discoverer and a theoretical pioneer of iron-based superconductor. - Abstract: Since the discovery of high Tc iron-based superconductors in early 2008, more than 15,000 papers have been published as a result of intensive research. This paper describes the current status of iron-based superconductors (IBSC) covering most up-to-date research progress along with the some background research, focusing on materials (bulk and thin film) and pairing mechanism

  16. UK provides "step increase" in funding for its science base

    CERN Multimedia

    1998-01-01

    The British government has come good on pre-election promises when this week, it agreed to inject an extra 700 million into the country's science base over the next three years. This extra funding is boosted by a further 400 million pounds from the Welcome Trust over the same period (1 page).

  17. Recognition of base pair inversions in duplex by chimeric (alpha,beta) triplex-forming oligonucleotides.

    Science.gov (United States)

    Timofeev, Edward N; Goryaeva, Baira V; Florentiev, Vladimir L

    2006-10-01

    DNA recognition by triplex-forming oligonucleotides (TFOs) is usually limited by homopurine-homopyrimidine sequence in duplexes. Modifications of the third strand may overcome this limitation. Chimeric alpha-beta TFOs are expected to form triplex DNA upon binding to non-regular sequence duplexes. In the present study we describe binding properties of chimeric alpha-beta oligodeoxynucleotides in the respect to short DNA duplexes with one, three, and five base pair inversions. Non-natural chimeric TFO's contained alpha-thymidine residues inside (GT) or (GA) core sequences. Modified residues were addressed to AT/TA inversions in duplexes. It was found in the non-denaturing gel-electrophoresis experiments that single or five adjacent base pair inversions in duplexes may be recognized by chimeric alpha-beta TFO's at 10 degrees C and pH 7.8. Three dispersed base pair inversions in the double stranded DNA prevented triplex formation by either (GT) or (GA) chimeras. Estimation of thermal stability of chimeric alpha-beta triplexes showed decrease in T(m) values as compared with unmodified complexes. PMID:16928141

  18. Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

    Science.gov (United States)

    Swasey, Steven M.; Gwinn, Elisabeth G.

    2016-04-01

    The thermal and chemical fragility of DNA nanomaterials assembled by Watson–Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag+, as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag+–DNA nanostructures. Our studies of Ag+-induced assembly of non-complementary DNA oligomers employ strands of 2–24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag+ can be achieved by optimizing solution conditions. These Ag+-mediated duplexes are stable to at least 60 mM Mg2+, higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag+-mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag+-mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’.

  19. CPK-based grid authentication: a step forward

    Institute of Scientific and Technical Information of China (English)

    WANG Hai-yan; WANG Ru-chuan

    2007-01-01

    Effective grid authentication plays a critical role in grid security, which has been recognized as a key issue in the designing and extension of grid technologies. At present, public key infrastructure (PKI) has been widely applied for grid authentication, and this article proposes a novel grid authentication mechanism, which is based on combined public key (CPK) employing elliptic curve cryptography (ECC). The designing structure of the new grid authentication mechanism and its implementation procedure are described in details.Property analysis of the new mechanism is also made in comparison with that of the globus security infrastructure (GSI) authentication, which leads to the conclusion that CPK-based grid authentication, may be applied as an optimized approach towards efficient and effective grid authentication.

  20. A self-adaptive step Cuckoo search algorithm based on dimension by dimension improvement

    Directory of Open Access Journals (Sweden)

    Lu REN

    2015-10-01

    Full Text Available The choice of step length plays an important role in convergence speed and precision of Cuckoo search algorithm. In the paper, a self-adaptive step Cuckoo search algorithm based on dimensional improvement is provided. First, since the step in the original self-adaptive step Cuckoo search algorithm is not updated when the current position of the nest is in the optimal position, simple modification of the step is made for the update. Second, evaluation strategy based on dimension by dimension update is introduced to the modified self-adaptive step Cuckoo search algorithm. The experimental results show that the algorithm can balance the contradiction between the global convergence ability and the precision of optimization. Moreover, the proposed algorithm has better convergence speed.

  1. Multi-agent System for Process Planning in Step-nc Based Manufacturing

    OpenAIRE

    Juan Du; Xianguo Yan

    2012-01-01

    In order to realize STEP-NC-oriented computer numerical control machining and achieve optimal performance in manufacturing, a multi-agent system for process planning in STEP-NC based manufacturing was designed. By analyzing the characteristic of STEP-NC data model, a manufacturing feature-oriented process planning method was proposed in this study and the distributed artificial intelligence methods, namely collaborative multi-agent was employed to accomplish process planning of part. The prop...

  2. Community-based Participatory Research: Necessary Next Steps

    Directory of Open Access Journals (Sweden)

    Zubaida Faridi, MBBS, MPH

    2007-07-01

    Full Text Available Community-based participatory research (CBPR is gaining increasing credence among public health researchers and practitioners. However, there is no standardization in assessing the quality of research methods, the effectiveness of the interventions, and the reporting requirements in the literature. The absence of standardization precludes meaningful comparisons of CBPR studies. Several authors have proposed a broad set of competencies required for CBPR research for both individuals and organizations, but the discussion remains fragmented. The Prevention Research Centers (PRC Program recently began a qualitative assessment of its national efforts, including an evaluation of how PRCs implement CBPR studies. Topics of interest include types of community partnerships; community capacity for research, evaluation, and training; and factors that help and hinder partner relationships. The assessment will likely contribute to the development of a standard set of competencies and resources required for effective CBPR.

  3. Prediction of plant promoters based on hexamers and random triplet pair analysis

    Directory of Open Access Journals (Sweden)

    Noman Nasimul

    2011-06-01

    Full Text Available Abstract Background With an increasing number of plant genome sequences, it has become important to develop a robust computational method for detecting plant promoters. Although a wide variety of programs are currently available, prediction accuracy of these still requires further improvement. The limitations of these methods can be addressed by selecting appropriate features for distinguishing promoters and non-promoters. Methods In this study, we proposed two feature selection approaches based on hexamer sequences: the Frequency Distribution Analyzed Feature Selection Algorithm (FDAFSA and the Random Triplet Pair Feature Selecting Genetic Algorithm (RTPFSGA. In FDAFSA, adjacent triplet-pairs (hexamer sequences were selected based on the difference in the frequency of hexamers between promoters and non-promoters. In RTPFSGA, random triplet-pairs (RTPs were selected by exploiting a genetic algorithm that distinguishes frequencies of non-adjacent triplet pairs between promoters and non-promoters. Then, a support vector machine (SVM, a nonlinear machine-learning algorithm, was used to classify promoters and non-promoters by combining these two feature selection approaches. We referred to this novel algorithm as PromoBot. Results Promoter sequences were collected from the PlantProm database. Non-promoter sequences were collected from plant mRNA, rRNA, and tRNA of PlantGDB and plant miRNA of miRBase. Then, in order to validate the proposed algorithm, we applied a 5-fold cross validation test. Training data sets were used to select features based on FDAFSA and RTPFSGA, and these features were used to train the SVM. We achieved 89% sensitivity and 86% specificity. Conclusions We compared our PromoBot algorithm to five other algorithms. It was found that the sensitivity and specificity of PromoBot performed well (or even better with the algorithms tested. These results show that the two proposed feature selection methods based on hexamer frequencies

  4. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).

  5. Prediction Equations of Energy Expenditure in Chinese Youth Based on Step Frequency during Walking and Running

    Science.gov (United States)

    Sun, Bo; Liu, Yu; Li, Jing Xian; Li, Haipeng; Chen, Peijie

    2013-01-01

    Purpose: This study set out to examine the relationship between step frequency and velocity to develop a step frequency-based equation to predict Chinese youth's energy expenditure (EE) during walking and running. Method: A total of 173 boys and girls aged 11 to 18 years old participated in this study. The participants walked and ran on a…

  6. One-step production of biodiesel from Nannochloropsis sp. on solid base Mg-Zr catalyst

    International Nuclear Information System (INIS)

    Nannochloropsis sp., one kind of green microalgae cultivated autotrophically and axenically in laboratory, is used as raw material to produce biodiesel by one-step method in an amended reactor. The effects of several reaction parameters on transesterification over Mg-Zr solid base catalyst were investigated through both conventional method and one-step method. One-step method could give a higher yield of methyl ester than conventional two-step method, which demonstrates that the present one-step method is suitable for biodiesel production from the microalgae Nannochloropsis sp. Moreover, the present one-step method realizes the convenient in situ separation of catalyst from microalgae residue which can be easily used consequently, reducing the procedure units as well as the overall costs.

  7. Removal of step-edges and corresponding Gibbs ringing in SQUID-based geomagnetic data

    International Nuclear Information System (INIS)

    We present a reliable post processing routine for the elimination of step-edges in SQUID-based geomagnetic data. A special feature of the algorithm is the correction of the A/D converters step response including the acquired Gibbs ringing, which results in smoothly reconstructed data. For this, the dependence of the step-edge shape on its sub-sample position is calculated. To locate the step-edges with sub-sample resolution, the local response of the undecimated wavelet transform to the step-edge is minimized by an optimization procedure. Due to the intrinsic quantization of the step-edge heights, a drift-free reconstruction of the measured quantity is possible. (paper)

  8. Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps

    Czech Academy of Sciences Publication Activity Database

    Šponer, Jiří; Jurečka, Petr; Marchan, I.; Luque, F.J.; Orozco, M.; Hobza, Pavel

    2006-01-01

    Roč. 12, č. 10 (2006), s. 2854-2865. ISSN 0947-6539 R&D Projects: GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z40550506 Keywords : ab initio calculations * DNA structures * nucleobases Subject RIV: BO - Biophysics Impact factor: 5.015, year: 2006

  9. Efficient and provable secure pairing-free security-mediated identity-based identification schemes.

    Science.gov (United States)

    Chin, Ji-Jian; Tan, Syh-Yuan; Heng, Swee-Huay; Phan, Raphael C-W

    2014-01-01

    Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user's secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI) was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions. PMID:25207333

  10. Efficient and Provable Secure Pairing-Free Security-Mediated Identity-Based Identification Schemes

    Directory of Open Access Journals (Sweden)

    Ji-Jian Chin

    2014-01-01

    Full Text Available Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user’s secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions.

  11. The Beyond 12/23 Restriction Is Imposed at the Nicking and Pairing Steps of DNA Cleavage during V(D)J Recombination▿

    OpenAIRE

    Drejer-Teel, Anna H.; Fugmann, Sebastian D.; Schatz, David G.

    2007-01-01

    The beyond 12/23 (B12/23) rule ensures inclusion of a Dβ gene segment in the assembled T-cell receptor (TCR) β variable region exon and is manifest by a failure of direct Vβ-to-Jβ gene segment joining. The restriction is enforced during the DNA cleavage step of V(D)J recombination by the recombination-activating gene 1 and 2 (RAG1/2) proteins and the recombination signal sequences (RSSs) flanking the TCRβ gene segments. Nothing is known about the step(s) at which DNA cleavage is defective or ...

  12. Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns

    Czech Academy of Sciences Publication Activity Database

    Kratochvílová, Irena; Todorciuc, Tatiana; Král, Karel; Němec, Hynek; Bunček, M.; Šebera, Jakub; Záliš, Stanislav; Vokáčová, Zuzana; Sychrovský, Vladimír; Bednárová, Lucie; Mojzeš, P.; Schneider, Bohdan

    2010-01-01

    Roč. 17, 1a (2010), L7-L7. ISSN 1211-5894. [Discussions in Structural Molecular Biology /8./. 18.03.2010-20.03.2010, Nové Hrady] R&D Projects: GA AV ČR KAN401770651; GA ČR GA203/08/1594 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z40550506; CEZ:AV0Z10100520; CEZ:AV0Z40400503; CEZ:AV0Z50520701 Keywords : base-pairing patterns * oligonucleotides * DNA Subject RIV: CF - Physical ; Theoretical Chemistry

  13. DFT Description of Intermolecular Forces between 9-Aminoacridines and DNA Base Pairs

    Directory of Open Access Journals (Sweden)

    Sandra Cotes Oyaga

    2013-01-01

    Full Text Available The B3LYP method with 6-31G* basis set was used to predict the geometries of five 9-aminoacridines (9-AA 1(a–e, DNA base pairs, and respective complexes. Polarizabilities, charge distribution, frontier molecular orbital (FMO, and dipole moments were used to analyze the nature of interactions that allow reasonable drug diffusion levels. The results showed that charge delocalization, high polarizabilities, and high dipole moments play an important role in intermolecular interactions with DNA. The interactions of 9-AA 1(a–e with GC are the strongest. 9-AA 1(d displayed the strongest interaction and 9-AA 1(b the weakest.

  14. Unconventional pairing originating from disconnected Fermi surfaces in the iron-based superconductor

    Energy Technology Data Exchange (ETDEWEB)

    Kuroki, Kazuhiko; Usui, Hidetomo [Department of Applied Physics and Chemistry, The University of Electro-Communications, Chofu, Tokyo 182-8585 (Japan); Onari, Seiichiro; Tanaka, Yukio [Department of Applied Physics, Nagoya University, Nagoya 464-8603 (Japan); Arita, Ryotaro [Department of Applied Physics, University of Tokyo, Hongo, Tokyo 113-8656 (Japan); Kontani, Hiroshi [Department of Physics, Nagoya University, Nagoya 464-8602 (Japan); Aoki, Hideo [Department of Physics, University of Tokyo, Hongo, Tokyo 113-0033 (Japan)], E-mail: kuroki@vivace.e-one.uec.ac.jp

    2009-02-15

    For an iron-based high T{sub c} superconductor LaFeAsO{sub 1-x}F{sub x}, we construct a minimal model where all of the five Fe d bands turn out to be involved. We then investigate the origin of superconductivity with a five-band random-phase approximation by solving the Eliashberg equation. We conclude that the spin fluctuation modes arising from the nesting between the disconnected Fermi pockets realize basically an extended s-wave pairing, where the gap changes sign across the nesting vector.

  15. Superior coexistence: systematicALLY regulatING land subsidence BASED on set pair theory

    Science.gov (United States)

    Chen, Y.; Gong, S.-L.

    2015-11-01

    Anthropogenic land subsidence is an environmental side effect of exploring and using natural resources in the process of economic development. The key points of the system for controlling land subsidence include cooperation and superior coexistence while the economy develops, exploring and using natural resources, and geological environmental safety. Using the theory and method of set pair analysis (SPA), this article anatomises the factors, effects, and transformation of land subsidence. Based on the principle of superior coexistence, this paper promotes a technical approach to the system for controlling land subsidence, in order to improve the prevention and control of geological hazards.

  16. A Multiparty Controlled Bidirectional Quantum Secure Direct Communication and Authentication Protocol Based on EPR Pairs

    Science.gov (United States)

    Chang, Yan; Zhang, Shi-Bin; Yan, Li-Li; Sheng, Zhi-Wei

    2013-06-01

    A multiparty controlled bidirectional quantum secure direct communication and authentication protocol is proposed based on EPR pair and entanglement swapping. The legitimate identities of communicating parties are encoded to Bell states which act as a detection sequence. Secret messages are transmitted by using the classical XOR operation, which serves as a one-time-pad. No photon with secret information transmits in the quantum channel. Compared with the protocols proposed by Wang et al. [Acta Phys. Sin. 56 (2007) 673; Opt. Commun. 266 (2006) 732], the protocol in this study implements bidirectional communication and authentication, which defends most attacks including the ‘man-in-the-middle’ attack efficiently.

  17. Theoretical study of metal ion binding in modified and natural cytosine-cytosine base pairs

    Czech Academy of Sciences Publication Activity Database

    Šebera, Jakub; Sugiyama, K.; Ono, A.; Mulder, J.; Bickelhaupt, F. M.; Tanaka, Y.; Sychrovský, Vladimír; Guerra, C. F.

    2013-01-01

    Roč. 20, č. 1 (2013), s. 39-39. ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /11./. 14.03.2013-16.03.2013, Nové Hrady] R&D Projects: GA ČR GAP205/10/0228; GA ČR(CZ) GAP304/10/1951; GA TA ČR TA01011165 Institutional support: RVO:61388963 Keywords : DFT * NMR * base pair * metal-mediated Subject RIV: CF - Physical ; Theoretical Chemistry

  18. Theoretical investigation of the hydrogen atom transfer in the hydrated A–T base pair

    International Nuclear Information System (INIS)

    Highlights: ► We study the hydrated A–T base pair with 2 and 4 water molecules. ► We consider the dynamics of hydrogen transfer in the hydrogen bridges. ► We compare this study with experimental data and simple schemes. - Abstract: The hydrated A–T base pair has been studied in order to understand the structural modifications and their electronic rearrangements induced by the movement of the hydrogen atoms in the H-bonds. The comparison of these results with that of the nonhydrated system can explain the role of the H-bonds of the water molecules in this system. Two naïve schemes have been considered, one where the hydrogen bonds of the water molecules are only indirectly involved in the hydrogen atoms transfer between the bases and another where the water molecules are directly involved in this transfer. The results support the idea that the real mechanisms are more complexes than these schemes. Some new stable structures of the A–T(H2O)2 and the A–T(H2O)4 systems have been found and the mechanisms of their generations have been analysed.

  19. The Beyond 12/23 Restriction Is Imposed at the Nicking and Pairing Steps of DNA Cleavage during V(D)J Recombination▿

    Science.gov (United States)

    Drejer-Teel, Anna H.; Fugmann, Sebastian D.; Schatz, David G.

    2007-01-01

    The beyond 12/23 (B12/23) rule ensures inclusion of a Dβ gene segment in the assembled T-cell receptor (TCR) β variable region exon and is manifest by a failure of direct Vβ-to-Jβ gene segment joining. The restriction is enforced during the DNA cleavage step of V(D)J recombination by the recombination-activating gene 1 and 2 (RAG1/2) proteins and the recombination signal sequences (RSSs) flanking the TCRβ gene segments. Nothing is known about the step(s) at which DNA cleavage is defective or how TCRβ locus sequences contribute to these defects. To address this, we examined the steps of DNA cleavage by the RAG proteins using TCRβ locus V, D, and J RSS oligonucleotide substrates. The results demonstrate that the B12/23 rule is enforced through slow nicking of Jβ substrates and to some extent through poor synapsis of Vβ and Jβ substrates. Nicking is controlled largely by the coding flank and, unexpectedly, the RSS spacer, while synapsis is controlled primarily by the RSS nonamer. The results demonstrate that different Jβ substrates are crippled at different steps of cleavage by distinct combinations of defects in the various DNA elements and strongly suggest that the DNA nicking step of V(D)J recombination can be rate limiting in vivo. PMID:17636023

  20. The beyond 12/23 restriction is imposed at the nicking and pairing steps of DNA cleavage during V(D)J recombination.

    Science.gov (United States)

    Drejer-Teel, Anna H; Fugmann, Sebastian D; Schatz, David G

    2007-09-01

    The beyond 12/23 (B12/23) rule ensures inclusion of a Dbeta gene segment in the assembled T-cell receptor (TCR) beta variable region exon and is manifest by a failure of direct Vbeta-to-Jbeta gene segment joining. The restriction is enforced during the DNA cleavage step of V(D)J recombination by the recombination-activating gene 1 and 2 (RAG1/2) proteins and the recombination signal sequences (RSSs) flanking the TCRbeta gene segments. Nothing is known about the step(s) at which DNA cleavage is defective or how TCRbeta locus sequences contribute to these defects. To address this, we examined the steps of DNA cleavage by the RAG proteins using TCRbeta locus V, D, and J RSS oligonucleotide substrates. The results demonstrate that the B12/23 rule is enforced through slow nicking of Jbeta substrates and to some extent through poor synapsis of Vbeta and Jbeta substrates. Nicking is controlled largely by the coding flank and, unexpectedly, the RSS spacer, while synapsis is controlled primarily by the RSS nonamer. The results demonstrate that different Jbeta substrates are crippled at different steps of cleavage by distinct combinations of defects in the various DNA elements and strongly suggest that the DNA nicking step of V(D)J recombination can be rate limiting in vivo. PMID:17636023

  1. A Web-Based Intervention to Encourage Walking (StepWise): Pilot Randomized Controlled Trial

    OpenAIRE

    Hargreaves, Elaine Anne; Mutrie, Nanette; Fleming, Jade Dallas

    2016-01-01

    Background Despite Internet-based interventions that incorporate pedometers with appropriate goal-setting processes and other theoretically-based behavior change strategies being proposed as a means of increasing walking behavior, few have incorporated all of these key features or assessed maintenance of behavior change. Objective The objective of our study was to investigate the effect of a 12-week pedometer step goal walking program individually tailored to baseline step counts, combined wi...

  2. A model for avian magnetoreception by coupling magnetite-based mechanism with radical-pair-based mechanism

    CERN Document Server

    Lu, Yan

    2012-01-01

    Many species of animals have been testified to use the geomagnetic field for their navigation, but the biophysical mechanism of magnetoreception has remained enigmatic. This paper presents a biophysical model consisting of magnetite-based mechanism and radical-pair-based mechanism for the avian magnetoreception. The amplitude of resultant magnetic field outside the magnetic particles correspond to the geomagnetic field direction and effect the yield of singlet/triplet state products in the radical pair reactions, therefore the yield of singlet/triplet state products can connect with the geomagnetic field information for orientational detection by the proposed model. The resultant magnetic fields corresponds to two materials with different magnetic properties were analysed under different directions of the geomagnetic field. The results shown that the ferromagnetic particles in organisms could provide more significant change of singlet state products than that of superparamagnetic particles, and the period of ...

  3. Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory

    Science.gov (United States)

    Jensen, Lasse; Govind, Niranjan

    2009-08-01

    In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.

  4. Damage mechanism of hydroxyl radicals toward adenine—thymine base pair

    International Nuclear Information System (INIS)

    The adenine—thymine base pair was studied in the presence of hydroxyl radicals in order to probe the hydrogen bond effect. The results show that the hydrogen bonds have little effect on the hydroxylation and dehydrogenation happened at the sites, which are not involved in a hydrogen bond, while at the sites involved in hydrogen bond formation in the base pair, the reaction becomes more difficult, both in view of the free energy barrier and the exothermicity. With a 6–311++G(d,p) level of description, both B3LYP and MP2 methods confirm that the C8 site of isolated adenine has the highest possibility to form covalent bond with the hydroxyl radicals, though with different energetics: B3LYP predicts a barrierless pathway, while MP2 finds a transition state with an energy of 106.1 kJ/mol. For the dehydrogenation reactions, B3LYP method predicts that the free energy barrier increases in the order of HN9 < HN61 < HN62 < H2 < H8. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  5. A Bilinear Pairing-Based Dynamic Key Management and Authentication for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Chin-Ling Chen

    2015-01-01

    Full Text Available In recent years, wireless sensor networks have been used in a variety of environments; a wireless network infrastructure, established to communicate and exchange information in a monitoring area, has also been applied in different environments. However, for sensitive applications, security is the paramount issue. In this paper, we propose using bilinear pairing to design dynamic key management and authentication scheme of the hierarchical sensor network. We use the dynamic key management and the pairing-based cryptography (PBC to establish the session key and the hash message authentication code (HMAC to support the mutual authentication between the sensors and the base station. In addition, we also embed the capability of the Global Positioning System (GPS to cluster nodes to find the best path of the sensor network. The proposed scheme can also provide the requisite security of the dynamic key management, mutual authentication, and session key protection. Our scheme can defend against impersonation attack, replay attack, wormhole attack, and message manipulation attack.

  6. Gapped graphene-based Josephson junction with d-wave pair coupling

    Energy Technology Data Exchange (ETDEWEB)

    Goudarzi, H., E-mail: h.goudarzi@urmia.ac.ir; Khezerlou, M., E-mail: m.khezerlou@urmia.ac.ir; Dezhaloud, T.

    2013-06-15

    Highlights: • We aim to study the influence of the Josephson current passing through a d-wave S/I/S gapped graphene-based junction. • We investigate how the Andreev bound states and the Josephson current are affected by characteristic of d-wave pairing asymmetry. • It is shown that the Josephson current for special range of phase vanishes and the position of the maximum current depends on the mass gap of graphene. -- Abstract: The Josephson current passing through a S/I/S gapped graphene-based junction, where superconductivity in the S region is induced by depositing unconventional d-wave superconductor is investigated. The energy levels of massive Dirac fermions are exactly found for Andreev bound states. We illustrate the effect of characteristic of d-wave pairing symmetry on the Andreev bound states and the Josephson current. It is shown that the Josephson current vanishes for special range of superconductivity phase, φ = φ{sub 1} − φ{sub 2} and the position of the maximum current depends on the mass gap of graphene. The critical supercurrent varies in an oscillatory manner as function of the barrier strength, so that the period of oscillations does not change by increasing the effective mass of quasiparticles.

  7. Gapped graphene-based Josephson junction with d-wave pair coupling

    International Nuclear Information System (INIS)

    Highlights: • We aim to study the influence of the Josephson current passing through a d-wave S/I/S gapped graphene-based junction. • We investigate how the Andreev bound states and the Josephson current are affected by characteristic of d-wave pairing asymmetry. • It is shown that the Josephson current for special range of phase vanishes and the position of the maximum current depends on the mass gap of graphene. -- Abstract: The Josephson current passing through a S/I/S gapped graphene-based junction, where superconductivity in the S region is induced by depositing unconventional d-wave superconductor is investigated. The energy levels of massive Dirac fermions are exactly found for Andreev bound states. We illustrate the effect of characteristic of d-wave pairing symmetry on the Andreev bound states and the Josephson current. It is shown that the Josephson current vanishes for special range of superconductivity phase, φ = φ1 − φ2 and the position of the maximum current depends on the mass gap of graphene. The critical supercurrent varies in an oscillatory manner as function of the barrier strength, so that the period of oscillations does not change by increasing the effective mass of quasiparticles

  8. Performance Comparison of Variable Step Size Techniques of Sato and Godard-Based Blind Equalizer

    Science.gov (United States)

    Suthendran, K.; Arivoli, T.

    2015-04-01

    The modern digital high speed wireless communication system demands quick convergence rate and low steady state error. The balancing between the demands can be achieved by opting step size. Thus, it is essential to define new algorithms to equalize channels and mitigate noise in communications. It is renowned that time varying step size blind equalization technique can speed up the convergence rate and minimize the misadjustment. This work presents a variable step size (VSS) approach based on godard blind equalization algorithm to resolve the conflict between the convergence rate and precision of the fixed step-size godard algorithm. The results of this projected approach is compared with the existing variable step size sato algorithm for a pulse amplitude modulated (PAM) input symbol.

  9. Effect of base-pair inhomogeneities on charge transport along the DNA molecule, mediated by twist and radial polarons

    International Nuclear Information System (INIS)

    Some recent results for a three-dimensional, semi-classical, tight-binding model for DNA show that there are two types of polarons, namely radial and twist polarons, which can transport charge along the DNA molecule. However, the existence of two types of base pairs in real DNA makes it crucial to find out if charge transport also exists in DNA chains with different base pairs. In this paper, we address this problem in its simple case, a homogeneous chain except for a single different base pair, which we call a base-pair inhomogeneity, and its effect on charge transport. Radial polarons experience either reflection or trapping. However, twist polarons are good candidates for charge transport along real DNA. This transport is also very robust with respect to weak parametric and diagonal disorder

  10. Research on test of product based on spatial sampling criteria and variable step sampling mechanism

    Science.gov (United States)

    Li, Ruihong; Han, Yueping

    2014-09-01

    This paper presents an effective approach for online testing the assembly structures inside products using multiple views technique and X-ray digital radiography system based on spatial sampling criteria and variable step sampling mechanism. Although there are some objects inside one product to be tested, there must be a maximal rotary step for an object within which the least structural size to be tested is predictable. In offline learning process, Rotating the object by the step and imaging it and so on until a complete cycle is completed, an image sequence is obtained that includes the full structural information for recognition. The maximal rotary step is restricted by the least structural size and the inherent resolution of the imaging system. During online inspection process, the program firstly finds the optimum solutions to all different target parts in the standard sequence, i.e., finds their exact angles in one cycle. Aiming at the issue of most sizes of other targets in product are larger than that of the least structure, the paper adopts variable step-size sampling mechanism to rotate the product specific angles with different steps according to different objects inside the product and match. Experimental results show that the variable step-size method can greatly save time compared with the traditional fixed-step inspection method while the recognition accuracy is guaranteed.

  11. Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems

    DEFF Research Database (Denmark)

    Börjesson, Karl; Preus, Søren; El-Sagheer, Afaf;

    2009-01-01

    We present the first nucleobase analog fluorescence resonance energy transfer (FRET)-pair. The pair consists of tCO, 1,3-diaza-2-oxophenoxazine, as an energy donor and the newly developed tC(nitro), 7-nitro-1,3-diaza-2-oxophenothiazine, as an energy acceptor. The FRET-pair successfully monitors d...

  12. Sheared-type G(anti).C(syn) base-pair: a unique d(GXC) loop closure motif.

    Science.gov (United States)

    Chin, Ko-Hsin; Chou, Shan-Ho

    2003-05-30

    Stable DNA loop structures closed by a novel G.C base-pair have been determined for the single-residue d(GXC) loops (X=A, T, G or C) in low-salt solution by high-resolution nuclear magnetic resonance (NMR) techniques. The closing G.C base-pair in these loops is not of the canonical Watson-Crick type, but adopts instead a unique sheared-type (trans Watson-Crick/sugar-edge) pairing, like those occurring in the sheared mismatched G.A or A.C base-pair, to draw the two opposite strands together. The cytidine residue in the closing base-pair is transformed into the rare syn domain to form two H-bonds with the guanine base and to prevent the steric clash between the G 2NH(2) and the C H-5 protons. Besides, the sugar pucker of the syn cytidine is still located in the regular C2'-endo domain, unlike the C3'-endo domain adopted for the pyrimidines of the out-of-alternation left-handed Z-DNA structure. The facile formation of the compact d(GXC) loops closed by a unique sheared-type G(anti).C(syn) base-pair demonstrates the great potential of the single-stranded d(GXC) triplet repeats to fold into stable hairpins. PMID:12758081

  13. Cloud Base Height Measurements at Manila Observatory: Initial Results from Constructed Paired Sky Imaging Cameras

    Science.gov (United States)

    Lagrosas, N.; Tan, F.; Antioquia, C. T.

    2014-12-01

    Fabricated all sky imagers are efficient and cost effective instruments for cloud detection and classification. Continuous operation of this instrument can result in the determination of cloud occurrence and cloud base heights for the paired system. In this study, a fabricated paired sky imaging system - consisting two commercial digital cameras (Canon Powershot A2300) enclosed in weatherproof containers - is developed in Manila Observatory for the purpose of determining cloud base heights at the Manila Observatory area. One of the cameras is placed on the rooftop of Manila Observatory and the other is placed on the rooftop of the university dormitory, 489m from the first camera. The cameras are programmed to simultaneously gather pictures every 5 min. Continuous operation of these cameras were implemented since the end of May of 2014 but data collection started end of October 2013. The data were processed following the algorithm proposed by Kassianov et al (2005). The processing involves the calculation of the merit function that determines the area of overlap of the two pictures. When two pictures are overlapped, the minimum of the merit function corresponds to the pixel column positions where the pictures have the best overlap. In this study, pictures of overcast sky prove to be difficult to process for cloud base height and were excluded from processing. The figure below shows the initial results of the hourly average of cloud base heights from data collected from November 2013 to July 2014. Measured cloud base heights ranged from 250m to 1.5km. These are the heights of cumulus and nimbus clouds that are dominant in this part of the world. Cloud base heights are low in the early hours of the day indicating low convection process during these times. However, the increase in the convection process in the atmosphere can be deduced from higher cloud base heights in the afternoon. The decrease of cloud base heights after 15:00 follows the trend of decreasing solar

  14. Ionic force field optimization based on single-ion and ion-pair solvation properties

    CERN Document Server

    Fyta, Maria; Dzubiella, Joachim; Vrbka, Lubos; Netz, Roland R

    2009-01-01

    Molecular dynamics simulations of ionic solutions depend sensitively on the force fields employed for the ions. To resolve the fine differences between ions of the same valence and roughly similar size and in particular to correctly describe ion-specific effects, it is clear that accurate force fields are necessary. In the past, optimization strategies for ionic force fields either considered single-ion properties (such as the solvation free energy at infinite dilution or the ion-water structure) or ion-pair properties (in the form of ion-ion distribution functions). In this paper we investigate strategies to optimize ionic force fields based on single-ion and ion-pair properties simultaneously. To that end, we simulate five different salt solutions, namely CsCl, KCl, NaI, KF, and CsI, at finite ion concentration. The force fields of these ions are systematically varied under the constraint that the single-ion solvation free energy matches the experimental value, which reduces the two-dimensional $\\{\\sigma,\\e...

  15. GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

    Science.gov (United States)

    Nemoto, Wataru; Yamanishi, Yoshihiro; Limviphuvadh, Vachiranee; Saito, Akira; Toh, Hiroyuki

    2016-09-01

    G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-dimers or higher-order molecular complexes. Many GPCRs exert a wide variety of molecular functions by forming specific combinations of GPCR subtypes. In addition, some GPCRs are reportedly associated with diseases. GPCR oligomerization is now recognized as an important event in various biological phenomena, and many researchers are investigating this subject. We have developed a support vector machine (SVM)-based method to predict interacting pairs for GPCR oligomerization, by integrating the structure and sequence information of GPCRs. The performance of our method was evaluated by the Receiver Operating Characteristic (ROC) curve. The corresponding area under the curve was 0.938. As far as we know, this is the only prediction method for interacting pairs among GPCRs. Our method could accelerate the analyses of these interactions, and contribute to the elucidation of the global structures of the GPCR networks in membranes. Proteins 2016; 84:1224-1233. © 2016 Wiley Periodicals, Inc. PMID:27191053

  16. Extruded polymer films pigmented with a heterogeneous ion-pair based lumophore for O2 sensing.

    Science.gov (United States)

    Mills, Andrew; Graham, Ashleigh

    2013-11-01

    A novel approach to polymeric Ru(II)-diimine luminescent O2 sensors is described. The Ru(II)-diimine, tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride ([Ru(dpp)3](2+)), is first ion-paired to the surface of heterogeneous TiO2 particles, rendered negatively charged due to the alkali nature of the aqueous solution, to produce an O2 sensitive pigment with a strikingly high oxygen sensitivity (i.e. PO2 (S = 1/2) = 0.002 atm, where PO2 (S = 1/2) is defined as the amount of oxygen required to reduce the initial, oxygen free luminescence by 50%), and a rapid response to oxygen. The pigment is extruded in low density polyethylene (LDPE) to produce a thin (60 μm), flexible, O2 sensing plastic film, with an O2 sensitivity (PO2 (S = 1/2) = 0.84 atm) comparable to the more traditional homogeneous lumophore ion-pair based O2 sensor ink films reported in the literature. PMID:24040643

  17. Exploiting bounded signal flow for graph orientation based on cause-effect pairs

    Directory of Open Access Journals (Sweden)

    Niedermeier Rolf

    2011-08-01

    Full Text Available Abstract Background We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases. Results We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances. Conclusions Several biologically relevant special cases of the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies.

  18. Homosexual Pairing within a Swarm-Based Mating System: The Case of the Chironomid Midge

    Directory of Open Access Journals (Sweden)

    Athol J. McLachlan

    2011-01-01

    Full Text Available Homosexuality has been dubbed the Darwinian paradox, because it raises the question of how behaviour that would seem to reduce the chance of successful mating can be maintained by natural selection. This question rests on the assumption that same sex mating is the result of active choice of partner, hardwired into the mating behaviour, but there is an alternative explanation for such behaviour. I refer to the possibility that same-sex mating is the result, not of adaptive behaviour at all, but rather of errors due to imprecise sensory machinery. Such an explanation finds support within the mating system of insects with swarm-based mating systems. To explore this case, I turn to the common chironomid midge. I show that homosexual pairing here, exclusively involving male/male pairs, is common. I attempt to show that this observation, together with data on insect predators of swarming midges, can be used to penetrate the mysteries of this fascinating but elusive mating system.

  19. Participation in 12-Step-Based Fellowships Among Dually-Diagnosed Persons

    OpenAIRE

    Laudet, Alexandre B.; Magura, Stephen; Vogel, Howard S.; Knight, Edward L.

    2003-01-01

    Twelve-step groups (12SG), a useful recovery resource, are underutilized by dually-diagnosed persons. There has been little empirical research in this area. This study followed members of a dual-focus 12-step-based fellowship (N = 277) over one year to gain a greater understanding of participation in both specialized dual focus and traditional 12SG among dually-diagnosed persons, including reasons for attending, perceived benefits of and obstacles to affiliation, and predictors of affiliation...

  20. Clamping down on weak terminal base pairs: oligonucleotides with molecular caps as fidelity-enhancing elements at the 5′- and 3′-terminal residues

    OpenAIRE

    Narayanan, Sukunath; Gall, Julia; Richert, Clemens

    2004-01-01

    The base-pairing fidelity of oligonucleotides depends on the identity of the nucleobases involved and the position of matched or mismatched base pairs in the duplex. Nucleobases forming weak base pairs, as well as a terminal position favor mispairing. We have searched for 5′-appended acylamido caps that enhance the stability and base-pairing fidelity of oligonucleotides with a 5′-terminal 2′-deoxyadenosine residue using combinatorial synthesis and MALDI-monitored nuclease selections. This pro...

  1. PID controller auto-tuning based on process step response and damping optimum criterion.

    Science.gov (United States)

    Pavković, Danijel; Polak, Siniša; Zorc, Davor

    2014-01-01

    This paper presents a novel method of PID controller tuning suitable for higher-order aperiodic processes and aimed at step response-based auto-tuning applications. The PID controller tuning is based on the identification of so-called n-th order lag (PTn) process model and application of damping optimum criterion, thus facilitating straightforward algebraic rules for the adjustment of both the closed-loop response speed and damping. The PTn model identification is based on the process step response, wherein the PTn model parameters are evaluated in a novel manner from the process step response equivalent dead-time and lag time constant. The effectiveness of the proposed PTn model parameter estimation procedure and the related damping optimum-based PID controller auto-tuning have been verified by means of extensive computer simulations. PMID:24035643

  2. Student Responses to a Context- and Inquiry-Based Three-Step Teaching Model

    Science.gov (United States)

    Walan, Susanne; Rundgren, Shu-Nu Chang

    2015-01-01

    Research has indicated that both context- and inquiry-based approaches could increase student interest in learning sciences. This case study aims to present a context- and inquiry-based combined teaching approach, using a three-step teaching model developed by the PROFILES project, and investigates Swedish students' responses to the activity. A…

  3. Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition

    Science.gov (United States)

    Kuznetsov, Nikita A.; Bergonzo, Christina; Campbell, Arthur J.; Li, Haoquan; Mechetin, Grigory V.; de los Santos, Carlos; Grollman, Arthur P.; Fedorova, Olga S.; Zharkov, Dmitry O.; Simmerling, Carlos

    2015-01-01

    Formamidopyrimidine-DNA glycosylase (Fpg) excises 8-oxoguanine (oxoG) from DNA but ignores normal guanine. We combined molecular dynamics simulation and stopped-flow kinetics with fluorescence detection to track the events in the recognition of oxoG by Fpg and its mutants with a key phenylalanine residue, which intercalates next to the damaged base, changed to either alanine (F110A) or fluorescent reporter tryptophan (F110W). Guanine was sampled by Fpg, as evident from the F110W stopped-flow traces, but less extensively than oxoG. The wedgeless F110A enzyme could bend DNA but failed to proceed further in oxoG recognition. Modeling of the base eversion with energy decomposition suggested that the wedge destabilizes the intrahelical base primarily through buckling both surrounding base pairs. Replacement of oxoG with abasic (AP) site rescued the activity, and calculations suggested that wedge insertion is not required for AP site destabilization and eversion. Our results suggest that Fpg, and possibly other DNA glycosylases, convert part of the binding energy into active destabilization of their substrates, using the energy differences between normal and damaged bases for fast substrate discrimination. PMID:25520195

  4. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs.

    Science.gov (United States)

    Fang, Wei; Chen, Ji; Rossi, Mariana; Feng, Yexin; Li, Xin-Zheng; Michaelides, Angelos

    2016-06-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  5. Theoretical studies on the intermolecular interactions of potentially primordial base-pair analogues

    Czech Academy of Sciences Publication Activity Database

    Šponer, Judit E.; Vázquez-Mayagoitia, Á.; Sumpter, B.G.; Leszczynski, J.; Šponer, Jiří; Otyepka, M.; Banáš, P.; Fuentes-Cabrera, M.

    2010-01-01

    Roč. 16, č. 10 (2010), s. 3057-3065. ISSN 0947-6539 R&D Projects: GA MŠk(CZ) LC06030; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476 Grant ostatní: GA MŠk(CZ) LC512; GA AV ČR(CZ) IAA400550701; GA ČR(CZ) GD203/09/H046 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : quantum chemistry * base pairing * origin of life Subject RIV: BO - Biophysics Impact factor: 5.476, year: 2010

  6. POINT PATTERN MATCHING ALGORITHM BASED ON POINT PAIR TOPOLOGICAL CHARACTERISTICS AND SPECTRAL MATCHING

    Institute of Scientific and Technical Information of China (English)

    Lu Chunyan; Zou Huanxin; Zhao Jian; Zhou Shilin

    2012-01-01

    Most of the Point Pattern Matching (PPM) algorithm performs poorly when the noise of the point's position and outliers exist.This paper presents a novel and robust PPM algorithm which combined Point Pair Topological Characteristics (PPTC) and Spectral Matching (SM) together to solve the afore mentioned issues.In which PPTC,a new shape descriptor,is firstly proposed.A new comparability measurement based on PPTC is defined as the matching probability.Finally,the correct matching results are achieved by the spectral matching method.The synthetic data experiments show its robustness by comparing with the other state-of-art algorithms and the real world data experiments show its effectiveness.

  7. Gapped graphene-based Josephson junction with d-wave pair coupling

    Science.gov (United States)

    Goudarzi, H.; Khezerlou, M.; Dezhaloud, T.

    2013-06-01

    The Josephson current passing through a S/I/S gapped graphene-based junction, where superconductivity in the S region is induced by depositing unconventional d-wave superconductor is investigated. The energy levels of massive Dirac fermions are exactly found for Andreev bound states. We illustrate the effect of characteristic of d-wave pairing symmetry on the Andreev bound states and the Josephson current. It is shown that the Josephson current vanishes for special range of superconductivity phase, φ = φ1 - φ2 and the position of the maximum current depends on the mass gap of graphene. The critical supercurrent varies in an oscillatory manner as function of the barrier strength, so that the period of oscillations does not change by increasing the effective mass of quasiparticles.

  8. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

    Science.gov (United States)

    2016-01-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  9. Comment Fail-Stop Blind Signature Scheme Design Based on Pairings

    Institute of Scientific and Technical Information of China (English)

    HU Xiaoming; HUANG Shangteng

    2006-01-01

    Fail-stop signature schemes provide security for a signer against forgeries of an enemy with unlimited computational power by enabling the signer to provide a proof of forgery when a forgery happens. Chang et al proposed a robust fail-stop blind signature scheme based on bilinear pairings. However, in this paper, it will be found that there are several mistakes in Chang et al' fail-stop blind signature scheme. Moreover, it will be pointed out that this scheme doesn' meet the property of a fail-stop signature: unconditionally secure for a signer. In Chang et al' scheme, a forger can forge a valid signature that can' be proved by a signer using the "proof of forgery". The scheme also doesn' possess the unlinkability property of a blind signature.

  10. Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.

    Directory of Open Access Journals (Sweden)

    Miguel M Fonseca

    Full Text Available BACKGROUND: Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates--the "codon-anticodon adaptation hypothesis" and the "wobble versatility hypothesis"--have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent "wobble cost hypothesis". PRINCIPAL FINDINGS: In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich. These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility. CONCLUSIONS/SIGNIFICANCE: Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".

  11. Alpha Beta Monitoring System Based on a Pair of Simultaneous Multi Wire Proportional Counters

    International Nuclear Information System (INIS)

    A new approach for a simultaneous alpha beta contamination monitoring system is presented. In nuclear environments or laboratories working with open radioactive sources there exists a risk of contamination. In order to avoid external contamination hazards, hand & foot alpha beta monitoring systems are needed. Usually, monitoring systems are based on large area Multi Wire Proportional Counters (MWPC).Generally, in the MWPC detectors the filling gas is supplied by a continuous gas supply system. The filling gas should not exhibit appreciable electron attachment coefficient. Typically, a noble gas such as Argon Methane, 90%Ar+10%CH4 is in use. This method of measurement is effective, yet it requires expensive maintenance costs due to gas flow control and periodical replacements. Several hand held commercial detectors such as Rotem Ind. PA-100, are based on free air flow alpha MWPC. Due to the energy released from the alpha particles in the filling gas a large number of ion pairs are formed. Despite the electron attachment coefficient of free air, a measurable pulse is obtained. Contrary to alpha sources, beta emitters deposit only a small part of their energy. In order to obtain a measurable pulse from beta interactions, oxygen free gas is required. Gas sealed detectors which are appropriate for beta measurements, require a relative thick entrance window in order to avoid gas leakage. Thick windows absorb alpha particles so that they are not appropriate for alpha measurement. The presented approach combines a pair of simultaneous MWPC assembled in a ôpancakeö type configuration; the sealed gas beta counter is located behind a free air alpha detector. This approach enables simultaneous alpha-beta measurement without needing continuous gas supply

  12. Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation

    DEFF Research Database (Denmark)

    Christensen, Ole Fredslund

    2012-01-01

    Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker-based rel......Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker......-based relationship matrix and the pedigree-based relationship matrix. The compatibility issue involves which allele frequencies to use in the marker-based relationship matrix, and also that adjustments of this matrix to the pedigree-based relationship matrix are needed. In addition, it has been overlooked that it...... base population. Here, two ideas are explored. The first idea is to instead adjust the pedigree-based relationship matrix to be compatible to the marker-based relationship matrix, whereas the second idea is to include the likelihood for the observed markers. A single-step method is used where the...

  13. Novel H+-Ion Sensor Based on a Gated Lateral BJT Pair

    Directory of Open Access Journals (Sweden)

    Heng Yuan

    2015-12-01

    Full Text Available An H+-ion sensor based on a gated lateral bipolar junction transistor (BJT pair that can operate without the classical reference electrode is proposed. The device is a special type of ion-sensitive field-effect transistor (ISFET. Classical ISFETs have the advantage of miniaturization, but  they are difficult to fabricate by a single fabrication process because of the bulky and brittle reference electrode materials. Moreover, the reference electrodes need to be separated from the sensor device in some cases. The proposed device is composed of two gated lateral BJT components, one of which had a silicide layer while the other was without the layer. The two components were operated under the metal-oxide semiconductor field-effect transistor (MOSFET-BJT hybrid mode, which can be controlled by emitter voltage and base current. Buffer solutions with different pH values were used as the sensing targets to verify the characteristics of the proposed device. Owing to their different sensitivities, both components could simultaneously detect the H+-ion concentration and function as a reference to each other. Per the experimental results, the sensitivity of the proposed device was found to be approximately 0.175 μA/pH. This experiment demonstrates enormous potential to lower the cost of the ISFET-based sensor technology.

  14. Effect of base-pair inhomogeneities on charge transport along DNA mediated by twist and radial polarons

    OpenAIRE

    Palmero, F.; Archilla, J. F. R.; Hennig, D.; Romero, F. R.

    2003-01-01

    Some recent results for a three--dimensional, semi--classical, tight--binding model for DNA show that there are two types of polarons, named radial and twist polarons, that can transport charge along the DNA molecule. However, the existence of two types of base pairs in real DNA, makes it crucial to find out if charge transport also exist in DNA chains with different base pairs. In this paper we address this problem in its simple case, an homogeneous chain except for a single different base p...

  15. Testing for direct genetic effects using a screening step in family-based association studies

    Directory of Open Access Journals (Sweden)

    Sharon M Lutz

    2013-11-01

    Full Text Available In genome wide association studies (GWAS, families based studies tend to have less power to detect genetic associations than population based studies, such as case-control studies. This can be an issue when testing if genes in a family based GWAS have a direct effect on the phenotype of interest or if the genes act indirectly through a secondary phenotype. When multiple SNPs are tested for a direct effect in the family based study, a screening step can be used to minimize the burden of multiple comparisons in the causal analysis. We propose a 2-stage screening step that can be incorporated into the family based association test (FBAT approach similar to the conditional mean model approach in the VanSteen-algorithm [1]. Simulations demonstrate that the type 1 error is preserved and this method is advantageous when multiple markers are tested. This method is illustrated by an application to the Framingham Heart Study.

  16. Simulation-based investigation of the paired-gear method in cod-end selectivity studies

    DEFF Research Database (Denmark)

    Herrmann, Bent; Frandsen, Rikke; Holst, René; O'Neill, F.G.

    had a small mesh cover. Thus, estimates of the selectivity parameters of the test cod-end can be made using both the paired-gear method and the covered cod-end method. These estimates are compared and, as it is assumed that the covered cod-end method is objective, we conclude that the paired...

  17. Pairing symmetries of several iron-based superconductor families and some similarities with cuprates and heavy-fermions

    Directory of Open Access Journals (Sweden)

    Das Tanmoy

    2012-03-01

    Full Text Available We show that, by using the unit-cell transformation between 1 Fe per unit cell to 2 Fe per unit cell, one can qualitatively understand the pairing symmetry of several families of iron-based superconductors. In iron-pnictides and iron-chalcogenides, the nodeless s±-pairing and the resulting magnetic resonance mode transform nicely between the two unit cells, while retaining all physical properties unchanged. However, when the electron-pocket disappears from the Fermi surface with complete doping in KFe2As2, we find that the unit-cell invariant requirement prohibits the occurrence of s±-pairing symmetry (caused by inter-hole-pocket nesting. However, the intra-pocket nesting is compatible here, which leads to a nodal d-wave pairing. The corresponding Fermi surface topology and the pairing symmetry are similar to Ce-based heavy-fermion superconductors. Furthermore, when the Fermi surface hosts only electron-pockets in KyFe2-xSe2, the inter-electron-pocket nesting induces a nodeless and isotropic d-wave pairing. This situation is analogous to the electron-doped cuprates, where the strong antiferromagnetic order creates similar disconnected electron-pocket Fermi surface, and hence nodeless d-wave pairing appears. The unit-cell transformation in KyFe2-xSe2 exhibits that the d-wave pairing breaks the translational symmetry of the 2 Fe unit cell, and thus cannot be realized unless a vacancy ordering forms to compensate for it. These results are consistent with the coexistence picture of a competing order and nodeless d-wave superconductivity in both cuprates and KyFe1.6Se2.

  18. Students' Errors in Solving the Permutation and Combination Problems Based on Problem Solving Steps of Polya

    Science.gov (United States)

    Sukoriyanto; Nusantara, Toto; Subanji; Chandra, Tjang Daniel

    2016-01-01

    This article was written based on the results of a study evaluating students' errors in problem solving of permutation and combination in terms of problem solving steps according to Polya. Twenty-five students were asked to do four problems related to permutation and combination. The research results showed that the students still did a mistake in…

  19. School-Based Intervention Strategies for School Phobia--A Ten-Step "Common Sense" Approach.

    Science.gov (United States)

    Want, Jerome H.

    1983-01-01

    Characteristic behaviors and personality features of school phobia (anxiety, willfulness, dependency, depression, and unrealistic self image) are described, and 10 steps in a school-based intervention approach are listed (including assessing the family constellation, preparing teachers for the student's return to school, and encouraging therapy…

  20. Step-based Exergames Used in Balance Training for Seniors: A Usability Study

    OpenAIRE

    Ystmark, Kristine Midjås

    2013-01-01

    This study explores the potential of the use of step-based exergames in balance training for senior citizens. Three exergames were tested and evaluated by healthy senior citizens to provide a basis for further development and use of these types of exergames.\

  1. Cryptanalysis on Identity-based Authenticated Key Agreement Protocols from Pairings

    Directory of Open Access Journals (Sweden)

    Mengbo Hou

    2010-07-01

    Full Text Available Two-party authenticated key agreement protocol is used to authenticate entities and establish session keys in an open network in order to provide secure communications between two parties. Several security attributes are highly desired for such protocols, such as perfect forward secrecy (the corruption of long-term keys of all the entities should not compromise any session key, PKG forward secrecy (the corruption of the PKG's master key in the ID-based system should not compromise the established session keys, and known session-key specific temporary information secrecy (The exposure of private temporary information should not compromise the secrecy of generated session keys. In 2005, Choie et al. proposed three identity-based authenticated key agreement protocols from pairings. Our analysis shows that they all didn't provide protection against known session-key specific temporary information attack and some of them are vulnerable against man-in-the-middle attack, such as the key replicating attack. We analyze some of the attacks under the BR93 security model.

  2. 2',4'-BNA bearing a 2-pyridine nucleobase for CG base pair recognition in the parallel motif triplex DNA.

    Science.gov (United States)

    Hari, Yoshiyuki; Matsugu, Sachiko; Inohara, Hiroyasu; Hatanaka, Yuri; Akabane, Masaaki; Imanishi, Takeshi; Obika, Satoshi

    2010-09-21

    We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py(B) in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py(B) units, triplex formation with dsDNA containing three CG base pairs was observed. PMID:20648389

  3. Pair Frames

    OpenAIRE

    Fereydooni, Abolhassan; Safapour, Ahmad

    2011-01-01

    In this paper a new concept related to the frame theory is introduced; the notion of pair frame. By investigating some properties of such frames, it is shown that pair frames are a generalization of ordinary frames. Some classes of of them are introduced such as (p, q)-pair frames and near identity pair frames.

  4. Monte Carlo simulations of biaxial structure in thin hybrid nematic film based upon spatially anisotropic pair potential

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhi-Dong; Chang Chun-Rui; Ma Dong-Lai

    2009-01-01

    Hybrid nematic films have been studied by Monte Carlo simulations using a lattice spin model,in which the pair potential is spatially anisotropic and dependent on elastic constants of liquid crystals.We confirm in the thin hybrid nematic film the existence of a biaxially nonbent structure and the structarc transition from the biaxial to the bent-director structure,which is similar to the result obtained using the Lebwohl-Lasher model.However,the step-like director's profile,characteristic for the biaxial structure,is spatially asymmetric in the film because the pair potential leads to K1≠K3.We estimate the upper cell thickness to be 69 spin layers,in which the biaxial structure can be found.

  5. Direct and two-step activity-based profiling of proteases and glycosidases

    OpenAIRE

    Willems, Lianne Irene

    2014-01-01

    Activity-based protein profiling provides a powerful approach for the monitoring of active enzyme populations in complex biological samples by making use of activity-based probes (ABPs), chemical probes that are designed to bind specifically to the active site of an enzyme (family). The research described in this thesis concerns two main topics. First, new techniques are developed for the two-step labeling of enzymatic activity, a strategy that involves the targeting of enzymes with an ABP fo...

  6. Nucleon-pair states of even-even Sn isotopes based on realistic effective interactions

    Science.gov (United States)

    Cheng, Y. Y.; Qi, C.; Zhao, Y. M.; Arima, A.

    2016-08-01

    In this paper we study yrast states of 128,126,124Sn and 104,106,108Sn by using the monopole-optimized realistic interactions in terms of both the shell model (SM) and the nucleon-pair approximation (NPA). For yrast states of 128,126Sn and 104,106Sn, we calculate the overlaps between the wave functions obtained in the full SM space and those obtained in the truncated NPA space, and find that most of these overlaps are very close to 1. Very interestingly, for most of these states with positive parity and even spin or with negative parity and odd spin, the SM wave function is found to be well represented by one nucleon-pair basis state, viz., a simple picture of "nucleon-pair states" (nucleon-pair configuration without mixings) emerges. In 128,126Sn, the positive-parity (or negative-parity) yrast states with spin J >10 (or J >7 ) are found to be well described by breaking one or two S pairs in the 101+ (or 71-) state, i.e., the yrast state of seniority-two, spin-maximum, and positive-parity (or negative-parity), into non-S pair(s). Similar regularity is also pointed out for 104,106Sn. The evolution of E 2 transition rates between low-lying states in 128,126,124Sn is discussed in terms of the seniority scheme.

  7. A Step Response Based Mixed-Signal BIST Approach for Continuous-time Linear Circuits

    Science.gov (United States)

    Walker, Alvernon; Lala, P. K.

    2001-01-01

    A new Mixed-Signal Built-in self-test approach that is based upon the step response of a reconfigurable (or multifunction) analog block is presented in this paper. The technique requires the overlapping step response of the Circuit Under Test (CUT) for two circuit configurations. Each configuration can be realized by changing the topology of the CUT or by sampling two CUT nodes with differing step responses. The technique can effectively detect both soft and hard faults and does not require an analog-to-digital converter (ADC) and/or digital-to-analog converter(DAC). It also does not require any precision voltage sources or comparators. This approach does not require any additional analog circuits to realize the test signal generator and sample circuits. The paper is concluded with the application of the proposed approach to a circuit found in the work of Epstein et al and two ITC 97 analog benchmark circuits.

  8. Interface-induced two-step RESET for filament-based multi-level resistive memory

    Science.gov (United States)

    Yuan, Fang; Shen, Shanshan; Zhang, Zhigang; Pan, Liyang; Xu, Jun

    2016-03-01

    In this paper, a two-step RESET switching behavior of Ag/Al2O3/HfO2/Pt bilayer resistive random access memory (RRAM) devices is investigated. The interface between the two oxide layers is responsible for the special two-step RESET switching. When the conducting filaments have ruptured in the lower layer, the interface can protect the Ag ions of the filaments from breaking in the upper layer due to the trapped charges or defects at the interface. Therefore, a stable middle resistance state (MRS) is realized and the device exhibits a terrace-like I-V curve during the RESET operations. A filament-based switching mechanism combined with the electron hopping theory is proposed to explain the physical nature of the two-step RESET behavior. Furthermore, a good multi-level resistive switching performance with excellent endurance and retention reliability is obtained.

  9. Multi-agent System for Process Planning in Step-nc Based Manufacturing

    Directory of Open Access Journals (Sweden)

    Juan Du

    2012-09-01

    Full Text Available In order to realize STEP-NC-oriented computer numerical control machining and achieve optimal performance in manufacturing, a multi-agent system for process planning in STEP-NC based manufacturing was designed. By analyzing the characteristic of STEP-NC data model, a manufacturing feature-oriented process planning method was proposed in this study and the distributed artificial intelligence methods, namely collaborative multi-agent was employed to accomplish process planning of part. The proposed multi-agent system consists of three types of autonomous agents, which are global manager agents, planning agents and manufacturing resource agents, respectively. Process planning can be automatically completed by multiple agents’ cooperation. Each agent is capable of communicating to each other through improved Knowledge Query and Manipulation Language (KQML. At last, one test part was designed and simulated to demonstrate the capabilities of this research in the study.

  10. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

    Energy Technology Data Exchange (ETDEWEB)

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Neese, Frank, E-mail: frank.neese@cec.mpg.de, E-mail: evaleev@vt.edu [Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr (Germany); Valeev, Edward F., E-mail: frank.neese@cec.mpg.de, E-mail: evaleev@vt.edu [Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061 (United States)

    2016-01-14

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  11. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

    International Nuclear Information System (INIS)

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  12. Sparse maps--A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory.

    Science.gov (United States)

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F; Neese, Frank

    2016-01-14

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  13. Interfacial molecular recognition of adenine, adenosine and ATP by a C60-uracil adduct via complementary base pairing

    Science.gov (United States)

    Marczak, Renata; Hoang, Vu T.; Noworyta, Krzysztof; Zandler, Melvin E.; Kutner, Wlodzimierz; D'Souza, Francis

    2002-10-01

    A new C60-uracil adduct was demonstrated to recognize adenine, adenosine, or adenosine 5'-triphosphate (ATP) via complementary base pairing which led to complex formation. The base-pairing mechanism was modeled by ab initio B3LYP/3-21G(*) calculations which revealed the Watson-Crick (A-T) interactions. Stable "expanded liquid" Langmuir films of the complexes were prepared with the limiting area per molecule increasing for different subphase composition in the order: water < adenine < adenosine < ATP solution. Comparison of experimental and calculated areas per molecule and dipole moments suggest both prevailing horizontal orientation of the complexes in films.

  14. Polarization entangled photon-pair source based on a type-II PPLN waveguide emitting at a telecom wavelength

    CERN Document Server

    Martin, A; Herrmann, H; Sohler, W; Ostrowsky, D B; Alibart, O; Tanzilli, S

    2010-01-01

    We report the realization of a fiber coupled polarization entangled photon-pair source at 1310 nm based on a birefringent titanium in-diffused waveguide integrated on periodically poled lithium niobate. By taking advantage of an original setup, we characterized the quantum properties of the pairs by measuring two-photon interference in both Hong-Ou-Mandel and standard Bell inequality configurations. We obtained, for the two sets of measurements, interference net visibilities reaching nearly 100%, which represent the best results ever reported for similar waveguide-based configurations. These results prove the relevance of our approach as an enabling technology for long-distance quantum communication.

  15. Model construction and pairing symmetry for the iron-based oxypnictides

    Energy Technology Data Exchange (ETDEWEB)

    Aoki, Hideo, E-mail: aoki@phys.s.u-tokyo.ac.j [Department of Physics, University of Tokyo, Hongo, Tokyo 113-0033 (Japan)

    2009-10-15

    PC-19-INV: In order to clarify the mechanism of superconductivity in the iron-based compound recently discovered by Hosono's group, we have first constructed a tight-binding model in terms of the maximally localized Wannier orbitals from a first-principles electronic structure calculation. The model has turned out to involve all the five Fe 3d bands. This is used to calculate the spin and charge susceptibilities with the five-band random-phase approximation, which are then plugged into the linearised Eliashberg equation. For a doped system we obtain an unconventional s-wave pairing with sign-reversing gap functions. To be more precise, the gap function is a 5x5 matrix, for which the diagonal elements mainly comprise d{sub x}{sup 2}{sub -y}{sup 2} and d{sub yz},d{sub xz} orbital components. The strong dependence of the gap between different orbitals may be observed experimentally.

  16. Simplified Aircraft-Based Paired Approach: Concept Definition and Initial Analysis

    Science.gov (United States)

    Johnson, Sally C.; Lohr, Gary W.; McKissick, Burnell T.; Abbott, Terence S.; Geurreiro, Nelson M.; Volk, Paul

    2013-01-01

    Simplified Aircraft-based Parallel Approach (SAPA) is an advanced concept proposed by the Federal Aviation Administration (FAA) to support dependent parallel approach operations to runways with lateral spacing closer than 2500 ft. At the request of the FAA, NASA performed an initial assessment of the potential performance and feasibility of the SAPA concept, including developing and assessing an operational implementation of the concept and conducting a Monte Carlo wake simulation study to examine the longitudinal spacing requirements. The SAPA concept was shown to have significant operational advantages in supporting the pairing of aircraft with dissimilar final approach speeds. The wake simulation study showed that support for dissimilar final approach speeds could be significantly enhanced through the use of a two-phased altitudebased longitudinal positioning requirement, with larger longitudinal positioning allowed for higher altitudes out of ground effect and tighter longitudinal positioning defined for altitudes near and in ground effect. While this assessment is preliminary and there are a number of operational issues still to be examined, it has shown the basic SAPA concept to be technically and operationally feasible.

  17. Decentralized supervisory based switching control for uncertain multivariable plants with variable input-output pairing.

    Science.gov (United States)

    Namaki-Shoushtari, Omid; Khaki-Sedigh, Ali

    2012-01-01

    In this paper, the design of decentralized switching control for uncertain multivariable plants is considered. In the proposed strategy, the uncertainty region is divided into smaller regions with a nominal model and specific control structure. The underlying design is based on the quantitative feedback theory (QFT). It is assumed that a MIMO-QFT controller exists for robust stability and performance of the individual uncertain sets. The proposed control structure is made up by these local decentralized controllers, which commute among themselves in accordance with the decision of a high level decision maker called the supervisor. The supervisor makes the decision by comparing the local models' behaviors with the one of the plant and selects the controller corresponding to the best fitted model. A hysteresis switching logic is used to slow down the switching to guarantee the overall closed loop stability. It is shown that this strategy provides a stable and robust adaptive controller to deal with complex multivariable plants with input-output pairing changes during the plant operation, which can facilitate the development of a reconfigurable decentralized control. Also, the multirealization technique is used to implement a family of controllers to achieve bumpless transfer. Simulation results are employed to show the effectiveness of the proposed method. PMID:21999896

  18. All-pairs Shortest Path Algorithm based on MPI+CUDA Distributed Parallel Programming Model

    Directory of Open Access Journals (Sweden)

    Qingshuang Wu

    2013-12-01

    Full Text Available In view of the problem that computing shortest paths in a graph is a complex and time-consuming process, and the traditional algorithm that rely on the CPU as computing unit solely can't meet the demand of real-time processing, in this paper, we present an all-pairs shortest paths algorithm using MPI+CUDA hybrid programming model, which can take use of the overwhelming computing power of the GPU cluster to speed up the processing. This proposed algorithm can combine the advantages of MPI and CUDA programming model, and can realize two-level parallel computing. In the cluster-level, we take use of the MPI programming model to achieve a coarse-grained parallel computing between the computational nodes of the GPU cluster. In the node-level, we take use of the CUDA programming model to achieve a GPU-accelerated fine grit parallel computing in each computational node internal. The experimental results show that the MPI+CUDA-based parallel algorithm can take full advantage of the powerful computing capability of the GPU cluster, and can achieve about hundreds of time speedup; The whole algorithm has good computing performance, reliability and scalability, and it is able to meet the demand of real-time processing of massive spatial shortest path analysis

  19. LiLEDDA: A Six-Step Forum-Based Netnographic Research Method for Nursing Science

    Directory of Open Access Journals (Sweden)

    MARTIN SALZMANN-ERIKSON

    2012-01-01

    Full Text Available Internet research methods in nursing science are less developed than in other sciences. We choose to present an approach to conducting nursing research on an internet-based forum. This paper presents LiLEDDA, a six-step forum-based netnographic research method for nursing science. The steps consist of: 1. Literature review and identification of the research question(s; 2. Locating the field(s online; 3. Ethical considerations; 4. Data gathering; 5. Data analysis and interpretation; and 6. Abstractions and trustworthiness. Traditional research approaches are limiting when studying non-normative and non-mainstream life-worlds and their cultures. We argue that it is timely to develop more up-to-date research methods and study designs applicable to nursing science that reflect social developments and human living conditions that tend to be increasingly online-based.

  20. Universal quantum gates for Single Cooper Pair Box based quantum computing

    Science.gov (United States)

    Echternach, P.; Williams, C. P.; Dultz, S. C.; Braunstein, S.; Dowling, J. P.

    2000-01-01

    We describe a method for achieving arbitrary 1-qubit gates and controlled-NOT gates within the context of the Single Cooper Pair Box (SCB) approach to quantum computing. Such gates are sufficient to support universal quantum computation.

  1. Uncertainty evaluation for three-dimensional scanning electron microscope reconstructions based on the stereo-pair technique

    DEFF Research Database (Denmark)

    Carli, Lorenzo; Genta, G; Cantatore, Angela; Barbato, G; De Chiffre, Leonardo; Levi, R

    2011-01-01

    multiple-view reconstructions of the cylindrical item under consideration. Uncertainty evaluation was performed starting from a modified version of the Piazzesi equation, enabling the calculation of the z-coordinate from a given stereo-pair. The metrological characteristics of each input variable have been......3D-SEM is a method, based on the stereophotogrammetry technique, which obtains three-dimensional topographic reconstructions starting typically from two SEM images, called the stereo-pair. In this work, a theoretical uncertainty evaluation of the stereo-pair technique, according to GUM (Guide to...... the Expression of Uncertainty in Measurement), was carried out, considering 3D-SEM reconstructions of a wire gauge with a reference diameter of 250 µm. Starting from the more commonly used tilting strategy, one based on the item rotation inside the SEM chamber was also adopted. The latter enables...

  2. Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs

    Energy Technology Data Exchange (ETDEWEB)

    Patra, Amritraj [Vanderbilt Univ., Nashville, TN (United States); Harp, Joel [Vanderbilt Univ., Nashville, TN (United States); Pallan, Pradeep S. [Vanderbilt Univ., Nashville, TN (United States); Zhao, Linlin [Vanderbilt Univ., Nashville, TN (United States); Abramov, Mikhail [Rega Inst. for Medical Research (Belgium); Herdewijn, Piet [Rega Inst. for Medical Research (Belgium); Univ. of Evry-Val-d' Essonne (France); Egli, Martin [Vanderbilt Univ., Nashville, TN (United States)

    2012-12-28

    The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium’s genome. Angew. Chem. Int. Ed., 50, 7109–7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.

  3. Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F

    2012-12-01

    Full Text Available Abstract Background Single-step methods provide a coherent and conceptually simple approach to incorporate genomic information into genetic evaluations. An issue with single-step methods is compatibility between the marker-based relationship matrix for genotyped animals and the pedigree-based relationship matrix. Therefore, it is necessary to adjust the marker-based relationship matrix to the pedigree-based relationship matrix. Moreover, with data from routine evaluations, this adjustment should in principle be based on both observed marker genotypes and observed phenotypes, but until now this has been overlooked. In this paper, I propose a new method to address this issue by 1 adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix instead of the reverse and 2 extending the single-step genetic evaluation using a joint likelihood of observed phenotypes and observed marker genotypes. The performance of this method is then evaluated using two simulated datasets. Results The method derived here is a single-step method in which the marker-based relationship matrix is constructed assuming all allele frequencies equal to 0.5 and the pedigree-based relationship matrix is constructed using the unusual assumption that animals in the base population are related and inbred with a relationship coefficient γ and an inbreeding coefficient γ / 2. Taken together, this γ parameter and a parameter that scales the marker-based relationship matrix can handle the issue of compatibility between marker-based and pedigree-based relationship matrices. The full log-likelihood function used for parameter inference contains two terms. The first term is the REML-log-likelihood for the phenotypes conditional on the observed marker genotypes, whereas the second term is the log-likelihood for the observed marker genotypes. Analyses of the two simulated datasets with this new method showed that 1 the parameters involved

  4. SVM with Quadratic Polynomial Kernel Function Based Nonlinear Model One-step-ahead Predictive Control

    Institute of Scientific and Technical Information of China (English)

    钟伟民; 何国龙; 皮道映; 孙优贤

    2005-01-01

    A support vector machine (SVM) with quadratic polynomial kernel function based nonlinear model one-step-ahead predictive controller is presented. The SVM based predictive model is established with black-box identification method. By solving a cubic equation in the feature space, an explicit predictive control law is obtained through the predictive control mechanism. The effect of controller is demonstrated on a recognized benchmark problem and on the control of continuous-stirred tank reactor (CSTR). Simulation results show that SVM with quadratic polynomial kernel function based predictive controller can be well applied to nonlinear systems, with good performance in following reference trajectory as well as in disturbance-rejection.

  5. A Randomized Controlled Pilot Study of Home-Based Step Training in Older People Using Videogame Technology

    OpenAIRE

    Schoene, Daniel; Lord, Stephen R; Delbaere, Kim; Severino, Connie; Davies, Thomas A.; Smith, Stuart T

    2013-01-01

    Background Stepping impairments are associated with physical and cognitive decline in older adults and increased fall risk. Exercise interventions can reduce fall risk, but adherence is often low. A new exergame involving step training may provide an enjoyable exercise alternative for preventing falls in older people. Purpose To assess the feasibility and safety of unsupervised, home-based step pad training and determine the effectiveness of this intervention on stepping performance and assoc...

  6. Photoinduced electron transfer in a Watson-Crick base-paired, 2-aminopurine:uracil-C60 hydrogen bonding conjugate.

    Science.gov (United States)

    D'Souza, Francis; Gadde, Suresh; Islam, D-M Shafiqul; Pang, Siew-Cheng; Schumacher, Amy Lea; Zandler, Melvin E; Horie, Rumiko; Araki, Yasuyaki; Ito, Osamu

    2007-02-01

    A fluorescent reporter molecule, 2-aminopurine was self-assembled via Watson-Crick base-pairing to a uracil appended fullerene to form a donor-acceptor conjugate; efficient photoinduced charge separation was confirmed by time-resolved emission and transient absorption spectral studies. PMID:17252101

  7. Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

    DEFF Research Database (Denmark)

    van Beest, M; Dooijes, D; van De Wetering, M; Kjaerulff, S; Bonvin, A; Nielsen, O; Clevers, H; Nielsen, Olaf

    2000-01-01

    promoter elements controlled by the yeast genes ste11 and Rox1 has indicated strict conservation of a larger DNA motif. By site selection, we identify a highly specific 12-base pair motif for Ste11, AGAACAAAGAAA. Similarly, we show that Tcf1, MatMc, and Sox4 bind unique, highly specific DNA motifs of 12...

  8. A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy

    NARCIS (Netherlands)

    de Brouwer, Arjan P. M.; Nabuurs, Sander B.; Verhaart, Ingrid E. C.; Oudakker, Astrid R.; Hordijk, Roel; Yntema, Helger G.; Hordijk-Hos, Jannet M.; Voesenek, Krysta; de Vries, Bert B. A.; van Essen, Ton; Chen, Wei; Hu, Hao; Chelly, Jamel; den Dunnen, Johan T.; Kalscheuer, Vera M.; Aartsma-Rus, Annemieke M.; Hamel, Ben C. J.; van Bokhoven, Hans; Kleefstra, Tjitske

    2014-01-01

    We have identified a deletion of 3 base pairs in the dystrophin gene (DMD), c.9711_9713del, in a family with nonspecific X-linked intellectual disability (ID) by sequencing of the exons of 86 known X-linked ID genes. This in-frame deletion results in the deletion of a single-amino-acid residue, Leu3

  9. Intrastrand base pairing in single-stranded deoxyribonucleic acid from ColE1-derived plasmid pCR1.

    OpenAIRE

    Edlind, T D; Ihler, G M

    1981-01-01

    Single strands of EcoRI-cleaved pCR1 deoxyribonucleic acid were examined by electron microscopy for intrastrand base pairing by using partial denaturing conditions. The locations of three stem and loop structures were mapped relative to the inverted repeat of Tn903. Potential roles and origins of these loops are discussed.

  10. Support vector machine based nonlinear model multi-step-ahead optimizing predictive control

    Institute of Scientific and Technical Information of China (English)

    ZHONG Wei-min; PI Dao-ying; SUN You-xian

    2005-01-01

    A support vector machine with guadratic polynomial kernel function based nonlinear model multi-step-ahead optimizing predictive controller was presented. A support vector machine based predictive model was established by black-box identification. And a quadratic objective function with receding horizon was selected to obtain the controller output. By solving a nonlinear optimization problem with equality constraint of model output and boundary constraint of controller output using Nelder-Mead simplex direct search method, a sub-optimal control law was achieved in feature space. The effect of the controller was demonstrated on a recognized benchmark problem and a continuous-stirred tank reactor. The simulation results show that the multi-step-ahead predictive controller can be well applied to nonlinear system, with better performance in following reference trajectory and disturbance-rejection.

  11. A Method of MPPT Control Based on Power Variable Step-size in Photovoltaic Converter System

    Directory of Open Access Journals (Sweden)

    Xu Hui-xiang

    2016-01-01

    Full Text Available Since the disadvantage of traditional MPPT algorithms of variable step-size, proposed power tracking based on variable step-size with the advantage method of the constant-voltage and the perturb-observe (P&O[1-3]. The control strategy modify the problem of voltage fluctuation caused by perturb-observe method, at the same time, introducing the advantage of constant-voltage method and simplify the circuit topology. With the theoretical derivation, control the output power of photovoltaic modules to change the duty cycle of main switch. Achieve the maximum power stabilization output, reduce the volatility of energy loss effectively, and improve the inversion efficiency[3,4]. Given the result of experimental test based theoretical derivation and the curve of MPPT when the prototype work.

  12. Reliability Estimation based on Step-Stress Accelerated Degradation Testing by Unequal Interval Time Series Analysis

    OpenAIRE

    Li Wang; Zaiwen Liu; Chongchong Yu

    2013-01-01

    This paper proposes a reliability estimation method based on Step-Stress Accelerated Degradation Testing (SSADT) data analysis using unequal interval time series analysis. A Multi-Regression Time Varying Auto-Regressive (MRTVAR) degradation time series model is proposed. Product SSADT data are treated as unequal interval composite time series and described using MRTVAR time series model and utilized to predict long-term trend of degradation. By using the suggested method, product reliability ...

  13. Plant trials of an on-stream iron ore analyser based on pair production

    International Nuclear Information System (INIS)

    An on-stream iron ore analyser, called Ironscan, has been developed in collaboration with Hamersley Iron Pty Limited for measuring the iron content of iron ore on conveyor belts. The analyser is based on pair production and irradiates the ore with gamma rays from a 226Ra source. A big advantage of the analyser is that it can be mounted under existing conveyor belts with minimal modifications to the conveyor structure, and the presence of steel reinforcement cables in the belt does not interfere once the analyser has been correctly calibrated. After dynamic trials of a laboratory prototype on a small conveyor facility at Port Melbourne to demonstrate the viability of the method for lumps (-30 + 6 mm particle size) and fines (-6 mm particle size), an industrial prototype was manufactured by Mineral Control Instrumentation Limited in Adelaide (now the Commonwealth Scientific and Industrial Research Organisation licensee) and extensively tested at the Hamersley Iron operations in Dampier and Mount Tom Price, Western Australia. At Dampier, it was installed on the main shiploading conveyor to assess its performance on the normal lumps and fines that are exported. The root mean square (RMS) deviation between single Ironscan measurements and conventional chemical analyses was about 0.4% Fe. The analyser was then evaluated on -150 mm ore from the primary crusher at Mount Tom Price. While it was clear that ore grade could be measured even at this coarse particle size, it was very difficult to obtain comparable chemical analyses and there was insufficient data to estimate the RMS deviation. (author). 6 refs, 7 figs, 1 tab

  14. Electromigration study of copper lines on steps prepared by a plasma-based etch process

    International Nuclear Information System (INIS)

    The electromigration phenomenon of the copper line etched with a plasma-based process over the SiNx step has been investigated. Two important factors, i.e., the dielectric topography and the stress temperature, were examined using the accelerated isothermal electromigration method. The activation energy of 0.73 eV to 0.89 eV indicates two possible mass transport pathways: interfacial and copper surface diffusions. The copper line on the SiNx step has a shorter lifetime and a smaller activation energy than the copper line on the flat surface has. For the former, voids were formed at the cusp region and perpendicular to the current flow direction. For the latter, voids were formed in series and parallel to the current flow direction. The ''neck'' structure at the cusp region, which is a result of the inappropriate etching condition, further decreased the lifetime and the activation energy. The lifetime of the ''neck-free'' copper line over the SiNx step was estimated to be 7.1 x 109 s under the high-speed IC operation condition. The thermal stress mismatch between the copper layer and TiW barrier layer as well as the underneath dielectric layer facilitated the void formation. The step effect on the lifetime was reduced when the test temperature was high because of the change of the local stress. In summary, the topography and the test temperature are critical factors for the copper line's lifetime.

  15. Damage identification in beam type structures based on statistical moment using a two step method

    Science.gov (United States)

    Wang, Dansheng; Xiang, Wei; Zhu, Hongping

    2014-02-01

    This paper defines a novel damage index-strain statistical moment, and formulates the fourth strain statistical moment (FSSM) of beam-type structures under white noise excitation. Based on this newly defined strain statistical moment index and the least square optimization algorithm, a two-step damage identification method is proposed. This two-step method is operated like this: first use the difference curves of FSSMs before and after damage to locate damage elements; then for those identified damage elements, employ the model updating method based on the least square algorithm to assess their damage severity. Numerical studies on a simply supported beam and a two-span continuous beam are performed and the study results show that the newly defined index is effective to locate damages, even when the noise intensity is as high as 15 percent. Integrating with the least square-based model updating technique, the damage severities of beam-type structures can also be determined quantitatively. In this way, the proposed two-step method is verified and found to be capable of identifying damage positions and severities of beam-type structures and insensitive to measurement noise.

  16. Carcinogenesis of asbestos switched on by inducing cross-linkage between DNA complementary pair bases

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Since the beginning of the 1980s, Dai Qianhuan predicted based upon his di-region theory that the carcinogenesis switched on by the so-called physical carcinogenic factors including radiation, asbestos and foreign matter implantation, is just initiated through the cross-linking between DNA complementary pair bases induced by them. In this note, it was evidenced with the DNA filter elution method that the oxygenase activated by asbestos induces the cross-linking between DNA inter-strands and DNA-protein with dosage correlation, in which over 80% of DNA inter-strand cross-link ratio account for the total cross-link ratio. Obviously, both of the cross-linkages are just induced by hydroxyl free radical, HO@, because the ferrous ion increased the cross-link ratios up to several times through Fenton reaction and vitamin C inhibited the cross-link ratios with factors of 8-9 by destroying the hydroxyl radical. Non-carcinogen but with lower free radical formation energy, pyrene, by culturing with asbestos gave 3-4 times cross-link ratios than the original ratios induced by asbestos only. Estradiol, an endogenous carcinogen, as a bio-electrophilic species but with higher free radical formation energy by culturing with asbestos, gave only 1.2 time cross-link ratios than expected ones. Ferrous ion which can increase HO@ concentration through Fenton reaction, increased the ratios to 2-2.5 times in the former case but only 1.2 time in the latter case. Vitamin C, a free radical scavenger, gave a powerful inhibition to the cross-linking with a factor of 8-11 in the former case but a weak inhibition with a factor of 1.2 only in the latter case. So, it is evidenced further that the cross-linkages induced by asbestos are originated from hydroxyl radical. Reasonable structures of the cross-linking products induced by asbestos or hydroxyl radical have been depicted based upon AM1 MO theory. These structures have been verified further by a reasonable explanation of the mutational

  17. A terrain-based paired-site sampling design to assess biodiversity losses from eastern hemlock decline

    Science.gov (United States)

    Young, J.A.; Smith, D.R.; Snyder, C.D.; Lemarie, D.P.

    2002-01-01

    Biodiversity surveys are often hampered by the inability to control extraneous sources of variability introduced into comparisons of populations across a heterogenous landscape. If not specifically accounted for a priori, this noise can weaken comparisons between sites, and can make it difficult to draw inferences about specific ecological processes. We developed a terrain-based, paired-site sampling design to analyze differences in aquatic biodiversity between streams draining eastern hemlock (Tsuga canadensis) forests, and those draining mixed hardwood forests in Delaware Water Gap National Recreation Area (USA). The goal of this design was to minimize variance due to terrain influences on stream communities, while representing the range of hemlock dominated stream environments present in the park. We used geographic information systems (GIS) and cluster analysis to define and partition hemlock dominated streams into terrain types based on topographic variables and stream order. We computed similarity of forest stands within terrain types and used this information to pair hemlock-dominated streams with hardwood counterparts prior to sampling. We evaluated the effectiveness of the design through power analysis and found that power to detect differences in aquatic invertebrate taxa richness was highest when sites were paired and terrain type was included as a factor in the analysis. Precision of the estimated difference in mean richness was nearly doubled using the terrain-based, paired site design in comparison to other evaluated designs. Use of this method allowed us to sample stream communities representative of park-wide forest conditions while effectively controlling for landscape variability.

  18. Solvation of deoxynucleosides in aqueous mixtures of organic solvents probed through their intrinsic fluorescence: Implications for open base pair states in DNA

    Science.gov (United States)

    Ababneh, Anas Mohammad

    Because of the importance of solvation in the function of DNA, there is considerable interest in understanding the solvation network of its constituent components. This is of particular importance in connection with the closing of base pairs that have been disrupted as a result of structural fluctuations. Following the opening of a base pair, the open base is exposed to a heterogeneous environment which involves polar as well as nonpolar interactions. Toward the goal of understanding how the open bases interact with such a heterogeneous environment, we have studied the intrinsic fluorescence properties of the purine and pyrimidine nucleosides (dG, dA, dT, and dC) in organic solvents in the presence of small amounts of water. Exposure of the nucleoside to water was done by preparing solutions in three different ways: (i) "premixed" solution in which the nucleoside is dissolved in a water-organic solvent mixture, (ii) "carry its own water" solution in which the nucleoside is first dissolved in water and then diluted in the organic solvent, and (iii) "injected" solution in which water is added to a solution of the nucleoside in the organic solvent. The organic solvents used in the present study were: n-butanol, acetonitrile, methanol, n-propanol, isopropanol, and isobutanol. We find that for n-butanol and acetonitrile, which have a high degree of amphiphilicity and weak hydrogen bonding ability, respectively, the fluorescence spectral properties of the purines are found to depend on the sequence of the steps in which the aqueous mixture was formed. By contrast, no such dependence was observed in the other organic solvents. On the other hand, no such dependence was observed for the pyrimidines in any of the organic solvents used in the present study. These findings suggest that the final solvation network around the purines is dependent on the nature of the environment to which they were initially exposed. This would tend to present an impediment to the closing of

  19. A 3-Step Algorithm Using Region-Based Active Contours for Video Objects Detection

    Directory of Open Access Journals (Sweden)

    Stéphanie Jehan-Besson

    2002-06-01

    Full Text Available We propose a 3-step algorithm for the automatic detection of moving objects in video sequences using region-based active contours. First, we introduce a very full general framework for region-based active contours with a new Eulerian method to compute the evolution equation of the active contour from a criterion including both region-based and boundary-based terms. This framework can be easily adapted to various applications, thanks to the introduction of functions named descriptors of the different regions. With this new Eulerian method based on shape optimization principles, we can easily take into account the case of descriptors depending upon features globally attached to the regions. Second, we propose a 3-step algorithm for detection of moving objects, with a static or a mobile camera, using region-based active contours. The basic idea is to hierarchically associate temporal and spatial information. The active contour evolves with successively three sets of descriptors: a temporal one, and then two spatial ones. The third spatial descriptor takes advantage of the segmentation of the image in intensity homogeneous regions. User interaction is reduced to the choice of a few parameters at the beginning of the process. Some experimental results are supplied.

  20. Quantum heat engine based on photon-assisted Cooper pair tunneling

    Science.gov (United States)

    Hofer, Patrick P.; Souquet, J.-R.; Clerk, A. Â. A.

    2016-01-01

    We propose and analyze a simple mesoscopic quantum heat engine that exhibits both high power and high efficiency. The system consists of a biased Josephson junction coupled to two microwave cavities, with each cavity coupled to a thermal bath. Resonant Cooper pair tunneling occurs with the exchange of photons between cavities, and a temperature difference between the baths can naturally lead to a current against the voltage, and hence work. As a consequence of the unique properties of Cooper-pair tunneling, the heat current is completely separated from the charge current. This combined with the strong energy selectivity of the process leads to an extremely high efficiency.

  1. Salt dependent premelting base pair opening probabilities of B and Z DNA Poly [d(G-C)] and significance for the B-Z transition

    OpenAIRE

    Chen, Y. Z.; Prohofsky, E W

    1993-01-01

    We calculate room temperature thermal fluctuational base pair opening probabilities of B and Z DNA Poly[d(G-C)] at various salt concentrations and discuss the significance of thermal fluctuation in facilitating base pair disruption during B to Z transition. Our calculated base pair opening probability of the B DNA at lower salt concentrations and the probability of the Z DNA at high salt concentrations are in agreement with observations. The salt dependence of the probabilities indicates a B ...

  2. Steps towards a SAR-based wind atlas in the Baltic Sea

    DEFF Research Database (Denmark)

    Hasager, Charlotte Bay; Badger, Merete; Pena Diaz, Alfredo;

    -2 meteorological mast data.The SAR-based results from the 12 existing and 42 planned offshore wind farm sites within the study area including parts of Danish, Swedish, German, and Polish Seas were extracted and showed variability in wind energy density from 300 to 800 W m-2. The wind energy density...... based on information of the atmospheric stability and the boundary layer height using WRF mesoscale results and applying this information to a model for the vertical profile in the marine boundary layer between 10 m and hub-height (Peña et al. 2008). The results of step 3 are currently in progress but...

  3. New schemes for high-voltage pulsed generators based on stepped transmission lines

    International Nuclear Information System (INIS)

    Wave processes were analyzed from the point of effective energy delivery in pulsed power systems based on transmission lines. A series of new schemes for the pulsed generators based on multistage stepped transmission lines both with the capacitive and inductive energy storage was found. These devices can provide voltage or current transformation up to 5-10 times due to wave processes if stage's characteristic impedances are in a certain correlation. The schemes suggested can be widely applied in the new powerful pulsed power accelerators. The theoretical conclusions are justified experimentally

  4. Interrupt-Based Step-Counting to Extend Battery Life in an Activity Monitor

    Directory of Open Access Journals (Sweden)

    Seung Young Kim

    2016-01-01

    Full Text Available Most activity monitors use an accelerometer and gyroscope sensors to characterize the wearer’s physical activity. The monitor measures the motion by polling an accelerometer or gyroscope sensor or both every 20–30 ms and frequent polling affects the battery life of a wearable device. One of the key features of a commercial daily-activity monitoring device is longer battery life so that the user can keep track of his or her activity for a week or so without recharging the battery of the monitoring device. Many low-power approaches for a step-counting system use either a polling-based algorithm or an interrupt-based algorithm. In this paper, we propose a novel approach that uses the tap interrupt of an accelerometer to count steps while consuming low power. We compared the accuracy of step counting and measured system-level power consumption to a periodic sensor-reading algorithm. Our tap interrupt approach shows a battery lifetime that is 175% longer than that of a 30 ms polling method without gyroscope. The battery lifetime can be extended up to 863% with a gyroscope by putting both the processor and the gyroscope into sleep state during the majority of operation time.

  5. Single-step scaffold-based cartilage repair in the knee: A systematic review.

    Science.gov (United States)

    Fischer, Stefan; Kisser, Agnes

    2016-12-01

    Chondral lesions are difficult-to-treat entities that often affect young and active people. Moreover, cartilage has limited intrinsic healing potential. The purpose of this systematic literature review was to analyse whether the single-step scaffold-based cartilage repair in combination with microfracturing (MFx) is more effective and safe in comparison to MFx alone. From the three identified studies, it seems that the single-step scaffold-assisted cartilage repair in combination with MFx leads to similar short- to medium-term (up to five years follow-up) results, compared to MFx alone. All of the studies have shown improvements regarding joint functionality, pain and partly quality of life. PMID:27408497

  6. Adjusted Wald Confidence Interval for a Difference of Binomial Proportions Based on Paired Data

    Science.gov (United States)

    Bonett, Douglas G.; Price, Robert M.

    2012-01-01

    Adjusted Wald intervals for binomial proportions in one-sample and two-sample designs have been shown to perform about as well as the best available methods. The adjusted Wald intervals are easy to compute and have been incorporated into introductory statistics courses. An adjusted Wald interval for paired binomial proportions is proposed here and…

  7. Ferrocene-based Lewis acids and Lewis pairs: Synthesis and structural characterization

    Indian Academy of Sciences (India)

    Pagidi Sudhakar; Pakkirisamy Thilagar

    2013-01-01

    Optically active Lewis acids and Lewis pairs were synthesized and characterized by multinuclear NMR, UV/Vis spectroscopy and elemental analysis. Optical rotation measurements were carried out and the absolute configuration of the new chiral molecules confirmed by single crystal X-ray diffraction.

  8. Classification between normal and tumor tissues based on the pair-wise gene expression ratio

    International Nuclear Information System (INIS)

    Precise classification of cancer types is critically important for early cancer diagnosis and treatment. Numerous efforts have been made to use gene expression profiles to improve precision of tumor classification. However, reliable cancer-related signals are generally lacking. Using recent datasets on colon and prostate cancer, a data transformation procedure from single gene expression to pair-wise gene expression ratio is proposed. Making use of the internal consistency of each expression profiling dataset this transformation improves the signal to noise ratio of the dataset and uncovers new relevant cancer-related signals (features). The efficiency in using the transformed dataset to perform normal/tumor classification was investigated using feature partitioning with informative features (gene annotation) as discriminating axes (single gene expression or pair-wise gene expression ratio). Classification results were compared to the original datasets for up to 10-feature model classifiers. 82 and 262 genes that have high correlation to tissue phenotype were selected from the colon and prostate datasets respectively. Remarkably, data transformation of the highly noisy expression data successfully led to lower the coefficient of variation (CV) for the within-class samples as well as improved the correlation with tissue phenotypes. The transformed dataset exhibited lower CV when compared to that of single gene expression. In the colon cancer set, the minimum CV decreased from 45.3% to 16.5%. In prostate cancer, comparable CV was achieved with and without transformation. This improvement in CV, coupled with the improved correlation between the pair-wise gene expression ratio and tissue phenotypes, yielded higher classification efficiency, especially with the colon dataset – from 87.1% to 93.5%. Over 90% of the top ten discriminating axes in both datasets showed significant improvement after data transformation. The high classification efficiency achieved suggested

  9. Adaptive Step Size Control of LMS-based Interference Cancellationfor ICS Repeater in Wibro Environment

    Institute of Scientific and Technical Information of China (English)

    Jeong-gon KIM; Won-geon BAE; Won-seok CHOI

    2010-01-01

    The use of repeater for the support of high rate data transmission and the extension of cell coverage is imperative for the Wibrc system,which based on the IEEE 8M.16e standardization.Generally,if the separation between transmitting and receiving antennas isnot sufficient,the oscillation of repeater and the interference due to the feedback signals from original transmitted signal may be ocerur.Hence,the Interference Cancellation System(ICS)should be implemented as the important part of the repeater system far the mobile cellular systems in order to eliminate unwanted signals from the corruptW signals in the receiver.In this paper,we propose an adaptive technique for the Least Mean Square(LMS)-based interference cancellation methods by changing the step size according to the variation of channel environment in order to improve the performance degradation which oceuurs by using the fixed step size approach.Simrlatim results show that the proposed sclxme attains a little lower Berafor Rate(BER)performance and much faster convergence speed compared to the conventional LMS-based interference cancellation techniques.The proposed scheme can be applied to other Orthogonal Frequency Division Multiple(OFDM)-based cellular systems and also be expected to achieve a similar performance improvement to W17-advanced system,which is called as the next generation mobile communication standards.

  10. Compatibility of pedigree-based and marker-based relationships for single-step genomic prediction

    DEFF Research Database (Denmark)

    Christensen, Ole Fredslund

    2012-01-01

    marker-based relationship matrix is constructed assuming all allele frequencies equal to 0.5 and the pedigree-based relationship matrix is constructed using the unusual assumption that animals in the base population are related and inbreed with relationship coefficient alpha and inbreeding coefficient...

  11. A Point Pairing Method Based on the Principle of Material Frame Indifference for the Characterization of Unknown Space Objects using Space-Based Non-Resolved Photometry Data

    Science.gov (United States)

    Chaudhary, A.; Payne, T.; Dao, P.; Murray-Krezan, J.; Lucas, K.; Mutschler, S.

    2013-09-01

    The point pairing method in this paper is based on set of simple physical truths for three-axis stabilized space objects in the geosynchronous orbit (GEO). It defines a method for the calculation of pairs of observation conditions (i.e. point pairs) that have a special property for three-axis stabilized GEO object characterization. An observation condition is defined to be the geometry of illumination for the solar panel and the body of the satellite and the geometry of its observation by a sensor. The physical truths are due to observation conditions that are equivalent with respect to either the solar panel or body for a pair of points, which can be identified analytically. When the observation conditions are equivalent for the solar panel, the contribution to the GEO object brightness by the solar panel at those pair of points is identical. Then the difference between the pair of brightness values cancels the solar panel contribution unconditionally and the remainder is only due to the body. Similarly, when the contribution of the body to the observed brightness is same for the point pair, the difference between the two brightness values cancels the body contribution unconditionally and the remainder is only due to the solar panels. This enables separation of the observed brightness data into contributions by the solar panels and the body, which is fundamental to space-object characterization. This separation of the solar panel or body contributions is feasible in each waveband of observation. Thus the point pairing is useful for the analysis of panchromatic as well as multi-spectral data. The desired observation conditions for point pairing occur routinely, typically within a week of each other. This work is supported by the Space Vehicles Directorate of the Air Force Materials Laboratory.

  12. Is ad-hoc plan adaptation based on 2-Step IMRT feasible?

    International Nuclear Information System (INIS)

    Background: The ability of a geometry-based method to expeditiously adapt a '2-Step' step and shoot IMRT plan was explored. Both changes of the geometry of target and organ at risk have to be balanced. A retrospective prostate planning study was performed to investigate the relative benefits of beam segment adaptation to the changes in target and organ at risk coverage. Methods: Four patients with six planning cases with extraordinarily large deformations of rectum and prostate were chosen for the study. A 9-field IMRT plan (A) using 2-Step IMRT segments was planned on an initial CT study. The plan had to fulfil all the requirements of a conventional high-quality step and shoot IMRT plan. To adapt to changes of the anatomy in a further CT data set, three approaches were considered: the original plan with optimized isocentre position (B), a newly optimized plan (C) and the original plan, adapted using the 2-Step IMRT optimization rules (D). DVH parameters were utilized for quantification of plan quality: D99 for the CTV and the central planning target volume (PTV), D95 for an outer PTV, V95, V80 and V50 for rectum and bladder. Results: The adapted plan (D) achieved almost the same target coverage as the newly optimized plan (C). Target coverage for plan B was poor and for the organs at risk, the rectum V80 was slightly increased. The volume with more than 95% of the target dose (V95) was 1.5 ± 1.5 cm3 for the newly optimized plan (C), compared to 2.2 ± 1.3 cm3 for the original plan (A) and 7.2 ± 4.8 cm3 (B) on the first and the second CT, respectively. The adapted plan resulted in 4.3 ± 2.1 cm3 (D), an intermediate dose load to the rectum. All other parameters were comparable for the newly optimized and the adapted plan. Conclusions: The first results for adaptation of interfractional changes using the 2-Step IMRT algorithm are encouraging. The plans were superior to plans with optimized isocentre position and only marginally inferior to a newly optimized plan.

  13. Star sub-pixel centroid calculation based on multi-step minimum energy difference method

    Science.gov (United States)

    Wang, Duo; Han, YanLi; Sun, Tengfei

    2013-09-01

    The star's centroid plays a vital role in celestial navigation, star images which be gotten during daytime, due to the strong sky background, have a low SNR, and the star objectives are nearly submerged in the background, takes a great trouble to the centroid localization. Traditional methods, such as a moment method, weighted centroid calculation method is simple but has a big error, especially in the condition of a low SNR. Gaussian method has a high positioning accuracy, but the computational complexity. Analysis of the energy distribution in star image, a location method for star target centroids based on multi-step minimum energy difference is proposed. This method uses the linear superposition to narrow the centroid area, in the certain narrow area uses a certain number of interpolation to pixels for the pixels' segmentation, and then using the symmetry of the stellar energy distribution, tentatively to get the centroid position: assume that the current pixel is the star centroid position, and then calculates and gets the difference of the sum of the energy which in the symmetric direction(in this paper we take the two directions of transverse and longitudinal) and the equal step length(which can be decided through different conditions, the paper takes 9 as the step length) of the current pixel, and obtain the centroid position in this direction when the minimum difference appears, and so do the other directions, then the validation comparison of simulated star images, and compare with several traditional methods, experiments shows that the positioning accuracy of the method up to 0.001 pixel, has good effect to calculate the centroid of low SNR conditions; at the same time, uses this method on a star map which got at the fixed observation site during daytime in near-infrared band, compare the results of the paper's method with the position messages which were known of the star, it shows that :the multi-step minimum energy difference method achieves a better

  14. One-step synthesis, biodegradation and biocompatibility of polyesters based on the metabolic synthon, dihydroxyacetone.

    Science.gov (United States)

    Korley, Julius N; Yazdi, Sara; McHugh, Kevin; Kirk, James; Anderson, James; Putnam, David

    2016-08-01

    The one-step synthesis of a polyester family containing dihydroxyacetone is described along with a quantitative analysis of in vitro/in vivo degradation kinetics and initial biocompatibility. Polyesters were synthesized by combining dihydroxyacetone, which is a diol found in the eukaryotic glucose metabolic pathway, with even-carbon aliphatic diacids (adipic, suberic, sebacic) represented in the long-chain alpha carboxylic acid metabolic pathway, by Schӧtten-Baumann acylation. We show that by using a crystalline monomeric form of dihydroxyacetone, well-defined polyesters can be formed in one step without protection and deprotection strategies. Both diacid length and polyester molecular weight were varied to influence polymer physical and thermal properties. Polyesters were generated with number-averaged (Mn) molecular weights ranging from 2200-11,500. Polydispersities were consistent with step-growth polymerization and ranged from 2 to 2.6. The melting (Tm) and recrystallization (Tc) temperatures were impacted in an unpredictable manner. Thermal transitions for the polyesters were highest for the adipic acid followed by suberic acid and sebacic acid, respectively. It was shown that the thermal response of the DHA-based polyesters was influenced by both the diacid length and molecular weight. In vitro degradation studies revealed first-order weight loss kinetics, the molecular weight loss followed first order kinetics with 25%-40% of the original mass remaining after 8 weeks. In vivo testing over 16 weeks highlighted that mass loss ranged from ∼70% to ∼6% depending upon initial molecular weight and diacid length. Histological analysis revealed rapid resolution of both acute and chronic inflammatory responses, normal foreign body responses were observed and no inflammation was present after week 4. This one-step synthesis proved robust with unique copolymers warranting further study as potential biomaterials. PMID:27179432

  15. A model for 3:2 HFQPO pairs in black hole binaries based on cosmic battery

    CERN Document Server

    Huang, Chang-Yin; Wang, Ding-Xiong; Li, Yang

    2016-01-01

    A model for 3:2 high-frequency quasi-periodic oscillations (HFQPOs) with 3:2 pairs observed in four black hole X-ray binaries (BHXBs) is proposed by invoking the epicyclic resonances with the magnetic connection (MC) between a spinning black hole (BH) with a relativistic accretion disc. It turns out that the MC can be worked out due to Poynting-Robertson cosmic battery (PRCB), and the 3:2 HFQPO pairs associated with the steep power-law states can be fitted in this model. Furthermore, the severe damping problem in the epicyclic resonance model can be overcome by transferring energy from the BH to the inner disc via the MC process for emitting X-rays with sufficient amplitude and coherence to produce the HFQPOs. In addition, we discuss the important role of the magnetic field in state transition of BHXBs.

  16. 3D broadband isotropic NRI metamaterial based on metallic cross-pairs

    International Nuclear Information System (INIS)

    In this paper, a new type of 3D metamaterial composed of double periodic array of metallic cross-pairs printed on the six sides of a cubic dielectric substrate was proposed to obtain the characteristics of broadband NRI and isotropy for the applications of super lenses. The behaviors of NRI, isotropy and polarization were analyzed using the CST Microwave Studio. The results show that the proposed metamaterial exhibits not only a broadband NRI whose relative bandwidth can be up to 56.7%, but also polarization-independence and isotropy. Thus, the proposed metamaterial is a good candidate material for 3D broadband isotropic NRI metamaterial. - Highlights: → 3D metamaterial is composed of double periodic array of metallic cross-pairs printed on the six sides of a cubic dielectric substrate. → Broadband negative refraction index (NRI) with relative bandwidth of 56.7%. → Polarization-independence and isotropy.

  17. Watson-Crick Base Pairing, Electronic and Photophysical Properties of Triazole Modified Adenine Analogues: A Computational Study

    KAUST Repository

    Das, Shubhajit

    2015-09-17

    We employ first-principles Density Functional Theory (DFT) and time-dependent DFT (TDDFT) to elucidate structural, electronic and optical properties of a few recently reported triazole adenine nucleobase analogues. The results are compared against the findings obtained for both natural adenine nucleobase and available experimental data. The optical absorption of these adenine analogues are calculated both in gas-phase and in solvent (methanol) using Polarized Continuum Model (PCM). We find that all the analogues show a red-shifted absorption profile as compared to adenine. Our simulated emission spectra in solvent compare fairly well with experimentally observed results. We investigate base paring ability of these adenine analogues with thymine. The calculations on the intrinsic stability of these base pairs ascertain that all the adenine analogues form the hydrogen bonded Watson-Crick base pair with similar H-bonding energy as obtained for natural adenine-thymine base pair. In our study, we provide a microscopic origin of the low-energy absorption and emission peaks, observed experimentally.

  18. A Practical Parallel Algorithm for All-Pair Shortest Path Based on Pipelining

    Institute of Scientific and Technical Information of China (English)

    Hua Wang; Ling Tian; Chun-Hua Jiang

    2008-01-01

    On the basis of Floyd algorithm with theextended path matrix, a parallel algorithm whichresolves all-pair shortest path (APSP) problem oncluster environment is analyzed and designed.Meanwhile, the parallel APSP pipelining algorithmmakes full use of overlapping technique betweencomputation and communication. Compared withbroadcast operation, the parallel algorithm reducescommunication cost. This algorithm has beenimplemented on MPI on PC-cluster. The theoreticalanalysis and experimental results show that the parallelalgorithm is an efficient and scalable algorithm.

  19. A Novel Three-Dimensional Wide-Angle Beam Propagation Method Based on Split-Step Fast Fourier Transform

    Institute of Scientific and Technical Information of China (English)

    ZANG Wei-Ping; CHENG Hua; TIAN Jian-Guo

    2009-01-01

    A novel three-dimensional wide-angle beam propagation method based on the split-step fast Fourier transform is developed. The formulation is based on the three-dimensional Helmholtz wave equation. Each propagation step is performed by utilizing both the FFT and split-step scheme. The solution of Helmholtz wave equation does not make the slowly varying envelope and one-way propagation approximations. To validate the efficiency and accuracy, numerical results for a propagation beam in a tilted step-index optical waveguide are compared with other beam propagation algorithms.

  20. A Study on the Storage Reliability of LSINS Based on Step-stress Accelerated Life Test

    Directory of Open Access Journals (Sweden)

    Teng Fei

    2015-01-01

    Full Text Available Based on the step-stress accelerated life test and the laser strap-down inertial navigation system, this paper studies the accelerated life model and the test method, provides the likelihood function, the likelihood equation and the two-order derivative when the stress level is k, evaluates the effectiveness of the method with the simulation test model established by MATLAB, applies the research findings in the storage reliability study of the XX laser strap-down inertial navigation system, and puts forward an effective evaluation method of the storage life of the inertial navigation system.

  1. Step-coordination Algorithm of Traffic Control Based on Multi-agent System

    Institute of Scientific and Technical Information of China (English)

    Hai-Tao Zhang; Fang Yu; Wen Li

    2009-01-01

    Aiming at the deficiency of conventional traffic control method, this paper proposes a new method based on multi-agent technology for traffic control. Different from many existing methods, this paper distinguishes traffic control on the basis of the agent technology from conventional traffic control method. The composition and structure of a multi-agent system (MAS) is first discussed. Then, the step-coordination strategies of intersection-agent, segment-agent, and area-agent are put forward. The advantages of the algorithm are demonstrated by a simulation study.

  2. A polarization entangled photon-pair source based on a type-II PPLN waveguide emitting at a telecom wavelength

    International Nuclear Information System (INIS)

    We report the realization of a fiber-coupled polarization entangled photon-pair source at 1310 nm based on a birefringent titanium in-diffused waveguide integrated into periodically poled lithium niobate. By making use of a dedicated and high-performance setup, we characterized the quantum properties of the pairs by measuring two-photon interference in both Hong-Ou-Mandel and standard Bell inequality configurations. For the two sets of measurements we obtained interference net visibilities reaching nearly 100%, which represent important and competitive results compared to those for the similar waveguide-based configurations already reported. These results prove the relevance of our approach as an enabling technology for long-distance quantum communication.

  3. Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

    Czech Academy of Sciences Publication Activity Database

    Morgado, C.A.; Svozil, D.; Turner, D.H.; Šponer, Jiří

    2012-01-01

    Roč. 14, č. 36 (2012), s. 12580-12591. ISSN 1463-9076 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional research plan: CEZ:AV0Z50040702 Keywords : GA base pairs * base stacking * RNA duplexes Subject RIV: BO - Biophysics Impact factor: 3.829, year: 2012

  4. PhosphoScan: A Probability-Based Method for Phosphorylation Site Prediction Using MS2/MS3 Pair Information

    OpenAIRE

    Wan, Yunhu; Cripps, Diane; Thomas, Stefani; Campbell, Patricia; Ambulos, Nicholas; CHEN Ting; Yang, Austin

    2008-01-01

    Phosphopeptide identification and phosphorylation site localization are crucial aspects of many biological studies. Furthermore, multiple phosphorylations of peptides make site localization even more difficult. We developed a probability-based method to unambiguously determine phosphorylation sites within phosphopeptides using MS2/3 pair information. A comparison test was performed with SEQUEST and MASCOT predictions using a spectral data set from a synthetic doubly phosphorylated peptide, an...

  5. A new image reconstruction method for 3-D PET based upon pairs of near-missing lines of response

    International Nuclear Information System (INIS)

    We formerly introduced a new image reconstruction method for three-dimensional positron emission tomography, which is based upon pairs of near-missing lines of response. This method uses an elementary geometric property of lines of response, namely that two lines of response which originate from radioactive isotopes located within a sufficiently small voxel, will lie within a few millimeters of each other. The effectiveness of this method was verified by performing a simulation using GATE software and a digital Hoffman phantom

  6. Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

    OpenAIRE

    Camila Ximenes; Eduardo Brandão; Paula Oliveira; Abraham Rocha; Tamisa Rego; Rafael Medeiros; Ana Aguiar-Santos; João Ferraz; Christian Reis; Paulo Araujo; Luiz Carvalho; Melo, Fabio L

    2014-01-01

    The Global Program for the Elimination of Lymphatic Filariasis (GPELF) aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR)-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuche...

  7. UvrD Helicase Unwinds DNA One Base Pair At A Time By A Two-Part Power Stroke

    OpenAIRE

    Lee, Jae Young; Yang, Wei

    2006-01-01

    Helicases use the energy derived from nucleoside triphosphate hydrolysis to unwind double helices in essentially every metabolic pathway involving nucleic acids. Earlier crystal structures have suggested that DNA helicases translocate along a single-stranded DNA in an inchworm fashion. We report here a series of crystal structures of the UvrD helicase complexed with DNA and ATP hydrolysis intermediates. These structures reveal that ATP binding alone leads to unwinding of 1 base pair by direct...

  8. Pair-Wise, Deformable Mirror, Image Plane-Based Diversity Electric Field Estimation for High Contrast Coronagraphy

    Science.gov (United States)

    Give'on, Amir; Kern, Brian D.; Shaklan, Stuart

    2011-01-01

    In this paper we describe the complex electric field reconstruction from image plane intensity measurements for high contrast coronagraphic imaging. A deformable mirror (DM) surface is modied with pairs of complementary shapes to create diversity in the image plane of the science camera where the intensity of the light is measured. Along with the Electric Field Conjugation correction algorithm, this estimation method has been used in various high contrast imaging testbeds to achieve the best contrasts to date both in narrow and in broad band light. We present the basic methodology of estimation in easy to follow list of steps, present results from HCIT and raise several open quations we are confronted with using this method.

  9. An FPGA-Based Multiple-Axis Velocity Controller and Stepping Motors Drives Design

    Directory of Open Access Journals (Sweden)

    Lai Chiu-Keng

    2016-01-01

    Full Text Available A Field Programmable Gate Array based system is a great hardware platform to support the implementation of hardware controllers such as PID controller and fuzzy controller. It is also programmed as hardware accelerator to speed up the mathematic calculation and greatly enhance the performance as applied to motor drive and motion control. Furthermore, the open structure of FPGA-based system is suitable for those designs with the ability of parallel processing or soft code processor embedded. In this paper, we apply the FPGA to a multi-axis velocity controller design. The developed system integrated three functions inside the FPGA chip, which are respectively the stepping motor drive, the multi-axis motion controller and the motion planning. Furthermore, an embedded controller with a soft code processor compatible to 8051 micro-control unit (MCU is built to handle the data transfer between the FPGA board and host PC. The MCU is also used to initialize the motion control and run the interpolator. The designed system is practically applied to a XYZ motion platform which is driven by stepping motors to verify its performance.

  10. A Practical Parallel Algorithm for All-Pair Shortest Path Based on Pipelining

    Institute of Scientific and Technical Information of China (English)

    Hua Wang; Ling Tian; Chun-Hua Jiang

    2008-01-01

    On the basis of Floyd algorithm with the extended path matrix, a parallel algorithm which resolves all-pair shortest path (APSP) problem on cluster environment is analyzed and designed. Meanwhile, the parallel APSP pipelining algorithm makes full use of overlapping technique between computation and communication. Compared with broadcast operation, the parallel algorithm reduces communication cost. This algorithm has been implemented on MPI on PC-cluster. The theoretical analysis and experimental results show that the parallel algorithm is an efficient and scalable algorithm.

  11. All-pairs Shortest Path Algorithm based on MPI+CUDA Distributed Parallel Programming Model

    OpenAIRE

    Qingshuang Wu; Chunya Tong; Qiang Wang; Xiangfu Cheng

    2013-01-01

    In view of the problem that computing shortest paths in a graph is a complex and time-consuming process, and the traditional algorithm that rely on the CPU as computing unit solely can't meet the demand of real-time processing, in this paper, we present an all-pairs shortest paths algorithm using MPI+CUDA hybrid programming model, which can take use of the overwhelming computing power of the GPU cluster to speed up the processing. This proposed algorithm can combine the advantages of MPI and ...

  12. The multiple time step r-RESPA procedure and polarizable potentials based on induced dipole moments

    Science.gov (United States)

    Masella, Michel

    In the present study, we present an accelerating scheme based on the reversible multiple time step r-RESPA method to be used in molecular dynamics simulations with polarizable potentials based on induced dipole moments. Even if the induced dipoles are estimated with an iterative self-consistent procedure, this scheme significantly reduces the CPU time needed to perform a molecular dynamics simulation, up to a factor 2, as compared to the Car-Parrinello method where additional dynamical variables are introduced for the treatment of the induced dipoles. The tests show that stable and reliable molecular dynamics trajectories can be generated with that scheme, and that the physical properties derived from the trajectories are equivalent to those computed with the classical all atom iterative approach and the Car-Parrinello one.

  13. Electrochemical model of polyaniline-based memristor with mass transfer step

    Energy Technology Data Exchange (ETDEWEB)

    Demin, V.A. [National Research Centre ' Kurchatov Institute' , 123182, Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), 141700, Dolgoprudny, Moscow Region (Russian Federation); Erokhin, V.V. [CNR-IMEM (National Research Council, Institute of Materials for Electronics and Magnetism) and University of Parma, Viale Usberti 7A, 42124, Parma (Italy); Kashkarov, P.K.; Kovalchuk, M.V. [National Research Centre ' Kurchatov Institute' , 123182, Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), 141700, Dolgoprudny, Moscow Region (Russian Federation); Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991, Moscow (Russian Federation)

    2015-03-10

    The electrochemical organic memristor with polyaniline active layer is a stand-alone device designed and realized for reproduction of some synapse properties in the innovative electronic circuits, such as the new field-programmable gate arrays or the neuromorphic networks capable for learning. In this work a new theoretical model of the polyaniline memristor is presented. The developed model of organic memristor functioning was based on the detailed consideration of possible electrochemical processes occuring in the active zone of this device including the mass transfer step of ionic reactants. Results of the calculation have demonstrated not only the qualitative explanation of the characteristics observed in the experiment, but also quantitative similarities of the resultant current values. This model can establish a basis for the design and prediction of properties of more complicated circuits and systems (including stochastic ones) based on the organic memristive devices.

  14. Electrochemical model of polyaniline-based memristor with mass transfer step

    International Nuclear Information System (INIS)

    The electrochemical organic memristor with polyaniline active layer is a stand-alone device designed and realized for reproduction of some synapse properties in the innovative electronic circuits, such as the new field-programmable gate arrays or the neuromorphic networks capable for learning. In this work a new theoretical model of the polyaniline memristor is presented. The developed model of organic memristor functioning was based on the detailed consideration of possible electrochemical processes occuring in the active zone of this device including the mass transfer step of ionic reactants. Results of the calculation have demonstrated not only the qualitative explanation of the characteristics observed in the experiment, but also quantitative similarities of the resultant current values. This model can establish a basis for the design and prediction of properties of more complicated circuits and systems (including stochastic ones) based on the organic memristive devices

  15. Direct Taxation in the Eu: The Common Corporate Tax Base as the Next Sub-Step towards Harmonization

    OpenAIRE

    Norbert Herzig; Johannes Kuhr

    2011-01-01

    This paper analyzes the Common Corporate Tax Base (CCTB) as an interim alternative to the proposal of a Council directive on a Common Consolidated Corporate Tax Base (CCCTB). The CCCTB concept does not only include common rules for determining the tax base like the CCTB but also the steps of consolidation and subsequent formula apportionment. Therefore, the paper starts by showing that particularly these second and third steps of the CCCTB project meet fierce political opposition from several...

  16. Uncertainty evaluation for three-dimensional scanning electron microscope reconstructions based on the stereo-pair technique

    International Nuclear Information System (INIS)

    3D-SEM is a method, based on the stereophotogrammetry technique, which obtains three-dimensional topographic reconstructions starting typically from two SEM images, called the stereo-pair. In this work, a theoretical uncertainty evaluation of the stereo-pair technique, according to GUM (Guide to the Expression of Uncertainty in Measurement), was carried out, considering 3D-SEM reconstructions of a wire gauge with a reference diameter of 250 µm. Starting from the more commonly used tilting strategy, one based on the item rotation inside the SEM chamber was also adopted. The latter enables multiple-view reconstructions of the cylindrical item under consideration. Uncertainty evaluation was performed starting from a modified version of the Piazzesi equation, enabling the calculation of the z-coordinate from a given stereo-pair. The metrological characteristics of each input variable have been taken into account and a SEM stage calibration has been performed. Uncertainty tables for the cases of tilt and rotation were then produced, leading to the calculation of expanded uncertainty. For the case of rotation, the largest uncertainty contribution resulted to be the rotational angle; however, for the case of tilt it resulted to be the pixel size. A relative expanded uncertainty equal to 5% and 4% was obtained for the case of rotation and tilt, respectively

  17. ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets

    OpenAIRE

    Pope, Bernard J.; Nguyen-Dumont, Tú; Hammet, Fleur; Park, Daniel J

    2014-01-01

    Background We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end sequencing can achieve complete overlap of read pairs. Variant calling from Hi-Plex-derived datasets can thus rely on the identification of variants appearing in both reads of read-pairs, permitting stringent filtering of sequencing chemistry-induced errors. These principles ...

  18. One-Step Targeted Minimum Loss-based Estimation Based on Universal Least Favorable One-Dimensional Submodels

    Science.gov (United States)

    van der Laan, Mark; Gruber, Susan

    2016-01-01

    Consider a study in which one observes n independent and identically distributed random variables whose probability distribution is known to be an element of a particular statistical model, and one is concerned with estimation of a particular real valued pathwise differentiable target parameter of this data probability distribution. The targeted maximum likelihood estimator (TMLE) is an asymptotically efficient substitution estimator obtained by constructing a so called least favorable parametric submodel through an initial estimator with score, at zero fluctuation of the initial estimator, that spans the efficient influence curve, and iteratively maximizing the corresponding parametric likelihood till no more updates occur, at which point the updated initial estimator solves the so called efficient influence curve equation. In this article we construct a one-dimensional universal least favorable submodel for which the TMLE only takes one step, and thereby requires minimal extra data fitting to achieve its goal of solving the efficient influence curve equation. We generalize these to universal least favorable submodels through the relevant part of the data distribution as required for targeted minimum loss-based estimation. Finally, remarkably, given a multidimensional target parameter, we develop a universal canonical one-dimensional submodel such that the one-step TMLE, only maximizing the log-likelihood over a univariate parameter, solves the multivariate efficient influence curve equation. This allows us to construct a one-step TMLE based on a one-dimensional parametric submodel through the initial estimator, that solves any multivariate desired set of estimating equations. PMID:27227728

  19. A Search for Spectral Galaxy Pairs of Overlapping Galaxies based on Fuzzy Recognition

    CERN Document Server

    Yang, Haifeng; Chen, Xiaoyan; Zhang, Jifu; Hou, Wen; Cai, Jianghui; Wei, Peng; Ren, Juanjuan; Liu, Xiaojie; Zhao, Yongheng

    2014-01-01

    The Spectral Galaxy Pairs (SGPs) are de?ned as the composite galaxy spectra which contain two independent redshift systems. These spectra are useful for studying dust properties of the foreground galaxies. In this paper, a total of 165 spectra of SGPs are mined out from Sloan Digital Sky Survey (SDSS) Data Release 9 (DR9) using the concept of membership degree from the fuzzy set theory particularly de?ned to be suitable for fuzzily identifying emission lines. The spectra and images of this sample are classi?ed according to the membership degree and their image features, respectively. Many of these 2nd redshift systems are too small or too dim to select from the SDSS images alone, making the sample a potentially unique source of information on dust e?ects in low-luminosity or low-surface-brightness galaxies that are underrepresented in morphological pair samples. The dust extinction of the objects with high membership degree is also estimated by Balmer decrement. Additionally, analyses for a series of spectros...

  20. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs

    OpenAIRE

    Ohkubo, Akihiro; Yamada, Kenji; Ito, Yu; Yoshimura, Kiichi; Miyauchi, Koichiro; Kanamori, Takashi; Masaki, Yoshiaki; Seio, Kohji; Yuasa, Hideya; Sekine, Mitsuo

    2015-01-01

    A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2’-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (dgC) residue for a C-G base pair have hi...

  1. DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

    International Nuclear Information System (INIS)

    To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH2 group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH2 group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes

  2. DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

    Energy Technology Data Exchange (ETDEWEB)

    Okutsu, N.; Shimamura, K.; Shimizu, E.; Kurita, N., E-mail: kurita@cs.tut.ac.jp [Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580 (Japan); Shulga, S. [Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv (Ukraine); Danilov, V. I. [Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv (Ukraine)

    2016-02-01

    To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.

  3. Ultrasensitive DNA detection based on two-step quantitative amplification on magnetic nanoparticles

    Science.gov (United States)

    Jin, Mingliang; Liu, Xia; van den Berg, Albert; Zhou, Guofu; Shui, Lingling

    2016-08-01

    Sensitive detection of a specific deoxyribo nucleic acid (DNA) sequence is important for biomedical applications. In this report, a two-step amplification strategy is developed based on magnetic nanoparticles (MNPs) to achieve ultrasensitive DNA fluorescence detection. The first level amplification is obtained from multiple binding sites on MNPs to achieve thousands of probe DNA molecules on one nanoparticle surface. The second level amplification is gained by enzymatic reaction to achieve fluorescence signal enhancement. MNPs functionalized by probe DNA (DNAp) are bound to target DNA (t-DNA) molecules with a ratio of 1:1 on a substrate with capture DNA (DNAc). After the MNPs with DNAp are released from the substrate, alkaline phosphatase (AP) is labelled to MNPs via hybridization reaction between DNAp on MNPs and detection DNAs (DNAd) with AP. The AP on MNPs catalyses non-fluorescent 4-methylumbelliferyl phosphate (4-MUP) to fluorescent 4-methylumbelliferone (4-MU) with high intensity. Finally, fluorescence intensity of the 4-MU is detected by a conventional fluorescence spectrophotometer. With this two-step amplification strategy, the limit of detection (LOD) of 2.8 × 10‑18 mol l‑1 for t-DNA has been achieved.

  4. Development of SmartStep: an insole-based physical activity monitor.

    Science.gov (United States)

    Sazonov, Edward S; Hegde, Nagaraj; Tang, Wenlong

    2013-01-01

    In our previous research we developed a SmartShoe--a shoe based physical activity monitor that can reliably differentiate between major postures and activities, accurately estimate energy expenditure of individuals, measure temporal gait parameters, and estimate body weights. In this paper we present the development of the next stage of the SmartShoe evolution--SmartStep, a physical activity monitor that is fully integrated into an insole, maximizing convenience and social acceptance of the monitor. Encapsulating the sensors, Bluetooth Low Energy wireless interface and the energy source within an assembly repeatedly loaded with high forces created during ambulation presented new design challenges. In this preliminary study we tested the ability of the SmartStep to measure the pressure differences between static weight-bearing and non-weight-bearing activities (such as no load vs. sitting vs. standing) as well as capture pressure variations during walking. We also measured long-term stability of the sensors and insole assembly under cyclic loading in a mechanical testing system. PMID:24111408

  5. First Steps Towards AN Integrated Citygml-Based 3d Model of Vienna

    Science.gov (United States)

    Agugiaro, G.

    2016-06-01

    This paper presents and discusses the results regarding the initial steps (selection, analysis, preparation and eventual integration of a number of datasets) for the creation of an integrated, semantic, three-dimensional, and CityGML-based virtual model of the city of Vienna. CityGML is an international standard conceived specifically as information and data model for semantic city models at urban and territorial scale. It is being adopted by more and more cities all over the world. The work described in this paper is embedded within the European Marie-Curie ITN project "Ci-nergy, Smart cities with sustainable energy systems", which aims, among the rest, at developing urban decision making and operational optimisation software tools to minimise non-renewable energy use in cities. Given the scope and scale of the project, it is therefore vital to set up a common, unique and spatio-semantically coherent urban model to be used as information hub for all applications being developed. This paper reports about the experiences done so far, it describes the test area and the available data sources, it shows and exemplifies the data integration issues, the strategies developed to solve them in order to obtain the integrated 3D city model. The first results as well as some comments about their quality and limitations are presented, together with the discussion regarding the next steps and some planned improvements.

  6. Quaternion-based Kalman Filter for AHRS Using an Adaptive-step Gradient Descent Algorithm

    Directory of Open Access Journals (Sweden)

    Li Wang

    2015-09-01

    Full Text Available This paper presents a quaternion-based Kalman filter for real-time estimation of the orientation of a quadrotor. Quaternions are used to represent rotation relationship between navigation frame and body frame. Processing of a 3-axis accelerometer using Adaptive-Step Gradient Descent (ASGD produces a computed quaternion input to the Kalman filter. The step-size in GD is set in direct proportion to the physical orientation rate. Kalman filter combines 3-axis gyroscope and computed quaternion to determine pitch and roll angles. This combination overcomes linearization error of the measurement equations and reduces the calculation cost. 3-axis magnetometer is separated from ASGD to independently calculate yaw angle for Attitude Heading Reference System (AHRS. This AHRS algorithm is able to remove the magnetic distortion impact. Experiments are carried out in the small-size flight controller and the real world flying test shows the proposed AHRS algorithm is adequate for the real-time estimation of the orientation of a quadrotor.

  7. Identifying typical patterns of vulnerability: A 5-step approach based on cluster analysis

    Science.gov (United States)

    Sietz, Diana; Lüdeke, Matthias; Kok, Marcel; Lucas, Paul; Carsten, Walther; Janssen, Peter

    2013-04-01

    Specific processes that shape the vulnerability of socio-ecological systems to climate, market and other stresses derive from diverse background conditions. Within the multitude of vulnerability-creating mechanisms, distinct processes recur in various regions inspiring research on typical patterns of vulnerability. The vulnerability patterns display typical combinations of the natural and socio-economic properties that shape a systems' vulnerability to particular stresses. Based on the identification of a limited number of vulnerability patterns, pattern analysis provides an efficient approach to improving our understanding of vulnerability and decision-making for vulnerability reduction. However, current pattern analyses often miss explicit descriptions of their methods and pay insufficient attention to the validity of their groupings. Therefore, the question arises as to how do we identify typical vulnerability patterns in order to enhance our understanding of a systems' vulnerability to stresses? A cluster-based pattern recognition applied at global and local levels is scrutinised with a focus on an applicable methodology and practicable insights. Taking the example of drylands, this presentation demonstrates the conditions necessary to identify typical vulnerability patterns. They are summarised in five methodological steps comprising the elicitation of relevant cause-effect hypotheses and the quantitative indication of mechanisms as well as an evaluation of robustness, a validation and a ranking of the identified patterns. Reflecting scale-dependent opportunities, a global study is able to support decision-making with insights into the up-scaling of interventions when available funds are limited. In contrast, local investigations encourage an outcome-based validation. This constitutes a crucial step in establishing the credibility of the patterns and hence their suitability for informing extension services and individual decisions. In this respect, working at

  8. Alpha-beta monitoring system based on pair of simultaneous Multi-Wire Proportional Counters

    Science.gov (United States)

    Wengrowicz, U.; Amidan, D.; Orion, I.

    2016-08-01

    A new approach for a simultaneous alpha-beta Multi-wire Proportional Counter (MWPC) is presented. The popular approach for alpha-beta monitoring systems consists of a large area MWPC using noble gas flow such as Argon Methane. This method of measurement is effective but requires large-scale and expensive maintenance due to the needs of gas flow control and periodic replacements. In this work, a pair of simultaneous MWPCs for alpha-beta measuring is presented. The developed detector consists of a sealed gas MWPC sensor for beta particles, behind a free air alpha sensor. This approach allows effective simultaneous detection and discrimination of both alpha and beta radiation without the maintenance cost noble gas flow required for unsealed detectors.

  9. A Step towards EEG-based brain computer interface for autism intervention.

    Science.gov (United States)

    Fan, Jing; Wade, Joshua W; Bian, Dayi; Key, Alexandra P; Warren, Zachary E; Mion, Lorraine C; Sarkar, Nilanjan

    2015-08-01

    Autism Spectrum Disorder (ASD) is a prevalent and costly neurodevelopmental disorder. Individuals with ASD often have deficits in social communication skills as well as adaptive behavior skills related to daily activities. We have recently designed a novel virtual reality (VR) based driving simulator for driving skill training for individuals with ASD. In this paper, we explored the feasibility of detecting engagement level, emotional states, and mental workload during VR-based driving using EEG as a first step towards a potential EEG-based Brain Computer Interface (BCI) for assisting autism intervention. We used spectral features of EEG signals from a 14-channel EEG neuroheadset, together with therapist ratings of behavioral engagement, enjoyment, frustration, boredom, and difficulty to train a group of classification models. Seven classification methods were applied and compared including Bayes network, naïve Bayes, Support Vector Machine (SVM), multilayer perceptron, K-nearest neighbors (KNN), random forest, and J48. The classification results were promising, with over 80% accuracy in classifying engagement and mental workload, and over 75% accuracy in classifying emotional states. Such results may lead to an adaptive closed-loop VR-based skill training system for use in autism intervention. PMID:26737113

  10. Phosphorus recovery by one or two-step technology with use of acids and bases

    Energy Technology Data Exchange (ETDEWEB)

    Stark, Kristina; Hultman, Bengt

    2003-07-01

    The method of using sludge fractionation is considered to be a sustainable solution where the sludge is seen as the raw material from which products are recovered. This paper will present solutions of advanced technology system for a large wastewater treatment plant. Use of enhanced biological phosphorus removal and fractionation of the sludge in two stages is advantageous both with respect to low necessary chemical and energy demands and recovery efficiency. Phosphorous recovery may be based on one- or two-step technology. Experimental studies have shown that it is possible to recover phosphorus from sludge by the combination of supercritical water oxidation process and alkaline leaching. When the concentration of sodium hydroxide is around 1 M, approximate 50 % of total phosphorus is recovered in room temperature. Meanwhile, over 98 % of the soluble phosphorus is recovered from the liquid phase by adding calcium chloride (CaCl{sub 2}). (author)

  11. Minimising complications in abdominoplasty: An approach based on the root cause analysis and focused preventive steps

    Directory of Open Access Journals (Sweden)

    Mohan Rangaswamy

    2013-01-01

    Full Text Available Significant complications still occur after abdominoplasty, the rate varies widely in different series. This variation suggests that there is a lot of scope for improvement. This paper reviews the various complications and also the technical improvements reported in the last 20 years. The root cause of each complication is analysed and preventive steps are suggested based on the literature and the author′s own personal series with very low complication rates. Proper case selection, risk stratified prophylaxis of thromboembolism, initial synchronous liposuction, flap elevation at the Scarpa fascia level, discontinuous incremental flap dissection, vascular preservation and obliteration of the sub-flap space by multiple sutures emerge as the strongest preventive factors. It is proposed that most of the complications of abdominoplasty are preventable and that it is possible to greatly enhance the aesthetic and safety profile of this surgery.

  12. GSM-MR compression algorithm with two step sorting based on similarity analysis

    Science.gov (United States)

    Cheng, Fei; Liu, Kai; Zhang, Jin; Ding, Wenwen; Li, Yunsong

    2015-05-01

    Collecting reliable and accurate MR data on time plays a vital role in the mobile communication network optimization. However, with the increment of the number of mobile users, network bandwidth cannot meet with mass transfer of MR. A high performance and high compression ratio GSM-MR compression algorithm is proposed to gain better transfer time. This algorithm utilizes two step sorting in order to reduce the distance between similar content, based on the analytic result about similarities of GSM-MR data sorting by different fields. Experimental results reveal that the algorithm does not only decrease compression consuming time, but also ascends compression ratio with the increment of the size of compression data.

  13. A Three Step B2B Sales Model Based on Satisfaction Judgments

    DEFF Research Database (Denmark)

    Grünbaum, Niels Nolsøe

    2015-01-01

    This paper aims to provide a coherent, detailed and integrative understanding of the mental processes (i.e. dimensions) that industrial buyers apply when forming satisfaction judgments in adjacent to new task buying situations. A qualitative inductive research strategy is utilized in this study....... The insights produces can be applied for selling companies to craft close collaborative customer relationships in a systematic ad efficient way. The process of building customer relationships will be guided through actions that yields higher satisfaction judgments leading to loyal customers and...... the selling companies‘ perspective. The buying center members applied satisfaction dimension when forming satisfaction judgments. Moreover, the focus and importance of the identified satisfaction dimensions fluctuated pending on the phase of the buying process. Based on the findings a three step sales...

  14. A Three Step B2B Sales Model Based on Satisfaction Judgments

    DEFF Research Database (Denmark)

    Grünbaum, Niels Nolsøe

    2015-01-01

    This paper aims to provide a coherent, detailed and integrative understanding of the mental processes (i.e. dimensions) that industrial buyers apply when forming satisfaction judgments in adjacent to new task buying situations. A qualitative inductive research strategy is utilized in this study....... The insights produces can be applied for selling companies to craft close collaborative customer relationships in a systematic a d efficient way. The process of building customer relationships will be guided through actions that yields higher satisfaction judgments leading to loyal customers and...... the selling companies’ perspective. The buying center members applied satisfaction dimension when forming satisfaction judgments. Moreover, the focus and importance of the identified satisfaction dimensions fluctuated pending on the phase of the buying process. Based on the findings a three step sales...

  15. One-step synthesis of natural silk sericin-based microcapsules with bionic structures.

    Science.gov (United States)

    Liu, Zhaogang; Cai, Yurong; Jia, Yaru; Liu, Lin; Kong, Xiangdong; Kundu, Subhas C; Yao, Juming

    2014-10-01

    Different techniques are being developed for fabricating microcapsules; it is still a challenge to fabricate them in an efficient and environment-friendly process. Here, a one-step green route to synthesize silk protein sericin-based microcapsules without any assistance of organic solvents is reported. By carefully changing the concentration of calcium ions accompanied with stirring, the morphology of the microcapsules can easily be regulated to form either discoidal, biconcave, cocoon-like, or tubular structures. The chelation of Ca(2+) and shearing force from agitation may induce the conformational transformation of sericin, which possibly results in the formation of microcapsules through the self-assembly of the protein subsequently. The as-prepared cocoon-like microcapsules exhibit pH-dependent stability. A potential application of microcapsules being fabricated from natural water-soluble silk protein sericin for controlled bioactive molecules loading and release system by a pH-triggered manner is quite feasible. PMID:25168858

  16. A Back-stepping Based Trajectory Tracking Controller for a Non-chained Nonholonomic Spherical Robot

    Institute of Scientific and Technical Information of China (English)

    Zhan Qiang; Liu Zengbo; Cai Yao

    2008-01-01

    Spherical robot has good static and dynamic stability, which provides it with strong viability in hostile environment, but the lack of effective control methods has hindered its application and development. This article deals with the dynamic trajectory tracking problem of the spherical robot BHQ-2 designed for unmanned environment exploration. The dynamic model of the spherical robot is established with a simplified Boltzmann-Hamel equation, based on which a trajectory tracking controller is designed by using the back-stepping method. The convergence of the controller is proved with the Lyapunov stability theory. Numerical simulations show that with the controller the robot can globally and asymptotically track desired trajectories, both linear and circular.

  17. Headwater thermal response to partial-retention forest harvesting: a process-based paired-catchment experiment

    Science.gov (United States)

    Moore, R. D.; Guenther, S. M.; Gomi, T.

    2008-12-01

    Paired-catchment experiments are the most rigorous empirical research design for estimating the effects of land use on aquatic systems. However, they have recently come under increasing criticism, in part because past studies typically treated catchments as black boxes. As a result, investigators could only speculate about the factors responsible for any observed effects, limiting their ability to generalize the experimental results in space and time. This study used a paired-catchment approach to investigate the effects of partial- retention forest harvesting with no riparian buffer on the thermal regime of a headwater stream in coastal British Columbia. In addition to monitoring stream temperature at three locations within the treatment reach, we monitored above-stream microclimate, water surface evaporation, bed temperature profiles, groundwater temperature, and reach-scale surface-subsurface interaction. Daily maximum stream temperatures increased after harvesting by over 5 °C during summer, with little effect in winter. The major driver of post- harvest warming was an increase in solar radiation, which was partially moderated by the increased effects of hyporheic exchange, bed heat conduction and evaporation. Incorporating process-based measurements into paired-catchment experiments not only allows the causes of treatment response to be assessed, but they provide a valuable data set for testing predictive models.

  18. The ALHAMBRA survey: an empirical estimation of the cosmic variance for merger fraction studies based on close pairs

    CERN Document Server

    López-Sanjuan, C; Hernández-Monteagudo, C; Varela, J; Molino, A; Arnalte-Mur, P; Ascaso, B; Castander, F J; Fernández-Soto, A; Huertas-Company, M; Márquez, I; Martínez, V J; Masegosa, J; Moles, M; Pović, M; Aguerri, J A L; Alfaro, E; Benítez, N; Broadhurst, T; Cabrera-Caño, J; Cepa, J; Cerviño, M; Cristóbal-Hornillos, D; Del Olmo, A; Delgado, R M González; Husillos, C; Infante, L; Perea, J; Prada, F; Quintana, J M

    2014-01-01

    Our goal is to estimate empirically, for the first time, the cosmic variance that affects merger fraction studies based on close pairs. We compute the merger fraction from photometric redshift close pairs with 10h^-1 kpc <= rp <= 50h^-1 kpc and Dv <= 500 km/s, and measure it in the 48 sub-fields of the ALHAMBRA survey. We study the distribution of the measured merger fractions, that follow a log-normal function, and estimate the cosmic variance sigma_v as the intrinsic dispersion of the observed distribution. We develop a maximum likelihood estimator to measure a reliable sigma_v and avoid the dispersion due to the observational errors (including the Poisson shot noise term). The cosmic variance of the merger fraction depends mainly on (i) the number density of the populations under study, both for the principal (n_1) and the companion (n_2) galaxy in the close pair, and (ii) the probed cosmic volume V_c. We find a significant dependence on neither the search radius used to define close companions, t...

  19. OECD benchmark on thermal fatigue problem - Second step: Evaluation based on FEM

    International Nuclear Information System (INIS)

    In the context of the OECD benchmark on thermal fatigue problem, this report corresponds to the second step of the procedure, i.e. integrity assessment in thermo-mechanical test interpretations. In this second step, participants were asked to estimate the number of cycles to crack initiation on the inner surface, without any initial notch. This report consists of evaluations based on FEM. Thermal and stress calculations are done by 3D-FEM, and based on these results, the number of cycles to crack initiation and propagation are estimated. The main conclusions are the following. Three dimensional Finite Element Analysis with JNC fatigue evaluation procedure estimated the most likely average crack initiation cycle as 2.8 x 104. The maximum Von Mises stress was 708 MPa, and the stress range was 653 MPa. The total strain was 0.48 pc. The estimated cracks are multiple longitudinal ones. Cracking area is from Z=213 to 198 mm and θ is equal to +/- 30 degrees. The cycle number for penetrating the thickness is estimated to be 4.6 x 103 and the crack will reach the outer surface during the planning test period. A detailed estimation of heat transfer coefficients Hwater and Houter is inevitable for a precise stress prediction. Precise estimations of thermal and mechanical properties, especially thermal conductivity, are important for a precise stress prediction. The difference among 3D, 2D, and 1D FEM is large; only 3D FEM can consider global circumstantial temperature difference, which leads to generate large membrane stress. With this membrane stress, the cycle number for crack penetration becomes 9 times shorter than the one without membrane stress. This effect is quite large and the precise estimation of the membrane stress is important

  20. Mutagenic Effects Induced by the Attack of NO2 Radical to the Guanine-Cytosine Base Pair

    Science.gov (United States)

    Cerón-Carrasco, José Pedro; Requena, Alberto; Zúñiga, José; Jacquemin, Denis

    2015-03-01

    We investigate the attack of the nitrogen dioxide radical (NO2) to the guanine-cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC-NO2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.

  1. Complex step derivative approximation of consistent tangent operators for viscoelasticity based on fractional calculus

    Science.gov (United States)

    Hürkamp, André; Tanaka, Masato; Kaliske, Michael

    2015-12-01

    In this contribution, the convergence behaviour of simulations with nonlinear viscoelastic models for rubber-like materials using fractional derivatives is investigated. Based on the complex step derivative approximation, numerical approximation schemes for tangent operators on the local and global algorithmic level are analysed. Material models including fractional derivatives usually exhibit numerical difficulties, since the entire stress history of the material has to be considered for the current stress state. Non-classical methods can help to reduce the numerical effort, but the convergence behaviour is not perfect. In this paper, a classical and a non-classical fractional element based viscoelastic material formulation are analysed. The local and the global convergence rate using analytically and numerically derived tangents are investigated and compared to the convergence behaviour of a standard nonlinear viscoelastic model. Numerical examples on rubber materials are exploited, showing the performance of the proposed methods. It can be proven that the outlined numerical differentiation schemes improve the convergence rate, as well as reduce the computation time for the fractional element based material models.

  2. Comprehensive evaluation of medium and long range correlated density functionals in TD-DFT investigation of DNA bases and base pairs: gas phase and water solution study

    Science.gov (United States)

    Shukla, Manoj K.; Leszczynski, Jerzy

    2010-11-01

    A comprehensive analysis of the performance of the TD-DFT method using different density functionals including recently developed medium and long-range correlation corrected density functionals have been carried out for lower-lying electronic singlet valence transitions of nucleic acid bases and the Watson-Crick base pairs in the gas phase and in the water solution. The standard 6-311++G(d,p) basis set was used. Ground state geometries of bases and base pairs were optimized at the M05-2X/6-311++G(d,p) level. The nature of potential energy surfaces (PES) was ascertained through the harmonic vibrational frequency analysis; all geometries were found to be minima at the respective PES. Electronic singlet vertical transition energies were also computed at the CC2/def2-TZVP level in the gas phase. The effect of state-specific water solvation on TD-DFT computed transition energies was considered using the PCM model. For the isolated bases the performance of the B3LYP functional was generally found to be superior among all functionals, but it measurably fails for charge-transfer states in the base pairs. The CC2/def2-TZVP computed transition energies were also revealed to be inferior compared with B3LYP results for the isolated bases. The performance of the ωB97XD, CAM-B3LYP and BMK functionals were found to be similar and comparable with the CC2 results for the isolated bases. However, for the Watson-Crick adenine-thymine and guanine-cytosine base pairs the performance of the ωB97XD functional was found to be the best among all the studied functionals in the present work in predicting the locally excited transitions as well as charge transfer states.

  3. A 2×2 SOI mach-zehnder thermo-optical switch based on strongly guided paired multimode interference couplers

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A silicon-on-insulator 2×2 Mach-Zehnder thermo-optical switch is developed based on strongly guided paired multimode interference couplers. The multimode-interference couplers were etched deeply for improving coupler characteristics such as self-imaging quality, uniformity and fabrication tolerance. The proposed switch achieves good performances, including a low insertion loss of -11 .OdB, a fiber-waveguide coupling loss of -4.3dB and a fast response speed measured to be 3.5 and 8.8 μs for raise and fall switching time, respectively.

  4. Unusual glass-forming ability of new Zr-Cu-based bulk glassy alloys containing an immiscible element pair

    International Nuclear Information System (INIS)

    We herein report the unusual glass-forming ability (GFA) of a new series of quinary Zr48Cu36-xNixAg8Al8 (048Cu36Ag8Al8 alloy. By cooper mold casting, an as-cast glassy rod with a diameter of 30 mm can be easily obtained for the representative alloy Zr48Cu32Ni4Ag8Al8. The possible reasons for the excellent GFA of the new quinary alloys with an immiscible element pair are discussed based on the atomic size distribution, chemical compatibility among the components and atomic structure of glassy alloys. (author)

  5. Cryptanalysis and Improvement on "Robust EPR-Pairs-Based Quantum Secure Communication with Authentication Resisting Collective Noise"

    Science.gov (United States)

    Yue, Qiu-Ling; Yu, Chao-Hua; Liu, Bin; Wang, Qing-Le

    2016-05-01

    Recently, Chang et al. [Sci Chin-Phys Mech Astron. 57(10), 1907-1912, 2014] proposed two robust quantum secure communication protocols with authentication based on Einstein-Podolsky-Rosen (EPR) pairs, which can resist collective noise. In this paper, we analyze the security of their protocols, and show that there is a kind of security flaw in their protocols. By a kind of impersonation attack, the eavesdropper can obtain half of the message on average. Furthermore, an improved method of their protocols is proposed to close the security loophole.

  6. Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

    Science.gov (United States)

    Sadeghi, Mehdi; Parto, Sahar; Arab, Shahriar; Ranjbar, Bijan

    2005-06-20

    We have used a statistical approach for protein secondary structure prediction based on information theory and simultaneously taking into consideration pairwise residue types and conformational states. Since the prediction of residue secondary structure by one residue window sliding make ambiguity in state prediction, we used a dynamic programming algorithm to find the path with maximum score. A score system for residue pairs in particular conformations is derived for adjacent neighbors up to ten residue apart in sequence. The three state overall per-residue accuracy, Q3, of this method in a jackknife test with dataset created from PDBSELECT is more than 70%. PMID:15936021

  7. Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations

    Czech Academy of Sciences Publication Activity Database

    Mládek, Arnošt; Sharma, P.; Mitra, A.; Bhattacharyya, D.; Šponer, Jiří; Šponer, Judit E.

    2009-01-01

    Roč. 113, č. 6 (2009), s. 1743-1755. ISSN 1520-6106 R&D Projects: GA AV ČR(CZ) IAA400550701; GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) 1QS500040581; GA MŠk(CZ) LC06030 Grant ostatní: GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : quantum chemical calculations * base pairing * RNA Subject RIV: BO - Biophysics Impact factor: 3.471, year: 2009

  8. Suggested Intense Positron Source based on (micropole) undulator induced pair production

    International Nuclear Information System (INIS)

    The construction of an Intense Positron Source (IPS) is suggested. The intensity of the produced positrons is to exceed that of any other existing source by orders of magnitude. The instantaneous intensity is to be 103 to 106 times higher yet. Fast positrons are to be produced in pulses of time duration ∼1 ns to 10 ps. Slow positron pulses of order +e-pairs will be produced by the generated gamma rays; 3) moderators to thermalize the produced positrons; and 4) a transport system through which the slow positrons will move. Spinoff benefits provided by the suggested device include the following: The equipment may be used to create (or destroy) nuclear isotopes in a controlled manner (i.e. without producing unwanted species); to produce (or destroy) in a controlled way chemical elements; to produce well collimated intense photon beams in the multi 100 MeV range for nuclear physics research, with intensities many orders of magnitude higher than can be achieved today; to generate intense bursts of neutrons; to supply fast positrons produced at high intensities (1016 to 1017 s-1) and within a small transverse phase space, to future high energy colliders, thereby perhaps even eliminating the need for damping rings. ((orig.))

  9. Dynamically tunable Fano resonance in planar structures based on periodically asymmetric graphene nanodisk pair

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhengren [School of Science, Chongqing Jiaotong University, Chongqing 400074 (China); Su, Xiaopeng [Department of Physics, Tongji University, Shanghai 200092 (China); Fan, Yuancheng [Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Department of Applied Physics, School of Science, Northwestern Polytechnical University, Xi' an 710129 (China); Yin, Pengfei [School of Science, Chongqing Jiaotong University, Chongqing 400074 (China); Zhang, Liwei [School of Physics and Chemistry, Henan Polytechnic University, Jiaozuo 454000 (China); Shi, Xi, E-mail: xishi@tongji.edu.cn [Department of Physics, Tongji University, Shanghai 200092 (China)

    2015-09-15

    We present a dynamically frequency tunable Fano resonance planar device composed of periodically asymmetric graphene nanodisk pair for the mid-infrared region. The two asymmetric graphene nanodisks can be directly excited by the light simultaneously and produce two kinds of reflected light with almost the same spectrum linewidth. By studying the local field distributions of our structure, we find that there are two kinds of modes for the two asymmetric graphene nanodisks, i.e., the symmetric mode and antisymmetric mode. Resonance coupling between the symmetric and antisymmetric modes generates the Fano resonance in our structure. This Fano resonance generation mechanism is different from it in traditional Fano resonance structure. In the traditional Fano resonance structure, the Fano resonance comes from the coupling effect between continuum and discrete structure. Moreover, we find that both of the Fano resonance amplitude and frequency of the structure can be dynamically controlled by varying the Fermi energy of graphene. Resonance transition in the structure is studied to reveal the physical mechanism behind it.

  10. PNA(T).DNA(AT) triplexes with Hoogsteen base pairing are more favorable

    Institute of Scientific and Technical Information of China (English)

    XIE Jun; LIU Ciquan; QU Lianghu

    2003-01-01

    Peptide nucleic acids (PNAs) are nucleic acid analogs with the deoxyribose phosphate backbone replaced by pseudo-peptide polymers to which the nucleobases are linked. The achiral, uncharged and rather flexible properties of the peptide backbone permit peptide nucleic acids more potential than oligonucleotides in application to antisence and antigenic reagents. The process of PNA binding to DNA duplex and forming triplex is the first step of PNA interacting with PNA. But there are no PNA.2DNA triplex crystal data up to date and little has been reported on the structure features and the force of the PNA.2DNA triplex. In this work,PNA(T).DNA(AT) triplexes are successfully built and the structures and forces to stabilize the triplex after optimizations and molecule dynamics are systematically examined,which are expected to aid in the application of PNAs as anticense and antigene agents.

  11. A six step approach for developing computer based assessment in medical education.

    Science.gov (United States)

    Hassanien, Mohammed Ahmed; Al-Hayani, Abdulmoneam; Abu-Kamer, Rasha; Almazrooa, Adnan

    2013-01-01

    Assessment, which entails the systematic evaluation of student learning, is an integral part of any educational process. Computer-based assessment (CBA) techniques provide a valuable resource to students seeking to evaluate their academic progress through instantaneous, personalized feedback. CBA reduces examination, grading and reviewing workloads and facilitates training. This paper describes a six step approach for developing CBA in higher education and evaluates student perceptions of computer-based summative assessment at the College of Medicine, King Abdulaziz University. A set of questionnaires were distributed to 341 third year medical students (161 female and 180 male) immediately after examinations in order to assess the adequacy of the system for the exam program. The respondents expressed high satisfaction with the first Saudi experience of CBA for final examinations. However, about 50% of them preferred the use of a pilot CBA before its formal application; hence, many did not recommend its use for future examinations. Both male and female respondents reported that the range of advantages offered by CBA outweighed any disadvantages. Further studies are required to monitor the extended employment of CBA technology for larger classes and for a variety of subjects at universities. PMID:23581891

  12. Five steps school based approach for screening of diabetes and hypertension

    Directory of Open Access Journals (Sweden)

    S.S. Karikatti

    2013-10-01

    Full Text Available Background: In India non communicable diseases accounted for 53% of all deaths in 2005. It is estimated to increase by 18% by 2015. Pre-mature onset of disease and death in India is a major concern. Issues like the limited resources, scarcity of trained health personnel and lack of motivation for community programme have increased the existing problems. Aim: To motivate community people for screening of diabetes & hypertension through school based approach. Materials and Methods: A cross sectional study was carried out at school settings. Five steps school based approach was used to motivate parents, family members, school staff and community people for screening of DM & HT and their risk factors. Screening camps were arranged and screening was done for hypertension and diabetes. The impact of motivation was assessed and yield rates were calculated. Results: Total 178 participants attended the screening camp. Of that 47(26.4% were men, 65 (36.60% were of low risk age group, 30 (16.9% were having hypertension [8/30 (26.7% people were newly detected]. Similarly, 21(11.8% were having diabetes and 7 / 21(33.3% were newly detected. Conclusion: In the present study yield of screening programme was quite good in which 34.8% community households were motivated.

  13. WRIST FORCE SENSOR'S DYNAMIC PERFORMANCE CALIBRATION BASED ON NEGATIVE STEP RESPONSE

    Institute of Scientific and Technical Information of China (English)

    ZHENG Hongmei

    2008-01-01

    Negative step response experimental method is used in wrist force sensor's dynamic performance calibration. The exciting manner of negative step response method is the same as wrist force sensor's load in working. This experimental method needn't special experiment equipments. Experiment's dynamic repeatability is good. So wrist force sensor's dynamic performance is suitable to be calibrated by negative step response method. A new correlation wavelet transfer method is studied. By wavelet transfer method, the signal is decomposed into two dimensional spaces of time-frequency. So the problem of negative step exciting energy concentrating in the low frequency band is solved. Correlation wavelet transfer doesn't require that wavelet primary function be orthogonal and needn't wavelet reconstruction. So analyzing efficiency is high. An experimental bench is designed and manufactured to load the wrist force sensor orthogonal excitation force/moment. A piezoelectric force sensor is used to setup soft trigger and calculate the value of negative step excitation. A wrist force sensor is calibrated. The pulse response function is calculated after negative step excitation and step response have been transformed to positive step excitation and step response. The pulse response function is transferred to frequency response function. The wrist force sensor's dynamic characteristics are identified by the frequency response function.

  14. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs.

    Science.gov (United States)

    Ohkubo, Akihiro; Yamada, Kenji; Ito, Yu; Yoshimura, Kiichi; Miyauchi, Koichiro; Kanamori, Takashi; Masaki, Yoshiaki; Seio, Kohji; Yuasa, Hideya; Sekine, Mitsuo

    2015-07-13

    A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2'-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (d(g)C) residue for a C-G base pair have higher binding and base recognition abilities than those containing 2'-OMe-4N-(2-guanidoethyl)-5-methylcytidine (2'-OMe (g)C), 2'-OMe-4N-(2-guanidoethyl)-5-methyl-2-thiocytidine (2'-OMe (g)Cs), d(g)C and 4S-(2-guanidoethyl)-4-thiothymidine ((gs)T). Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine ((DA)Nac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives. On the basis of this knowledge, we successfully synthesized a fully modified TFO containing (DA)Nac, d(g)C, 2'-OMe-2-thiothymidine (2'-OMe (s)T) and 2'-OMe-8-thioxoadenosine (2'-OMe (s)A) with high binding and base recognition abilities. To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions. PMID:26013815

  15. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition.

    Science.gov (United States)

    Harika, Narinder K; Paul, Ananya; Stroeva, Ekaterina; Chai, Yun; Boykin, David W; Germann, Markus W; Wilson, W David

    2016-06-01

    Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor-surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a (15)N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents. PMID:27131382

  16. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition

    Science.gov (United States)

    Harika, Narinder K.; Paul, Ananya; Stroeva, Ekaterina; Chai, Yun; Boykin, David W.; Germann, Markus W.; Wilson, W. David

    2016-01-01

    Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents. PMID:27131382

  17. Stepped Fault Line Selection Method Based on Spectral Kurtosis and Relative Energy Entropy of Small Current to Ground System

    OpenAIRE

    Xiaowei Wang; Xiangxiang Wei; Jie Gao; Yaxiao Hou; Yanfang Wei

    2014-01-01

    This paper proposes a stepped selection method based on spectral kurtosis relative energy entropy. Firstly, the length and type of window function are set; then when fault occurs, enter step 1: the polarity of first half-wave extremes is analyzed; if the ratios of extremes between neighboring lines are positive, the bus bar is the fault line, else, the SK relative energy entropies are calculated, and then enter step 2: if the obtained entropy multiple is bigger than the threshold or equal to ...

  18. Algorithm of axial fuel optimization based in progressive steps of turned search

    International Nuclear Information System (INIS)

    The development of an algorithm for the axial optimization of fuel of boiling water reactors (BWR) is presented. The algorithm is based in a serial optimizations process in the one that the best solution in each stage is the starting point of the following stage. The objective function of each stage adapts to orient the search toward better values of one or two parameters leaving the rest like restrictions. Conform to it advances in those optimization stages, it is increased the fineness of the evaluation of the investigated designs. The algorithm is based on three stages, in the first one are used Genetic algorithms and in the two following Tabu Search. The objective function of the first stage it looks for to minimize the average enrichment of the one it assembles and to fulfill with the generation of specified energy for the operation cycle besides not violating none of the limits of the design base. In the following stages the objective function looks for to minimize the power factor peak (PPF) and to maximize the margin of shutdown (SDM), having as restrictions the one average enrichment obtained for the best design in the first stage and those other restrictions. The third stage, very similar to the previous one, it begins with the design of the previous stage but it carries out a search of the margin of shutdown to different exhibition steps with calculations in three dimensions (3D). An application to the case of the design of the fresh assemble for the fourth fuel reload of the Unit 1 reactor of the Laguna Verde power plant (U1-CLV) is presented. The obtained results show an advance in the handling of optimization methods and in the construction of the objective functions that should be used for the different design stages of the fuel assemblies. (Author)

  19. Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA

    International Nuclear Information System (INIS)

    Base-pair sequences for 5S and 5.8S RNAs are not readily extracted from proton homonuclear nuclear Overhauser enhancement (NOE) connectivity experiments alone, due to extensive peak overlap in the downfield (11-15 ppm) proton NMR spectrum. In this paper, we introduce a new method for base-pair proton peak assignment for ribosomal RNAs, based upon the distance-dependent broadening of the resonances of base-pair protons spatially proximal to a paramagnetic group. Introduction of a nitroxide spin-label covalently attached to the 3'-terminal ribose provides an unequivocal starting point for base-pair hydrogen-bond proton NMR assignment. Subsequent NOE connectivities then establish the base-pair sequence for the terminal stem of a 5S RNA. Periodate oxidation of yeast 5S RNA, followed by reaction with 4-amino-2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO-NH2) and sodium borohydride reduction, produces yeast 5S RNA specifically labeled with a paramagnetic nitroxide group at the 3'-terminal ribose. Comparison of the 500-MHz 1H NMR spectra of native and 3'-terminal spin-labeled yeast 5S RNA serves to identify the terminal base pair (G1 . C120) and its adjacent base pair (G2 . U119) on the basis of their proximity to the 3'-terminal spin-label. From that starting point, we have then identified (G . C, A . U, or G . U) and sequenced eight of the nine base pairs in the terminal helix via primary and secondary NOE's

  20. Young Foreign Language Learners' Interactions during Task-Based Paired Assessments

    Science.gov (United States)

    Butler, Yuko Goto; Zeng, Wei

    2014-01-01

    Despite the popularity of task-based language teaching (TBLT) in foreign language (FL) education at elementary school, it remains unclear how young learners' FL abilities can best be evaluated with tasks. The present study seeks to understand developmental differences in interactions among elementary-school students during task-based language…

  1. The Effect of 12-Step Based Fellowship Participation on Abstinence Among Dually Diagnosed Persons: A Two-Year Longitudinal Study†

    OpenAIRE

    Laudet, Alexandra B.; Magura, Stephen; Cleland, Charles M.; Vogel, Howard S.; Knight, Edward L.; Rosenblum, Andrew

    2004-01-01

    A large percentage of individuals are dually-diagnosed with a psychiatric disorder and a substance use disorder. Such persons typically face more difficulties and have poorer outcomes than do single disorder substance users. Among noncomorbid substance users, treatment and participation in 12-Step groups have been shown to enhance the likelihood of abstinence from substance misuse. Specialized 12-Step based fellowships have recently emerged to address the recovery needs of dually-diagnosed pe...

  2. The Distribution of Technetium in U/Pu Partition Step of Advanced Purex Process Based on Organic Reagents

    Institute of Scientific and Technical Information of China (English)

    WANG; Hui; WEI; Yan; LIU; Fang; JIA; Yong-fen; LIU; Zhan-yuan

    2012-01-01

    <正>Advanced Purex process based on organic reagents (APOR) is an advanced Purex process, where monomethylhydrazine (MMH)-dimethylhydroxylamine (DMHAN) are adopted as salt-free plutonium- reductant in the partition step. During this step, technetium mainly goes into aqueous plutonium stream, and the aim of our work is to explain this phenomena. Reaction kinetic experiments and process experiments with mixer-settler were carried out for this purpose.

  3. A comparison of intravascular source designs based on the beta particle emitter 114mIn/114In Line source versus stepping source

    International Nuclear Information System (INIS)

    Background: Catheter-based intravascular brachytherapy (IVB) sources of the next generation will have to meet high demands in terms of miniaturization, flexibility, safety, reliability, costs and versatility. The radionuclide pair 114mIn/114In (half-life 49.51 days, maximum beta energy 2.0 MeV, average beta energy 0.78 MeV) is an attractive beta emitter for application in such a source. Methods: Since metallic indium is unfit for the manufacture of a brachytherapy source, the feasibility, safety and dosimetric properties of a design concept comprising a linear array of ceramic In2O3 spheres within a thin-walled, superelastic Ni/Ti capsule are investigated. Results: Neutron activation of enriched In2O3 spheres yields a specific activity sufficiently high for the manufacture of a stepping source, keeping treatment times limited to a few minutes. Although 114mIn/114In also emits some gamma radiation, the effective doses received by members of the medical staff are an order of magnitude lower than those received from fluoroscopy. The dose distributions about a 40-mm line source and a 5-mm stepping source (outer diameter 0.36 mm) are calculated using MCNP4C. Dose-volume histograms (DVHs) are calculated for the line source (centered and noncentered) and the stepping source (centered) using the geometry of a human coronary artery. Conclusion: The results show that a centered stepping source with optimized dwell times delivers the most homogenous dose within the target volume

  4. Chain propagation and termination mechanisms for polymerization of conjugated polar alkenes by [Al]-based frustrated Lewis pairs

    KAUST Repository

    He, Jianghua

    2014-11-25

    A combined experimental and theoretical study on mechanistic aspects of polymerization of conjugated polar alkenes by frustrated Lewis pairs (FLPs) based on N-heterocyclic carbene (NHC) and Al(C6F5)3 pairs is reported. This study consists of three key parts: structural characterization of active propagating intermediates, propagation kinetics, and chain-termination pathways. Zwitterionic intermediates that simulate the active propagating species in such polymerization have been generated or isolated from the FLP activation of monomers such as 2-vinylpyridine and 2-isopropenyl-2-oxazoline-one of which, IMes+-CH2C(Me)=(C3H2NO)Al(C6F5)3 - (2), has been structurally characterized. Kinetics performed on the polymerization of 2-vinylpyridine by ItBu/Al(C6F5)3 revealed that the polymerization follows a zero-order dependence on monomer concentration and a first-order dependence on initiator (ItBu) and activator [Al(C6F5)3] concentrations, indicating a bimolecular, activated monomer propagation mechanism. The Lewis pair polymerization of conjugate polar alkenes such as methacrylates is accompanied by competing chain-termination side reactions; between the two possible chain-termination pathways, the one that proceeds via intramolecular backbiting cyclization involving nucleophilic attack of the activated ester group of the growing polymer chain by the O-ester enolate active chain end to generate a six-membered lactone (δ-valerolactone)-terminated polymer chain is kinetically favored, but thermodynamically disfavored, over the pathway leading to the -ketoester-terminated chain, as revealed by computational studies.

  5. Post Hartree-Fock studies of the canonical Watson-Crick DNA base pairs: molecular structure and the nature of stability.

    Science.gov (United States)

    Danilov, Victor I; Anisimov, Victor M

    2005-02-01

    Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G-C and A-T base pairs; while HF and DFT methods predict perfect planar or almost planar geometry of the base pairs. Supposedly the nonplanarity of the pairs is caused by pyramidalization of the amino nitrogen atoms, which is underestimated by the HF and DFT methods. This justifies the importance of geometry optimization at the MP2 level for obtaining reliable prediction of the charge distribution, molecular dipole moments and geometrical structure of the base pairs. The Morokuma-Kitaura and the Reduced Variational Space methods of the decomposition for molecular HF interaction energies were used for investigation of the hydrogen bonding in the Watson-Crick base pairs. It is shown that the HF stability of the hydrogen-bonded DNA base pairs originates mainly from electrostatic interactions. At the same time, the calculated magnitude of the second order intramolecular correlation correction to the Coulomb energy showed that electron correlation reduces the contribution of the electrostatic term to the attractive interaction for the A-T and G-C base pairs. Polarization, charge transfer and dispersion interactions also make considerable contribution to the attraction energy of bases. PMID:15588110

  6. Prestack nonstationary deconvolution based on variable-step sampling in the radial trace domain

    Institute of Scientific and Technical Information of China (English)

    Li Fang; Wang Shou-Dong; Chen Xiao-Hong; Liu Guo-Chang; Zheng Qiang

    2013-01-01

    The conventional nonstationary convolutional model assumes that the seismic signal is recorded at normal incidence. Raw shot gathers are far from this assumption because of the effects of offsets. Because of such problems, we propose a novel prestack nonstationary deconvolution approach. We introduce the radial trace (RT) transform to the nonstationary deconvolution, we estimate the nonstationary deconvolution factor with hyperbolic smoothing based on variable-step sampling (VSS) in the RT domain, and we obtain the high-resolution prestack nonstationary deconvolution data. The RT transform maps the shot record from the offset and traveltime coordinates to those of apparent velocity and traveltime. The ray paths of the traces in the RT better satisfy the assumptions of the convolutional model. The proposed method combines the advantages of stationary deconvolution and inverse Q filtering, without prior information for Q. The nonstationary deconvolution in the RT domain is more suitable than that in the space-time (XT) domain for prestack data because it is the generalized extension of normal incidence. Tests with synthetic and real data demonstrate that the proposed method is more effective in compensating for large-offset and deep data.

  7. Primary step for endoscopic sinonasal tract and anterior skull base robotics

    Directory of Open Access Journals (Sweden)

    Crampette Louis

    2011-12-01

    Full Text Available Introduction: Surgeons have evolved a lot their surgical procedures in sinus surgery and are now able to resect malignant tumors. These progresses are now leading new difficulties like impairing vision (bleeding and LCR flow and necessity of multiple simultaneous tasks. With the aim of designing a new endoscope-holder, primary step was to characterize the surgeon gesture, the kinematics, and the type of man-machine interface acceptable by the surgeon. Methods: We worked on thirteen sinonasal tracts of cadaver heads. Surgical procedures were: opening all the sinuses, the carotid, the sella turcica, the lamina papyracea and the anterior skull base. We used conventional instruments which were instrumented with a force-torque sensor and a navigation system. Then we have experimentally evaluated robots with three different kinematics and two types of man-machine interfaces. Results: We collected enough position and force data as well as kinematics constraints and interface requirements to specify a robot for endoscopic sinus surgery.

  8. A Dynamic Era-Based Time-Symmetric Block Time-Step Algorithm with Parallel Implementations

    CERN Document Server

    Kaplan, M

    2012-01-01

    The time-symmetric block time--step (TSBTS) algorithm is a newly developed efficient scheme for $N$--body integrations. It is constructed on an era-based iteration. In this work, we re-designed the TSBTS integration scheme with dynamically changing era size. A number of numerical tests were performed to show the importance of choosing the size of the era, especially for long time integrations. Our second aim was to show that the TSBTS scheme is as suitable as previously known schemes for developing parallel $N$--body codes. In this work, we relied on a parallel scheme using the copy algorithm for the time-symmetric scheme. We implemented a hybrid of data and task parallelization for force calculation to handle load balancing problems that can appear in practice. Using the Plummer model initial conditions for different numbers of particles, we obtained the expected efficiency and speedup for a small number of particles. Although parallelization of the direct $N$--body codes is negatively affected by the commun...

  9. A high-contrast imaging polarimeter with a stepped-transmission filter based coronagraph

    Science.gov (United States)

    Liu, Cheng-Chao; Ren, De-Qing; Zhu, Yong-Tian; Dou, Jiang-Pei; Guo, Jing

    2016-05-01

    The light reflected from planets is polarized mainly due to Rayleigh scattering, but starlight is normally unpolarized. Thus it provides an approach to enhance the imaging contrast by inducing the imaging polarimetry technique. In this paper, we propose a high-contrast imaging polarimeter that is optimized for the direct imaging of exoplanets, combined with our recently developed stepped-transmission filter based coronagraph. Here we present the design and calibration method of the polarimetry system and the associated test of its high-contrast performance. In this polarimetry system, two liquid crystal variable retarders (LCVRs) act as a polarization modulator, which can extract the polarized signal. We show that our polarimeter can achieve a measurement accuracy of about 0.2% at a visible wavelength (632.8 nm) with linearly polarized light. Finally, the whole system demonstrates that a contrast of 10‑9 at 5λ/D is achievable, which can be used for direct imaging of Jupiter-like planets with a space telescope.

  10. New in silico approach to assessing RNA secondary structures with non-canonical base pairs

    OpenAIRE

    Rybarczyk, Agnieszka; Szostak, Natalia; Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Adamiak, Ryszard; Blazewicz, Jacek; Szachniuk, Marta

    2015-01-01

    Background The function of RNA is strongly dependent on its structure, so an appropriate recognition of this structure, on every level of organization, is of great importance. One particular concern is the assessment of base-base interactions, described as the secondary structure, the knowledge of which greatly facilitates an interpretation of RNA function and allows for structure analysis on the tertiary level. The RNA secondary structure can be predicted from a sequence using in silico meth...

  11. Novel coronene-naphthalene dimide-based donor-acceptor pair for tunable charge-transfer nanostructures.

    Science.gov (United States)

    Kumar, Mohit; George, Subi J

    2014-09-01

    Charge-transfer (CT) assemblies of aromatic donor (D) and acceptor (A) molecules have recently gained attention as a promising material for organic electronics and ferroelectrics. Two major factors which govern their functions are the strength of CT interaction and their supramolecular nanostructuring. Here we present coronene-naphthalenediimide (NDI)-based novel D-A pairs that form alternately stacked CT assemblies. Through systematic substitution of the NDI derivatives and studying their CT interactions with coronene, a clear understanding of the secondary forces responsible for controlling their association is gained. Finally, the use of CT-based supramolecular amphiphiles for their nanostructural engineering into ordered one-dimensional (1-D) assemblies is demonstrated. PMID:25045008

  12. Theoretical analysis of novel fiber grating pair

    Science.gov (United States)

    Wang, Liao; Jia, Hongzhi; Fang, Liang; You, Bei

    2016-06-01

    A novel fiber grating pair that consists of a conventional long-period fiber grating and a fiber Bragg cladding grating (FBCG) is proposed. The FBCG is a new type of fiber grating in which refractive index modulation is formed in the cladding. Through the coupled-mode theory, we accurately calculate the coupling coefficients between modes supported in the fibers. And some other mode coupling features in the fiber cladding gratings are analyzed in detail. The calculation of the modes involved in this paper is based on a model of three-layer step-index fiber geometry. Then, we have investigated the sensitivity characteristics for variation of the modulation strengths of the fiber Bragg cladding gratings' resonance peaks and the long-period cladding gratings' (LPCGs) dual resonant peaks. Finally, the modulation strength sensitivity of the grating pair's three resonant peaks is demonstrated, and the results indicate that these grating pairs may find potential applications in optical fiber sensing.

  13. A base-paired hairpin structure essential for the functional priming signal for DNA replication of the broad host range plasmid RSF1010.

    OpenAIRE

    Miao, D M; Honda, Y; Tanaka, K.; Higashi, A.; Nakamura, T.(International Center for Elementary Particle Physics and Department of Physics, The University of Tokyo, Tokyo, Japan); TAGUCHI, Y.; Sakai, H.; Komano, T; Bagdasarian, M

    1993-01-01

    The two single-strand DNA initiation signals, ssiA(RSF1010) and ssiB(RSF1010) of the broad host-range plasmid RSF1010 contain proposed stem-loop structures. Nine single base-change mutations in the stem of the ssiA structure, each of which destroyed a relevant base pairing, damaged the ssiA activity. A second single-base change was introduced into each of the nine ssiA mutants in such a way that the base pairing was restored. Only three out of nine second base changes that restored the base p...

  14. Identification of Mine-Shaped Objects based on an Efficient Phase Stepped-Frequency Radar Approach

    DEFF Research Database (Denmark)

    Sørensen, Helge Bjarup Dissing; Jakobsen, Kaj Bjarne; Nymann, Ole

    A computational efficient approach to identify very small mine-shaped plastic objects, e.g. M56 Anti-Personnel (AP) mines buried in the ground, is presented. The size of the objects equals the smallest AP-mines in use today, i.e., the most difficult mines to detect with respect to humanitarian mine...... clearance. Our approach consists of three stages, the phase stepped-frequency radar method, generation of a quarternary image and template crosscorrelation. The phase stepped-frequency radar method belongs to the class of stepped-frequency radar methods. In a two-dimensional mesh-grid above the ground a...

  15. Spin fluctuations and unconventional superconducting pairing in iron-based superconductors

    Institute of Scientific and Technical Information of China (English)

    Yu Shun-Li; Li Jian-Xin

    2013-01-01

    In this article,we review the recent theoretical works on the spin fluctuations and superconductivity in iron-based superconductors.Using the fluctuation exchange approximation and multi-orbital tight-binding models,we study the characteristics of the spin fluctuations and the symmetries of the superconducting gaps for different iron-based superconductors.We explore the systems with both electron-like and hole-like Fermi surfaces (FS) and the systems with only the electronlike FS.We argue that the spin-fluctuation theories are successful in explaining at least the essential part of the problems,indicating that the spin fluctuation is the common origin of superconductivity in iron-based superconductors.

  16. A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

    Science.gov (United States)

    Lemons, Patrick R.; Marshall, T.C.; McCloskey, Sarah E.; Sethi, S.A.; Schmutz, Joel A.; Sedinger, James S.

    2015-01-01

    Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artifacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.

  17. Demonstration of polarization sensitivity of emulsion-based pair conversion telescope for cosmic gamma-ray polarimetry

    CERN Document Server

    Ozaki, Keita; Aoki, Shigeki; Kamada, Keiki; Kaneyama, Taichi; Nakagawa, Ryo; Rokujo, Hiroki

    2016-01-01

    Linear polarization of high-energy gamma-rays (10 MeV-100 GeV) can be detected by measuring the azimuthal angle of electron-positron pairs and observing the modulation of the azimuthal distribution. To demonstrate the gamma-ray polarization sensitivity of emulsion, we conducted a test using a polarized gamma-ray beam at SPring-8/LEPS. Emulsion tracks were reconstructed using scanning data, and gamma-ray events were selected automatically. Using an optical microscope, out of the 2381 gamma-ray conversions that were observed, 1372 remained after event selection, on the azimuthal angle distribution of which we measured the modulation. From the distribution of the azimuthal angles of the selected events, a modulation factor of 0.21 + 0.11 - 0.09 was measured, from which the detection of a non-zero modulation was established with a significance of 3.06 $\\sigma$. This attractive polarimeter will be applied to the GRAINE project, a balloon-borne experiment that observes cosmic gamma-rays with an emulsion-based pair ...

  18. Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

    Directory of Open Access Journals (Sweden)

    Camila Ximenes

    2014-12-01

    Full Text Available The Global Program for the Elimination of Lymphatic Filariasis (GPELF aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuchereria bancrofti were collected during the day. Conventional PCR and semi-nested PCR assays were optimised. The detection limit of the technique for purified W. bancrofti DNA extracted from adult worms was 10 fg for the internal systems (WbF/Wb2 and 0.1 fg by using semi-nested PCR. The specificity of the primers was confirmed experimentally by amplification of 1 ng of purified genomic DNA from other species of parasites. Evaluation of the paired urine and serum samples by the semi-nested PCR technique indicated only two of the 20 tested individuals were positive, whereas the simple internal PCR system (WbF/Wb2, which has highly promising performance, revealed that all the patients were positive using both samples. This study successfully demonstrated the possibility of using the PCR technique on urine for the diagnosis of W. bancrofti infection.

  19. Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA.

    Science.gov (United States)

    Hithell, Gordon; Shaw, Daniel J; Donaldson, Paul M; Greetham, Gregory M; Towrie, Michael; Burley, Glenn A; Parker, Anthony W; Hunt, Neil T

    2016-05-01

    Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA. PMID:27079484

  20. Pairing based threshold cryptography improving on Libert-Quisquater and Baek-Zheng

    DEFF Research Database (Denmark)

    Desmedt, Yvo; Lange, Tanja

    In this paper we apply techniques from secret sharing and threshold decryption to show how to properly design an ID-based threshold system in which one assumes no trust in any party. In our scheme: We avoid that any single machine ever knew the master secret s of the trusted authority (TA). Inste...

  1. Stacked base-pair structures of adenine nucleosides stabilized by the formation of hydrogen-bonding network involving the two sugar groups

    International Nuclear Information System (INIS)

    Highlights: ► A combination of laser desorption and supersonic jet-cooling is used to produce base pairs of adenine nucleosides. ► Stacked base-pair structure of N6,N6-dimethyladnosine is identified by IR vibrational spectroscopy. ► Anharmonic vibrational calculation is employed to analyze the vibrational mode coupling in the stacked base pair. - Abstract: We have employed a laser desorption technique combined with supersonic-jet cooling for producing base pairs of adenine nucleosides, adenosine (Ado) and N6,N6-dimethyladenosine (DMAdo) under low-temperature conditions. The resulting base pairs are then ionized through resonant two-photon ionization (R2PI) and analyzed by time-of-flight mass spectrometry. It is found that dimers of these adenine nucleosides are stable, especially in the case of DMAdo, with respect to those of the corresponding bases, i.e., adenine and N6,N6-dimethyladenine. Structural analysis of the DMAdo dimer is performed based on the IR–UV double resonance measurements and theoretical calculations. The result demonstrates that the dimer possesses a stacked structure being stabilized by the formation of hydrogen-bonding network involving the two sugar groups. The occurrence of the frequency shift and broadening is explained satisfactorily based on the anharmonic coupling of the OH stretching modes with specific bending modes and low-frequency modes of base and sugar moieties

  2. A PMU-Based Three-Step Controlled Separation with Transient Stability Considerations

    OpenAIRE

    Wang, C; Hou, Y.

    2014-01-01

    Controlled separation has been identified as one of the critical strategies to prevent a blackout of a bulk power system following a severe disturbance. To implement this critical strategy, optimal splitting points have to be identified subject to a series of steady-state and dynamic constraints. In this paper, a systematic controlled separation with three steps is proposed to cover steady-state and dynamic constraints with PMU measurements. At the first step, the power flow tracing method is...

  3. Subradiant split Cooper pairs

    OpenAIRE

    Cottet, Audrey; Kontos, Takis; Yeyati, Alfredo Levy

    2011-01-01

    We suggest a way to characterize the coherence of the split Cooper pairs emitted by a double-quantum-dot based Cooper pair splitter (CPS), by studying the radiative response of such a CPS inside a microwave cavity. The coherence of the split pairs manifests in a strongly nonmonotonic variation of the emitted radiation as a function of the parameters controlling the coupling of the CPS to the cavity. The idea to probe the coherence of the electronic states using the tools of Cavity Quantum Ele...

  4. Neuronal synapse as a memristor: modeling pair- and triplet-based STDP rule.

    Science.gov (United States)

    Cai, Weiran; Ellinger, Frank; Tetzlaff, Ronald

    2015-02-01

    We propose a new memristive model for the neuronal synapse based on the spike-timing-dependent plasticity (STDP) protocol, considering both long-term and short-term plasticity in the synapse. Higher-order behavior is modeled by a memristor with adaptive thresholds, which realizes the well-established suppression principle of Froemke. We assume a mechanism of variable thresholds adapting to synaptic potentiation (LTP) and depression (LTD), which reproduces the refractory time in the weight modification. The corresponding dynamical process is governed by a set of ordinary differential equations. Interestingly, the Froemke's model and our memristive model, based on two completely different mechanisms, are found to be quantitatively equivalent for the 'pre-post-pre' case and 'post-pre-post' case. A relation of the adaptive thresholds to short-term plasticity is addressed. PMID:24960611

  5. GBAS Ionospheric Anomaly Monitoring Based on a Two-Step Approach.

    Science.gov (United States)

    Zhao, Lin; Yang, Fuxin; Li, Liang; Ding, Jicheng; Zhao, Yuxin

    2016-01-01

    As one significant component of space environmental weather, the ionosphere has to be monitored using Global Positioning System (GPS) receivers for the Ground-Based Augmentation System (GBAS). This is because an ionospheric anomaly can pose a potential threat for GBAS to support safety-critical services. The traditional code-carrier divergence (CCD) methods, which have been widely used to detect the variants of the ionospheric gradient for GBAS, adopt a linear time-invariant low-pass filter to suppress the effect of high frequency noise on the detection of the ionospheric anomaly. However, there is a counterbalance between response time and estimation accuracy due to the fixed time constants. In order to release the limitation, a two-step approach (TSA) is proposed by integrating the cascaded linear time-invariant low-pass filters with the adaptive Kalman filter to detect the ionospheric gradient anomaly. The performance of the proposed method is tested by using simulated and real-world data, respectively. The simulation results show that the TSA can detect ionospheric gradient anomalies quickly, even when the noise is severer. Compared to the traditional CCD methods, the experiments from real-world GPS data indicate that the average estimation accuracy of the ionospheric gradient improves by more than 31.3%, and the average response time to the ionospheric gradient at a rate of 0.018 m/s improves by more than 59.3%, which demonstrates the ability of TSA to detect a small ionospheric gradient more rapidly. PMID:27240367

  6. GBAS Ionospheric Anomaly Monitoring Based on a Two-Step Approach

    Science.gov (United States)

    Zhao, Lin; Yang, Fuxin; Li, Liang; Ding, Jicheng; Zhao, Yuxin

    2016-01-01

    As one significant component of space environmental weather, the ionosphere has to be monitored using Global Positioning System (GPS) receivers for the Ground-Based Augmentation System (GBAS). This is because an ionospheric anomaly can pose a potential threat for GBAS to support safety-critical services. The traditional code-carrier divergence (CCD) methods, which have been widely used to detect the variants of the ionospheric gradient for GBAS, adopt a linear time-invariant low-pass filter to suppress the effect of high frequency noise on the detection of the ionospheric anomaly. However, there is a counterbalance between response time and estimation accuracy due to the fixed time constants. In order to release the limitation, a two-step approach (TSA) is proposed by integrating the cascaded linear time-invariant low-pass filters with the adaptive Kalman filter to detect the ionospheric gradient anomaly. The performance of the proposed method is tested by using simulated and real-world data, respectively. The simulation results show that the TSA can detect ionospheric gradient anomalies quickly, even when the noise is severer. Compared to the traditional CCD methods, the experiments from real-world GPS data indicate that the average estimation accuracy of the ionospheric gradient improves by more than 31.3%, and the average response time to the ionospheric gradient at a rate of 0.018 m/s improves by more than 59.3%, which demonstrates the ability of TSA to detect a small ionospheric gradient more rapidly. PMID:27240367

  7. Determination of the rate of base-pair substitution and insertion mutations in retrovirus replication.

    OpenAIRE

    Dougherty, J P; Temin, H M

    1988-01-01

    We recently described a protocol for determination of retrovirus mutation rates, that is, the mutation frequency in a single cycle of retrovirus replication (J.P. Dougherty and H.M. Temin, Mol. Cell. Biol. 6:4378-4395, 1987; J.P. Dougherty and H.M. Temin, p. 18-23, in J. H. Miller and M. P. Calos, ed., Gene Transfer Vectors for Mammalian Cells, 1987). We used this protocol to determine the mutation rates for defined mutations in a replicating retrovirus by using a spleen necrosis virus-based ...

  8. The Analysis of the Atomic Pair Distribution Function of Pmn-Based Nanopowders by X-Ray Diffraction

    Science.gov (United States)

    Ghasemifard, M.; Khorrami, Gh. H.

    The three-dimensional atomic-scale structure around Mg, Nb, Ti and Zr atoms in a series ferroelectric material such as PMN, PZT, PMN-PZT and PMN-PT has been studied using X-ray diffraction (MoKα), Rietveld refinement and the atomic pair distribution function (PDF) technique. The structure and particle size of the powders was determined by X-ray diffraction and TEM observation. The studies show that the materials are disordered at nanometer length distances. The three-dimensional atomic ordering in PMN-based nanopowders may well be described by a cubic structure of the perovskite type, similar to that occurring in the bulk crystals. At the end, the analyzed data show that the sizes of ZrO6 octahedral are larger than TiO6 octahedral.

  9. Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions

    DEFF Research Database (Denmark)

    Orum, H; Nielsen, Henrik; Engberg, J

    1991-01-01

    We have identified and characterized the full set of spliceosomal small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) from the ciliated protozoan Tetrahymena thermophila. With the exception of U4 snRNA, the sizes of the T. thermophila snRNAs are closely similar to their metazoan homologues. The T....... thermophila snRNAs all have unique 5' ends, which start with an adenine residue. In contrast, with the exception of U6, their 3' ends show some size heterogeneity. The primary sequences of the T. thermophila snRNAs contain the sequence motifs shown, or proposed, to be of functional importance in other...... organisms. Furthermore, secondary structures closely similar to phylogenetically proven models can be inferred from the T. thermophila data. Analysis of the snRNA sequences identifies three potential snRNA-snRNA base-pairing interactions, all of which are consistent with available phylogenetic data. Two of...

  10. Cyanine-based probe\\tag-peptide pair fluorescence protein imaging and fluorescence protein imaging methods

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2013-01-15

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  11. Electron pairing without superconductivity

    Science.gov (United States)

    Levy, Jeremy

    Strontium titanate (SrTiO3) is the first and best known superconducting semiconductor. It exhibits an extremely low carrier density threshold for superconductivity, and possesses a phase diagram similar to that of high-temperature superconductors--two factors that suggest an unconventional pairing mechanism. Despite sustained interest for 50 years, direct experimental insight into the nature of electron pairing in SrTiO3 has remained elusive. Here we perform transport experiments with nanowire-based single-electron transistors at the interface between SrTiO3 and a thin layer of lanthanum aluminate, LaAlO3. Electrostatic gating reveals a series of two-electron conductance resonances--paired electron states--that bifurcate above a critical pairing field Bp of about 1-4 tesla, an order of magnitude larger than the superconducting critical magnetic field. For magnetic fields below Bp, these resonances are insensitive to the applied magnetic field; for fields in excess of Bp, the resonances exhibit a linear Zeeman-like energy splitting. Electron pairing is stable at temperatures as high as 900 millikelvin, well above the superconducting transition temperature (about 300 millikelvin). These experiments demonstrate the existence of a robust electronic phase in which electrons pair without forming a superconducting state. Key experimental signatures are captured by a model involving an attractive Hubbard interaction that describes real-space electron pairing as a precursor to superconductivity. Support from AFOSR, ONR, ARO, NSF, DOE and NSSEFF is gratefully acknowledged.

  12. Simulation and Prototype Design of Variable Step Angle Techniques Based Asteroid Deflection for Future Planetary Mission

    Science.gov (United States)

    Sathiyavel, C.

    2016-07-01

    Asteroids are minor planets, especially those of the inner Solar System. The most desirable asteroids for cross the geo-synchronous orbit are the carbonaceous C-type asteroids that are deemed by the astronomy community to have a planetary protection categorization of unrestricted Earth return. The mass of near earth Asteroids (assuming spherical asteroid) as a function of its diameter varies from 2 m to 10m, the corresponding densities from 1.9/cm3 to 3.8 g/cm3. For example, a 6.5-m diameter asteroid with a density of 2.8 g/cm3 has a mass of order 4,00,000 kg. If this Asteroid falls on earth then the earth will be destroyed at when the equally of inclination angle both of earth and Asteroid. My proposed work is how we can avert this great danger for near feature the above mass of Asteroid. The present work is Simulation and Prototype Design of a Variable Step Angle Techniques Based Asteroid Deflection for future planetary Mission. Proposed method is comparing with previous method that will be very useful to achieving hit the ion velocity to asteroid surface in several direction at static position of Asteroid deviate mission[ADM].The deviate angle α1 to α2 with help of Variable step angle techniques, it is containing Stepper Motor with attach of Ion propulsion module system.VASAT module is locating the top edge on the three axis stabilized Method in ADM.The three axis stabilized method is including the devices are like Gyroscope sensor ,Arduino Microcontroller system and ion propulsion techniques. Arduino Microcontroller system determines the orientation from gyroscope sensor. Then it uses ion Propulsion techniques modules to control the required motion like pitch, yaw and roll attitude of the ADM. The exhaust thrust value is 1500 mN and velocity is 10,000 m/s [from simulation results but experimental output results is small because low quality of Components is used in research lab] .The propulsion techniques also used as a static position of ADM Mission [both

  13. Maximizing Expected Base Pair Accuracy in RNA Secondary Structure Prediction by Joining Stochastic Context-Free Grammars Method

    Directory of Open Access Journals (Sweden)

    Shahira M. Habashy

    2012-03-01

    Full Text Available The identification of RNA secondary structures has been among the most exciting recent developments in biology and medical science. Prediction of RNA secondary structure is a fundamental problem in computational structural biology. For several decades, free energy minimization has been the most popular method for prediction from a single sequence. It is based on a set of empirical free energy change parameters derived from experiments using a nearest-neighbor model. Accurate prediction of RNA secondary structure from the base sequence is an unsolved computational challenge. The accuracy of predictions made by free energy minimization is limited by the quality of the energy parameters in the underlying free energy model. More recently, stochastic context-free grammars (SCFGs have emerged as an alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands of experimentally -measured thermodynamic parameters, SCFGs use fully-automated statistical learning algorithms to derive model parameters. This paper proposes a new algorithm that computes base pairing pattern for RNA molecule. Complex internal structures in RNA are fully taken into account. It supports the calculation of stochastic context-free grammars (SCFGs, and equilibrium concentrations of duplex structures. This new algorithm is compared with dynamic programming benchmark mfold and algorithms (Tfold, and MaxExpect. The results showed that the proposed algorithm achieved better performance with respect to sensitivity and positive predictive value.

  14. Next Step for STEP

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Claire [CTSI; Bremner, Brenda [CTSI

    2013-08-09

    The Siletz Tribal Energy Program (STEP), housed in the Tribe’s Planning Department, will hire a data entry coordinator to collect, enter, analyze and store all the current and future energy efficiency and renewable energy data pertaining to administrative structures the tribe owns and operates and for homes in which tribal members live. The proposed data entry coordinator will conduct an energy options analysis in collaboration with the rest of the Siletz Tribal Energy Program and Planning Department staff. An energy options analysis will result in a thorough understanding of tribal energy resources and consumption, if energy efficiency and conservation measures being implemented are having the desired effect, analysis of tribal energy loads (current and future energy consumption), and evaluation of local and commercial energy supply options. A literature search will also be conducted. In order to educate additional tribal members about renewable energy, we will send four tribal members to be trained to install and maintain solar panels, solar hot water heaters, wind turbines and/or micro-hydro.

  15. A model for gamma-ray binaries, based on the effect of pair production feedback in shocked pulsar winds

    CERN Document Server

    Derishev, E

    2016-01-01

    We analyze the model of gamma-ray binaries, consisting of a massive star and a pulsar with ultrarelativistic wind. We consider radiation from energetic particles, accelerated at the pulsar wind termination shock, and feedback of this radiation on the wind through production of secondary electron-positron pairs. We show that the pair feedback limits the Lorentz factor of the pulsar wind and creates a population of very energetic pairs, whose radiation may be responsible for the observed gamma-ray signal.

  16. Vocational Assessment in the School Setting: A Curriculum Based Model. Secondary Transition and Employment Project: STEP.

    Science.gov (United States)

    Baumgart, Diane; Perino, Daniel M.

    The guide, developed by the Secondary Transition and Employment Project (STEP) in Idaho, describes a rationale and model for implementing secondary/vocational assessment of students with disabilities that is integrated with curriculum and transition strategies. Assessment and curricular strategies are particularly intended for students in rural…

  17. Estimating Digital Inter-Symbol Interference Channel Blindly Based on the One-Step Branch Transition Rules in Trellises

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A novel discrete-time digital inter-symbol interference (ISI) channel blind estimation sub-optimal algorithm is proposed. This algorithm reduces the complexity of the optimal maximum likelihood sequence estimation(MLSE) considerably based on the one-step branch transition rules in trellises, and is suitable for the estimation of the channels with small lengths of ISI.

  18. Life Cost Based FMEA Manual: A Step by Step Guide to Carrying Out a Cost-based Failure Modes and Effects Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Rhee, Seung; Spencer, Cherrill; /Stanford U. /SLAC

    2009-01-23

    definition of detection difficulty (D) is how well the organization controls the development process. Another definition relates to the detectability of a particular failure in the product when it is in the hands of the customer. The former asks 'What is the chance of catching the problem before we give it to the customer'? The latter asks 'What is the chance of the customer catching the problem before the problem results in a catastrophic failure?' (Palady, 1995) These differing definitions confuse the FMEA users when one tries to determine detection difficulty. Are we trying to measure how easy it is to detect where a failure has occurred or when it has occurred? Or are we trying to measure how easy or difficult it is to prevent failures? Ordinal scale variables are used to rank-order industries such as, hotels, restaurants, and movies (Note that a 4 star hotel is not necessarily twice as good as a 2 star hotel). Ordinal values preserve rank in a group of items, but the distance between the values cannot be measured since a distance function does not exist. Thus, the product or sum of ordinal variables loses its rank since each parameter has different scales. The RPN is a product of 3 independent ordinal variables, it can indicate that some failure types are 'worse' than others, but give no quantitative indication of their relative effects. To resolve the ambiguity of measuring detection difficulty and the irrational logic of multiplying 3 ordinal indices, a new methodology was created to overcome these shortcomings, Life Cost-Based FMEA. Life Cost-Based FMEA measures failure/risk in terms of monetary cost. Cost is a universal parameter that can be easily related to severity by engineers and others. Thus, failure cost can be estimated using the following simplest form: Expected Failure Cost = {sup n}{Sigma}{sub i=1}p{sub i}c{sub i}, p: Probability of a particular failure occurring; c: Monetary cost associated with that particular failure; and

  19. Surface chemical modification of TEOS based silica aerogels synthesized by two step (acid-base) sol-gel process

    International Nuclear Information System (INIS)

    The present paper describes the comparative studies on the hydrophobic and physical properties of the tetraethoxysilane (TEOS) based silica aerogels prepared by two step sol-gel process followed by supercritical drying. Silica alcogels were prepared by keeping the molar ratio of TEOS:methanol (MeOH):H2O (acidic):H2O (basic) constant at 1:33:3.5:3.5 with oxalic acid and ammonium hydroxide concentrations fixed at 0.001 and 1 M, respectively. In all, nine different co-precursors (CP) of the type R nSiX4-n, have been used. The aerogels have been characterized by density, porosity, percentage of volume shrinkage, optical transmission, contact angle and thermal conductivity measurements. The surface chemical modification of silica aerogels was confirmed by the presence of C-H and Si-C peaks at 2900, 1450 and 840 cm-1, respectively, from the Fourier transform-infrared spectroscopy (FT-IR). The microstructure of the aerogels was studied using transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques. In addition to these studies, the stability of the hydrophobic aerogels against an organic impurity (methanol, in the present studies) in water has also been studied

  20. ATMS Step By Step.

    Science.gov (United States)

    National Library of Australia, Canberra.

    This manual is designed to provide an introduction and basic guide to the use of IBM's Advanced Text Management System (ATMS), the text processing system to be used for the creation of Australian data bases within AUSINET. Instructions are provided for using the system to enter, store, retrieve, and modify data, which may then be displayed at the…

  1. Direct Taxation in the Eu: The Common Corporate Tax Base as the Next Sub-Step towards Harmonization

    Directory of Open Access Journals (Sweden)

    Norbert Herzig

    2011-12-01

    Full Text Available This paper analyzes the Common Corporate Tax Base (CCTB as an interim alternative to the proposal of a Council directive on a Common Consolidated Corporate Tax Base (CCCTB. The CCCTB concept does not only include common rules for determining the tax base like the CCTB but also the steps of consolidation and subsequent formula apportionment. Therefore, the paper starts by showing that particularly these second and third steps of the CCCTB project meet fierce political opposition from several Member States and do leave leeway for tax planning. Afterwards, the CCCTB proposal's approach to common rules for determining the tax base is evaluated, i.e. tested for its suitability as a point of departure for drafting a CCTB. Finally, various other aspects of the proposal are examined in light of a CCTB without consolidation.

  2. Energy and exergy analyses of a new four-step copper-chlorine cycle for geothermal-based hydrogen production

    International Nuclear Information System (INIS)

    In this paper, energy and exergy analyses of the geothermal-based hydrogen production via thermochemical water decomposition using a new, four-step copper-chlorine (Cu-Cl) cycle are conducted, and the respective cycle energy and exergy efficiencies are examined. Also, a parametric study is performed to investigate how each step of the cycle and its overall cycle performance are affected by reference environment temperatures, reaction temperatures, as well as energy efficiency of the geothermal power plant itself. As a result, overall energy and exergy efficiencies of the cycle are found to be 21.67% and 19.35%, respectively, for a reference case.

  3. Novel transmission pricing scheme based on point-to-point tariff and transaction pair matching for pool market

    International Nuclear Information System (INIS)

    Transmission pricing scheme is a key component in the infrastructure of power market, and pool is an indispensable pattern of market organization; meanwhile, pay-as-bid (PAB) serves as a main option to determine market prices in pool. In this paper, a novel transmission pricing scheme is proposed for pool power market based on PAB. The new scheme is developed by utilizing point-to-point (PTP) tariff and introducing an approach of transaction pair matching (TPM). The model and procedure of the new scheme are presented in detail. Apart from the advantages of existing transmission pricing schemes, such as ensuing open, fair and non-discriminatory access, proper recovery for investment as well as transparency, the new scheme provides economic signals to promote the maximum use of the existing transmission network, encourages appropriate bidding behaviors in pool, and helps to reduce the possibility of the enforcement of market power and the appearing of price spikes; thus improves market operation efficiency and trading effects. In order to testify the effectiveness of the proposed scheme, a case based on IEEE 30-bus system is studied. (author)

  4. Design of A 5-Bit Fully Parallel Analog to Digital Converter Using Common Gate Differrential Mos Pair-Based Comparator

    Science.gov (United States)

    Aytar, Oktay

    2015-09-01

    This paper presents a novel comparator structure based on the common gate differential MOS pair. The proposed comparator has been applied to fully parallel analog to digital converter (A/D converter). Furthermore, this article presents 5 bit fully parallel A/D Converter design using the cadence IC5141 design platform and NCSU(North Carolina State University) design kit with 0.18 μm CMOS technology library. The proposed fully parallel A/D converter consist of resistor array block, comparator block, 1-n decoder block and programmable logic array. The 1-n decoder block includes latch block and thermometer code circuit that is implemented using transmission gate based multiplexer circuit. Thus, sampling frequency and analog bandwidth are increased. The INL and DNL of the proposed fully parallel A/D converter are (0/ + 0.63) LSB and (-0.26/ + 0.31) LSB at a sampling frequency of 5 GS/s with an input signal of 50 MHz, respectively. The proposed fully parallel A/D Converter consumes 340 mW from 1.8 V supply.

  5. Effect of single interstitial impurity in iron-based superconductors with sign-changed s-wave pairing symmetry

    Science.gov (United States)

    Yu, Xiang-Long; Liu, Da-Yong; Quan, Ya-Min; Zheng, Xiao-Jun; Zou, Liang-Jian

    2015-12-01

    We employ the self-consistent Bogoliubov-de Gennes (BdG) formulation to investigate the effect of single interstitial nonmagnetic/magnetic impurity in iron-based superconductors with s ± -wave pairing symmetry. We find that both the nonmagnetic and magnetic impurities can induce bound states within the superconducting (SC) gap and a π phase shift of SC order parameter at the impurity site. However, different from the interstitial-nonmagnetic-impurity case characterized by two symmetric peaks with respect to zero energy, the interstitial magnetic one only induces single bound-state peak. In the strong scattering regime this peak can appear at the Fermi level, which has been observed in the recent scanning tunneling microscope (STM) experiment of Fe(Te,Se) superconductor with interstitial Fe impurities (Yin et al. 2015 [44]). This novel single in-gap peak feature also distinguishes the interstitial case from the substitutional one with two peaks. These results provide important information for comparing the different impurity effects in the iron-based superconductors.

  6. Excited state properties of naphtho-homologated xxDNA bases and effect of methanol solution, deoxyribose, and base pairing.

    Science.gov (United States)

    Zhang, Laibin; Ren, Tingqi; Tian, Jianxiang; Yang, Xiuqin; Zhou, Liuzhu; Li, Xiaoming

    2013-04-18

    Design and synthesis of fluorescent nucleobase analogues for studying structures and dynamics of nucleic acids have attracted much attention in recent years. In the present work, a comprehensive theoretical study of electronic transitions of naphtho-homologated base analogues, namely, xxC, xxT, xxA, and xxG, was performed. The nature of the low-lying excited states was discussed, and the results were compared with those of x-bases. Geometrical characteristics of the lowest excited singlet ππ* states were explored using the CIS method. The calculated excitation maxima are 423, 397, 383, and 357 nm for xxA, xxG, xxC, and xxT, respectively, and they are greatly red-shifted compared with x-bases and natural bases, allowing them to be selectively excited in the presence of the natural bases. In the gas phase, the fluorescence from them would be expected to occur around 497, 461, 457, and 417 nm, respectively. The effects of methanol solution, deoxyribose, and base paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were also examined. PMID:23531077

  7. Two-Step SPD Processing of a Trimodal Al-Based Nano-Composite

    Science.gov (United States)

    Zhang, Yuzheng; Sabbaghianrad, Shima; Yang, Hanry; Topping, Troy D.; Langdon, Terence G.; Lavernia, Enrique J.; Schoenung, Julie M.; Nutt, Steven R.

    2015-12-01

    An ultrafine-grained (UFG) aluminum nano-composite was fabricated using two severe plastic deformation steps: cryomilling of powders (and subsequent consolidation of blended powders by forging) followed by high-pressure torsion (HPT). The forged bulk composite featured a trimodal structure comprised of UFG, coarse grain (CG) regions, and ceramic particles. The additional HPT processing introduced finer grain sizes and altered the morphology and spatial distribution of the ductile CG regions. As a result, both strength and ductility increased substantially compared to those of the Al nano-composite prior to HPT. The increases were attributed to the more optimal shape and spacing of the CG regions which promoted uniform elongation and yielding during tensile loading. Microstructural changes were characterized at each processing step to establish the evolution of microstructure and to elucidate structure-property relationships. The toughening effect of the CG regions was documented via fracture analysis, providing a potential strategy for designing microstructures with enhanced strength and toughness.

  8. Mechanical design and driving mechanism of an isokinetic functional electrical stimulation-based leg stepping trainer.

    Science.gov (United States)

    Hamzaid, N A; Fornusek, C; Ruys, A; Davis, G M

    2007-12-01

    The mechanical design of a constant velocity (isokinetic) leg stepping trainer driven by functional electrical stimulation-evoked muscle contractions was the focus of this paper. The system was conceived for training the leg muscles of neurologically-impaired patients. A commercially available slider crank mechanism for elliptical stepping exercise was adapted to a motorized isokinetic driving mechanism. The exercise system permits constant-velocity pedalling at cadences of 1-60 rev x min(-1). The variable-velocity feature allows low pedalling forces for individuals with very weak leg muscles, yet provides resistance to higher pedalling effort in stronger patients. In the future, the system will be integrated with a computer-controlled neuromuscular stimulator and a feedback control unit to monitor training responses of spinal cord-injured, stroke and head injury patients. PMID:18274073

  9. Multi-step-prediction of chaotic time series based on co-evolutionary recurrent neural network

    International Nuclear Information System (INIS)

    This paper proposes a co-evolutionary recurrent neural network (CERNN) for the multi-step-prediction of chaotic time series, it estimates the proper parameters of phase space reconstruction and optimizes the structure of recurrent neural networks by co-evolutionary strategy. The searching space was separated into two subspaces and the individuals are trained in a parallel computational procedure. It can dynamically combine the embedding method with the capability of recurrent neural network to incorporate past experience due to internal recurrence. The effectiveness of CERNN is evaluated by using three benchmark chaotic time series data sets: the Lorenz series, Mackey-Glass series and real-world sun spot series. The simulation results show that CERNN improves the performances of multi-step-prediction of chaotic time series

  10. Investigation on the ion pair amphiphiles and their in vitro release of amantadine drug based on PLGA–PEG–PLGA gel

    International Nuclear Information System (INIS)

    The amantadine drug and oleic acid surfactant are used to form amantadine-based ion pair amphiphiles based on proton transfer reaction between the drug and the surfactant molecules. The ion pair amphiphiles are characterized by 1H-nuclear magnetic resonance, Fourier transform infrared spectroscopy, and X-ray diffraction. Self-assembly properties of amantadine-based ion pair amphiphiles are studied by surface tension determination, transmission electron microscopy, zeta potential, and dynamic light scattering. The aggregation behavior studies indicate that the as-prepared ion pair amphiphiles can self-assemble into vesicles with the size of 200–300 nm in aqueous solution. The drug release results show that the amantadine release rate could be well controlled by incorporating the amantadine-based ion pair vesicles in poly (lactic-co-glycolic acid)-poly (ethylene glycol)-poly (lactic-co-glycolic acid) (PLGA–PEG–PLGA) copolymer hydrogel. The drug release from the AT–OA vesicle-loaded PLGA–PEG–PLGA hydrogel is significantly inhibited in comparison with the AT-loaded PLGA–PEG–PLGA hydrogel. The present work thus demonstrates that the vesicle-loaded hydrogel is a good candidate for the drug delivery system with long-term controlled drug release behavior

  11. Investigation on the ion pair amphiphiles and their in vitro release of amantadine drug based on PLGA–PEG–PLGA gel

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaoxia, E-mail: yxx-678@163.com; Ji, Xiaoqing; Shi, Chunhuan; Liu, Jing [Shandong University, School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems (China); Wang, Haiyang [Institute of Materia Medica Shandong Academy of Medical Sciences, Shandong Taitian Newdrug Discovery Co.Ltd (China); Luan, Yuxia, E-mail: yuxialuan@sdu.edu.cn [Shandong University, School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems (China)

    2014-12-15

    The amantadine drug and oleic acid surfactant are used to form amantadine-based ion pair amphiphiles based on proton transfer reaction between the drug and the surfactant molecules. The ion pair amphiphiles are characterized by {sup 1}H-nuclear magnetic resonance, Fourier transform infrared spectroscopy, and X-ray diffraction. Self-assembly properties of amantadine-based ion pair amphiphiles are studied by surface tension determination, transmission electron microscopy, zeta potential, and dynamic light scattering. The aggregation behavior studies indicate that the as-prepared ion pair amphiphiles can self-assemble into vesicles with the size of 200–300 nm in aqueous solution. The drug release results show that the amantadine release rate could be well controlled by incorporating the amantadine-based ion pair vesicles in poly (lactic-co-glycolic acid)-poly (ethylene glycol)-poly (lactic-co-glycolic acid) (PLGA–PEG–PLGA) copolymer hydrogel. The drug release from the AT–OA vesicle-loaded PLGA–PEG–PLGA hydrogel is significantly inhibited in comparison with the AT-loaded PLGA–PEG–PLGA hydrogel. The present work thus demonstrates that the vesicle-loaded hydrogel is a good candidate for the drug delivery system with long-term controlled drug release behavior.

  12. A Large Scale Daylighting System Based on a Stepped Thickness Waveguide

    Directory of Open Access Journals (Sweden)

    Ngoc Hai Vu

    2016-01-01

    Full Text Available This paper presents a study on the use of optical fiber and a solar concentrator for a building daylighting system. Daylighting is essential for improving indoor environments and reducing electric lighting power consumption in office buildings. Traditionally, optical fiber daylighting systems were implemented only on a small scale. More complicated technologies are required for more amounts of daylight over further distance via a smaller light guider. The proposed solar lighting system with optical fiber is composed of an array of linear Fresnel lenses and a stepped thickness waveguide. The linear Fresnel lenses collect light into the stepped thickness waveguide. The stepped-thickness waveguide is an optical component which redirects focused sunlight from the vertical direction to the horizontal direction, and it guides light to the attached optical fiber. Simulation models were developed using commercial optical simulation tools (LightTools™. The optical efficiency and angular tolerance of the system are analyzed. The overall system cost is also estimated. Some considerations on the economic expansion of the system in terms of efficiency and estimated annual average energy saving are discussed. The results show that the presented optical fiber daylighting system is a strong candidate for low-price and highly efficient solution for solar energy application to building energy savings.

  13. SmartFit: A Step Count Based Mobile Application for Engagement in Physical Activities

    Directory of Open Access Journals (Sweden)

    Atifa Sarwar

    2015-08-01

    Full Text Available Research has found that relatively few people en-gage in regular exercise or other physical activities. Despite the availability of numerous mobile applications and specialized devices for self-tracking, people mostly lack the motivation for performing physical activities. In this article we present SmartFit, a mobile application that uses step count for promoting the physical activities in adults. This article points out that while considering walk, activity duration is not sufficient for deter-mining users activeness state. Step count is another factor that should be taken into account. For this we propose an approach for converting the steps into duration for which activity has been performed. This duration is then used in Smartfit for categorizing user into different activeness levels. Gamification techniques have been incorporated in SmartFit as they are found to serve the purpose of motivating and encouraging the user. Gamification is used for awarding/deducting points to user in order to keep them engaged for longer period. Furthermore feedback is also provided to users depending upon their goal and achieved progress. The objective is to facilitate and motivate the user and then keep them engaged in carrying out the recommended level of physical activities.

  14. Coupled Inductor Based High Step-Up DC-DC Converter for Multi Input PV System

    Directory of Open Access Journals (Sweden)

    G. Shiny Vikram

    2014-09-01

    Full Text Available With the shortage of the energy and ever increasing of the oil price, research on the renewable and green energy sources, especially the solar arrays and the fuel cells, becomes more and more important. How to achieve high step-up and high efficiency DC/DC converters is the major consideration in the renewable power applications due to the low voltage of PV arrays and fuel cells. In this paper a coupled inductor dc-dc converter for photovoltaic system is proposed. The circuit configuration of the proposed converter is very simple. Thus, the proposed converter has higher step-up and step-down voltage gains than the conventional bidirectional dc–dc boost/buck converter. Under same electric specifications for the proposed converter and the conventional bidirectional boost/buck converter, the average value of the switch current in the proposed converter is less than the conventional bidirectional boost/buck converter. The operating principles have been applied to multi input photovoltaic system and outputs have been observed.

  15. On Candlestick-based Trading Rules Profitability Analysis via Parametric Bootstraps and Multivariate Pair-Copula based Models

    OpenAIRE

    Andreea Röthig; Andreas Röthig; Carl Chiarella

    2015-01-01

    This study analyses the profitability of candlestick-based technical trading rules in currency futures markets. The main feature of this type of technical analysis is that it generates signals based on the relationships between several price series, i.e. open, high, low and close prices. Since the trading rules are not precise and mainly based on causal knowledge of traders, we use a fuzzy-system to mathematize and classify them. The profitability of the trading rules is then tested by means ...

  16. Implementasi Sistem Step By Step Switching Menggunakan Komponen Terintegrasi

    OpenAIRE

    Suherman

    2009-01-01

    Sentral yang menggunakan sistem step by step switching telah lama ditinggalkan. Teknologi telah beralih ke sistem switching digital common control, bahkan berbasis packet switching khususnya penggunaan IP based Network. Namun demikian, teknologi switching step by step yang dahulu berbasis sistem mekanis masih dapat diperbaharui dengan memanfaatkan komponen terintegrasi (integrates cicuit, IC). Sistem switching step by step dengan komponen terintegrasi ini dapat dimanfaatkan untuk membentuk...

  17. Property (RD) for Hecke Pairs

    Energy Technology Data Exchange (ETDEWEB)

    Shirbisheh, Vahid, E-mail: shirbisheh@gmail.com

    2012-06-15

    As the first step towards developing noncommutative geometry over Hecke C{sup Asterisk-Operator }-algebras, we study property (RD) (Rapid Decay) for Hecke pairs. When the subgroup H in a Hecke pair (G, H) is finite, we show that the Hecke pair (G, H) has (RD) if and only if G has (RD). This provides us with a family of examples of Hecke pairs with property (RD). We also adapt Paul Jolissant's works in Jolissaint (J K-Theory 2:723-735, 1989; Trans Amer Math Soc 317(1):167-196, 1990) to the setting of Hecke C{sup Asterisk-Operator }-algebras and show that when a Hecke pair (G, H) has property (RD), the algebra of rapidly decreasing functions on the set of double cosets is closed under holomorphic functional calculus of the associated (reduced) Hecke C{sup Asterisk-Operator }-algebra. Hence they have the same K{sub 0}-groups.

  18. Property (RD) for Hecke Pairs

    Science.gov (United States)

    Shirbisheh, Vahid

    2012-06-01

    As the first step towards developing noncommutative geometry over Hecke C ∗-algebras, we study property (RD) (Rapid Decay) for Hecke pairs. When the subgroup H in a Hecke pair ( G, H) is finite, we show that the Hecke pair ( G, H) has (RD) if and only if G has (RD). This provides us with a family of examples of Hecke pairs with property (RD). We also adapt Paul Jolissant's works in Jolissaint (J K-Theory 2:723-735, 1989; Trans Amer Math Soc 317(1):167-196, 1990) to the setting of Hecke C ∗-algebras and show that when a Hecke pair ( G, H) has property (RD), the algebra of rapidly decreasing functions on the set of double cosets is closed under holomorphic functional calculus of the associated (reduced) Hecke C ∗-algebra. Hence they have the same K 0-groups.

  19. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition.

    Directory of Open Access Journals (Sweden)

    Edze R Westra

    Full Text Available Discriminating self and non-self is a universal requirement of immune systems. Adaptive immune systems in prokaryotes are centered around repetitive loci called CRISPRs (clustered regularly interspaced short palindromic repeat, into which invader DNA fragments are incorporated. CRISPR transcripts are processed into small RNAs that guide CRISPR-associated (Cas proteins to invading nucleic acids by complementary base pairing. However, to avoid autoimmunity it is essential that these RNA-guides exclusively target invading DNA and not complementary DNA sequences (i.e., self-sequences located in the host's own CRISPR locus. Previous work on the Type III-A CRISPR system from Staphylococcus epidermidis has demonstrated that a portion of the CRISPR RNA-guide sequence is involved in self versus non-self discrimination. This self-avoidance mechanism relies on sensing base pairing between the RNA-guide and sequences flanking the target DNA. To determine if the RNA-guide participates in self versus non-self discrimination in the Type I-E system from Escherichia coli we altered base pairing potential between the RNA-guide and the flanks of DNA targets. Here we demonstrate that Type I-E systems discriminate self from non-self through a base pairing-independent mechanism that strictly relies on the recognition of four unchangeable PAM sequences. In addition, this work reveals that the first base pair between the guide RNA and the PAM nucleotide immediately flanking the target sequence can be disrupted without affecting the interference phenotype. Remarkably, this indicates that base pairing at this position is not involved in foreign DNA recognition. Results in this paper reveal that the Type I-E mechanism of avoiding self sequences and preventing autoimmunity is fundamentally different from that employed by Type III-A systems. We propose the exclusive targeting of PAM-flanked sequences to be termed a target versus non-target discrimination mechanism.

  20. A randomized controlled pilot study of home-based step training in older people using videogame technology.

    Directory of Open Access Journals (Sweden)

    Daniel Schoene

    Full Text Available BACKGROUND: Stepping impairments are associated with physical and cognitive decline in older adults and increased fall risk. Exercise interventions can reduce fall risk, but adherence is often low. A new exergame involving step training may provide an enjoyable exercise alternative for preventing falls in older people. PURPOSE: To assess the feasibility and safety of unsupervised, home-based step pad training and determine the effectiveness of this intervention on stepping performance and associated fall risk in older people. DESIGN: Single-blinded two-arm randomized controlled trial comparing step pad training with control (no-intervention. SETTING/PARTICIPANTS: Thirty-seven older adults residing in independent-living units of a retirement village in Sydney, Australia. INTERVENTION: Intervention group (IG participants were provided with a computerized step pad system connected to their TVs and played a step game as often as they liked (with a recommended dose of 2-3 sessions per week for 15-20 minutes each for eight weeks. In addition, IG participants were asked to complete a choice stepping reaction time (CSRT task once each week. MAIN OUTCOME MEASURES: CSRT, the Physiological Profile Assessment (PPA, neuropsychological and functional mobility measures were assessed at baseline and eight week follow-up. RESULTS: Thirty-two participants completed the study (86.5%. IG participants played a median 2.75 sessions/week and no adverse events were reported. Compared to the control group, the IG significantly improved their CSRT (F31,1 = 18.203, p<.001, PPA composite scores (F31,1 = 12.706, p = 0.001, as well as the postural sway (F31,1 = 4.226, p = 0.049 and contrast sensitivity (F31,1 = 4.415, p = 0.044 PPA sub-component scores. In addition, the IG improved significantly in their dual-task ability as assessed by a timed up and go test/verbal fluency task (F31,1 = 4.226, p = 0.049. CONCLUSIONS: Step pad training can

  1. A new Salmonella tester strain (TA102) with A X T base pairs at the site of mutation detects oxidative mutagens.

    OpenAIRE

    Levin, D E; Hollstein, M; Christman, M.F.; Schwiers, E A; Ames, B N

    1982-01-01

    A new tester strain, TA102, is described as an addition to the set of strains for the Salmonella/microsome mutagenicity test. This strain contains A X T base pairs at the site of the mutation (determined by DNA sequence analysis) in contrast to the other Salmonella tester strains that detect mutagens damaging G X C base pairs. This strain differs from previous tester strains in that the mutation has been introduced into a multicopy plasmid, so that approximately equal to 30 copies of the muta...

  2. A Novel Face Recognition Approach Based on Two-Step Test Sample Representation

    OpenAIRE

    Zun-xiong Liu; Zhi-qiang Huang; Heng Zhang

    2013-01-01

    The two-step test sample representation method is proposed for face recognition. It first identifies k “representative” samples from each category training samples for the test sample then produces a weighted sum of all the “representative” samples that well approximates the test sample. This method assigns the test sample to the class whose training samples have the smallest deviation from the test sample. As the method proposed in this paper is able to reduce the side-effect of the other tr...

  3. Implementation of FFT by using MATLAB: SIMULINK on Xilinx Virtex-4 FPGAs: Performance of a Paired Transform Based FFT

    Directory of Open Access Journals (Sweden)

    Ranganadh Narayanam

    2013-06-01

    Full Text Available Discrete Fourier Transform is principal mathematical method for the frequency analysis and is having wide applications in Engineering and Sciences. Because the DFT is so ubiquitous, fast methods for computing DFT have been studied extensively, and continuous to be an active research. The way of splitting the DFT gives out various fast algorithms. In this paper, we present the implementation of two fast algorithms for the DFT for evaluating their performance. One of them is the popular radix-2 Cooley-Tukey fast Fourier transform algorithm (FFT [1] and the other one is the Grigoryan FFT based on the splitting by the paired transform [2]. We evaluate the performance of these algorithms by implementing them on the Xilinx Virtex-4 FPGAs [3], by developing our own FFT processor architectures. Finally we show that the Grigoryan FFT is working faster than Cooley-Tukey FFT, consequently it is useful for higher sampling rates. Operating at higher sampling rates is a challenge in DSP applications.

  4. Spectrophotometric Determination of Cefixime Trihydrate in Pharmaceutical Formulations Based on Ion-Pair Reaction with Bromophenol Blue.

    Science.gov (United States)

    Keskar, Mrudul R; Jugade, Ravin M

    2015-01-01

    Cefixime trihydrate is a broad spectrum cephalosporin antibiotic, effective against gram-positive and gram-negative bacterial infections. Simple and rapid method has been developed for the determination of cefixime trihydrate in bulk and pharmaceutical formulations. This method was based on the formation of bluish-green ion-pair complex of cefixime trihydrate with bromophenol blue in dimethyl sulfoxide (DMSO)-acetonitrile medium. Different parameters were studied and optimized. A 2:1 complex was formed between the drug and reagent almost instantaneously at room temperature which has λmax of 610 nm. Under optimum conditions, calibration curve was found to be linear over the range of 10-130 μg mL(-1). The method was subjected to analytical quality control. The limit of detection was found to be 1.08 μg mL(-1). Recovery studies and interference studies were carried out. The proposed method was successfully applied to the determination of cefixime trihydrate in bulk and pharmaceutical formulations with high precision and accuracy. PMID:26279621

  5. High yield and ultrafast sources of electrically triggered entangled-photon pairs based on strain-tunable quantum dots.

    Science.gov (United States)

    Zhang, Jiaxiang; Wildmann, Johannes S; Ding, Fei; Trotta, Rinaldo; Huo, Yongheng; Zallo, Eugenio; Huber, Daniel; Rastelli, Armando; Schmidt, Oliver G

    2015-01-01

    Triggered sources of entangled photon pairs are key components in most quantum communication protocols. For practical quantum applications, electrical triggering would allow the realization of compact and deterministic sources of entangled photons. Entangled-light-emitting-diodes based on semiconductor quantum dots are among the most promising sources that can potentially address this task. However, entangled-light-emitting-diodes are plagued by a source of randomness, which results in a very low probability of finding quantum dots with sufficiently small fine structure splitting for entangled-photon generation (∼10(-2)). Here we introduce strain-tunable entangled-light-emitting-diodes that exploit piezoelectric-induced strains to tune quantum dots for entangled-photon generation. We demonstrate that up to 30% of the quantum dots in strain-tunable entangled-light-emitting-diodes emit polarization-entangled photons. An entanglement fidelity as high as 0.83 is achieved with fast temporal post selection. Driven at high speed, that is 400 MHz, strain-tunable entangled-light-emitting-diodes emerge as promising devices for high data-rate quantum applications. PMID:26621073

  6. LifeSteps: An Evidence-based Health Promotion Program for Underserved Populations – A Community Service Learning Approach

    Directory of Open Access Journals (Sweden)

    Melanie Austin-McCain

    2015-04-01

    Full Text Available Chronic diseases are the most common, costly, and preventable of all health problems in the United States. Chronic diseases represent the leading causes of death and are experienced at higher rates by minority populations (CDC, 2012. Innovative community-based health promotion programs are recommended that meet the diverse needs of underserved populations (Yeary, et al., 2011. LifeSteps is being developed as an evidence-based health promotion program focusing on health and wellness, a domain area defined within the Occupational Therapy Practice Framework (OTPF, 2008. LifeSteps will utilize a client-centered approach to coach individuals in making health behavior changes. Fieldwork and service-learning components are incorporated integrating clinical practice, academic study, and collaboration with community providers. Program evaluation measures based on the Transtheoretical Model (TTM have been identified to address all phases of program planning. The LifeSteps health promotion program aligns with local, national, and international objectives and addresses the need for programs that meet the diverse needs of underserved populations. Occupational therapists are in a unique position for implementing community-based interventions that promote health and contribute to a healthier society.

  7. Unravelling the interaction dynamics of a carbonatite-silicate magmatic pair: A numerical approach based on Korteweg Stress theory

    Science.gov (United States)

    Valentini, L.; Moore, K. R.; Chazot, G.

    2009-04-01

    Most of the worldwide carbonatites occur in spatial association with silicate rocks. Even when unquestionable evidence for the associated carbonatite and silicate rocks to represent contemporaneous liquids exists, the modes of interaction between the two liquids can be difficult to infer. In general, the retrieval of information about the mechanisms of interaction between magmas can be complicated by the intrinsic dynamical nature of such systems. The development of new physico-chemical equilibria (e.g. hybridization) can erase any information about the previous stages of interaction. However, the occurrence of magmatic heterogeneities, such as enclaves and flow bands, as well as mineral disequilibrium textures, may serve as dynamic markers for the underlying interaction processes. Small-scale heterogeneities, in the form of micron to millimetre sized globules, characterized by more or less smooth interfaces, are frequently observed in carbonatite-silicate pairs. Textural observation, as well as the lack of suitable mechanisms for the dispersion of a discrete magmatic liquid in the form of a small-scale emulsion, have lead many petrologists to advocate immiscible separation as the process capable of forming such textures. However, the geochemical criteria for liquid immiscibility are not always met, and when not coupled with geochemical and dynamical arguments, textural observation may lead to ambiguous conclusions. In this study we adopted an integrated approach in order to infer the details of magmatic interaction of a carbonatite-silicate pair from Massif Central (France). The studied samples display emulsion-like textures, formed by micro-scale dolomitic globules dispersed in a trachytic glassy matrix. Our approach is based on a novel numerical method, coupled with textural observation and geochemical analyses. The novelty of our numerical model consists in the inclusion, in the adopted advection-diffusion equations, of a term that takes into account the effect

  8. Defining a competency framework: the first step toward competency-based medical education.

    Directory of Open Access Journals (Sweden)

    Azim Mirzazadeh

    2014-09-01

    Full Text Available Despite the existence of a large variety of competency frameworks for medical graduates, there is no agreement on a single set of outcomes. Different countries have attempted to define their own set of competencies to respond to their local situations. This article reports the process of developing medical graduates' competency framework as the first step in the curriculum reform in Tehran University of Medical Sciences (TUMS. A participatory approach was applied to develop a competency framework in Tehran University of Medical Sciences (TUMS. Following literature review, nominal group meetings with students and faculty members were held to generate the initial list of expectations, and 9 domains was proposed. Then, domains were reviewed, and one of the domains was removed. The competency framework was sent to Curriculum Reform Committee for consideration and approval, where it was decided to distribute electronic and paper forms among all faculty members and ask them for their comments. Following incorporating some of the modifications, the document was approved by the committee. The TUMS competency framework consists of 8 domains: Clinical skills; Communication skills; Patient management; Health promotion and disease prevention; Personal development; Professionalism, medical ethics and law; Decision making, reasoning and problem-solving; and Health system and the corresponding role of physicians. Development of a competency framework through a participatory approach was the first step towards curriculum reform in TUMS, aligned with local needs and conditions. The lessons learned through the process may be useful for similar projects in the future.

  9. Seven-step problem-based learning in an interaction design course

    DEFF Research Database (Denmark)

    Schultz, Nette; Christensen, Hans Peter

    2004-01-01

    The objective in this paper is the implementation of the highly structured seven-step PBL procedure as part of the learning process in a human-computer interaction design course at the Technical University of Denmark, taking into account the common learning processes in PBL and the interaction de...... others in a single course. The evaluation results showed that the students definitely took a deep approach to learning, and indicated clearly that the students had obtained competences not only within the traditional HCI curriculum but also in terms of team-work skills.......The objective in this paper is the implementation of the highly structured seven-step PBL procedure as part of the learning process in a human-computer interaction design course at the Technical University of Denmark, taking into account the common learning processes in PBL and the interaction...... individual reports after each case in the PBL-process in order to explore the students’ inter- and intra-personal team skills development in the learning process. Different qualitative and quantitative evaluation methods have been used to obtain a thorough evaluation of PBL used as a learning method among...

  10. An improved algorithm to convert CAD model to MCNP geometry model based on STEP file

    International Nuclear Information System (INIS)

    Highlights: • Fully exploits common features of cells, making the processing efficient. • Accurately provide the cell position. • Flexible to add new parameters in the structure. • Application of novel structure in INP file processing, conveniently evaluate cell location. - Abstract: MCNP (Monte Carlo N-Particle Transport Code) is a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron, or coupled neutron/photon/electron transport. Its input file, the INP file, has the characteristics of complicated form and is error-prone when describing geometric models. Due to this, a conversion algorithm that can solve the problem by converting general geometric model to MCNP model during MCNP aided modeling is highly needed. In this paper, we revised and incorporated a number of improvements over our previous work (Yang et al., 2013), which was proposed and targeted after STEP file and INP file were analyzed. Results of experiments show that the revised algorithm is more applicable and efficient than previous work, with the optimized extraction of geometry and topology information of the STEP file, as well as the production efficiency of output INP file. This proposed research is promising, and serves as valuable reference for the majority of researchers involved with MCNP-related researches

  11. Modified normal-phase ion-pair chromatographic methods for the facile separation and purification of imidazolium-based ionic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Urban, ND; Schenkel, MR; Robertson, LA; Noble, RD; Gin, DL

    2012-07-04

    lmidazolium- and oligo(imidazolium)-based ionic organic compounds are important in the design of room-temperature ionic liquid materials; however, the chromatographic analysis and separation of such compounds are often difficult. A convenient and inexpensive method for effective thin-layer chromatography (TLC) analysis and column chromatography separation of imidazolium-based ionic compounds is presented. Normal-phase ion-pair TLC is used to effectively analyze homologous mixtures of these ionic compounds. Subsequent separation of the mixtures is performed using ion-pair flash chromatography on normal-phase silica gel, yielding high levels of recovery. This method also results in a complete exchange of the counter anion on the imidazolium compounds to the anion of the ion-pair reagent. (C) 2012 Elsevier Ltd. All rights reserved.

  12. Statistical inference about the relative efficiency of a new survey protocol, based on paired-tow survey calibration data

    OpenAIRE

    Cadigan, Noel G.; Dowden, Jeff J.

    2010-01-01

    Paired-tow calibration studies provide information on changes in survey catchability that may occur because of some necessary change in protocols (e.g., change in vessel or vessel gear) in a fish stock survey. This information is important to ensure the continuity of annual time-series of survey indices of stock size that provide the basis for fish stock assessments. There are several statistical models used to analyze the paired-catch data from calibration studies. Our main contribu...

  13. An unstructured finite volume solver for two phase water/vapour flows based on an elliptic oriented fractional step method

    International Nuclear Information System (INIS)

    Based on experience gained at EDF and Cea, a more general and robust 3-dimensional (3D) multiphase flow solver has been being currently developed for over three years. This solver, based on an elliptic oriented fractional step approach, is able to simulate multicomponent/multiphase flows. Discretization follows a 3D full unstructured finite volume approach, with a collocated arrangement of all variables. The non linear behaviour between pressure and volume fractions and a symmetric treatment of all fields are taken into account in the iterative procedure, within the time step. It greatly enforces the realizability of volume fractions (i.e 0 < α < 1), without artificial numerical needs. Applications to widespread test cases as static sedimentation, water hammer and phase separation are shown to assess the accuracy and the robustness of the flow solver in different flow conditions, encountered in nuclear reactors pipes. (authors)

  14. Process for separating carbon dioxide from flue gas using sweep-based membrane separation and absorption steps

    Science.gov (United States)

    Wijmans, Johannes G.; Baker, Richard W.; Merkel, Timothy C.

    2012-08-21

    A gas separation process for treating flue gases from combustion processes, and combustion processes including such gas separation. The invention involves routing a first portion of the flue gas stream to be treated to an absorption-based carbon dioxide capture step, while simultaneously flowing a second portion of the flue gas across the feed side of a membrane, flowing a sweep gas stream, usually air, across the permeate side, then passing the permeate/sweep gas to the combustor.

  15. Comparative analysis of phase extraction methods based on phase-stepping and shifting curve in grating interferometry

    International Nuclear Information System (INIS)

    Two phase extraction methods which are based separately on phase-stepping and shifting curve are mainly used in phase-sensitive imaging in gating interferometry to determine the x-ray phase shift induced by an object in the beam. In this paper, the authors perform a full comparative analysis and present the main virtues and limitations of these two methods according to the theoretical analysis of the grating interferometry. (general)

  16. ACL2 Meets the GPU: Formalizing a CUDA-based Parallelizable All-Pairs Shortest Path Algorithm in ACL2

    Directory of Open Access Journals (Sweden)

    David S. Hardin

    2013-04-01

    Full Text Available As Graphics Processing Units (GPUs have gained in capability and GPU development environments have matured, developers are increasingly turning to the GPU to off-load the main host CPU of numerically-intensive, parallelizable computations. Modern GPUs feature hundreds of cores, and offer programming niceties such as double-precision floating point, and even limited recursion. This shift from CPU to GPU, however, raises the question: how do we know that these new GPU-based algorithms are correct? In order to explore this new verification frontier, we formalized a parallelizable all-pairs shortest path (APSP algorithm for weighted graphs, originally coded in NVIDIA's CUDA language, in ACL2. The ACL2 specification is written using a single-threaded object (stobj and tail recursion, as the stobj/tail recursion combination yields the most straightforward translation from imperative programming languages, as well as efficient, scalable executable specifications within ACL2 itself. The ACL2 version of the APSP algorithm can process millions of vertices and edges with little to no garbage generation, and executes at one-sixth the speed of a host-based version of APSP coded in C – a very respectable result for a theorem prover. In addition to formalizing the APSP algorithm (which uses Dijkstra's shortest path algorithm at its core, we have also provided capability that the original APSP code lacked, namely shortest path recovery. Path recovery is accomplished using a secondary ACL2 stobj implementing a LIFO stack, which is proven correct. To conclude the experiment, we ported the ACL2 version of the APSP kernels back to C, resulting in a less than 5% slowdown, and also performed a partial back-port to CUDA, which, surprisingly, yielded a slight performance increase.

  17. Paired fuzzy sets

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco de los Ríos, Camilo; Gómez, Daniel;

    2015-01-01

    In this paper we want to stress the relevance of paired fuzzy sets, as already proposed in previous works of the authors, as a family of fuzzy sets that offers a unifying view for different models based upon the opposition of two fuzzy sets, simply allowing the existence of different types of...

  18. Industrial Process Identification and Control Design Step-test and Relay-experiment-based Methods

    CERN Document Server

    Liu, Tao

    2012-01-01

      Industrial Process Identification and Control Design is devoted to advanced identification and control methods for the operation of continuous-time processes both with and without time delay, in industrial and chemical engineering practice.   The simple and practical step- or relay-feedback test is employed when applying the proposed identification techniques, which are classified in terms of common industrial process type: open-loop stable; integrating; and unstable, respectively. Correspondingly, control system design and tuning models that follow are presented for single-input-single-output processes.   Furthermore, new two-degree-of-freedom control strategies and cascade control system design methods are explored with reference to independently-improving, set-point tracking and load disturbance rejection. Decoupling, multi-loop, and decentralized control techniques for the operation of multiple-input-multiple-output processes are also detailed. Perfect tracking of a desire output trajectory is realiz...

  19. Usability of an internet-based platform (Next.Step for adolescent weight management

    Directory of Open Access Journals (Sweden)

    Pedro Sousa

    2015-02-01

    Full Text Available OBJECTIVE: The current study evaluates the usability perception of an e-therapeutic platform (supported by electronic processes and communication, aiming to promote the behavior change and to improve the adolescent health status through increased and interactive contact between the adolescent and the clinical staff. METHODS: This was a correlational study with a sample of 48 adolescents (12-18 years who attended a Pediatric Obesity Clinic between January and August of 2012. Participants were invited to access, during 24 weeks, the e-therapeutic multidisciplinary platform (Next.Step in addition to the standard treatment program. A usability questionnaire was administered and the platform performance and utilization indicators were analyzed. RESULTS: The users' perception of satisfaction, efficiency, and effectiveness regarding the Next.Step platform was clearly positive. However, only 54.17% of the enrolled adolescents accessed the platform, with a mean task-completion rate of 14.55% (SD = 18.853. The higher the number of the platform consulted resources, the greater the tendency to enjoy the platform, to consider it exciting and quick, to consider that the time spent in it was useful, to consider the access to information easy, and to login easier. Post-intervention assessment revealed a significant reduction in anthropometric and behavioral variables, including body mass index z-score, waist circumference percentile, hip circumference, and weekly screen time. CONCLUSION: These results highlight the importance of information and communication technologies in the health information access and the healthcare provision. Despite the limited adherence rate, platform users expressed a positive overall perception of its usability and presented a positive anthropometric and behavioral progress.

  20. Multiple-Step Injection Molding for Fibrin-Based Tissue-Engineered Heart Valves.

    Science.gov (United States)

    Weber, Miriam; Gonzalez de Torre, Israel; Moreira, Ricardo; Frese, Julia; Oedekoven, Caroline; Alonso, Matilde; Rodriguez Cabello, Carlos J; Jockenhoevel, Stefan; Mela, Petra

    2015-08-01

    Heart valves are elaborate and highly heterogeneous structures of the circulatory system. Despite the well accepted relationship between the structural and mechanical anisotropy and the optimal function of the valves, most approaches to create tissue-engineered heart valves (TEHVs) do not try to mimic this complexity and rely on one homogenous combination of cells and materials for the whole construct. The aim of this study was to establish an easy and versatile method to introduce spatial diversity into a heart valve fibrin scaffold. We developed a multiple-step injection molding process that enables the fabrication of TEHVs with heterogeneous composition (cell/scaffold material) of wall and leaflets without the need of gluing or suturing components together, with the leaflets firmly connected to the wall. The integrity of the valves and their functionality was proved by either opening/closing cycles in a bioreactor (proof of principle without cells) or with continuous stimulation over 2 weeks. We demonstrated the potential of the method by the two-step molding of the wall and the leaflets containing different cell lines. Immunohistology after stimulation confirmed tissue formation and demonstrated the localization of the different cell types. Furthermore, we showed the proof of principle fabrication of valves using different materials for wall (fibrin) and leaflets (hybrid gel of fibrin/elastin-like recombinamer) and with layered leaflets. The method is easy to implement, does not require special facilities, and can be reproduced in any tissue-engineering lab. While it has been demonstrated here with fibrin, it can easily be extended to other hydrogels. PMID:25654448

  1. Young Learners' Interactional Development in Task-Based Paired-Assessment in Their First and Foreign Languages: A Case of English Learners in China

    Science.gov (United States)

    Butler, Yuko Goto; Zeng, Wei

    2015-01-01

    In response to the growing interest in evaluating young learners' foreign language (FL) performance, this study aims to deepen our understanding of young learners' developmental differences in interaction during task-based paired-language assessments. To examine age effects separately from the effect of general language proficiency, we analysed…

  2. Structures, physicochemical properties, and applications of T-Hg-II-T, C-Ag-I-C, and other metallo-base-pairs

    Czech Academy of Sciences Publication Activity Database

    Tanaka, Y.; Kondo, J.; Sychrovský, Vladimír; Šebera, Jakub; Dairaku, T.; Saneyoshi, H.; Urata, H.; Torigoe, H.; Ono, A.

    2015-01-01

    Roč. 51, č. 98 (2015), s. 17343-17360. ISSN 1359-7345 R&D Projects: GA ČR GAP205/10/0228 Institutional support: RVO:61388963 Keywords : metal-mediated base-pairs * T–Hg–T * C–Ag–C Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.834, year: 2014

  3. Self-deflection of bright soliton in a separate bright-dark screening soliton pair based on higher-order space charge field

    Institute of Scientific and Technical Information of China (English)

    Zhonghua Hao(郝中华); Jinsong Liu(刘劲松)

    2003-01-01

    Based on the interaction of the separate soliton pair, the self-deflection of the bright screening soliton in a bright-dark pair is studied by taking the higher order space charge field into account. Both numerical and analytical methods are adopted to obtain the result that the higher order of space charge field can enhance the deflection process of the bright soliton and varying the peak intensity of the dark soliton can influence the self-deflection strongly. The expression of the deflection distance with the dark soliton's peak intensity is derived, and some corresponding properties of the self-deflection process are figured out.

  4. Three-dimensional paper-based slip device for one-step point-of-care testing

    OpenAIRE

    Han, Kwi Nam; Choi, Jong-Soon; Kwon, Joseph

    2016-01-01

    In this study, we developed a new type of paper-based analytical device (PAD), the three-dimensional (3D) slip-PAD, to detect infectious human norovirus for global healthcare. The 3D configuration of the papers combined with a slip design provides unique features and versatility that overcome the limitations of fluidic manipulation and sensitivity in point-of-care (POC) tests. The assay can be carried out in a single step based on a moveable slip design, making it suitable for unskilled users...

  5. Efficient Certificateless Signcryption Scheme from Weil Pairing

    Directory of Open Access Journals (Sweden)

    Gang Yu

    2011-08-01

    Full Text Available Certificateless signcryption has both the advantage of certificateless public key cryptography, which overcome the escrow problem inherited from identity based cryptography without the use of certificates as in traditional public key cryptography, and signcryption which can fulfill both the functions of signature and encryption in a logical signal step. In this paper, we explicit the security model for certificateless signcryption and propose an efficient certificateless signcryption scheme from Weil pairings. The new scheme not only can be proved to be secure in our model but also can simultaneously provide public verifiability and forward security. Furthermore, compared with existing schemes, the new scheme is more efficient.

  6. Preonset studies of spondyloepiphyseal dysplasia tarda caused by a novel 2-base pair deletion in SEDL encoding sedlin.

    Science.gov (United States)

    Mumm, S; Zhang, X; Gottesman, G S; McAlister, W H; Whyte, M P

    2001-12-01

    Spondyloepiphyseal dysplasia tarda (SEDT), an X-linked recessive skeletal disorder, presents with disproportionate short stature and "barrel-chest" deformity in affected (hemizygous) adolescent boys. In four reported families to date, mutations in a gene designated SEDL (spondyloepiphyseal dysplasia late) cosegregate with SEDT. We diagnosed SEDT in a short-stature, kyphotic 15-year-old boy because of his characteristic vertebral malformations. Clinical manifestations of SEDT were evident in at least four previous generations. A novel 2-base pair (bp) deletion in exon 5 of SEDL was found in the propositus by polymerase chain reaction (PCR) amplification and sequencing of all four coding exons. The mutation ATdel241-242 cosegregated with the kindred's skeletal disease. The deletion is adjacent to a noncanonical splice site for exon 5 but does not alter splicing. Instead, it deletes 2 bp from the coding sequence, causing a frameshift. A maternal aunt and her three young sons were investigated subsequently. Radiographs showed subtle shaping abnormalities of her pelvis and knees, suggesting heterozygosity. X-rays of the spine and pelvis of her 8-year-old son revealed characteristic changes of SEDT, but her younger sons (aged 6 years and 3 years) showed no abnormalities. SEDL analysis confirmed that she and only her eldest boy had the 2-bp deletion. Molecular testing of SEDL enables carrier detection and definitive diagnosis before clinical or radiographic expression of SEDT. Although there is no specific treatment for SEDT, preexpression molecular testing of SEDL could be helpful if avoiding physical activities potentially injurious to the spine and the joints proves beneficial. PMID:11760838

  7. Do not Lose Your Students in Large Lectures: A Five-Step Paper-Based Model to Foster Students’ Participation

    Directory of Open Access Journals (Sweden)

    Mona Hassan Aburahma

    2015-07-01

    Full Text Available Like most of the pharmacy colleges in developing countries with high population growth, public pharmacy colleges in Egypt are experiencing a significant increase in students’ enrollment annually due to the large youth population, accompanied with the keenness of students to join pharmacy colleges as a step to a better future career. In this context, large lectures represent a popular approach for teaching the students as economic and logistic constraints prevent splitting them into smaller groups. Nevertheless, the impact of large lectures in relation to student learning has been widely questioned due to their educational limitations, which are related to the passive role the students maintain in lectures. Despite the reported feebleness underlying large lectures and lecturing in general, large lectures will likely continue to be taught in the same format in these countries. Accordingly, to soften the negative impacts of large lectures, this article describes a simple and feasible 5-step paper-based model to transform lectures from a passive information delivery space into an active learning environment. This model mainly suits educational establishments with financial constraints, nevertheless, it can be applied in lectures presented in any educational environment to improve active participation of students. The components and the expected advantages of employing the 5-step paper-based model in large lectures as well as its limitations and ways to overcome them are presented briefly. The impact of applying this model on students’ engagement and learning is currently being investigated.

  8. 2012 IUPAP C10 Young Scientist Prize on the Structure and Dynamics of Condensed Matter Lecture: Spin Fluctuations and Pairing in Fe-based Superconductors

    Science.gov (United States)

    Christianson, A. D.

    2012-02-01

    The origin of superconductivity in the Fe-based superconductors, like that in other unconventional superconductors, remains shrouded in mystery. How the pairing bosons emerge either due to or in spite of the strong magnetic interactions found in the Fe-based superconductors is one of the most thoroughly investigated questions in the field. A prominent example of the interplay of superconductivity and magnetism is the dramatic shift of spectral weight from the low energy spin excitations to an energy which is related to the superconducting gap resulting in a peak in the spin excitation spectrum localized in both momentum and energy which occurs at the onset of superconductivity. The appearance of the new peak in the spin excitation spectrum below the superconducting transition temperature is referred to as s spin resonance and is most commonly interpreted as indicating a sign change of the superconducting order parameter on different portions of the Fermi surface and thus is consistent with an extended s-wave or s± pairing symmetry in many Fe-based superconductors. We will review the observations and implications of the spin resonance across the Fe-based superconductors. In particular we will examine the relationship between the resonance energy and the superconducting transition temperature as a function of chemical doping and pressure. While the spin resonance provides important information about pairing symmetry, there does not appear to be sufficient spectral to explain the pairing strength. Thus the remainder of the spin excitation spectrum must be examined to determine if spin fluctuations are ultimately responsible for pairing in the Fe-based materials. Consequently, we will discuss in detail the way in which the spin excitations evolve from the nonsuperconducting compounds to their superconducting relatives as a function of chemical doping.

  9. High Output Voltage Based Multiphase Step-Up DC-DC Converter Topology with Voltage Doubler Rectifiers

    Directory of Open Access Journals (Sweden)

    Liao Xiaozhong

    2013-02-01

    Full Text Available High Output Voltage Based Multiphase Step-Up DC-DC Converter topology with voltage doubler rectifiers is presented in this paper. High output voltage is obtained due to the series combination of voltage doubler rectifiers on the secondary side of high frequency transformers. This topology is useful in the application where the output voltage is greater than the input. The two loop control strategy has been developed in order to analyze the stable and effective working of the converter topology. Therefore the working mode analysis of the converter topology has been described in detail. The multiphase step-up DC-DC converter topology is first simulated on MATLAB and then a prototype has been designed in order to verify the simulation and experimental results. Finally the simulation and experimental results are found to be satisfactory.

  10. Direct micro/nano metal patterning based on two-step transfer printing of ionic metal nano-ink

    International Nuclear Information System (INIS)

    We present a direct metal patterning method by a two-step transfer printing process of non-particle, ionic metal nano-ink solution. This fabrication method allows a simple direct patterning of various micro/nanoscale metallic structures. Complex structures such as multilayer line arrays, patterns along non-flat topologies, and micro/nanoscale hybrid patterns can be achieved by using this process. Also, the low temperature and pressure process conditions are compatible with the fabrication of electronic structures and devices on flexible substrates such as polyimide film and photographic papers. As an application of this process, we fabricated ZnO nanowire-based flexible UV sensors, where metal electrodes were fabricated by two-step transfer printing. In the case of ZnO nanowire sensors, highly sensitive and fast responding performances to UV illumination and good mechanical robustness against repeated bending conditions could be verified. (paper)

  11. Asymmetric cryptosystem and software design based on two-step phase-shifting interferometry and elliptic curve algorithm

    Science.gov (United States)

    Fan, Desheng; Meng, Xiangfeng; Wang, Yurong; Yang, Xiulun; Peng, Xiang; He, Wenqi; Dong, Guoyan; Chen, Hongyi

    2013-11-01

    We propose an asymmetric cryptosystem based on two-step phase-shifting interferometry (PSI) and elliptic curve (EC) public-key cryptographic algorithm, in which one image is encrypted to two interferograms by double random-phase encoding (DRPE) in Fresnel domain and two-step PSI, and the session keys such as geometrical parameters and pseudo-random seeds, are asymmetrically encoded and decoded with the aid of EC algorithm. The receiver, who possesses the corresponding private key generated by EC algorithm, can successfully decipher the transmitted data using the extracted session keys. The utilization of EC asymmetric cryptosystem solves the problem of key management and dispatch, which is inevitable in the conventional optical symmetric cryptosystems. Not only computer simulation, but also software design and development are carried out to verify the feasibility of the proposed cryptosystem.

  12. A NUFFT Based Step-frequency Chirp Signal High Resolution Imaging Algorithm and Target Recognition Algorithm

    Directory of Open Access Journals (Sweden)

    Xiang Yin

    2015-12-01

    Full Text Available Radar Automatic Target Recognition (RATR is the key technique to be breaked through in the fuure development of intelligent weapon system. Compared to the 2-D SAR image target recognition, High Resolution Range Profile (HRRP target recognition has the advantage of low data dimension, low requirement of radar system's calculation and storage ability, and the imaging algorithm is also not complicated. HRRP imaging is the first and the key process in target recognition, its speed and imaging quality can directly influence the real-time capability and accuracy of target recognition. In this paper a new HRRP imaging algorithm — NUFFT algorithm is proposed, the derivation of mathematical expression is given, both for the echo simulation process and the imaging process. In the meantime, by analyzing each step's calculation complexity, we compared the calculation complexity of four different imaging algorithms, we also simulate two target's imaging and target recognition processing. Theoretical analysis and simulation both prove that the proposed algorithm's calculation complexity is improved in various degree compared with the others, thus can be effectively used in target recognition.

  13. One step gold (bio)functionalisation based on CS{sub 2}-amine reaction

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Ines [Centro de Quimica e Bioquimica, Faculdade de Ciencias da Universidade de Lisboa, Ed. C8, Campo Grande, 1749-016 Lisboa (Portugal); Cascalheira, Antonio C. [Lumisense, Lda, Campus Faculdade de Ciencias da Universidade de Lisboa, Ed. ICAT, Campo Grande, 1749-016 Lisboa (Portugal); Viana, Ana S., E-mail: anaviana@fc.ul.p [Centro de Quimica e Bioquimica, Faculdade de Ciencias da Universidade de Lisboa, Ed. C8, Campo Grande, 1749-016 Lisboa (Portugal)

    2010-12-01

    Dithiocarbamates have been regarded as alternative anchor groups to thiols on gold surfaces, and claimed to be formed in situ through the reaction between secondary amines and carbon disulphide. In this paper, we further exploit this methodology for a convenient one step biomolecule immobilisation onto gold surfaces. First, the reactivity between CS{sub 2} and electroactive compounds containing amines, primary (dopamine), secondary (epinephrine), and an amino acid (tryptophan) has been investigated by electrochemical methods. Cyclic voltammetric characterisation of the modified electrodes confirmed the immobilisation of all the target compounds, allowing the estimation of their surface concentration. The best result was obtained with epinephrine, a secondary amine, for which a typical quasi-reversible behaviour of surface confined electroactive species could be clearly depicted. Electrochemical reductive desorption studies enabled to infer on the extent of the reaction and on the relative stability of the generated monolayers. Bio-functionalisation studies have been accomplished through the reaction of CS{sub 2} with glucose oxidase in aqueous medium, and the catalytic activity of the immobilised enzyme was evaluated towards glucose, by electrochemical methods in the presence of a redox mediator. Scanning tunnelling microscopy (STM) and Atomic force microscopy (AFM) were used respectively, to characterize the gold electrodes and Glucose Oxidase coverage and distribution on the modified surfaces.

  14. Ring-dot-shaped multilayer piezoelectric step-down transformers using PZT-based ceramics

    International Nuclear Information System (INIS)

    In this study, multilayer piezo stack transformers for switching mode power supply (SMPS) application were manufactured using 0.01Pb(Ni1/3Nb2/3)O3 - 0.08Pb(Mn1/3Nb2/3)O3 - 0.91Pb(Zr0.505Ti0.495)O3 (PNN-PMN-PZT) ceramics. The voltage ratio of a multilayer piezo stack transformer showed a maximum at the resonance frequency of the input and then increased with increasing load resistance. The efficiency of the multilayer piezo stack transformer showed its highest value at around the matching load. The output power increased with increasing input voltage. The temperature of the multilayer piezo stack transformer increased with increasing output power and load resistance. The manufactured multilayer piezo stack transformer could be used up to 5 W at a resonance frequency of 70.25 kHz for SMPS application because the temperature rise from room temperature is believed to about 20 .deg. C and because the transformer is electrically stable. The newly-developed ring-dot-type step-down multilayer piezo stack transformer shows possible applications as SMPS for electronic power sources with excellent input-to-output properties.

  15. Managing chronic pathologies with a stepped mHealth-based approach in clinical psychology and medicine

    Directory of Open Access Journals (Sweden)

    Gianluca Castelnuovo

    2015-04-01

    Full Text Available Chronic diseases and conditions typically require long-term monitoring and treatment protocols both in traditional settings and in out-patient frameworks. The economic burden of chronic conditions is a key challenge and new and mobile technologies could offer good solutions. mHealth could be considered an evolution of ehealth and could be defined as the practice of medicine and public health supported by mobile communication devices. mHealth approach could overcome limitations linked with the traditional, restricted and highly expensive in-patient treatment of many chronic pathologies. Possible applications include stepped mHealth approach, where patients can be monitored and treated in their everyday contexts. Unfortunately, many barriers for the spread of mHealth are still present. Due the significant impact of psychosocial factors on disease evolution, psychotherapies have to be included into the chronic disease protocols. Existing psychological theories of health behavior change have to be adapted to the new technological contexts and requirements. In conclusion, clinical psychology and medicine have to face the chronic care management challenge in both traditional and mHealth settings.

  16. One step gold (bio)functionalisation based on CS2-amine reaction

    International Nuclear Information System (INIS)

    Dithiocarbamates have been regarded as alternative anchor groups to thiols on gold surfaces, and claimed to be formed in situ through the reaction between secondary amines and carbon disulphide. In this paper, we further exploit this methodology for a convenient one step biomolecule immobilisation onto gold surfaces. First, the reactivity between CS2 and electroactive compounds containing amines, primary (dopamine), secondary (epinephrine), and an amino acid (tryptophan) has been investigated by electrochemical methods. Cyclic voltammetric characterisation of the modified electrodes confirmed the immobilisation of all the target compounds, allowing the estimation of their surface concentration. The best result was obtained with epinephrine, a secondary amine, for which a typical quasi-reversible behaviour of surface confined electroactive species could be clearly depicted. Electrochemical reductive desorption studies enabled to infer on the extent of the reaction and on the relative stability of the generated monolayers. Bio-functionalisation studies have been accomplished through the reaction of CS2 with glucose oxidase in aqueous medium, and the catalytic activity of the immobilised enzyme was evaluated towards glucose, by electrochemical methods in the presence of a redox mediator. Scanning tunnelling microscopy (STM) and Atomic force microscopy (AFM) were used respectively, to characterize the gold electrodes and Glucose Oxidase coverage and distribution on the modified surfaces.

  17. Huge electric field enhancement and highly sensitive sensing based on the Fano resonance effect in an asymmetric nanorod pair

    International Nuclear Information System (INIS)

    A sharp plasmonic Fano resonance is found to appear in a silver nanorod pair structure with broken length symmetry. It is shown that it arises from strong interference between a narrow plasmon mode of inter-nanorod near-field coupling and broad scattering from the nanorod. The inter-nanorod coupling is the result of the magnetic dipole plasmon resonance induced by the anti-parallel current of the nanorod pair, while the broad scattering is caused by electric dipole oscillation. The numerical results show that a giant local field enhancement (197), a high quality factor (52) and a sensing sensitivity of 1426 nm per refractive index unit in the symmetry-broken nanorod pair with a displacement Δl = 40 nm originated from a pronounced Fano resonance in the near-infrared spectrum. Huge local field enhancement and high sensitivity make this simple structure promising for surface enhanced Raman spectroscopy and sensing applications. (paper)

  18. Multi-risk assessment and users' perception: a futher step towards ecosystem-based beach management

    OpenAIRE

    Lozoya Azcárate, Juan Pablo

    2012-01-01

    This thesis deals with the need to move towards a holistic, truly integrated and ecosystem-based beach management that allows a sustainable use of these systems within the socio-ecological paradigm. However, the scarcity of frameworks for such management has been identified as a major constraint. The goal of this thesis was to apply and develop a set of methodologies based on the introduction of the Ecosystem Approach principles to beach management. These tools would be part of the Ecosystem ...

  19. Common consolidated corporate tax base: step towards company tax harmonization in European Union

    OpenAIRE

    Stravinskaitė, Vaida

    2013-01-01

    The European Commission on 16 March 2011 proposed a harmonized system for the tax base calculation of companies operating in the EU. The proposed Common Consolidated Corporate Tax Base (CCCTB) indicates that businesses would benefit from a "one-stop-shop" system for filing their tax returns and would be able to consolidate all the profits and losses they incur across the EU. Member States would maintain their full sovereign right to set their own corporate tax rate. However, many Member State...

  20. Synthesis of 5-[3-(2-aminopyrimidin-4-yl)aminopropyn-1-yl]uracil derivative that recognizes Ade-Thy base pairs in double-stranded DNA.

    Science.gov (United States)

    Ito, Yu; Masaki, Yoshiaki; Kanamori, Takashi; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

    2016-01-01

    5-[3-(2-Aminopyrimidin-4-yl)aminopropyn-1-yl]uracil (Ura(Pyr)) was designed as a new nucleobase to recognize Ade-Thy base pair in double-stranded DNA. We successfully synthesized the dexoynucleoside phosphoramidite having Ura(Pyr) and incorporated it into triplex forming oligonucleotides (TFOs). Melting temperature analysis revealed that introduction of Ura(Pyr) into TFOs could effectively stabilize their triplex structures without loss of base recognition capabilities. PMID:26602276

  1. Change of the sign of superconducting intraband order parameters induced by interband pair hopping interaction in iron-based high-temperature superconductors

    International Nuclear Information System (INIS)

    Iron based superconductors are characterized by the s± gap symmetry, where the gap changes its sign between pockets of the Fermi surface. We discuss another sign change mechanism of the superconducting order parameter (OP)—the interband Cooper pairs hopping interaction. In the minimal two-orbital model of iron based superconductors we show that this interaction can lead to a change of the sign of the intraband superconducting OP regardless of its symmetry. (paper)

  2. Trunk, head, and step characteristics during normal and narrow-based walking under deteriorated sensory conditions.

    Science.gov (United States)

    Deshpande, Nandini; Zhang, Fang

    2014-01-01

    The ability to maintain stability in the frontal plane (medialateral direction) while walking is commonly included as a component of motor performance assessment. Postural control in the frontal plane may deteriorate faster and earlier with increasing age, compared to that in the sagittal plane (anteroposterior direction). Fifteen young (20-30 years old) and 15 older (>65 years old) healthy participants were recruited to investigate age-related differences in postural control during the normal and narrow-based walking when performed under suboptimal vestibular and lower limb somatosensory conditions achieved by galvanic stimulation and compliant surfaces, respectively. Gait speed decreased in the narrow-based walking condition, with larger decrease in the elderly (by 6%). In the elderly head roll increased with perturbed vestibular information in impaired somatosensory condition (by 40.70%). In both age groups trunk roll increased under impaired somatosensation in the narrow-based walking condition (by 43.62%) but not in normal walking condition. Older participants adopted a more cautious strategy characterized by lower walking speed when walking on a narrow base and exhibited deteriorated integrative ability of the CNS for head control. Accurate lower limb somatosensation may play a critical role in narrow-based walking. PMID:24528161

  3. Effect of BrU on the transition between wobble Gua-Thy and tautomeric Gua-Thy base-pairs: ab initio molecular orbital calculations

    International Nuclear Information System (INIS)

    We investigated transition states (TS) between wobble Guanine-Thymine (wG-T) and tautomeric G-T base-pair as well as Br-containing base-pairs by MP2 and density functional theory (DFT) calculations. The obtained TS between wG-T and G*-T (asterisk is an enol-form of base) is different from TS got by the previous DFT calculation. The activation energy (17.9 kcal/mol) evaluated by our calculation is significantly smaller than that (39.21 kcal/mol) obtained by the previous calculation, indicating that our TS is more preferable. In contrast, the obtained TS and activation energy between wG-T and G-T* are similar to those obtained by the previous DFT calculation. We furthermore found that the activation energy between wG-BrU and tautomeric G-BrU is smaller than that between wG-T and tautomeric G-T. This result elucidates that the replacement of CH3 group of T by Br increases the probability of the transition reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G base is accelerated by the introduction of wG-BrU base-pair.

  4. Effect of BrU on the transition between wobble Gua-Thy and tautomeric Gua-Thy base-pairs: ab initio molecular orbital calculations

    Science.gov (United States)

    Nomura, Kazuya; Hoshino, Ryota; Hoshiba, Yasuhiro; Danilov, Victor I.; Kurita, Noriyuki

    2013-04-01

    We investigated transition states (TS) between wobble Guanine-Thymine (wG-T) and tautomeric G-T base-pair as well as Br-containing base-pairs by MP2 and density functional theory (DFT) calculations. The obtained TS between wG-T and G*-T (asterisk is an enol-form of base) is different from TS got by the previous DFT calculation. The activation energy (17.9 kcal/mol) evaluated by our calculation is significantly smaller than that (39.21 kcal/mol) obtained by the previous calculation, indicating that our TS is more preferable. In contrast, the obtained TS and activation energy between wG-T and G-T* are similar to those obtained by the previous DFT calculation. We furthermore found that the activation energy between wG-BrU and tautomeric G-BrU is smaller than that between wG-T and tautomeric G-T. This result elucidates that the replacement of CH3 group of T by Br increases the probability of the transition reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G base is accelerated by the introduction of wG-BrU base-pair.

  5. An electrochemical one-step system for assaying methyltransferase activity based on transport of a quantum dot signaling tracer.

    Science.gov (United States)

    Baek, Songyi; Won, Byoung Yeon; Park, Ki Soo; Park, Hyun Gyu

    2013-11-15

    A one-step, electrochemical method for assaying methyltransferase (MTase) activity, based on the convective transport of a quantum dot (QD) signaling tracer, has been developed. The assay chip used in this system was prepared by modifying a gold matrix with CdSe/ZnS QD-tagged dsDNA, which contains a specific methylation site (5'-GATC-3') recognized by MTase. Treatment of the chip with DNA adenine methylation (Dam) MTase, generates a methylated sequence (5'-GAmTC-3') within the dsDNA. The methylated dsDNA is then subjected to a cleavage reaction, induced by DpnI, which leads to release from the gold matrix of a DNA fragment tethered to a QD. Detection of the released QD, using square wave anodic stripping voltammetry (SWASV) on a glassy carbon (GC) electrode, enables the reliable quantitation of the methylated DNA. Because it is accomplished in a simple and convenient one step and does not require any complicated secondary or tedious washing steps, the new assay method holds great promise for epigenetic analysis in facility-limited environments or point-of-care testing (POCT) applications. PMID:23777705

  6. A Novel Variable Step Size Adjustment Method Based on Autocorrelation of Error Signal for the Constant Modulus Blind Equalization Algorithm

    Directory of Open Access Journals (Sweden)

    M. A. Demir

    2012-04-01

    Full Text Available Blind equalization is a technique for adaptive equalization of a communication channel without the use of training sequence. Although the constant modulus algorithm (CMA is one of the most popular adaptive blind equalization algorithms, because of using fixed step size it suffers from slow convergence rate. A novel enhanced variable step size CMA algorithm (VSS-CMA based on autocorrelation of error signal has been proposed to improve the weakness of CMA for application to blind equalization in this paper. The new algorithm resolves the conflict between the convergence rate and precision of the fixed step-size conventional CMA algorithm. Computer simulations have been performed to illustrate the performance of the proposed method in simulated frequency selective Rayleigh fading channels and experimental real communication channels. The obtained simulation results using single carrier (SC IEEE 802.16-2004 protocol have demonstrated that the proposed VSS-CMA algorithm has considerably better performance than conventional CMA, normalized CMA (N-CMA and the other VSS-CMA algorithms.

  7. Cooper pairs in atomic nuclei

    International Nuclear Information System (INIS)

    We describe recent efforts to study Cooper pairs in atomic nuclei. We consider a self-consistent Hartree Fock mean field for the even Sm isotopes and compare results based on three treatments of pairing correlations: a BCS treatment, a number-projected BCS treatment and an exact treatment using the Richardson Ansatz. Significant differences are seen in the pairing correlation energies. Furthermore, because it does not average over the properties of the fermion pairs, the Richardson solution permits a more meaningful definition of the Cooper wave function and of the fraction of pairs that are collective. Our results confirm that only a few pairs near the Fermi surface in realistic atomic nuclei are collective. (Author)

  8. Cooper pairs in atomic nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Pittel, S. [Bartol Research Institute and Department of Physics and Astronomy, University of Delaware, Newark, 19716 Delaware (United States); Dussel, G. G. [Departamento de Fisica J.J. Giambiagi, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Dukelsky, J.; Sarriguren, P. [Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid (Spain)

    2008-12-15

    We describe recent efforts to study Cooper pairs in atomic nuclei. We consider a self-consistent Hartree Fock mean field for the even Sm isotopes and compare results based on three treatments of pairing correlations: a BCS treatment, a number-projected BCS treatment and an exact treatment using the Richardson Ansatz. Significant differences are seen in the pairing correlation energies. Furthermore, because it does not average over the properties of the fermion pairs, the Richardson solution permits a more meaningful definition of the Cooper wave function and of the fraction of pairs that are collective. Our results confirm that only a few pairs near the Fermi surface in realistic atomic nuclei are collective. (Author)

  9. First steps in the logic-based assessment of post-composed phenotypic descriptions

    CERN Document Server

    Jimenez-Ruiz, Ernesto; Berlanga, Rafael; Rebholz-Schuhmann, Dietrich

    2010-01-01

    In this paper we present a preliminary logic-based evaluation of the integration of post-composed phenotypic descriptions with domain ontologies. The evaluation has been performed using a description logic reasoner together with scalable techniques: ontology modularization and approximations of the logical difference between ontologies.

  10. Pairing the Volcano

    CERN Document Server

    Ionica, Sorina

    2011-01-01

    Isogeny volcanoes are graphs whose vertices are elliptic curves and whose edges are $\\ell$-isogenies. Algorithms allowing to travel on these graphs were developed by Kohel in his thesis (1996) and later on, by Fouquet and Morain (2001). However, up to now, no method was known, to predict, before taking a step on the volcano, the direction of this step. Hence, in Kohel's and Fouquet-Morain algorithms, many steps are taken before choosing the right direction. In particular, ascending or horizontal isogenies are usually found using a trial-and-error approach. In this paper, we propose an alternative method that efficiently finds all points $P$ of order $\\ell$ such that the subgroup generated by $P$ is the kernel of an horizontal or an ascending isogeny. In many cases, our method is faster than previous methods. This is an extended version of a paper published in the proceedings of ANTS 2010. In addition, we treat the case of 2-isogeny volcanoes and we derive from the group structure of the curve and the pairing ...

  11. QM/MM Simulation of the Hydrogen Bond Dynamics of an Adenine:Uracil Base Pair in Solution. Geometric Correlations and Infrared Spectrum

    CERN Document Server

    Yan, Yun-an

    2009-01-01

    Hybrid QM(DFT)/MM molecular dynamics simulations have been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. Trajectories are analyzed putting special attention to the geometric correlations of the $\\NHN$ and $\\NHO$ hydrogen bonds in the base pair. Further, based on empirical correlations between the hydrogen bond bond length and the fundamental NH stretching frequency its fluctuations are obtained along the trajectory. Using the time dependent frequencies the infrared lineshape is determined assuming the validity of a second order cumulant expansion. The deviations for the fundamental transition frequencies are calculated to amount to less than 2% as compared with experiment. The width of the spectrum for the $\\NHN$ bond is in reasonable agreement with experiment while that for the $\\NHO$ case is underestimated by the present model. Comparing the performance of different pseudopotentials it is found that the Troulli...

  12. Improvement in conductivity and thermal stability of polystyrene with two-step reduced graphene oxide based nanocomposite graphene/polystyrene

    International Nuclear Information System (INIS)

    In in situ microemulsion synthesis, we have synthesized successfully nanocomposite based on polystyrene (PS) and two-step reduced graphene oxide sheets with heat and NaBH4 agent after they had been treated by monoglyceride. Resulted nanocomposite has been better in electrical conductivity (approximately 2.01x10-2 S/cm), thermal stability (increased about 120 oC) and physical properties (glass transition temperature increases of over 6.40 oC, elastic modulus increases by 45%) than pure PS properties. (author)

  13. Mutants of the Base Excision Repair Glycosylase, Endonuclease III: DNA Charge Transport as a First Step in Lesion Detection

    OpenAIRE

    Romano, Christine A.; Sontz, Pamela A.; Barton, Jacqueline K.

    2011-01-01

    Endonuclease III (EndoIII) is a base excision repair glycosylase that targets damaged pyrimidines and contains a [4Fe-4S] cluster. We have proposed a model where BER proteins that contain redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in the detection of DNA lesions. Here, several mutants of EndoIII were prepared to probe their efficiency of DNA/protein charge transport. Cyclic voltammetry experiments on DNA-modified electrodes show that aromatic residues F30...

  14. Web based health surveys: Using a Two Step Heckman model to examine their potential for population health analysis.

    Science.gov (United States)

    Morrissey, Karyn; Kinderman, Peter; Pontin, Eleanor; Tai, Sara; Schwannauer, Mathias

    2016-08-01

    In June 2011 the BBC Lab UK carried out a web-based survey on the causes of mental distress. The 'Stress Test' was launched on 'All in the Mind' a BBC Radio 4 programme and the test's URL was publicised on radio and TV broadcasts, and made available via BBC web pages and social media. Given the large amount of data created, over 32,800 participants, with corresponding diagnosis, demographic and socioeconomic characteristics; the dataset are potentially an important source of data for population based research on depression and anxiety. However, as respondents self-selected to participate in the online survey, the survey may comprise a non-random sample. It may be only individuals that listen to BBC Radio 4 and/or use their website that participated in the survey. In this instance using the Stress Test data for wider population based research may create sample selection bias. Focusing on the depression component of the Stress Test, this paper presents an easy-to-use method, the Two Step Probit Selection Model, to detect and statistically correct selection bias in the Stress Test. Using a Two Step Probit Selection Model; this paper did not find a statistically significant selection on unobserved factors for participants of the Stress Test. That is, survey participants who accessed and completed an online survey are not systematically different from non-participants on the variables of substantive interest. PMID:27394193

  15. Present and next steps of the JAERI superconducting rf linac based FEL program

    International Nuclear Information System (INIS)

    The JAERI superconducting rf linac based FEL has successfully been lased to produce a 0.3 kW FEL light and 100 kW or larger electron beam output in quasi continuous wave operation in 1999. The 1 kW class output as our present program goal will be achieved to improve the optical out coupling method in the FEL optical resonator, the electron gun, and the electron beam optics in the JAERI FEL driver. As our next 5 year program goal is the 100 kW class FEL light and a few tens MW class electron beam output in average, quasi continuous wave operation of the light and electron beam will be planned in the JAERI superconducting rf linac based FEL facility. Conceptual design options needed for such a very high power operation and shorter wavelength light sources will be discussed to improve and to upgrade the exciting facility. (author)

  16. First Steps towards Evidence-Based Preventive Home Visits: Experiences Gathered in a Swedish Municipality

    Directory of Open Access Journals (Sweden)

    Charlotte Löfqvist

    2012-01-01

    Full Text Available The purpose of preventive home visits is to promote overall health and wellbeing in old age. The aim of this paper was to describe the process of the development of evidence-based preventive home visits, targeting independent community-living older persons. The evidence base was generated from published studies and practical experiences. The results demonstrate that preventive home visits should be directed to persons 80 years old and older and involve various professional competences. The visits should be personalized, lead to concrete interventions, and be followed up. The health areas assessed should derive from a broad perspective and include social, psychological, and medical aspects. Core components in the protocol developed in this study captured physical, medical, psychosocial, and environmental aspects. Results of a pilot study showed that the protocol validly identified health risks among older people with different levels of ADL dependence.

  17. Initial steps of the base excision repair pathway within the nuclear architecture

    International Nuclear Information System (INIS)

    Oxidative stress induced lesions threaten aerobic organisms by representing a major cause of genomic instability. A common product of guanine oxidation, 8-oxo-guanine (8- oxoG) is particularly mutagenic by provoking G to T transversions. Removal of oxidised bases from DNA is initiated by the recognition and excision of the damaged base by a DNA glycosylase, initiating the base excision repair (BER) pathway. In mammals, 8-oxoG is processed by the 8-oxoG-DNA-glycosylase I (OGG1), which biochemical mechanisms has been well characterised in vitro. However how and where this enzyme finds the modified base within the complex chromatin architecture is not yet understood. We show that upon induction of 8-oxoG, OGG1, together with at least two other proteins involved in BER, is recruited from a soluble fraction to chromatin. Formation kinetics of this patches correlates with 8-oxoG excision, suggesting a direct link between presence of this chromatin-associated complexes and 8-oxoG repair. More precisely, these repair patches are specifically directed to euchromatin regions, and completely excluded from heterochromatin regions. Inducing of artificial chromatin compaction results in a complete inhibition of the in vivo repair of 8-oxoG, probably by impeding the access of OGG1 to the lesion. Using OGG1 mutants, we show that OGG1 direct recognition of 8-oxoG did not trigger its re-localisation to the chromatin. We conclude that in response to the induction of oxidative DNA damage, the DNA glycosylase is actively recruited to regions of open chromatin allowing the access of the BER machinery to the lesions. (author)

  18. Entity Model Based Quality Management: A First Step Towards High Reliability Organization Management

    OpenAIRE

    Engelbrecht, Sabine; Radestock, Christine; Bohle, Detlev

    2010-01-01

    A management system built upon a generic entity model is presented as an approach towards management systems for High Reliability Organizations (HRO). The entity model is derived from the Ground Systems and Operations standard of the European Cooperation for Space Standardization (ECSS). DLR has launched a first application of the model in its Applied Remote Sensing Cluster, especially for the Center for Satellite based Crisis Information. It is proposed that a management system built...

  19. Nano-Sim: A Step Wise Equivalent Conductance based Statistical Simulator for Nanotechnology Circuit Design

    OpenAIRE

    Sukhwani, Bharat; Padmanabhan, Uday; Wang, Janet M.

    2005-01-01

    New nanotechnology based devices are replacing CMOS devices to overcome CMOS technology's scaling limitations. However, many such devices exhibit non-monotonic I-V characteristics and uncertain properties which lead to the negative differential resistance (NDR) problem and the chaotic performance. This paper proposes a new circuit simulation approach that can effectively simulate nanotechnology devices with uncertain input sources and negative differential resistance (NDR) problem. The experi...

  20. Steps toward subject-specific classification in ECG-based detection of sleep apnea

    International Nuclear Information System (INIS)

    This study deals with ECG-based recognition of sleep apnea in epochs of 1 min duration using spectral- and correlation-based features extracted from the modulation of QRS amplitude, respiratory myogram interference and RR intervals. On a database comprising 140 simultaneous recordings of polysomnograms (PSGs) and 8-lead Holter-ECGs, it is shown that a single-parameter ROC threshold classification can achieve high detection rates up to 81.0% sensitivity and 85.6% specificity. Still, individual accuracy may be low, and the improvement employing feature combination by means of second order polynomial classifiers is only marginal. We speculate that individual differences, like co-morbidities, and even intra-individual confounding factors, like nocturnal changes in body position (BP), are major reasons for the difficulties to significantly raise the detection rate using multivariate techniques, which is evident in virtually all papers on that subject. Using the BP information in the PSG, we show a potential benefit for individualized single-feature classifiers by comparing the maximally achievable individual and global accuracy when either one optimal global threshold for the total dataset, individual threshold values for each subject or individual thresholds for each BP are applied. We developed an ECG-based BP segmentation algorithm and finally suggest a potential strategy to derive individually optimized subject-specific threshold values

  1. Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations.

    Science.gov (United States)

    Jain, Alok; Krishna Deepak, R N V; Sankararamakrishnan, Ramasubbu

    2014-07-01

    Three-dimensional structures of biomolecules are stabilized by a large number of non-covalent interactions and some of them such as van der Waals, electrostatic and hydrogen bond interactions are well characterized. Delocalized π-electron clouds of aromatic residues are known to be involved in cation-π, CH-π, OH-π and π-π interactions. In proteins, many examples have been found in which the backbone carbonyl oxygen of one residue makes close contact with the aromatic center of aromatic residues. Quantum chemical calculations suggest that such contacts may provide stability to the protein secondary structures. In this study, we have systematically analyzed the experimentally determined high-resolution DNA crystal structures and identified 91 examples in which the aromatic center of one base is in close contact (interactions between the bases in base pairs with oxygen-aromatic contacts are energetically favorable. Decomposition of interaction energies indicates that dispersion forces are the major cause for energetically stable interaction in these base pairs. We speculate that oxygen-aromatic contacts in intra-strand base pairs in a DNA structure may have biological significance. PMID:24816369

  2. Fews-Risk: A step towards risk-based flood forecasting

    Science.gov (United States)

    Bachmann, Daniel; Eilander, Dirk; de Leeuw, Annemargreet; Diermanse, Ferdinand; Weerts, Albrecht; de Bruijn, Karin; Beckers, Joost; Boelee, Leonore; Brown, Emma; Hazlewood, Caroline

    2015-04-01

    Operational flood prediction and the assessment of flood risk are important components of flood management. Currently, the model-based prediction of discharge and/or water level in a river is common practice for operational flood forecasting. Based on the prediction of these values decisions about specific emergency measures are made within operational flood management. However, the information provided for decision support is restricted to pure hydrological or hydraulic aspects of a flood. Information about weak sections within the flood defences, flood prone areas and assets at risk in the protected areas are rarely used in a model-based flood forecasting system. This information is often available for strategic planning, but is not in an appropriate format for operational purposes. The idea of FEWS-Risk is the extension of existing flood forecasting systems with elements of strategic flood risk analysis, such as probabilistic failure analysis, two dimensional flood spreading simulation and the analysis of flood impacts and consequences. Thus, additional information is provided to the decision makers, such as: • Location, timing and probability of failure of defined sections of the flood defence line; • Flood spreading, extent and hydraulic values in the hinterland caused by an overflow or a breach flow • Impacts and consequences in case of flooding in the protected areas, such as injuries or casualties and/or damages to critical infrastructure or economy. In contrast with purely hydraulic-based operational information, these additional data focus upon decision support for answering crucial questions within an operational flood forecasting framework, such as: • Where should I reinforce my flood defence system? • What type of action can I take to mend a weak spot in my flood defences? • What are the consequences of a breach? • Which areas should I evacuate first? This presentation outlines the additional required workflows towards risk-based flood

  3. A truly international lunar base as the next logical step for human spaceflight

    Science.gov (United States)

    Bonneville, Richard

    Recent fora (e.g. the ISECG’s Global Exploration Roadmap) have highlighted a human mission to Mars as the long term goal for space exploration, with intermediate stages such as missions to the Moon and/or to asteroids. But actually a human mission to Mars will not be feasible before several decades, whereas in the meantime robotic missions will be able to provide an enormous amount of information on the history and the environment of the red planet, at a rather moderate cost. And if we consider missions to asteroids, introducing a human in the loop will require a considerably higher complexity and cost than using robots, with no significant additional benefit. The only sensible and feasible objective of a near-term human spaceflight program would be the edification of a lunar base, under the condition that this base is built as a true international venture. Science will not be the main driver; it has to be acknowledged from the beginning that the true main goal will be peace and a nucleus of international cooperation between the big countries. The ISS in the 1990’s had illustrated a calmed relation between the USA, together with Europe, Canada and Japan, and Russia. A lunar base should be the symbol of a similar calmed relation between the same partners and China. For the benefit of all humankind this extra continent, the Moon, will be used only for peaceful purposes, like Antarctica today, and will not become the theatre or the stake of conflicts. The financial cost of that venture will be high, but not that high if it is compared with the cost of recent wars; so let us go to the Moon, OK, but let us get there together.

  4. A Step Forward To Component-based Software Cost Estimation in Object-oriented Environment

    CERN Document Server

    Ahmed, Nadeem; Qureshi, M Rizwan Jameel

    2012-01-01

    Software cost estimation (SCE) of a project is pivotal to the acceptance or rejection of the development of software project. Various SCE techniques have been in practice with their own strengths and limitations. The latest of these is object-oriented one. Currently object-oriented approach for SCE is based on Line of Code (LOC), function points, functions and classes etc. Relatively less attention has been paid to the SCE in component-based software engineering (CBSE). So there is a pressing need to search parameters/variables that have a vital role for the SCE using CBSE which is taken up in this paper. This paper further looks at level of significance of all the parameters/variables thus searched. The time is being used as an independent variable because time is a parameter which is almost, all previous in one. Therefore this approach may be in a way an alternate of all previous approaches. Infact the underlying research ultimately may lead towards SCE of complex systems, using CBSE, in a scientific, syste...

  5. Achieving the Desired Transformation: Thoughts on Next Steps for Outcomes-Based Medical Education.

    Science.gov (United States)

    Holmboe, Eric S; Batalden, Paul

    2015-09-01

    Since the introduction of the outcomes-based medical education (OBME) movement, progress toward implementation has been active but challenging. Much of the angst and criticism has been directed at the approaches to assessment that are associated with outcomes-based or competency frameworks, particularly defining the outcomes. In addition, these changes to graduate medical education (GME) are concomitant with major change in health care systems--specifically, changes to increase quality and safety while reducing cost. Every sector, from medical education to health care delivery and financing, is in the midst of substantial change and disruption.The recent release of the Institute of Medicine's report on the financing and governance of GME highlights the urgent need to accelerate the transformation of medical education. One source of continued tension within the medical education community arises from the assumption that the much-needed increases in value and improvement in health care can be achieved by holding the current educational structures and architecture of learning in place while concomitantly withdrawing resources. The authors of this Perspective seek to reframe the important and necessary debate surrounding the current challenges to implementing OBME. Building on recent change and service theories (e.g., Theory U and coproduction), they propose several areas of redirection, including reexamination of curricular models and greater involvement of learners, teachers, and regulators in cocreating new training models, to help facilitate the desired transformation in medical education. PMID:26083400

  6. Analysis of Renal Cell Carcinoma as a First Step for Developing Mass Spectrometry-Based Diagnostics

    Science.gov (United States)

    Yoshimura, Kentaro; Chen, Lee Chuin; Mandal, Mridul Kanti; Nakazawa, Tadao; Yu, Zhan; Uchiyama, Takahito; Hori, Hirokazu; Tanabe, Kunio; Kubota, Takeo; Fujii, Hideki; Katoh, Ryohei; Hiraoka, Kenzo; Takeda, Sen

    2012-10-01

    Immediate diagnosis of human specimen is an essential prerequisites in medical routines. This study aimed to establish a novel cancer diagnostics system based on probe electrospray ionization-mass spectrometry (PESI-MS) combined with statistical data processing. PESI-MS uses a very fine acupuncture needle as a probe for sampling as well as for ionization. To demonstrate the applicability of PESI-MS for cancer diagnosis, we analyzed nine cases of clear cell renal cell carcinoma (ccRCC) by PESI-MS and processed the data by principal components analysis (PCA). Our system successfully delineated the differences in lipid composition between non-cancerous and cancerous regions. In this case, triacylglycerol (TAG) was reproducibly detected in the cancerous tissue of nine different individuals, the result being consistent with well-known profiles of ccRCC. Moreover, this system enabled us to detect the boundaries of cancerous regions based on the expression of TAG. These results strongly suggest that PESI-MS will be applicable to cancer diagnosis, especially when the number of data is augmented.

  7. ADAPTIVE CHANNEL EQUALIZATION FOR FBMC BASED ON VARIABLE LENGTH STEP SIZE AND MEAN-SQUARED ERROR

    Directory of Open Access Journals (Sweden)

    Mashhoor AlTarayrah

    2014-03-01

    Full Text Available Recently, increasing data transmission rates and the demand of more bandwidth at the same time have been a challenge. The trend now is to support high data rates in wireless communications. Multicarrier systems have overcome many challenges of high bandwidth efficiency and at the same time provided also high spectral efficiency. Filter bank multicarrier systems (FBMC provide some advantages more than the traditional orthogonal frequency division multiplexing (OFDM with cyclic prefix (CP. FBMC systems provide a much better spectral shaping of the subcarriers than orthogonal frequency division multiplexing (OFDM. Therefore, the most obvious difference between the two techniques is in frequency selectivity. In this paper, we will present a least-meansquare (LMS algorithm which is based on well-known cost functions, which is the mean-squared error (MSE adapted for FBMC system with offset QAM modulation (OQAM. This leads to a per-subchannel adaptive equalizer solution with low complexity. The proposed simulations have used practical channel information based on the International Telecommunications Union (ITU Standards. Moreover, we will discuss how the proposed algorithm will optimize and evaluate the convergence characteristic curves of LMS equalization algorithm per-subcarrier.

  8. Homogeneous DNA Detection Based on Fluorescence Quenching by Nanoparticles in Single-step Format :Target-Induced Configuration Transform

    Institute of Scientific and Technical Information of China (English)

    ZHANG,Songbai; WU,Zaisheng; XIE,Ming; SHEN,Guoli; YU,Ruqin

    2009-01-01

    A new strategy for homogeneous detection of DNA hybridization in single-step format was developed based on fluorescence quenching by gold nanoparticles.The gold nanoparticle is functionalized with 5'-thiolated 48-base oligonucleotide(probe sequence),whose 3'-terminus is labeled with fluorescein(FAM),a negatively charged fluo-rescencc dye.The oligonucleotide adopts all extended configuration due to the electrostatic repulsion between nega-tively charged gold nanoparticle and the FAM-attached probe sequence.After addition of the complementary target sequence,specific DNA hybridization induces a conformation change of the probe from an extended stmcture to an arch.1ike configuration,which brings the fluorophore and the gold nanoparticle in close proximity.The fluorescence is efficiently quenched by gold nanoparticles.The fluorescence quenching efficiency is related to the target concen.tration,which allows the quantitative detection for target sequence in a sample.A linear detection range from 1.6 to 209.4 nmoI/L Was obtained under the optimized experimental conditions with a detection limit of 0.1 nmol,L.In the assay system,the gold nanoparticles act as both nanoscaffolds and nanoquenchers.Furthermore,the proposed strategy.in which only two DNA sequences arc involved,is not only different from the traditional molecular bea-cons or reverse molecular beacons but also different from the commonly used sandwich hybridization methods.In addition,the DNA hybridization detection was achieved in homogenous solution in a single-step format,which al-lows real.time detection and quantification with other advantages such as easy operation and elimination of washing steps.

  9. A novel metric for bone marrow cells chromosome pairing.

    Science.gov (United States)

    Khmelinskii, Artem; Ventura, Rodrigo; Sanches, João

    2010-06-01

    Karyotyping is a set of procedures, in the scope of the cytogenetics, that produces a visual representation of the 46 chromosomes observed during the metaphase step of the cellular division, called mitosis, paired and arranged in decreasing order of size. Automatic pairing of bone marrow cells is a difficult task because these chromosomes appear distorted, overlapped, and their images are usually blurred with undefined edges and low level of detail. In this paper, a new metric is proposed to compare this type of chromosome images toward the design of an automatic pairing algorithm for leukemia diagnostic purposes. Besides the features used in the traditional karyotyping procedures, a new feature, based on mutual information , is proposed to increase the discriminate power of the G-banding pattern dissimilarity between chromosomes and improve the performance of the classifier. The pairing algorithm is formulated as a combinatorial optimization problem where the distances between homologous chromosomes are minimized and the distances between nonhomologous ones are maximized. The optimization task is solved by using an integer programming approach. A new bone marrow chromosome dataset--Lisbon-K1 (LK1) chromosome dataset with 9200 chromosomes---was build for this study. These chromosomes have much lower quality than the classic Copenhagen, Edinburgh, and Philadelphia datasets, and its classification and pairing is therefore more difficult. Experiments using real images from the LK(1) and Grisan et al. datasets based on a leave-one-out cross-validation strategy are performed to test and validate the pairing algorithm. PMID:20172790

  10. Double side multicrystalline silicon passivation by one step stain etching-based porous silicon

    Energy Technology Data Exchange (ETDEWEB)

    Mohamed, Seifeddine Belhadj; Ben Rabha, Mohamed; Bessais, Brahim [Laboratoire de Photovoltaique, Centre de Recherches et des Technologies de l' Energie, Technopole de Borj-Cedria, BP 95, 2050 Hammam-Lif (Tunisia)

    2012-10-15

    In this paper, we investigate the effect of stain etching-based porous silicon on the double side multicrystalline silicon. Special attention is given to the use of the stain etched PS as an antireflection coating as well as for surface passivating capabilities. Stain etching of double side multicrystalline silicon leads to the formation of PS nanostructures, that dramatically decrease the surface reflectivity from 30% to about 7% and increase the effective lifetime from 1 {mu}s to 10 {mu}s at a minority carrier density ({Delta}n) of 10{sup 15} cm{sup -3}. These results let us correlate the rise of the lifetime values to the photoluminescence intensity to the hydrogen and oxide passivation as shown by FTIR analysis. This low-cost PS formation process can be applied in the photovoltaic cell technology as a standard procedure (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  11. One step shift towards flexible supercapacitors based on carbon nanotubes - A review

    International Nuclear Information System (INIS)

    Supercapacitors have emerged as prominent energy storage devices that offer high energy density compared to conventional capacitors and high power density which is not found in batteries. Carbon nanotubes (CNTs) because of their high surface area and tremendous electrical properties are used as electrode material for supercapacitors. In this review we focused on the factors like surface area, role of the electrolyte and techniques adopted to improve performance of CNTs based supercapacitors. The supercapacitors are widely tested in liquid electrolytes which are normally hazardous in nature, toxic, flammable and their leakage has safety concerns. This review also focuses on research which is replacing these unsafe electrolytes by solid electrolytes with the combination of low cost CNTs deposited flexible supports for supercapacitors

  12. One step shift towards flexible supercapacitors based on carbon nanotubes - A review

    Energy Technology Data Exchange (ETDEWEB)

    Yar, A., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com; Dennis, J. O., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com; Mohamed, N. M., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com; Mumtaz, A., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com; Irshad, M. I., E-mail: asfandyarhargan@gmail.com, E-mail: johndennis@petronas.com.my, E-mail: noranimuti-mohamed@petronas.com.my, E-mail: asad-032@yahoo.com, E-mail: imrancssp@gmail.com [Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS (Malaysia); Ahmad, F., E-mail: ahmad-1234farooq@yahoo.com [Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS (Malaysia)

    2014-10-24

    Supercapacitors have emerged as prominent energy storage devices that offer high energy density compared to conventional capacitors and high power density which is not found in batteries. Carbon nanotubes (CNTs) because of their high surface area and tremendous electrical properties are used as electrode material for supercapacitors. In this review we focused on the factors like surface area, role of the electrolyte and techniques adopted to improve performance of CNTs based supercapacitors. The supercapacitors are widely tested in liquid electrolytes which are normally hazardous in nature, toxic, flammable and their leakage has safety concerns. This review also focuses on research which is replacing these unsafe electrolytes by solid electrolytes with the combination of low cost CNTs deposited flexible supports for supercapacitors.

  13. Analysing a reading strategy based on the elaboration of questions and the pair of answers and questions

    OpenAIRE

    Wilmo Ernesto Francisco Junior

    2011-01-01

    This paper describes a reading activity developed with chemistry students. The main aim was to analyse the reflections produced after reading three articles about experimentation. This study was performed with 17 chemistry students from a federal university. The reading strategy involved writing productions. Questions and the pair of questions and answers elaborated from articles were analysed, as well as the contribution of the socialization of knowledge by means of discussions and a debate....

  14. Temperature Dependence of the Average Energy Expended Per e-h Pair for Germanium-Based Dark Matter Experiments

    OpenAIRE

    Wei, W. -Z.; Wang, L.; Mei, D.-M.

    2016-01-01

    We report a new method to determine the temperature-dependent average energy expended per electron-hole (e-h) pair, $\\varepsilon$, for germanium detectors. As a result, the Fano factor and $\\varepsilon$ can be determined separately. Subsequently, we illustrate the variation of $\\varepsilon$ as a function of temperature. The impact of $\\varepsilon$ on the energy threshold and energy scale for germanium detectors at a given temperature is evaluated.

  15. Estimation of the Contribution of Intrinsic Currents to Motoneuron Firing Based on Paired Motoneuron Discharge Records in the Decerebrate Cat

    OpenAIRE

    Powers, Randall K.; Nardelli, Paul; Cope, T. C.

    2008-01-01

    Motoneuron activation is strongly influenced by persistent inward currents (PICs) flowing through voltage-sensitive channels. PIC characteristics and their contribution to the control of motoneuron firing rate have been extensively described in reduced animal preparations, but their contribution to rate modulation in human motoneurons is controversial. It has recently been proposed that the analysis of discharge records of a simultaneously recorded pair of motor units can be used to make quan...

  16. Multiple regression approach to mapping of quantitative trait loci (QTL) based on sib-pair data: a theoretical analysis

    OpenAIRE

    Xiong, Momiao; Guo, Sunwei

    2000-01-01

    The interval mapping method has been shown to be a powerful tool for mapping QTL. However, it is still a challenge to perform a simultaneous analysis of several linked QTLs, and to isolate multiple linked QTLs. To circumvent these problems, multiple regression analysis has been suggested for experimental species. In this paper, the multiple regression approach is extended to human sib-pair data through multiple regression of the squared difference in trait values between two...

  17. Step-by-Step Design of an FPGA-Based Digital Compensator for DC/DC Converters Oriented to an Introductory Course

    Science.gov (United States)

    Zumel, P.; Fernandez, C.; Sanz, M.; Lazaro, A.; Barrado, A.

    2011-01-01

    In this paper, a short introductory course to introduce field-programmable gate array (FPGA)-based digital control of dc/dc switching power converters is presented. Digital control based on specific hardware has been at the leading edge of low-medium power dc/dc switching converters in recent years. Besides industry's interest in this topic, from…

  18. Microfluidics-based single-step preparation of injection-ready polymeric nanosystems for medical imaging and drug delivery

    Science.gov (United States)

    Liu, Kegang; Zhu, Zhen; Wang, Xueya; Gonçalves, Daniel; Zhang, Bei; Hierlemann, Andreas; Hunziker, Patrick

    2015-10-01

    Translation of therapeutic polymeric nanosystems to patients and industry requires simplified, reproducible and scalable methods for assembly and loading. A single-step in-line process based on nanocoprecipitation of oxazoline-siloxane block copolymers in flow-focusing poly(dimethylsiloxane) microfluidics was designed to manufacture injection-ready nanosystems. Nanosystem characteristics could be controlled by copolymer concentration, block length and chemistry, microchannel geometry, flow rate, aqueous/organic flow rate ratio and payload concentration. The well-tolerated nanosystems exhibited differential cell binding and payload delivery and could confer sensitivity to photodynamic therapy to HeLa cancer cells. Such injection-ready nanosystems carrying drugs, diagnostic or functional materials may facilitate translation to clinical application.Translation of therapeutic polymeric nanosystems to patients and industry requires simplified, reproducible and scalable methods for assembly and loading. A single-step in-line process based on nanocoprecipitation of oxazoline-siloxane block copolymers in flow-focusing poly(dimethylsiloxane) microfluidics was designed to manufacture injection-ready nanosystems. Nanosystem characteristics could be controlled by copolymer concentration, block length and chemistry, microchannel geometry, flow rate, aqueous/organic flow rate ratio and payload concentration. The well-tolerated nanosystems exhibited differential cell binding and payload delivery and could confer sensitivity to photodynamic therapy to HeLa cancer cells. Such injection-ready nanosystems carrying drugs, diagnostic or functional materials may facilitate translation to clinical application. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03543k

  19. A Knowledge-Based Step Length Estimation Method Based on Fuzzy Logic and Multi-Sensor Fusion Algorithms for a Pedestrian Dead Reckoning System

    Directory of Open Access Journals (Sweden)

    Ying-Chih Lai

    2016-05-01

    Full Text Available The demand for pedestrian navigation has increased along with the rapid progress in mobile and wearable devices. This study develops an accurate and usable Step Length Estimation (SLE method for a Pedestrian Dead Reckoning (PDR system with features including a wide range of step lengths, a self-contained system, and real-time computing, based on the multi-sensor fusion and Fuzzy Logic (FL algorithms. The wide-range SLE developed in this study was achieved by using a knowledge-based method to model the walking patterns of the user. The input variables of the FL are step strength and frequency, and the output is the estimated step length. Moreover, a waist-mounted sensor module has been developed using low-cost inertial sensors. Since low-cost sensors suffer from various errors, a calibration procedure has been utilized to improve accuracy. The proposed PDR scheme in this study demonstrates its ability to be implemented on waist-mounted devices in real time and is suitable for the indoor and outdoor environments considered in this study without the need for map information or any pre-installed infrastructure. The experiment results show that the maximum distance error was within 1.2% of 116.51 m in an indoor environment and was 1.78% of 385.2 m in an outdoor environment.

  20. The Healthy Steps Study: A randomized controlled trial of a pedometer-based Green Prescription for older adults. Trial protocol

    Directory of Open Access Journals (Sweden)

    Schluter Philip J

    2009-11-01

    Full Text Available Abstract Background Graded health benefits of physical activity have been demonstrated for the reduction of coronary heart disease, some cancers, and type-2 diabetes, and for injury reduction and improvements in mental health. Older adults are particularly at risk of physical inactivity, and would greatly benefit from successful targeted physical activity interventions. Methods/Design The Healthy Steps study is a 12-month randomized controlled trial comparing the efficacy of a pedometer-based Green Prescription with the conventional time-based Green Prescription in increasing and maintaining physical activity levels in low-active adults over 65 years of age. The Green Prescription interventions involve a primary care physical activity prescription with 3 follow-up telephone counselling sessions delivered by trained physical activity counsellors over 3 months. Those in the pedometer group received a pedometer and counselling based around increasing steps that can be monitored on the pedometer, while those in the standard Green Prescription group received counselling using time-based goals. Baseline, 3 month (end of intervention, and 12 month measures were assessed in face-to-face home visits with outcomes measures being physical activity (Auckland Heart Study Physical Activity Questionnaire, quality of life (SF-36 and EQ-5D, depressive symptoms (Geriatric Depression Scale, blood pressure, weight status, functional status (gait speed, chair stands, and tandem balance test and falls and adverse events (self-report. Utilisation of health services was assessed for the economic evaluation carried out alongside this trial. As well, a process evaluation of the interventions and an examination of barriers and motives for physical activity in the sample were conducted. The perceptions of primary care physicians in relation to delivering physical activity counselling were also assessed. Discussion The findings from the Healthy Steps trial are due in late

  1. A one-step method of designing an observer-based modified repetitive-control system

    Science.gov (United States)

    Zhou, Lan; She, Jinhua; Wu, Min

    2015-10-01

    A method of designing a robust observer-based modified repetitive-control system for a class of strictly proper linear plants with periodic uncertainties has been developed. These plants have no direct path from the input to the output. First, the periodicity and continuity of repetitive control are exploited to construct a continuous-discrete two-dimensional (2D) model that allows the preferential adjustment of control and learning through regulation of the 2D feedback gains. Next, Lyapunov stability theory and the singular-value decomposition of the output matrix are used to establish two stability conditions. The conditions convert (a) the problem of designing the maximum cut-off angular frequency of the low-pass filter into a standard generalised eigenvalue optimisation problem, and (b) the problem of independently designing a state observer and a stabilising controller into a feasibility problem for linear matrix inequalities (LMIs). Two tuning parameters in one of the LMIs determine the selection of the 2D feedback gains. Then, the combination of two design conditions yields an iterative algorithm that simultaneously optimises the maximum cut-off angular frequency of the low-pass filter and the gains of the stabilising controller. It solves the trade-off problem between stability and tracking performance. Finally, a simulation example demonstrates the validity of the method.

  2. Systematic exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the expansion of the genetic alphabet

    Czech Academy of Sciences Publication Activity Database

    Dhami, K.; Malyshev, D. A.; Ordoukhanian, P.; Kubelka, Tomáš; Hocek, Michal; Romesberg, F. E.

    2014-01-01

    Roč. 42, č. 16 (2014), s. 10235-10244. ISSN 0305-1048 R&D Projects: GA ČR GBP206/12/G151 Institutional support: RVO:61388963 Keywords : unnatural base pairs * DNA * dTPT3-dNaM Subject RIV: CE - Biochemistry Impact factor: 9.112, year: 2014 http://nar.oxfordjournals.org/content/42/16/10235

  3. DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental-Theoretical Case Study of the AT Homo-Oligonucleotide.

    Science.gov (United States)

    Di Meo, Florent; Pedersen, Morten N; Rubio-Magnieto, Jenifer; Surin, Mathieu; Linares, Mathieu; Norman, Patrick

    2015-02-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment. PMID:26261947

  4. Transcription modulation in vitro of the fibroin gene exerted by a 200-base-pair region upstream from the "TATA" box.

    OpenAIRE

    Tsuda, M; Suzuki, Y

    1983-01-01

    We have previously reported that the 5'-flanking sequence upstream from the "TATA" box modulates the faithful transcription initiation of the fibroin gene in a homologous whole cell extract prepared from the silk glands, whereas such a modulating effect is not observed in a HeLa cell extract. Subsequently we have determined that major signals responsible for the modulating effect are located within a 200-base-pair region upstream from the TATA box, mainly in a distal region between nucleotide...

  5. Growing Right Onto Wellness (GROW): A Family-Centered, Community-Based Obesity Prevention Randomized Controlled Trial for Preschool Child-Parent Pairs

    OpenAIRE

    Po’e, Eli K.; Heerman, William J.; Mistry, Rishi S.; Barkin, Shari L.

    2013-01-01

    Growing Right Onto Wellness (GROW) is a randomized controlled trial that tests the efficacy of a family-centered, community-based, behavioral intervention to prevent childhood obesity among preschool-aged children. Focusing on parent-child pairs, GROW utilizes a multi-level framework, which accounts for macro (i.e., built-environment) and micro (i.e., genetics) level systems that contribute to the childhood obesity epidemic.

  6. First Steps Toward K-12 Teacher Professional Development Using Internet-based Telescopes

    Science.gov (United States)

    Berryhill, K. J.; Gershun, D.; Slater, T. F.; Armstrong, J. D.

    2012-12-01

    How can science teachers become more familiar with emerging technology, excite their students and give students a taste of astronomy research? Astronomy teachers do not always have research experience, so it is difficult for them to convey to students how researchers use telescopes. The nature of astronomical observation (e.g., remote sites, expensive equipment, and odd hours) has been a barrier to providing teachers with insight into the process. Robotic telescopes (operated automatically with queued observing schedules) and remotely controlled telescopes (controlled by the user via the Internet) allow scientists to conduct observing sessions on research-grade telescopes half a world away. The same technology can now be harnessed by STEM educators to engage students and reinforce what is being taught in the classroom, as seen in some early research in elementary schools (McKinnon and Mainwaring 2000 and McKinnon and Geissinger 2002), and middle/high schools (Sadler et al. 2001, 2007 and Gehret et al. 2005). However, teachers need to be trained to use these resources. Responding to this need, graduate students and faculty at the University of Wyoming and CAPER Center for Astronomy & Physics Education Research are developing teacher professional development programs using Internet-based telescopes. We conducted an online course in the science education graduate program at the University of Wyoming. This course was designed to sample different types of Internet-based telescopes to evaluate them as resources for teacher professional development. The 10 participants were surveyed at the end of the course to assess their experiences with each activity. In addition, pre-test/post-test data were collected focusing specifically on one of the telescopes (Gershun, Berryhill and Slater 2012). Throughout the course, the participants learned to use a variety of robotic and remote telescopes including SLOOH Space Camera (www.slooh.com), Sky Titan Observatory (www

  7. One step towards the fabrication of a nanoscale Si-nc based laser cavity

    International Nuclear Information System (INIS)

    In this paper, we report on the design of two major components of a laser architecture using Si-nc embedded in SiO2 as the optical gain medium and sub-wavelength periodic structures to form the resonant cavity. Dimensions of the structures have been matched to near-infrared wavelengths (∼850 nm) of the maximum photoluminescent emission where optical gain has been observed from Si-nc. Both the front (FM) and rear (RM) mirrors have been fabricated by the implantation of Si ions (50 keV, 2x1017 Si+/cm2) through a mask, in order to produce a Bragg reflector by optical index contrast between the implanted and the non-implanted zones. Two closely spaced Bragg reflectors are used in the FM structure to allow a narrow bandpass (partial transmission) centered at 850 nm. The implanted structures have been annealed to produce Si-nc and passivation. Scanning electron microscopy (SEM) images show that the design dimensions of the structure have been obtained. Characterization of the structures by laser excitation reveals an optical gap in both mirrors between 825 and 870 nm, as per the design parameters. A quality factor Q∼95 and a reflectivity R∼0.2 have been measured for the FM. These results support the concept that a complete Si-nc based laser cavity can be built to emit coherent light. - Research Highlights: → Ion implantation through a mask has been used to produce sub-wavelength periodic structures. → Bragg mirror has been tested as a part of Si-nanocrystals' laser architecture. → Numerical simulations have revealed an optical band gap as per the design parameters.

  8. Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing

    Science.gov (United States)

    Lee, Myeong H.; Sankey, Otto F.

    2009-01-01

    We report a first-principles study of electron ballistic transport through a molecular junction containing deoxycytidine-monophosphate (dCMP) connected to metal electrodes. A guanidinium ion and guanine nucleobase are tethered to gold electrodes on opposite sides to form hydrogen bonds with the dCMP molecule providing an electric circuit. The circuit mimics a component of a potential device for sequencing unmodified single-stranded DNA. The molecular conductance is obtained from DFT Green's function scattering methods and is compared to estimates from the electron tunneling decay constant obtained from the complex band structure. The result is that a complete molecular dCMP circuit of 'linker((CH2)2)-guanidinium-phosphate-deoxyribose-cytosine-guanine' has a very low conductance (of the order of fS) while the hydrogen-bonded guanine-cytosine base-pair has a moderate conductance (of the order of tens to hundreds of nS). Thus, while the transverse electron transfer through base-pairing is moderately conductive, electron transfer through a complete molecular dCMP circuit is not. The gold Fermi level is found to be aligned very close to the HOMO for both the guanine-cytosine base-pair and the complete molecular dCMP circuit. Results for two different plausible geometries of the hydrogen-bonded dCMP molecule reveal that the conductance varies from fS for an extended structure to pS for a slightly compressed structure.

  9. Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes – A comparative study of group-I intron structures

    Indian Academy of Sciences (India)

    K Chandrasekhar; R Malathi

    2003-09-01

    In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non-Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.

  10. Observation of H-bond mediated 3hJH2H3coupling constants across Watson-Crick AU base pairs in RNA

    International Nuclear Information System (INIS)

    3hJH2H3trans-hydrogen bond scalar coupling constants have been observed for the first time in Watson-Crick AU base pairs in uniformly 15N-labeled RNA oligonucleotides using a new 2hJNN-HNN-E. COSY experiment. The experiment utilizes adenosine H2 (AH2) for original polarization and detection, while employing 2hJNNcouplings for coherence transfer across the hydrogen bonds (H-bonds). The H3 protons of uracil bases are unperturbed throughout the experiment so that these protons appear as passive spins in E. COSY patterns. 3hJH2H3coupling constants can therefore be accurately measured in the acquisition dimension from the displacement of the E. COSY multiplet components, which are separated by the relatively large 1JH3N3coupling constants in the indirect dimension of the two-dimensional experiment. The 3hJH2H3scalar coupling constants determined for AU base pairs in the two RNA hairpins examined here have been found to be positive and range in magnitude up to 1.8 Hz. Using a molecular fragment representation of an AU base pair, density functional theory/finite field perturbation theory (DFT/FPT) methods have been applied to attempt to predict the relative contributions of H-bond length and angular geometry to the magnitude of 3hJH2H3coupling constants. Although the DFT/FPT calculations did not reproduce the full range of magnitude observed experimentally for the 3hJH2H3coupling constants, the calculations do predict the correct sign and general trends in variation in size of these coupling constants. The calculations suggest that the magnitude of the coupling constants depends largely on H-bond length, but can also vary with differences in base pair geometry. The dependency of the 3hJH2H3coupling constant on H-bond strength and geometry makes it a new probe for defining base pairs in NMR studies of nucleic acids

  11. One Step Forward--Half a Step Back: A Status Report on Bias-Based Bullying of Asian American Students in New York City Schools

    Science.gov (United States)

    Asian American Legal Defense and Education Fund, 2013

    2013-01-01

    In September 2008, Mayor Michael Bloomberg and former Schools Chancellor, Joel Klein announced Chancellor's Regulation A-832, which established policies and procedures on how New York City schools should respond to bias-based harassment, intimidation, and bullying in schools. The Asian American Legal Defense and Education Fund (AALDEF), the…

  12. Gadolinium trace determination in biomedical samples by diode-laser-based multi-step resonance ionization mass spectrometry

    International Nuclear Information System (INIS)

    Diode laser based multi-step resonance ionization mass spectrometry (RIMS), which has been developed primarily for ultra trace analysis of long lived radioactive isotopes has been adapted for the application to elements within the sequence of the rare earths. First investigations concern Gd isotopes. Here high suppression of isobars, as provided by RIMS, is mandatory. Using a three step resonant excitation scheme into an autoionizing state, which has been the subject of preparatory spectroscopic investigations, high efficiency of >1x10-6 and good isobaric selectivity >107 was realized. Additionally the linearity of the method has been demonstrated over six orders of magnitude. Avoiding contaminations from the Titanium-carrier foil resulted in a suppression of background of more than one order of magnitude and a correspondingly low detection limit of 4x109 atoms, equivalent to lpg of Gd. The technique has been applied for trace determination of the Gd-content in animal tissue. Bio-medical micro samples were analyzed shortly after Gd-chelat, which is used as the primary contrast medium for magnetic resonance imaging (MRI) in biomedical investigations, has been injected. Correlated in-vivo magnetic resonance images have been taken. The RIMS measurements show high reproducibility as a well as good precision, and contribute to new insight into the distribution and kinetics of Gd within different healthy and cancerous tissues

  13. Fueling our future: four steps to a new, reliable, cleaner, decentralized energy supply based on hydrogen and fuel cells

    International Nuclear Information System (INIS)

    'Full text:' This manuscript demonstrates the possible driving factors and necessary elements needed to move Hydrogen and Fuel Cells (H2/FC) to worldwide commercialisation. Focusing not only on the technology itself, we look at the 'bigger picture' explaining how certain trends have impacted the progress of new technologies developments in the past. In this process, the consumer has played and will continue to play the key and leading role. We also examine different Distributed Generation scenarios including distributed generation via fuel cells for automotive applications which may be the catalyst to the Hydrogen Economy. One possible step could be the use of Personal Power Cars equipped with Fuel Cells which not only drive on Hydrogen, but also supply (while standing) electricity /heat to residential and commercial buildings. With 1.3 billion potential customers, P.R. China is one country where such a scenario may fit. The up-and-coming Chinese H2/FC industry deals with applied fundamental research such as advances in Hydrogen production from Natural Gas, Methanol and Gasoline. The current activities in P.R. China certain to further accelerate the trend towards the coming Hydrogen Economy, together with the steps necessary to achieve a new reliable, cleaner and decentralized Energy Supply based on H2/FC are examined. (author)

  14. Average Energy Expended Per e-h Pair and Energy Scale Function for Germanium-Based Dark Matter Experiments

    CERN Document Server

    Wei, W -Z; Mei, D -M

    2016-01-01

    We report a new method to determine the temperature-dependent average energy expended per electron-hole (e-h) pair, $\\varepsilon$, for germanium detectors. As a result, the Fano factor and $\\varepsilon$ can be determined separately. Subsequently, we illustrate the variation of $\\varepsilon$ as a function of temperature. The impact of $\\varepsilon$ on the energy threshold and energy scale for germanium detectors at a given temperature is evaluated. We demonstrate an absolute energy scale function of low-energy recoils for germanium detectors in the direct detection of dark matter particles.

  15. Atomic-Level Organization of Vicinal Acid-Base Pairs through the Chemisorption of Aniline and Derivatives onto Mesoporous SBA15

    KAUST Repository

    Basset, Jean-Marie

    2016-06-09

    The design of novel heterogeneous catalysts with multiple adjacent functionalities is of high interest for heterogeneous catalysis. Herein, we report a method to obtain a majority bifunctional acid-base pairs on SBA15. Aniline reacts with SBA15 by opening siloxane bridges leading to N-phenylsilanamine-silanol pairs. In contrast with ammonia treated surfaces, the material is stable under air/moisture. Advanced solid state MAS NMR: 2D ¹H-¹H double-quantum, ¹H-¹³C HETCOR experiments and dynamic nuclear polarization enhanced ²⁹Si and ¹⁵N spectra demonstrate both the close proximity between the two moieties and the formation of a covalent Si-N surface bond and confirm the design of vicinal acid-base pairs. This approach was successfully applied to the design of a series of aniline derivatives bifunctional SBA15. A correlation of the substituents effects on the aromatic ring (Hammet parameters) on the kinetics of the model reaction of Knoevenagel is observed.

  16. Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

    Directory of Open Access Journals (Sweden)

    Sándor Suhai

    2003-09-01

    Full Text Available Abstract: The structure of two isomeric stacked dimers of Watson-Crick 9-methyladenine-1-methylthymine pairs was fully optimized using an approximate density functional theory (DFT method augmented with an empirical dispersion interaction. The results of the calculations reveal that head-to-tail (AT-TA and head-to-head (AT-AT dimers possess a significantly different geometry. The structure of both complexes is stabilized by vertical CH…O and C-H…N hydrogen bonds with the participation of the hydrogen atoms of the methyl groups. The energy of hydrogen bonding and stacking interactions was additionally calculated using the MP2/6-31G*(0.25 method. Differences in the mutual arrangement of the base pairs in two isomeric dimers lead to significant changes of intra and interstrand stacking interaction energies.

  17. Fiber-based photon-pair source capable of hybrid entanglement in frequency and transverse mode, controllably scalable to higher dimensions

    Science.gov (United States)

    Cruz-Delgado, D.; Ramirez-Alarcon, R.; Ortiz-Ricardo, E.; Monroy-Ruz, J.; Dominguez-Serna, F.; Cruz-Ramirez, H.; Garay-Palmett, K.; U’Ren, A. B.

    2016-01-01

    We have designed and implemented a photon-pair source, based on the spontaneous four wave mixing (SFWM) process in a few-mode fiber, in a geometry which permits multiple, simultaneous SFWM processes, each associated with a distinct combination of transverse modes for the four participating waves. In our source: i) each process is group-velocity-matched so that it is, by design, nearly-factorable, and ii) the spectral separation between neighboring processes is greater than the marginal spectral width of each process. Consequently, there is a direct correspondence between the joint amplitude of each process and each of the Schmidt mode pairs of the overall two-photon state. Our approach permits hybrid entanglement in discrete frequency and in transverse mode, whereby control of the number of supported fiber transverse modes allows scalability to higher dimensions while spectral filtering may be used for straightforward Schmidt mode discrimination. PMID:27271284

  18. Fiber-based photon-pair source capable of hybrid entanglement in frequency and transverse mode, controllably scalable to higher dimensions

    Science.gov (United States)

    Cruz-Delgado, D.; Ramirez-Alarcon, R.; Ortiz-Ricardo, E.; Monroy-Ruz, J.; Dominguez-Serna, F.; Cruz-Ramirez, H.; Garay-Palmett, K.; U’Ren, A. B.

    2016-06-01

    We have designed and implemented a photon-pair source, based on the spontaneous four wave mixing (SFWM) process in a few-mode fiber, in a geometry which permits multiple, simultaneous SFWM processes, each associated with a distinct combination of transverse modes for the four participating waves. In our source: i) each process is group-velocity-matched so that it is, by design, nearly-factorable, and ii) the spectral separation between neighboring processes is greater than the marginal spectral width of each process. Consequently, there is a direct correspondence between the joint amplitude of each process and each of the Schmidt mode pairs of the overall two-photon state. Our approach permits hybrid entanglement in discrete frequency and in transverse mode, whereby control of the number of supported fiber transverse modes allows scalability to higher dimensions while spectral filtering may be used for straightforward Schmidt mode discrimination.

  19. Preparation of Thermo-Responsive Poly(ionic liquids-Based Nanogels via One-Step Cross-Linking Copolymerization

    Directory of Open Access Journals (Sweden)

    Jing Zhang

    2015-09-01

    Full Text Available In this study, thermo-responsive polymeric nanogels were facilely prepared via one-step cross-linking copolymerization of ethylene glycol dimethacrylate/divinylbenzene and ionic liquid (IL-based monomers, 1,n-dialkyl-3,3′-bis-1-vinyl imidazolium bromides ([CnVIm]Br; n = 6, 8, 12 in selective solvents. The results revealed that stable and blue opalescent biimidazolium (BIm-based nanogel solutions could be obtained without any precipitation when the copolymerizations were conducted in methanol. Most importantly, these novel nanogels were thermo-response, and could reversibly transform to precipitation in methanol with temperature changes. Turbidity analysis and dynamic light scatting (DLS measurement illustrated that PIL-based nanogel solutions presented the phase transform with upper critical solution temperature (UCST in the range of 5–25 °C. The nanogels were characterized using Fourier transform infrared (FTIR, thermogravimetric analyses (TGA, and scanning electron microscopy (SEM. In addition, BIm-based nanogels could also be used as highly active catalysts in the cycloaddition reaction of CO2 and epoxides. As a result, our attributes build a robust platform suitable for the preparation of polymeric nanomaterials, as well as CO2 conversion.

  20. Dislocation network with pair-coupling structure in {111} γ/γ' interface of Ni-based single crystal superalloy.

    Science.gov (United States)

    Ru, Yi; Li, Shusuo; Zhou, Jian; Pei, Yanling; Wang, Hui; Gong, Shengkai; Xu, Huibin

    2016-01-01

    The γ/γ' interface dislocation network is reported to improve the high temperature creep resistance of single crystal superalloys and is usually found to deposit in {001} interface. In this work, a new type of dislocation network was found in {111} γ/γ' interface at a single crystal model superalloy crept at 1100 °C/100 MPa. The dislocations in the network are screw with Burgers vectors of 1/2 a and most interestingly, they exhibit a pair-coupling structure. Further investigation indicates that the formation of {111} interface dislocation network occurs when the γ' raft structure begins to degrade by the dislocations cutting into the rafted γ' through the interface. In this condition, the pair-coupling structure is established by the dislocations gliding in a single {111} plane of γ', in order to remove the anti-phase boundary in γ'; these dislocations also act as diffusion channels for dissolving of the γ' particle that is unstable under the interfacial stress from lattice misfit, which leads to the formation of {111}-type zigzag interface. The formation of this network arises as a consequence of more negative misfit, low-alloying γ' particle and proper test conditions of temperature and stress. PMID:27511822

  1. Synthesis and integration of Fe-soc-MOF cubes into colloidosomes via a single-step emulsion-based approach

    KAUST Repository

    Pang, Maolin

    2013-07-17

    Bottom-up fabrication of complex 3D hollow superstructures from nonspherical building blocks (BBs) poses a significant challenge for scientists in materials chemistry and physics. Spherical colloidal silica or polystyrene particles are therefore often integrated as BBs for the preparation of an emerging class of materials, namely colloidosomes (using colloidal particles for Pickering stabilization and fusing them to form a permeable shell). Herein, we describe for the first time a one-step emulsion-based technique that permits the assembly of metal-organic framework (MOF) faceted polyhedral BBs (i.e., cubes instead of spheres) into 3D hollow superstructures (or "colloidosomes" ). The shell of each resultant hollow MOF colloidosome is constructed from a monolayer of cubic BBs, whose dimensions can be precisely controlled by varying the amount of emulsifier used in the synthesis. © 2013 American Chemical Society.

  2. One-step fabrication of 3D silver paste electrodes into microfluidic devices for enhanced droplet-based cell sorting

    Directory of Open Access Journals (Sweden)

    Lang Rao

    2015-05-01

    Full Text Available 3D microelectrodes are one-step fabricated into a microfluidic droplet separator by filling conductive silver paste into PDMS microchambers. The advantages of 3D silver paste electrodes in promoting droplet sorting accuracy are systematically demonstrated by theoretical calculation, numerical simulation and experimental validation. The employment of 3D electrodes also helps to decrease the droplet sorting voltage, guaranteeing that cells encapsulated in droplets undergo chip-based sorting processes are at better metabolic status for further potential cellular assays. At last, target droplet containing single cell are selectively sorted out from others by an appropriate electric pulse. This method provides a simple and inexpensive alternative to fabricate 3D electrodes, and it is expected our 3D electrode-integrated microfluidic droplet separator platform can be widely used in single cell operation and analysis.

  3. S-1-Based versus capecitabine-based preoperative chemoradiotherapy in the treatment of locally advanced rectal cancer: a matched-pair analysis.

    Directory of Open Access Journals (Sweden)

    Meng Su

    Full Text Available OBJECTIVE: The aim of this paper was to compare the efficacy and safety of S-1-based and capecitabine-based preoperative chemoradiotherapy regimens in patients with locally advanced rectal cancer through a retrospective matched-pair analysis. MATERIALS AND METHODS: Between Jan 2010 and Mar 2014, 24 patients with locally advanced rectal cancer who received preoperative radiotherapy concurrently with S-1 were individually matched with 24 contemporary patients with locally advanced rectal cancer who received preoperative radiotherapy concurrently with capecitabine according to clinical stage (as determined by pelvic magnetic resonance imaging and computed tomography and age (within five years. All these patients performed mesorectal excision 4-8 weeks after the completion of chemoradiotherapy. RESULTS: The tumor volume reduction rates were 55.9±15.1% in the S-1 group and 53.8±16.0% in the capecitabine group (p = 0.619. The overall downstaging, including both T downstaging and N downstaging, occurred in 83.3% of the S-1 group and 70.8% of the capecitabine group (p = 0.508. The significant tumor regression, including regression grade I and II, occurred in 33.3% of S-1 patients and 25.0% of capecitabine patients (p = 0.754. In the two groups, Grade 4 adverse events were not observed and Grade 3 consisted of only two cases of diarrhea, and no patient suffered hematologic adverse event of Grade 2 or higher. However, the incidence of diarrhea (62.5% vs 33.3%, p = 0.014 and hand-foot syndrome (29.2% vs 0%, p = 0.016 were higher in capecitabine group. Other adverse events did not differ significantly between two groups. CONCLUSIONS: The two preoperative chemoradiotherapy regimens were effective and safe for patients of locally advanced rectal cancer, but regimen with S-1 exhibited a lower incidence of adverse events.

  4. First Step Towards a Non-Adiabatic Description of the Fission Process Based on the Generator Coordinate Method

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, R; Goutte, H; Gogny, D; Dubray, N; Lacroix, D

    2009-11-24

    Among the different theoretical approaches able to describe fission, microscopic ones can help us in the understanding of this process, as they have the advantage of describing the nuclear structure and the dynamics in a consistent manner. The sole input of the calculations is the nucleon-nucleon interaction. Such a microscopic time-dependent and quantum mechanical formalism has already been used, based on the Gaussian Overlap Approximation of the Generator Coordinate Method with the adiabatic approximation, to analyze the collective dynamics of low-energy fission in {sup 238}U. However, at higher energies, a few MeV above the barrier, the adiabatic approximation doesn't seem valid anymore. Indeed, manifestations of proton pair breaking have been observed in {sup 238}U and {sup 239}U for an excitation energy of 2.3 MeV above the barrier. Taking the intrinsic excitations into account during the fission process will enable us to determine the coupling between collective and intrinsic degrees of freedom, in particular from saddle to scission. Guidelines of the new formalism under development are presented and some preliminary results on overlaps between non excited and excited states are discussed.

  5. First step towards a non-adiabatic description of the fission process based on the Generator Coordinate Method

    Directory of Open Access Journals (Sweden)

    Lacroix D.

    2010-03-01

    Full Text Available Among the different theoretical approaches able to describe fission, microscopic ones can help us in the understanding of this process, as they have the advantage of describing the nuclear structure and the dynamics in a consistent manner. The sole input of the calculations is the nucleon-nucleon interaction. Such a microscopic time-dependent and quantum mechanical formalism has already been used, based on the Gaussian Overlap Approximation of the Generator Coordinate Method with the adiabatic approximation, to analyze the collective dynamics of low-energy fission in 238U [1]. However, at higher energies, a few MeV above the barrier, the adiabatic approximation doesn’t seem valid anymore. Indeed, manifestations of proton pair breaking have been observed in 238U and 239U for an excitation energy of 2.3 MeV above the barrier [2–4]. Taking the intrinsic excitations into account during the fission process will enable us to determine the coupling between collective and intrinsic degrees of freedom, in particular from saddle to scission. Guidelines of the new formalism under development are presented and some preliminary results on overlaps between non excited and excited states are discussed.

  6. Adjoint of Pair Frames

    OpenAIRE

    Fereydooni, Abolhassan; Safapour, Ahmad; Rahimi , Asghar

    2012-01-01

    The concept of (p,q)-pair frames is generalized to (l,l^*)-pair frames. Adjoint (conjugate) of a pair frames for dual space of a Banach space is introduced and some conditions for the existence of adjoint (conjugate) of pair frames are presented.

  7. A 2-D process-based model for suspended sediment dynamics: a first step towards ecological modeling

    Science.gov (United States)

    Achete, F. M.; van der Wegen, M.; Roelvink, D.; Jaffe, B.

    2015-06-01

    In estuaries suspended sediment concentration (SSC) is one of the most important contributors to turbidity, which influences habitat conditions and ecological functions of the system. Sediment dynamics differs depending on sediment supply and hydrodynamic forcing conditions that vary over space and over time. A robust sediment transport model is a first step in developing a chain of models enabling simulations of contaminants, phytoplankton and habitat conditions. This works aims to determine turbidity levels in the complex-geometry delta of the San Francisco estuary using a process-based approach (Delft3D Flexible Mesh software). Our approach includes a detailed calibration against measured SSC levels, a sensitivity analysis on model parameters and the determination of a yearly sediment budget as well as an assessment of model results in terms of turbidity levels for a single year, water year (WY) 2011. Model results show that our process-based approach is a valuable tool in assessing sediment dynamics and their related ecological parameters over a range of spatial and temporal scales. The model may act as the base model for a chain of ecological models assessing the impact of climate change and management scenarios. Here we present a modeling approach that, with limited data, produces reliable predictions and can be useful for estuaries without a large amount of processes data.

  8. One Step Quick Detection of Cancer Cell Surface Marker by Integrated NiFe-based Magnetic Biosensing Cell Cultural Chip

    Institute of Scientific and Technical Information of China (English)

    Chenchen Bao; Lei Chen; Tao Wang; Chong Lei; Furong Tian; Daxiang Cui; Yong Zhou

    2013-01-01

    RGD peptides has been used to detect cell surface integrin and direct clinical effective therapeutic drug selection. Herein we report that a quick one step detection of cell surface marker that was realized by a specially designed NiFe-based magnetic biosensing cell chip combined with functionalized magnetic nanoparti-cles. Magnetic nanoparticles with 20-30 nm in diameter were prepared by coprecipitation and modified with RGD-4C, and the resultant RGD-functionalized magnetic nanoparticles were used for targeting cancer cells cul-tured on the NiFe-based magnetic biosensing chip and distinguish the amount of cell surface receptor-integrin. Cell lines such as Calu3, Hela, A549, CaFbr, HEK293 and HUVEC exhibiting different integrin expression were chosen as test samples. Calu3, Hela, HEK293 and HUVEC cells were successfully identified. This approach has advantages in the qualitative screening test. Compared with traditional method, it is fast, sensitive, low cost, easy-operative, and needs very little human intervention. The novel method has great potential in applications such as fast clinical cell surface marker detection, and diagnosis of early cancer, and can be easily extended to other biomedical applications based on molecular recognition.

  9. Volume holographic recording in photopolymerizable nanocomposite materials based on radical-mediated thiol-yne step-growth polymerizations

    Science.gov (United States)

    Mitsube, Ken; Nishimura, Yuki; Takayama, Shingo; Nagaya, Kohta; Tomita, Yasuo

    2013-05-01

    We propose the use of radical-mediated thiol-yne step-growth photopolymerizations for volume holographic recording in NPC films to overcome the drawback of low crosslinking densities but retain the advantage of low shrinkage in the thiol-ene photopolymerizations. The thiol-yne photopolymerization mechanism is different from the thiol-ene photopolymeriztions in the sense that each alkyne functional group can react consecutively with two thiol functional groups. We show that thiol-yne based NPC films dispersed with silica nanoparticles give the saturated refractive index change as large as 0.008 and the material recording sensitivity as high as 2005 cm/J at a wavelength of 532 nm, larger than the minimum acceptable values of 0.005 and 500 cm/J, respectively, for holographic data storage. We also show that the shrinkage of a recorded hologram can be as low as that of thiol-ene based NPC films and that the thermal stability is improved better. In addition, we demonstrate digital data page recording in thiol-yne based NPC films, showing a low symbol error rate and a high signal-to-noise ratio to be 2.8×10-4 and 8, respectively.

  10. A pair of novel Cd(II) enantiomers based on lactate derivatives: Synthesis, crystal structures and properties

    Science.gov (United States)

    Xu, Zhong-Xuan; Ao, Ke-Hou; Zhang, Jian

    2016-09-01

    A pair of novel 3D homochiral metal-organic frameworks (HMOFs), namely [Cd2.5((R)-CIA)6(1,4-DIB)(H2O)2]·((CH3)2NH2)·H2O (1-D), [Cd2.5((S)-CIA)6(1,4-DIB)(H2O)2]·((CH3)2NH2)·H2O (1-L), have been synthesized using lactic acid derivative ligands ((R)-H3CIA and (S)-H3CIA) and 1,4-DIB. Crystallographic analyses indicate that the complexes 1-D and 1-L are packed by cage substructures. Some physical characteristics, such as solid-state circular dichroism (CD), thermal stabilities and photoluminescent properties are also investigated. Our results highlight the effective method to apply lactic acid derivative ligands to form interesting HMOFs.

  11. New Theoretical Insight into the Interactions and Properties of Formic Acid: Development of a Quantum-Based Pair Potential for Formic Acid.

    Energy Technology Data Exchange (ETDEWEB)

    Roszak, S; Gee, R; Balasubramanian, K; Fried, L

    2005-08-08

    We performed ab initio quantum chemical studies for the development of intra and intermolecular interaction potentials for formic acid for use in molecular dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter-molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment.

  12. New theoretical insight into the interactions and properties of formic acid: development of a quantum-based pair potential for formic acid.

    Science.gov (United States)

    Roszak, Szczepan; Gee, Richard H; Balasubramanian, Krishnan; Fried, Laurence E

    2005-10-01

    We performed ab initio quantum-chemical studies for the development of intra- and intermolecular interaction potentials for formic acid for use in molecular-dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen-bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular-dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular-dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment. PMID:16238411

  13. Key Roles of Lewis Acid-base Pairs on ZnxZryOz in Direct Ethanol/Acetone to Isobutene Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Junming; Baylon, Rebecca A.; Liu, Changjun; Mei, Donghai; Martin, Kevin J.; Venkitasubramanian, Padmesh; Wang, Yong

    2016-01-20

    The effects of surface acidity on the cascade ethanol-to-isobutene conversion were studied using ZnxZryOz catalysts. The ethanol-to-isobutene reaction was found to be limited by the secondary reaction of the key intermediate, acetone, namely the acetone-to-isobutene reaction. Although the catalysts with coexisting Brønsted acidity could catalyze the rate-limiting acetone-to-isobutene reaction, the presence of Brønsted acidity is also detrimental. First, secondary isobutene isomerization is favored, producing a mixture of butene isomers. Second, undesired polymerization and coke formation prevail, leading to rapid catalyst deactivation. Most importantly, both steady-state and kinetic reaction studies as well as FTIR analysis of adsorbed acetone-d6 and D2O unambiguously showed that a highly active and selective nature of balanced Lewis acid-base pairs was masked by the coexisting Brønsted acidity in the aldolization and self-deoxygenation of acetone to isobutene. As a result, ZnxZryOz catalysts with only Lewis acid-base pairs were discovered, on which nearly a theoretical selectivity to isobutene (~88.9%) was successfully achieved, which has never been reported before. Moreover, the absence of Brønsted acidity in such ZnxZryOz catalysts also eliminates the side isobutene isomerization and undesired polymerization/coke reactions, resulting in the production of high purity isobutene with significantly improved catalyst stability (< 2% activity loss after 200 h time-on-stream). This work not only demonstrates a balanced Lewis acid-base pair for the highly active and selective cascade ethanol-to-isobutene reaction, but also sheds light on the rational design of selective and robust acid-base catalyst for C-C coupling via aldolization reaction.

  14. The first photoexcitation step of ruthenium-based models for artificial photosynthesis highlighted by resonance Raman spectroscopy.

    Science.gov (United States)

    Herrmann, Carmen; Neugebauer, Johannes; Presselt, Martin; Uhlemann, Ute; Schmitt, Michael; Rau, Sven; Popp, Jürgen; Reiher, Markus

    2007-05-31

    Ruthenium-polypyridine and related complexes play an important role as models for light-harvesting antenna systems to be employed in artificial photosynthesis. In this theoretical and experimental work, the first photoexcitation step of a tetranuclear [Ru2Pd2] complex composed of two ruthenium-bipyridyl subunits and two palladium-based fragments, {[(tbbpy)2Ru(tmbi)]2[Pd(allyl)]2}2+ (tbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine, tmbi = 5,6,5',6'-tetramethyl-2,2'-bibenzimidazolate), is investigated by means of experimental and theoretical resonance Raman spectroscopy. The calculated spectra, which were obtained within the short-time approximation combined with time-dependent density functional theory (TDDFT), reproduce the experimental spectrum with excellent agreement. We also compared calculations on off-resonance Raman spectra, for which a completely different theoretical approach has to be used, to experimental ones and again found very good agreement. The [Ru2Pd2] complex represents the probably largest system for which a quantum chemical frequency analysis and a calculation of conventional Raman as well as resonance Raman spectra with reasonable basis sets have been performed. A comparison between the resonance Raman spectra of the [Ru2Pd2] complex and its mononuclear [Ru] building block [(tbbpy)2Ru(tmbi)]2+ and a normal-mode analysis reveal that the [Ru2Pd2] resonance Raman spectrum is composed uniquely from peaks arising from the [Ru] fragment. This observation and an analysis of the Kohn-Sham orbitals mainly involved in the initial electronic excitation in the TDDFT description of the [Ru2Pd2] system support the hypothesis that the initial photoexcitation step of [Ru2Pd2] is a charge-transfer excitation from the ruthenium atoms to the adjacent butyl-2,2'-bipyridine ligands. PMID:17489631

  15. Fueling our future: four steps to a new reliable, cleaner, decentralized energy supply based on Hydrogen and fuel cells

    International Nuclear Information System (INIS)

    In examining various market strategies, this presentation demonstrates the possible driving factors and necessary elements needed to move Hydrogen and Fuel Cells (H2/FC) to worldwide commercialisation. Focusing not only on the technology itself, this presentation looks at the 'bigger picture' explaining how certain trends have impacted the progress of new technologies developments in the past. The presentation demonstrates how these models can be applied to our present day situation. In this process, the consumer has played and will continue to play the key and leading role. Due to such strong influence, the consumer will ultimately fuel the future of H2/FC commercialisation by a desire for new and not yet discovered products and services. Examining different Distributed Generation scenarios, the catalyst to the Hydrogen Economy may be found through distributed generation via fuel cells. One possible step could be the use of Personal Power Cars equipped with Fuel Cells which not only drive on Hydrogen, but also supply (while standing) electricity /heat to residential and commercial buildings. The incentive for car owners driving and using these vehicles is twofold: either save (at his own home) or earn (at his office) money while their cars are parked and plugged into buildings via smart docking stations available at key parking sites. Cars parked at home in the garage will supply electricity to the homes and additionally, replace the function of the existing boiler. Car owners can earn money by selling the electricity generated (but not needed at that time) to the utilities and feed it into the existing electricity grid. The inter-dependability between supply and consumer-driven demand (or better, demand and supply) and other examples are explained. The steps necessary to achieve a new, reliable, cleaner and decentralized Energy Supply based on H2/FC are also presented and examined. (author)

  16. Non-enzymatic Glucose Biosensor Based on Cu/SWNTs Composite Film Fabricated by One-step Electrodeposition

    Institute of Scientific and Technical Information of China (English)

    SUN Fang; LIU Peng; LI Li; LIANYong-fu

    2011-01-01

    Based on the adsorption of copper ions on single-walled carbon nanotubes(SWNTs)in electrolyte,Cu/SWNTs nanocomposite film was initially prepared on indium-doped tin oxide(ITO)substrate by one-step electrodeposition.This method may provide a versatile and facile pathway to fabricate other SWNTs-supported metal composite films.Electrochemical experiments revealed that the obtained Cu/SWNTs/ITO electrode offered an excellent electrocatalytic activity towards the oxidation of glucose and could be applied to the construction of non-enzymatic glucose biosensor.The linear range of the sensor was 1.0× 10-6to 6.0× 10-4 mol/L and the response time was within 2 s.Particularly,its sensitivity reached as high as 1434.67 μA.L·mmol-1·cm-2,which was superior to any other non-enzymatic glucose biosensor based on copper-carbon nanotubes electrode reported previously.

  17. Three-dimensional paper-based slip device for one-step point-of-care testing

    Science.gov (United States)

    Han, Kwi Nam; Choi, Jong-Soon; Kwon, Joseph

    2016-05-01

    In this study, we developed a new type of paper-based analytical device (PAD), the three-dimensional (3D) slip-PAD, to detect infectious human norovirus for global healthcare. The 3D configuration of the papers combined with a slip design provides unique features and versatility that overcome the limitations of fluidic manipulation and sensitivity in point-of-care (POC) tests. The assay can be carried out in a single step based on a moveable slip design, making it suitable for unskilled users. The 3D fluidic network developed by layered construction of wax-patterned papers provides different fluidic paths for the sequential delivery of multiple fluids without the need for peripheral equipment. The release and mixing of enhancement reagents on the device improved the sensitivity and detection limit. The assay results could be visualized by naked eye within 10 min, with subsequent amplification of the signal over time (human norovirus. These results demonstrate that the 3D slip-PAD is a sensitive diagnostic assay for detecting human norovirus infection that is particularly suitable for POC testing in regions where resources are scarce.

  18. Antibody-Free Colorimetric Detection of Total Aflatoxins in Rice Based on a Simple Two-Step Chromogenic Reaction.

    Science.gov (United States)

    Du, Bibai; Su, Xiaoou; Yang, Kunhao; Pan, Long; Liu, Qingju; Gong, Lingling; Wang, Peilong; Yang, Jingkui; He, Yujian

    2016-04-01

    The prevalently used immunoassays for fast screening of aftatoxins (AFs) usually cannot meet the requirement for simultaneous determination of total AFs (aflatoxin B1 + aflatoxin B2 + aflatoxin G1 + aflatoxin G2) due to the deficiency of highly group-specific antibodies. This paper describes a two-step chromogenic reaction based method to quantitatively detect total AFs in rice using colorimetric measurement without antibody. In the method, colorless AFs transform into green-colored indophenol products through the reaction with sodium hydroxide and 2,6-dibromoquinone-4-chloroimide (DBQC) successively, allowing selectively determining total AFs up to 3.9 μg/kg over other competitive mycotoxins under optimal conditions by a UV-vis spectrophotometer. In addition, the colorimetric measurement results of the rice samples agree well with that of a standard HPLC method, demonstrating the good reliability and applicability of the method. Uniquely, the method has potential for on-site detection of total AFs in rice when using a nylon membrane-based device. PMID:26938207

  19. Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI.

    Science.gov (United States)

    Edgell, David R; Stanger, Matthew J; Belfort, Marlene

    2003-05-27

    Homing endonucleases initiate mobility of their host group I introns by binding to and cleaving lengthy recognition sequences that are typically centered on the intron insertion site (IS) of intronless alleles. Because the intron interrupts the endonucleases' recognition sequence, intron-containing alleles are immune to cleavage by their own endonuclease. I-TevI and I-BmoI are related GIY-YIG endonucleases that bind a homologous stretch of thymidylate synthase (TS)-encoding DNA but use different strategies to distinguish intronless from intron-containing substrates. I-TevI discriminates between substrates at the level of DNA binding, as its recognition sequence is centered on the intron IS. I-BmoI, in contrast, possesses a very asymmetric recognition sequence with respect to the intron IS, binds both intron-containing and intronless TS-encoding substrates, but efficiently cleaves only intronless substrate. Here, we show that I-BmoI is extremely tolerant of multiple substitutions around its cleavage sites and has a low specific activity. However, a single G-C base pair, at position -2 of a 39-base pair recognition sequence, is a major determinant for cleavage efficiency and distinguishes intronless from intron-containing alleles. Strikingly, this G-C base pair is universally conserved in phylogenetically diverse TS-coding sequences; this finding suggests that I-BmoI has evolved exquisite cleavage requirements to maximize the potential to spread to variant intronless alleles, while minimizing cleavage at its own intron-containing allele. PMID:12781137

  20. Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes

    Indian Academy of Sciences (India)

    Ying Yan; Jing Yan; Xianyu Piao; Tianbiao Zhang; Yifu Guan

    2012-06-01

    Locked nucleic acid (LNA) and 2′--methyl nucleotide (OMeN) are the most extensively studied nucleotide analogues. Although both LNA and OMeN are characterized by the C3′-endo sugar pucker conformation, which is dominant in A-form DNA and RNA nucleotides, they demonstrate different binding behaviours. Previous studies have focused attention on their properties of duplex stabilities, hybridization kinetics and resistance against nuclease digestion; however, their ability to discriminate mismatched hybridizations has been explored much less. In this study, LNA- and OMeN-modified oligonucleotide probes have been prepared and their effects on the DNA duplex stability have been examined: LNA modifications can enhance the duplex stability, whereas OMeN modifications reduce the duplex stability. Next, we studied how the LNA:DNA and OMeN:DNA mismatches reduced the duplex stability. Melting temperature measurement showed that different LNA:DNA or OMeN:DNA mismatches indeed influence the duplex stability differently. LNA purines can discriminate LNA:DNA mismatches more effectively than LNA pyrimidines as well as DNA nucleotides. Furthermore, we designed five LNA- and five OMeN-modified oligonucleotide probes to simulate realistic situations where target–probe duplexes contain a complementary LNA:DNA or OMeN:DNA base pairs and a DNA:DNA mismatch simultaneously. The measured collective effect showed that the duplex stability was enhanced by the complementary LNA:DNA base pair but decreased by the DNA:DNA mismatch in a position-dependent manner regardless of the chemical identity and position of the complementary LNA:DNA base pair. On the other hand, the OMeN-modified probes also showed that the duplex stability was reduced by both the OMeN modification and the OMeN:DNA mismatch in a position-dependent manner.